Sample records for bergportal.ch

  1. Avalanche risk in backcountry terrain based on usage frequency and accident data

    NASA Astrophysics Data System (ADS)

    Techel, F.; Zweifel, B.; Winkler, K.

    2014-08-01

    In Switzerland, the vast majority of avalanche accidents occurs during recreational activities. Risk analysis studies mostly rely on accident statistics without considering exposure (or the elements at risk), i.e. how many and where people are recreating. We compared the accident data (backcountry touring) with reports from two social media mountaineering networks - bergportal.ch"target="_blank">bergportal.ch and camptocamp.org. On these websites, users reported more than 15 000 backcountry tours during the five winters 2009/2010 to 2013/2014. We noted similar patterns in avalanche accident data and user data like demographics of recreationists, distribution of the day of the week (weekday vs. weekend) or weather conditions (fine vs. poor weather). However, we also found differences such as the avalanche danger conditions on days with activities and accidents, but also the geographic distribution. While backcountry activities are concentrated in proximity to the main population centres in the West and North of the Swiss Alps, a large proportion of the severe avalanche accidents occurred in the inner-alpine, more continental regions with frequently unfavorably snowpack structure. This suggests that even greater emphasis should be put on the type of avalanche problem in avalanche education and avalanche forecasting to increase the safety of backcountry recreationists.

  2. CH-TRU Waste Content Codes (CH-TRUCON)

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Washington TRU Solutions LLC

    2007-08-15

    The CH-TRU Waste Content Codes (CH-TRUCON) document describes the inventory of the U.S. Department of Energy (DOE) CH-TRU waste within the transportation parameters specified by the Contact-Handled Transuranic Waste Authorized Methods for Payload Control (CH-TRAMPAC). The CH-TRAMPAC defines the allowable payload for the Transuranic Package Transporter-II (TRUPACT-II) and HalfPACT packagings. This document is a catalog of TRUPACT-II and HalfPACT authorized contents and a description of the methods utilized to demonstrate compliance with the CH-TRAMPAC. A summary of currently approved content codes by site is presented in Table 1. The CH-TRAMPAC describes "shipping categories" that are assigned to each payload container.more » Multiple shipping categories may be assigned to a single content code. A summary of approved content codes and corresponding shipping categories is provided in Table 2, which consists of Tables 2A, 2B, and 2C. Table 2A provides a summary of approved content codes and corresponding shipping categories for the "General Case," which reflects the assumption of a 60-day shipping period as described in the CH-TRAMPAC and Appendix 3.4 of the CH-TRU Payload Appendices. For shipments to be completed within an approximately 1,000-mile radius, a shorter shipping period of 20 days is applicable as described in the CH-TRAMPAC and Appendix 3.5 of the CH-TRU Payload Appendices. For shipments to WIPP from Los Alamos National Laboratory (LANL), Nevada Test Site, and Rocky Flats Environmental Technology Site, a 20-day shipping period is applicable. Table 2B provides a summary of approved content codes and corresponding shipping categories for "Close-Proximity Shipments" (20-day shipping period). For shipments implementing the controls specified in the CH-TRAMPAC and Appendix 3.6 of the CH-TRU Payload Appendices, a 10-day shipping period is applicable. Table 2C provides a summary of approved content codes and corresponding shipping categories for "Controlled

  3. CH-TRU Waste Content Codes (CH-TRUCON)

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Washington TRU Solutions LLC

    2007-06-15

    The CH-TRU Waste Content Codes (CH-TRUCON) document describes the inventory of the U.S. Department of Energy (DOE) CH-TRU waste within the transportation parameters specified by the Contact-Handled Transuranic Waste Authorized Methods for Payload Control (CH-TRAMPAC). The CH-TRAMPAC defines the allowable payload for the Transuranic Package Transporter-II (TRUPACT-II) and HalfPACT packagings. This document is a catalog of TRUPACT-II and HalfPACT authorized contents and a description of the methods utilized to demonstrate compliance with the CH-TRAMPAC. A summary of currently approved content codes by site is presented in Table 1. The CH-TRAMPAC describes "shipping categories" that are assigned to each payload container.more » Multiple shipping categories may be assigned to a single content code. A summary of approved content codes and corresponding shipping categories is provided in Table 2, which consists of Tables 2A, 2B, and 2C. Table 2A provides a summary of approved content codes and corresponding shipping categories for the "General Case," which reflects the assumption of a 60-day shipping period as described in the CH-TRAMPAC and Appendix 3.4 of the CH-TRU Payload Appendices. For shipments to be completed within an approximately 1,000-mile radius, a shorter shipping period of 20 days is applicable as described in the CH-TRAMPAC and Appendix 3.5 of the CH-TRU Payload Appendices. For shipments to WIPP from Los Alamos National Laboratory (LANL), Nevada Test Site, and Rocky Flats Environmental Technology Site, a 20-day shipping period is applicable. Table 2B provides a summary of approved content codes and corresponding shipping categories for "Close-Proximity Shipments" (20-day shipping period). For shipments implementing the controls specified in the CH-TRAMPAC and Appendix 3.6 of the CH-TRU Payload Appendices, a 10-day shipping period is applicable. Table 2C provides a summary of approved content codes and corresponding shipping categories for "Controlled

  4. CH-TRU Waste Content Codes (CH-TRUCON)

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Washington TRU Solutions LLC

    2007-09-20

    The CH-TRU Waste Content Codes (CH-TRUCON) document describes the inventory of the U.S. Department of Energy (DOE) CH-TRU waste within the transportation parameters specified by the Contact-Handled Transuranic Waste Authorized Methods for Payload Control (CH-TRAMPAC). The CH-TRAMPAC defines the allowable payload for the Transuranic Package Transporter-II (TRUPACT-II) and HalfPACT packagings. This document is a catalog of TRUPACT-II and HalfPACT authorized contents and a description of the methods utilized to demonstrate compliance with the CH-TRAMPAC. A summary of currently approved content codes by site is presented in Table 1. The CH-TRAMPAC describes "shipping categories" that are assigned to each payload container.more » Multiple shipping categories may be assigned to a single content code. A summary of approved content codes and corresponding shipping categories is provided in Table 2, which consists of Tables 2A, 2B, and 2C. Table 2A provides a summary of approved content codes and corresponding shipping categories for the "General Case," which reflects the assumption of a 60-day shipping period as described in the CH-TRAMPAC and Appendix 3.4 of the CH-TRU Payload Appendices. For shipments to be completed within an approximately 1,000-mile radius, a shorter shipping period of 20 days is applicable as described in the CH-TRAMPAC and Appendix 3.5 of the CH-TRU Payload Appendices. For shipments to WIPP from Los Alamos National Laboratory (LANL), Nevada Test Site, and Rocky Flats Environmental Technology Site, a 20-day shipping period is applicable. Table 2B provides a summary of approved content codes and corresponding shipping categories for "Close-Proximity Shipments" (20-day shipping period). For shipments implementing the controls specified in the CH-TRAMPAC and Appendix 3.6 of the CH-TRU Payload Appendices, a 10-day shipping period is applicable. Table 2C provides a summary of approved content codes and corresponding shipping categories for "Controlled

  5. CH-TRU Waste Content Codes (CH-TRUCON)

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Washington TRU Solutions LLC

    2006-06-20

    The CH-TRU Waste Content Codes (CH-TRUCON) document describes the inventory of the U.S. Department of Energy (DOE) CH-TRU waste within the transportation parameters specified by the Contact-Handled Transuranic Waste Authorized Methods for Payload Control (CH-TRAMPAC). The CH-TRAMPAC defines the allowable payload for the Transuranic Package Transporter-II (TRUPACT-II) and HalfPACT packagings. This document is a catalog of TRUPACT-II and HalfPACT authorized contents and a description of the methods utilized to demonstrate compliance with the CH-TRAMPAC. A summary of currently approved content codes by site is presented in Table 1. The CH-TRAMPAC describes "shipping categories" that are assigned to each payload container.more » Multiple shipping categories may be assigned to a single content code. A summary of approved content codes and corresponding shipping categories is provided in Table 2, which consists of Tables 2A, 2B, and 2C. Table 2A provides a summary of approved content codes and corresponding shipping categories for the "General Case," which reflects the assumption of a 60-day shipping period as described in the CH-TRAMPAC and Appendix 3.4 of the CH-TRU Payload Appendices. For shipments to be completed within an approximately 1,000-mile radius, a shorter shipping period of 20 days is applicable as described in the CH-TRAMPAC and Appendix 3.5 of the CH-TRU Payload Appendices. For shipments to WIPP from Los Alamos National Laboratory (LANL), Nevada Test Site, and Rocky Flats Environmental Technology Site, a 20-day shipping period is applicable. Table 2B provides a summary of approved content codes and corresponding shipping categories for "Close-Proximity Shipments" (20-day shipping period). For shipments implementing the controls specified in the CH-TRAMPAC and Appendix 3.6 of the CH-TRU Payload Appendices, a 10-day shipping period is applicable. Table 2C provides a summary of approved content codes and corresponding shipping categories for "Controlled

  6. CH-TRU Waste Content Codes (CH-TRUCON)

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Washington TRU Solutions LLC

    2006-01-18

    The CH-TRU Waste Content Codes (CH-TRUCON) document describes the inventory of the U.S. Department of Energy (DOE) CH-TRU waste within the transportation parameters specified by the Contact-Handled Transuranic Waste Authorized Methods for Payload Control (CH-TRAMPAC). The CH-TRAMPAC defines the allowable payload for the Transuranic Package Transporter-II (TRUPACT-II) and HalfPACT packagings. This document is a catalog of TRUPACT-II and HalfPACT authorized contents and a description of the methods utilized to demonstrate compliance with the CH-TRAMPAC. A summary of currently approved content codes by site is presented in Table 1. The CH-TRAMPAC describes "shipping categories" that are assigned to each payload container.more » Multiple shipping categories may be assigned to a single content code. A summary of approved content codes and corresponding shipping categories is provided in Table 2, which consists of Tables 2A, 2B, and 2C. Table 2A provides a summary of approved content codes and corresponding shipping categories for the "General Case," which reflects the assumption of a 60-day shipping period as described in the CH-TRAMPAC and Appendix 3.4 of the CH-TRU Payload Appendices. For shipments to be completed within an approximately 1,000-mile radius, a shorter shipping period of 20 days is applicable as described in the CH-TRAMPAC and Appendix 3.5 of the CH-TRU Payload Appendices. For shipments to WIPP from Los Alamos National Laboratory (LANL), Nevada Test Site, and Rocky Flats Environmental Technology Site, a 20-day shipping period is applicable. Table 2B provides a summary of approved content codes and corresponding shipping categories for "Close-Proximity Shipments" (20-day shipping period). For shipments implementing the controls specified in the CH-TRAMPAC and Appendix 3.6 of the CH-TRU Payload Appendices, a 10-day shipping period is applicable. Table 2C provides a summary of approved content codes and corresponding shipping categories for "Controlled

  7. CH-TRU Waste Content Codes (CH-TRUCON)

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Washington TRU Solutions LLC

    2006-08-15

    The CH-TRU Waste Content Codes (CH-TRUCON) document describes the inventory of the U.S. Department of Energy (DOE) CH-TRU waste within the transportation parameters specified by the Contact-Handled Transuranic Waste Authorized Methods for Payload Control (CH-TRAMPAC). The CH-TRAMPAC defines the allowable payload for the Transuranic Package Transporter-II (TRUPACT-II) and HalfPACT packagings. This document is a catalog of TRUPACT-II and HalfPACT authorized contents and a description of the methods utilized to demonstrate compliance with the CH-TRAMPAC. A summary of currently approved content codes by site is presented in Table 1. The CH-TRAMPAC describes "shipping categories" that are assigned to each payload container.more » Multiple shipping categories may be assigned to a single content code. A summary of approved content codes and corresponding shipping categories is provided in Table 2, which consists of Tables 2A, 2B, and 2C. Table 2A provides a summary of approved content codes and corresponding shipping categories for the "General Case," which reflects the assumption of a 60-day shipping period as described in the CH-TRAMPAC and Appendix 3.4 of the CH-TRU Payload Appendices. For shipments to be completed within an approximately 1,000-mile radius, a shorter shipping period of 20 days is applicable as described in the CH-TRAMPAC and Appendix 3.5 of the CH-TRU Payload Appendices. For shipments to WIPP from Los Alamos National Laboratory (LANL), Nevada Test Site, and Rocky Flats Environmental Technology Site, a 20-day shipping period is applicable. Table 2B provides a summary of approved content codes and corresponding shipping categories for "Close-Proximity Shipments" (20-day shipping period). For shipments implementing the controls specified in the CH-TRAMPAC and Appendix 3.6 of the CH-TRU Payload Appendices, a 10-day shipping period is applicable. Table 2C provides a summary of approved content codes and corresponding shipping categories for "Controlled

  8. CH-TRU Waste Content Codes (CH-TRUCON)

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Washington TRU Solutions LLC

    2006-12-20

    The CH-TRU Waste Content Codes (CH-TRUCON) document describes the inventory of the U.S. Department of Energy (DOE) CH-TRU waste within the transportation parameters specified by the Contact-Handled Transuranic Waste Authorized Methods for Payload Control (CH-TRAMPAC). The CH-TRAMPAC defines the allowable payload for the Transuranic Package Transporter-II (TRUPACT-II) and HalfPACT packagings. This document is a catalog of TRUPACT-II and HalfPACT authorized contents and a description of the methods utilized to demonstrate compliance with the CH-TRAMPAC. A summary of currently approved content codes by site is presented in Table 1. The CH-TRAMPAC describes "shipping categories" that are assigned to each payload container.more » Multiple shipping categories may be assigned to a single content code. A summary of approved content codes and corresponding shipping categories is provided in Table 2, which consists of Tables 2A, 2B, and 2C. Table 2A provides a summary of approved content codes and corresponding shipping categories for the "General Case," which reflects the assumption of a 60-day shipping period as described in the CH-TRAMPAC and Appendix 3.4 of the CH-TRU Payload Appendices. For shipments to be completed within an approximately 1,000-mile radius, a shorter shipping period of 20 days is applicable as described in the CH-TRAMPAC and Appendix 3.5 of the CH-TRU Payload Appendices. For shipments to WIPP from Los Alamos National Laboratory (LANL), Nevada Test Site, and Rocky Flats Environmental Technology Site, a 20-day shipping period is applicable. Table 2B provides a summary of approved content codes and corresponding shipping categories for "Close-Proximity Shipments" (20-day shipping period). For shipments implementing the controls specified in the CH-TRAMPAC and Appendix 3.6 of the CH-TRU Payload Appendices, a 10-day shipping period is applicable. Table 2C provides a summary of approved content codes and corresponding shipping categories for "Controlled

  9. CH-TRU Waste Content Codes (CH-TRUCON)

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Washington TRU Solutions LLC

    2007-02-15

    The CH-TRU Waste Content Codes (CH-TRUCON) document describes the inventory of the U.S. Department of Energy (DOE) CH-TRU waste within the transportation parameters specified by the Contact-Handled Transuranic Waste Authorized Methods for Payload Control (CH-TRAMPAC). The CH-TRAMPAC defines the allowable payload for the Transuranic Package Transporter-II (TRUPACT-II) and HalfPACT packagings. This document is a catalog of TRUPACT-II and HalfPACT authorized contents and a description of the methods utilized to demonstrate compliance with the CH-TRAMPAC. A summary of currently approved content codes by site is presented in Table 1. The CH-TRAMPAC describes "shipping categories" that are assigned to each payload container.more » Multiple shipping categories may be assigned to a single content code. A summary of approved content codes and corresponding shipping categories is provided in Table 2, which consists of Tables 2A, 2B, and 2C. Table 2A provides a summary of approved content codes and corresponding shipping categories for the "General Case," which reflects the assumption of a 60-day shipping period as described in the CH-TRAMPAC and Appendix 3.4 of the CH-TRU Payload Appendices. For shipments to be completed within an approximately 1,000-mile radius, a shorter shipping period of 20 days is applicable as described in the CH-TRAMPAC and Appendix 3.5 of the CH-TRU Payload Appendices. For shipments to WIPP from Los Alamos National Laboratory (LANL), Nevada Test Site, and Rocky Flats Environmental Technology Site, a 20-day shipping period is applicable. Table 2B provides a summary of approved content codes and corresponding shipping categories for "Close-Proximity Shipments" (20-day shipping period). For shipments implementing the controls specified in the CH-TRAMPAC and Appendix 3.6 of the CH-TRU Payload Appendices, a 10-day shipping period is applicable. Table 2C provides a summary of approved content codes and corresponding shipping categories for "Controlled

  10. CH-TRU Waste Content Codes (CH-TRUCON)

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Washington TRU Solutions LLC

    2006-09-15

    The CH-TRU Waste Content Codes (CH-TRUCON) document describes the inventory of the U.S. Department of Energy (DOE) CH-TRU waste within the transportation parameters specified by the Contact-Handled Transuranic Waste Authorized Methods for Payload Control (CH-TRAMPAC). The CH-TRAMPAC defines the allowable payload for the Transuranic Package Transporter-II (TRUPACT-II) and HalfPACT packagings. This document is a catalog of TRUPACT-II and HalfPACT authorized contents and a description of the methods utilized to demonstrate compliance with the CH-TRAMPAC. A summary of currently approved content codes by site is presented in Table 1. The CH-TRAMPAC describes "shipping categories" that are assigned to each payload container.more » Multiple shipping categories may be assigned to a single content code. A summary of approved content codes and corresponding shipping categories is provided in Table 2, which consists of Tables 2A, 2B, and 2C. Table 2A provides a summary of approved content codes and corresponding shipping categories for the "General Case," which reflects the assumption of a 60-day shipping period as described in the CH-TRAMPAC and Appendix 3.4 of the CH-TRU Payload Appendices. For shipments to be completed within an approximately 1,000-mile radius, a shorter shipping period of 20 days is applicable as described in the CH-TRAMPAC and Appendix 3.5 of the CH-TRU Payload Appendices. For shipments to WIPP from Los Alamos National Laboratory (LANL), Nevada Test Site, and Rocky Flats Environmental Technology Site, a 20-day shipping period is applicable. Table 2B provides a summary of approved content codes and corresponding shipping categories for "Close-Proximity Shipments" (20-day shipping period). For shipments implementing the controls specified in the CH-TRAMPAC and Appendix 3.6 of the CH-TRU Payload Appendices, a 10-day shipping period is applicable. Table 2C provides a summary of approved content codes and corresponding shipping categories for "Controlled

  11. Kinetics of OH- and Cl-initiated oxidation of CH2dbnd CHC(O)O(CH2)2CH3 and CH2dbnd CHCH2C(O)O(CH2)2CH3 and fate of the alkoxy radicals formed

    NASA Astrophysics Data System (ADS)

    Rivela, Cynthia; Blanco, María B.; Teruel, Mariano A.

    2016-05-01

    Rate coefficients of the reactions of OH and Cl radicals with vinyl and allyl butyrate were determined for the first time at 298 K and 1 atm using the relative method to be (in cm3 molecule-1 s-1): k1(OH + CH2dbnd CHC(O)O(CH2)2CH3) = (2.61 ± 0.31) × 10-11, k2(Cl + CH2dbnd CHC(O)O(CH2)2CH3) = (2.48 ± 0.89) × 10-10, k3(OH + CH2dbnd CHCH2C(O)O(CH2)2CH3) = (2.89 ± 0.31) × 10-11, and k4(Cl + CH2dbnd CHCH2C(O)O(CH2)2CH3) = (2.25 ± 0.96) × 10-10. Reactivity trends and atmospheric lifetimes of esters are presented. Additionally, a product study shown butyric acid and polifunctional products for the reactions of vinyl and allyl butyrate, respectively and general mechanism is proposed.

  12. Unimolecular reactivity of organotrifluoroborate anions, RBF3- , and their alkali metal cluster ions, M(RBF3 )2- (M = Na, K; R = CH3 , CH3 CH2 , CH3 (CH2 )3 , CH3 (CH2 )5 , c-C3 H5 , C6 H5 , C6 H5 CH2 , CH2 CHCH2 , CH2 CH, C6 H5 CO).

    PubMed

    Bathie, Fiona L B; Bowen, Chris J; Hutton, Craig A; O'Hair, Richard A J

    2018-07-15

    Potassium organotrifluoroborates (RBF 3 K) are important reagents used in organic synthesis. Although mass spectrometry is commonly used to confirm their molecular formulae, the gas-phase fragmentation reactions of organotrifluoroborates and their alkali metal cluster ions have not been previously reported. Negative-ion mode electrospray ionization (ESI) together with collision-induced dissociation (CID) using a triple quadrupole mass spectrometer were used to examine the fragmentation pathways for RBF 3 - (where R = CH 3 , CH 3 CH 2 , CH 3 (CH 2 ) 3 , CH 3 (CH 2 ) 5 , c-C 3 H 5 , C 6 H 5 , C 6 H 5 CH 2 , CH 2 CHCH 2 , CH 2 CH, C 6 H 5 CO) and M(RBF 3 ) 2 - (M = Na, K), while density functional theory (DFT) calculations at the M06/def2-TZVP level were used to examine the structures and energies associated with fragmentation reactions for R = Me and Ph. Upon CID, preferentially elimination of HF occurs for RBF 3 - ions for systems where R = an alkyl anion, whereas R - formation is favoured when R = a stabilized anion. At higher collision energies loss of F - and additional HF losses are sometimes observed. Upon CID of M(RBF 3 ) 2 - , formation of RBF 3 - is the preferred pathway with some fluoride transfer observed only when M = Na. The DFT-calculated relative thermochemistry for competing fragmentation pathways is consistent with the experiments. The main fragmentation pathways of RBF 3 - are HF elimination and/or R - loss. This contrasts with the fragmentation reactions of other organometallate anions, where reductive elimination, beta hydride transfer and bond homolysis are often observed. The presence of fluoride transfer upon CID of Na(RBF 3 ) 2 - but not K(RBF 3 ) 2 - is in agreement with the known fluoride affinities of Na + and K + and can be rationalized by Pearson's HSAB theory. Copyright © 2018 John Wiley & Sons, Ltd.

  13. ChIP-seq.

    PubMed

    Kim, Tae Hoon; Dekker, Job

    2018-05-01

    Owing to its digital nature, ChIP-seq has become the standard method for genome-wide ChIP analysis. Using next-generation sequencing platforms (notably the Illumina Genome Analyzer), millions of short sequence reads can be obtained. The densities of recovered ChIP sequence reads along the genome are used to determine the binding sites of the protein. Although a relatively small amount of ChIP DNA is required for ChIP-seq, the current sequencing platforms still require amplification of the ChIP DNA by ligation-mediated PCR (LM-PCR). This protocol, which involves linker ligation followed by size selection, is the standard ChIP-seq protocol using an Illumina Genome Analyzer. The size-selected ChIP DNA is amplified by LM-PCR and size-selected for the second time. The purified ChIP DNA is then loaded into the Genome Analyzer. The ChIP DNA can also be processed in parallel for ChIP-chip results. © 2018 Cold Spring Harbor Laboratory Press.

  14. ChIP and ChIP-Related Techniques: Expanding the Fields of Application and Improving ChIP Performance.

    PubMed

    Visa, Neus; Jordán-Pla, Antonio

    2018-01-01

    Protein-DNA interactions in vivo can be detected and quantified by chromatin immunoprecipitation (ChIP). ChIP has been instrumental for the advancement of epigenetics and has set the groundwork for the development of a number of ChIP-related techniques that have provided valuable information about the organization and function of genomes. Here, we provide an introduction to ChIP and discuss the applications of ChIP in different research areas. We also review some of the strategies that have been devised to improve ChIP performance.

  15. ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data

    PubMed Central

    2010-01-01

    Background Chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing (ChIP-seq) or ChIP followed by genome tiling array analysis (ChIP-chip) have become standard technologies for genome-wide identification of DNA-binding protein target sites. A number of algorithms have been developed in parallel that allow identification of binding sites from ChIP-seq or ChIP-chip datasets and subsequent visualization in the University of California Santa Cruz (UCSC) Genome Browser as custom annotation tracks. However, summarizing these tracks can be a daunting task, particularly if there are a large number of binding sites or the binding sites are distributed widely across the genome. Results We have developed ChIPpeakAnno as a Bioconductor package within the statistical programming environment R to facilitate batch annotation of enriched peaks identified from ChIP-seq, ChIP-chip, cap analysis of gene expression (CAGE) or any experiments resulting in a large number of enriched genomic regions. The binding sites annotated with ChIPpeakAnno can be viewed easily as a table, a pie chart or plotted in histogram form, i.e., the distribution of distances to the nearest genes for each set of peaks. In addition, we have implemented functionalities for determining the significance of overlap between replicates or binding sites among transcription factors within a complex, and for drawing Venn diagrams to visualize the extent of the overlap between replicates. Furthermore, the package includes functionalities to retrieve sequences flanking putative binding sites for PCR amplification, cloning, or motif discovery, and to identify Gene Ontology (GO) terms associated with adjacent genes. Conclusions ChIPpeakAnno enables batch annotation of the binding sites identified from ChIP-seq, ChIP-chip, CAGE or any technology that results in a large number of enriched genomic regions within the statistical programming environment R. Allowing users to pass their own annotation data such

  16. Selenium carboxylic acids betaine; 3,3‧,3″-selenotris(propanoic acid) betaine, Se(CH2CH2COOH)2(CH2CH2COO)

    NASA Astrophysics Data System (ADS)

    Doudin, Khalid; Törnroos, Karl W.

    2017-06-01

    Attempts to prepare [Se(CH2CH2COOH)3]+Cl- from Se(CH2CH2COOH)2 and H2Cdbnd CHCOOH in concentrated hydrochloric acid, for the corresponding sulfonium salt, led exclusively to the Se-betaine, Se(CH2CH2COOH)2(CH2CH2COO). The Se-betaine crystallises in the space group P2l/c with the cell dimensions at 223 K, a = 5.5717(1), b = 24.6358(4), c = 8.4361(1) Å, β = 104.762(1)°, V = 1119.74(3) Å3, Z = 4, Dcalc = 1.763 Mgm- 3, μ = 3.364 Mm-1. The structure refined to RI = 0.0223 for 2801 reflections with Fo > 4σ(Fo). In the crystalline state the molecule is intermolecularly linked to neighbouring molecules by a number of hydrogen bonds; a very strong carboxylic-carboxylate bond with an O⋯O distance of 2.4435(16) Å, a medium strong carboxylic-carboxylate bond with an O⋯O distance of 2.6431(16) Å and several weak O⋯H(CH2) with O⋯C distances between 3.2 and 3.3 Å. In the carboxylic group involved in the very strong hydrogen bond the O⋯H bond is antiperiplanar to the Cdbnd O bond while the Osbnd H bond is periplanar to the Cdbnd O bond in the second carboxylic group. Based upon the Csbnd O bond lengths and the elongation of the Osbnd H bond involved in the strong hydrogen bond one may describe the compound as strongly linked units of Se(CH2CH2COOH)(CH2CH2COO)2 rather than Se(CH2CH2COOH)2(CH2CH2COO). The selenium atom forms two strong intramolecular 1,5-Se⋯O contacts, with a carboxylate oxygen atom, 2.9385(12) Å, and with a carboxylic oxygen atom, 2.8979(11) Å. To allow for these contacts the two organic fragments have been forced into the periplanar conformation. The molecule is only slightly asymmetric with regard to the Csbnd Sesbnd C bond angles but is very asymmetric with regard to the torsion angles.

  17. Laboratory Spectroscopy of CH(+) and Isotopic CH

    NASA Technical Reports Server (NTRS)

    Pearson, John C.; Drouin, Brian J.

    2006-01-01

    The A1II - X1(Epsilon) electronic band of the CH(+) ion has been used as a probe of the physical and dynamical conditions of the ISM for 65 years. In spite of being one of the first molecular species observed in the ISM and the very large number of subsequent observations with large derived column densities, the pure rotational spectra of CH+ has remained elusive in both the laboratory and in the ISM as well. We report the first laboratory measurement of the pure rotation of the CH(+) ion and discuss the detection of CH-13(+) in the ISM. Also reported are the somewhat unexpected chemical conditions that resulted in laboratory production.

  18. libChEBI: an API for accessing the ChEBI database.

    PubMed

    Swainston, Neil; Hastings, Janna; Dekker, Adriano; Muthukrishnan, Venkatesh; May, John; Steinbeck, Christoph; Mendes, Pedro

    2016-01-01

    ChEBI is a database and ontology of chemical entities of biological interest. It is widely used as a source of identifiers to facilitate unambiguous reference to chemical entities within biological models, databases, ontologies and literature. ChEBI contains a wealth of chemical data, covering over 46,500 distinct chemical entities, and related data such as chemical formula, charge, molecular mass, structure, synonyms and links to external databases. Furthermore, ChEBI is an ontology, and thus provides meaningful links between chemical entities. Unlike many other resources, ChEBI is fully human-curated, providing a reliable, non-redundant collection of chemical entities and related data. While ChEBI is supported by a web service for programmatic access and a number of download files, it does not have an API library to facilitate the use of ChEBI and its data in cheminformatics software. To provide this missing functionality, libChEBI, a comprehensive API library for accessing ChEBI data, is introduced. libChEBI is available in Java, Python and MATLAB versions from http://github.com/libChEBI, and provides full programmatic access to all data held within the ChEBI database through a simple and documented API. libChEBI is reliant upon the (automated) download and regular update of flat files that are held locally. As such, libChEBI can be embedded in both on- and off-line software applications. libChEBI allows better support of ChEBI and its data in the development of new cheminformatics software. Covering three key programming languages, it allows for the entirety of the ChEBI database to be accessed easily and quickly through a simple API. All code is open access and freely available.

  19. Impact of artifact removal on ChIP quality metrics in ChIP-seq and ChIP-exo data

    PubMed Central

    Carroll, Thomas S.; Liang, Ziwei; Salama, Rafik; Stark, Rory; de Santiago, Ines

    2014-01-01

    With the advent of ChIP-seq multiplexing technologies and the subsequent increase in ChIP-seq throughput, the development of working standards for the quality assessment of ChIP-seq studies has received significant attention. The ENCODE consortium's large scale analysis of transcription factor binding and epigenetic marks as well as concordant work on ChIP-seq by other laboratories has established a new generation of ChIP-seq quality control measures. The use of these metrics alongside common processing steps has however not been evaluated. In this study, we investigate the effects of blacklisting and removal of duplicated reads on established metrics of ChIP-seq quality and show that the interpretation of these metrics is highly dependent on the ChIP-seq preprocessing steps applied. Further to this we perform the first investigation of the use of these metrics for ChIP-exo data and make recommendations for the adaptation of the NSC statistic to allow for the assessment of ChIP-exo efficiency. PMID:24782889

  20. On the Jupiter's ephemeris in the Ch'i-Yao Jang-Tsai-Chüch.

    NASA Astrophysics Data System (ADS)

    Niu, Weixing; Jiang, Xiaoyuan

    Jupiter's ephemeris preserved in the Ch'i-Yao Jang-Tsai-Chüch is interpreted. Then the time and position coordinates of Jupiter's first stationary point, second stationary point, first visibility in the east and last visibility in the west, which recorded in the ephemeris are analysed. The accuracy of the ephemeris is also discussed. Finally, it is identified that the ephemeris has been used as an astrological handbook by Japanese astrologers in 973 - 1132.

  1. Rate constants for the reactions of OH with CH3Cl, CH2Cl2, CHCl3, and CH3Br

    NASA Technical Reports Server (NTRS)

    Hsu, K.-J.; Demore, W. B.

    1994-01-01

    Rate constants for the reactions of OH with CH3Cl, CH2Cl2, CHCl3, and CH3Br have been measured by a relative rate technique in which the reaction rate of each compound was compared to that of HFC-152a (CH3CHF2) and (for CH2Cl2) HFC-161 (CH3CH2F). Using absolute rate constants for HFC-152a and HFC-161, which we have determined relative to those for CH4, CH3CCl3, and C2H6, temperature dependent rate constants of both compounds were derived. The derived rate constant for CH3Br is in good agreement with recent absolute measurements. However, for the chloromethanes all the rate constants are lower at atmospheric temperatures than previously reported, especially for CH2Cl2 where the present rate constant is about a factor of 1.6 below the JPL 92-20 value. The new rate constant appears to resolve a discrepancy between the observed atmospheric concentrations and those calculated from the previous rate constant and estimated release rates.

  2. Cholinesterase (ChE) response and related mortality among birds fed ChE inhibitors

    USGS Publications Warehouse

    Ludke, J.L.; Hill, E.F.; Dieter, M.P.

    1975-01-01

    Patterns of mortality and inhibition of brain and plasma ChE in birds treated with ChE inhibitors were studied in an attempt to determine the validity of using ChE activity as a monitoring and diagnostic technique. Analysis of brain ChE activity proved to be reliable for diagnosing and monitoring effects of selected ChE inhibitors in birds. Brain ChE inhibition exceeding 20% indicated exposure, and inhibition greater than 50% was sufficient for diagnosing cause of death. Individuals that died from dietary exposure to parathion or carbofuran had brain ChE activities below 55% of normal; although individuals could survive with brain ChE activity lower than 50%. Problems associated with collection, storage, and analysis of tissues for ChE activity are discussed.

  3. Ice chemistry of acetaldehyde reveals competitive reactions in the first step of the Strecker synthesis of alanine: formation of HO-CH(CH3)-NH2 vs. HO-CH(CH3)-CN

    NASA Astrophysics Data System (ADS)

    Fresneau, Aurélien; Danger, Grégoire; Rimola, Albert; Duvernay, Fabrice; Theulé, Patrice; Chiavassa, Thierry

    2015-08-01

    The understanding of compound formation in laboratory simulated astrophysical environments is an important challenge in obtaining information on the chemistry occurring in these environments. We here investigate by means of both laboratory experiments and quantum chemical calculations the ice-based reactivity of acetaldehyde (CH3CHO) with ammonia (NH3) and hydrogen cyanide (HCN) in excess of water (H2O) promoted by temperature. A priori, this study should give information on alanine (2HN-CH(CH3)-COOH) formation (the simplest chiral amino acid detected in meteorites), since these reactions concern the first steps of its formation through the Strecker synthesis. However, infrared spectroscopy, mass spectrometry with HC14N or HC15N isotopologues and B3LYP-D3 results converge to indicate that an H2O-dominated ice containing CH3CHO, NH3 and HCN not only leads to the formation of α-aminoethanol (2HN-CH(CH3)-OH, the product compound of the first step of the Strecker mechanism) and its related polymers (2HN-(CH(CH3)-O)n-H) due to reaction between CH3CHO and NH3, but also to the 2-hydroxypropionitrile (HO­-CH(CH3)-CN) and its related polymers (H-(O-CH(CH3))n-CN) from direct reaction between CH3CHO and HCN. The ratio between these two species depends on the initial NH3/HCN ratio in the ice. Formation of α-aminoethanol is favoured when the NH3 concentration is larger than HCN. We also show that the presence of water is essential for the formation of HO­-CH(CH3)-CN, contrarily to 2HN-CH(CH3)-OH whose formation also takes place in absence of H2O ice. As in astrophysical ices NH3 is more abundant than HCN, formation of α-aminoethanol should consequently be favoured compared to 2-hydroxypropionitrile, thus pointing out α-aminoethanol as a plausible intermediate species for alanine synthesis through the Strecker mechanism in astrophysical ices.

  4. New superhindered polydentate polyphosphine ligands P(CH2CH2P(t)Bu2)3, PhP(CH2CH2P(t)Bu2)2, P(CH2CH2CH2P(t)Bu2)3, and their ruthenium(II) chloride complexes.

    PubMed

    Gilbert-Wilson, Ryan; Field, Leslie D; Bhadbhade, Mohan M

    2012-03-05

    The synthesis and characterization of the extremely hindered phosphine ligands, P(CH(2)CH(2)P(t)Bu(2))(3) (P(2)P(3)(tBu), 1), PhP(CH(2)CH(2)P(t)Bu(2))(2) (PhP(2)P(2)(tBu), 2), and P(CH(2)CH(2)CH(2)P(t)Bu(2))(3) (P(3)P(3)(tBu), 3) are reported, along with the synthesis and characterization of ruthenium chloro complexes RuCl(2)(P(2)P(3)(tBu)) (4), RuCl(2)(PhP(2)P(2)(tBu)) (5), and RuCl(2)(P(3)P(3)(tBu)) (6). The bulky P(2)P(3)(tBu) (1) and P(3)P(3)(tBu) (3) ligands are the most sterically encumbered PP(3)-type ligands so far synthesized, and in all cases, only three phosphorus donors are able to bind to the metal center. Complexes RuCl(2)(PhP(2)P(2)(tBu)) (5) and RuCl(2)(P(3)P(3)(tBu)) (6) were characterized by crystallography. Low temperature solution and solid state (31)P{(1)H} NMR were used to demonstrate that the structure of RuCl(2)(P(2)P(3)(tBu)) (4) is probably analogous to that of RuCl(2)(PhP(2)P(2)(tBu)) (5) which had been structurally characterized.

  5. ChIA-PET2: a versatile and flexible pipeline for ChIA-PET data analysis

    PubMed Central

    Li, Guipeng; Chen, Yang; Snyder, Michael P.; Zhang, Michael Q.

    2017-01-01

    ChIA-PET2 is a versatile and flexible pipeline for analyzing different types of ChIA-PET data from raw sequencing reads to chromatin loops. ChIA-PET2 integrates all steps required for ChIA-PET data analysis, including linker trimming, read alignment, duplicate removal, peak calling and chromatin loop calling. It supports different kinds of ChIA-PET data generated from different ChIA-PET protocols and also provides quality controls for different steps of ChIA-PET analysis. In addition, ChIA-PET2 can use phased genotype data to call allele-specific chromatin interactions. We applied ChIA-PET2 to different ChIA-PET datasets, demonstrating its significantly improved performance as well as its ability to easily process ChIA-PET raw data. ChIA-PET2 is available at https://github.com/GuipengLi/ChIA-PET2. PMID:27625391

  6. Co-processing CH4 and oxygenates on Mo/H-ZSM-5: 2. CH4-CO2 and CH4-HCOOH mixtures.

    PubMed

    Bedard, Jeremy; Hong, Do-Young; Bhan, Aditya

    2013-08-07

    Co-processing of formic acid or carbon dioxide with CH4 (FA/CH4 = 0.01-0.03 and CO2/CH4 = 0.01-0.03) on Mo/H-ZSM-5 catalysts at 950 K with the prospect of kinetically coupling dehydrogenation and deoxygenation cycles results instead in a two-zone, staged bed reactor configuration consisting of upstream oxygenate/CH4 reforming and downstream CH4 dehydroaromatization. The addition of an oxygenate co-feed (oxygenate/CH4 = 0.01-0.03) causes oxidation of the active molybdenum carbide catalyst while producing CO and H2 until completely converted. Forward rates of C6H6 synthesis are unaffected by the introduction of an oxygenate co-feed after rigorously accounting for the thermodynamic reversibility caused by the H2 produced in oxygenate reforming reactions and the fraction of the active catalyst deemed unavailable for CH4 DHA. All effects of co-processing oxygenates with CH4 can be construed in terms of an approach to equilibrium.

  7. ChIP-re-ChIP: Co-occupancy Analysis by Sequential Chromatin Immunoprecipitation.

    PubMed

    Beischlag, Timothy V; Prefontaine, Gratien G; Hankinson, Oliver

    2018-01-01

    Chromatin immunoprecipitation (ChIP) exploits the specific interactions between DNA and DNA-associated proteins. It can be used to examine a wide range of experimental parameters. A number of proteins bound at the same genomic location can identify a multi-protein chromatin complex where several proteins work together to regulate gene transcription or chromatin configuration. In many instances, this can be achieved using sequential ChIP; or simply, ChIP-re-ChIP. Whether it is for the examination of specific transcriptional or epigenetic regulators, or for the identification of cistromes, the ability to perform a sequential ChIP adds a higher level of power and definition to these analyses. In this chapter, we describe a simple and reliable method for the sequential ChIP assay.

  8. Anharmonic Effect in CH3CH2C(=O)OCH2CH3 Decomposition

    NASA Astrophysics Data System (ADS)

    Ding, Yang; Song, Liguo; Yao, Li; Xia, Wenwen

    2017-12-01

    In this paper, using the B3LYP functional and CCSD(T) method with 6-311++G** basis set, the harmonic and anharmonic rate constants in the unimolecular dissociation of ethyl propanoate have been calculated using Rice-Ramsperger-Kassel-Marcus theory. The anharmonic rate constants of the title reaction have also been examined, the comparison shows that, the anharmonic effect especially in the case of high total energies and temperature for channels 3 to 6 is significant, so that the anharmonic effect cannot be neglected for unimolecular dissociation reaction of CH3CH2C(=O)OCH2CH3 both in microcanonical and canonical systems.

  9. ChIP-chip.

    PubMed

    Kim, Tae Hoon; Dekker, Job

    2018-05-01

    ChIP-chip can be used to analyze protein-DNA interactions in a region-wide and genome-wide manner. DNA microarrays contain PCR products or oligonucleotide probes that are designed to represent genomic sequences. Identification of genomic sites that interact with a specific protein is based on competitive hybridization of the ChIP-enriched DNA and the input DNA to DNA microarrays. The ChIP-chip protocol can be divided into two main sections: Amplification of ChIP DNA and hybridization of ChIP DNA to arrays. A large amount of DNA is required to hybridize to DNA arrays, and hybridization to a set of multiple commercial arrays that represent the entire human genome requires two rounds of PCR amplifications. The relative hybridization intensity of ChIP DNA and that of the input DNA is used to determine whether the probe sequence is a potential site of protein-DNA interaction. Resolution of actual genomic sites bound by the protein is dependent on the size of the chromatin and on the genomic distance between the probes on the array. As with expression profiling using gene chips, ChIP-chip experiments require multiple replicates for reliable statistical measure of protein-DNA interactions. © 2018 Cold Spring Harbor Laboratory Press.

  10. Luminescent Copper(I) Halide Butterfly Dimers Coordinated to [Au(CH3imCH2py)2]BF4 and [Au(CH3imCH2quin)2]BF4

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Catalano, V.; Moore, A; Shearer, J

    2009-01-01

    The coordination chemistry of copper(I) halides to the homoleptic, N-heterocyclic carbene Au(I) complexes [Au(CH{sub 3}imCH{sub 2}quin){sub 2}]BF{sub 4} and [Au(CH{sub 3}imCH{sub 2}py){sub 2}]BF{sub 4} was explored. The reaction of CuX (X = Cl, Br, I) with either [Au(CH{sub 3}imCH{sub 2}quin){sub 2}]BF{sub 4} or [Au(CH{sub 3}imCH{sub 2}py){sub 2}]BF{sub 4} produces trimetallic complexes containing Cu{sub 2}X{sub 2}-butterfly copper clusters coordinated to the two imine moieties. The triangular arrangement of the metals places the gold(I) center in close proximity ({approx}2.5-2.6 {angstrom}) to the centroid of the Cu-Cu vector. The Cu-Cu separations vary as a function of bridging halide with the shortest Cu-Cu separationsmore » of {approx}2.5 {angstrom} found in the iodo-complexes and the longest separations of 2.9 {angstrom} found in the bridging chloride complexes. In all six complexes the Au-Cu separations range from {approx}2.8 to 3.0 {angstrom}. In the absence of halides, the dimetallic complex [AuCu(CH{sub 3}imCH{sub 2}py){sub 2}(NCCH{sub 3}){sub 2}](BF{sub 4}){sub 2}, containing a long Au-Cu distance of {approx}4.72 {angstrom} is formed. Additionally, as the byproduct of the reaction of CuBr with [Au(CH{sub 3}imCH{sub 2}quin){sub 2}]BF{sub 4} the deep-red, dimetallic compound, AuCuBr{sub 2}(CH{sub 3}imCH{sub 2}quin){sub 2}, was isolated in very low yield. All of these complexes were studied by NMR spectroscopy, mass spectrometry, and the copper containing species were additionally characterized by X-ray crystallography. In solution the copper centers dissociate from the gold complexes, but as shown by XANES and EXAFS spectroscopy, at low temperature the Cu-Cu linkage is broken, and the individual copper(I) halides reposition themselves to opposite sides of the gold complex while remaining coordinated to one imine moiety. In the solid state all of the complexes are photoluminescent, though the nature of the excited state was not determined.« less

  11. CH-53K Heavy Lift Replacement Helicopter (CH-53K)

    DTIC Science & Technology

    2015-12-01

    Selected Acquisition Report (SAR) RCS: DD-A&T(Q&A)823-390 CH-53K Heavy Lift Replacement Helicopter (CH-53K) As of FY 2017 President’s Budget...December 2015 SAR March 4, 2016 10:04:18 UNCLASSIFIED 4 Col Henry Vanderborght PMA-261 Heavy Lift Helicopters Program Executive Office - Air, Anti...Replacement Helicopter (CH-53K) DoD Component Navy Responsible Office References SAR Baseline (Development Estimate) Defense Acquisition Executive (DAE

  12. Dynamics of the F(-) + CH3I → HF + CH2I(-) Proton Transfer Reaction.

    PubMed

    Zhang, Jiaxu; Xie, Jing; Hase, William L

    2015-12-17

    Direct chemical dynamics simulations, at collision energies Erel of 0.32 and 1.53 eV, were performed to obtain an atomistic understanding of the F(-) + CH3I reaction dynamics. There is only the F(-) + CH3I → CH3F + I(-) bimolecular nucleophilic substitution SN2 product channel at 0.32 eV. Increasing Erel to 1.53 eV opens the endothermic F(-) + CH3I → HF + CH2I(-) proton transfer reaction, which is less competitive than the SN2 reaction. The simulations reveal proton transfer occurs by two direct atomic-level mechanisms, rebound and stripping, and indirect mechanisms, involving formation of the F(-)···HCH2I complex and the roundabout. For the indirect trajectories all of the CH2I(-) is formed with zero-point energy (ZPE), while for the direct trajectories 50% form CH2I(-) without ZPE. Without a ZPE constraint for CH2I(-), the reaction cross sections for the rebound, stripping, and indirect mechanisms are 0.2 ± 0.1, 1.2 ± 0.4, and 0.7 ± 0.2 Å(2), respectively. Discarding trajectories that do not form CH2I(-) with ZPE reduces the rebound and stripping cross sections to 0.1 ± 0.1 and 0.7 ± 0.5 Å(2). The HF product is formed rotationally and vibrationally unexcited. The average value of J is 2.6 and with histogram binning n = 0. CH2I(-) is formed rotationally excited. The partitioning between CH2I(-) vibration and HF + CH2I(-) relative translation energy depends on the treatment of CH2I(-) ZPE. Without a CH2I(-) ZPE constraint the energy partitioning is primarily to relative translation with little CH2I(-) vibration. With a ZPE constraint, energy partitioning to CH2I(-) rotation, CH2I(-) vibration, and relative translation are statistically the same. The overall F(-) + CH3I rate constant at Erel of both 0.32 and 1.53 eV is in good agreement with experiment and negligibly affected by the treatment of CH2I(-) ZPE, since the SN2 reaction is the major contributor to the total reaction rate constant. The potential energy surface and reaction dynamics for F

  13. Capture and dissociation in the complex-forming CH + H2 → CH2 + H, CH + H2 reactions.

    PubMed

    González, Miguel; Saracibar, Amaia; Garcia, Ernesto

    2011-02-28

    The rate coefficients for the capture process CH + H(2)→ CH(3) and the reactions CH + H(2)→ CH(2) + H (abstraction), CH + H(2) (exchange) have been calculated in the 200-800 K temperature range, using the quasiclassical trajectory (QCT) method and the most recent global potential energy surface. The reactions, which are of interest in combustion and in astrochemistry, proceed via the formation of long-lived CH(3) collision complexes, and the three H atoms become equivalent. QCT rate coefficients for capture are in quite good agreement with experiments. However, an important zero point energy (ZPE) leakage problem occurs in the QCT calculations for the abstraction, exchange and inelastic exit channels. To account for this issue, a pragmatic but accurate approach has been applied, leading to a good agreement with experimental abstraction rate coefficients. Exchange rate coefficients have also been calculated using this approach. Finally, calculations employing QCT capture/phase space theory (PST) models have been carried out, leading to similar values for the abstraction rate coefficients as the QCT and previous quantum mechanical capture/PST methods. This suggests that QCT capture/PST models are a good alternative to the QCT method for this and similar systems.

  14. Conformational and spectroscopic study of xanthogen ethyl formates, ROC(S)SC(O)OCH2CH3. Isolation of CH3CH2OC(O)SH

    NASA Astrophysics Data System (ADS)

    Juncal, Luciana C.; Cozzarín, Melina V.; Romano, Rosana M.

    2015-03-01

    ROC(S)SC(O)OCH2CH3, with R = CH3sbnd , (CH3)2CHsbnd and CH3(CH2)2sbnd , were obtained through the reaction between potassium xanthate salts, ROC(S)SK, and ethyl chloroformate, ClC(O)OCH2CH3. The liquid compounds were identified and characterized by 1H and 13C NMR and mass spectrometry. The conformations adopted by the molecules were studied by DFT methods. 6 conformers were theoretically predicted for R = CH3sbnd and (CH3)2CHsbnd , while the conformational flexibility of the n-propyl substituent increases the total number of feasible rotamers to 21. For the three molecules, the conformers can be associated in 3 groups, being the most stable the AS forms - the Cdbnd S double bond anti (A) with respect to the Csbnd S single bond and the Ssbnd C single bond syn (S) with respect to the Cdbnd O double bond - followed by AA and SS conformers. The vibrational spectra were interpreted in terms of the predicted conformational equilibrium, presenting the ν(Cdbnd O) spectral region signals corresponding to the three groups of conformers. A moderated pre-resonance Raman enhancement of the ν(Cdbnd S) vibrational mode of CH3(CH2)2OC(S)SC(O)OCH2CH3 was detected, when the excitation radiation approaches the energy of a n → π∗ electronic transition associated with the Cdbnd S chromophore. UV-visible spectra in different solvents were measured and interpreted in terms of TD-DFT calculations. The unknown molecule CH3CH2OC(O)SH was isolated by the UV-visible photolysis of CH3OC(S)SC(O)OCH2CH3 isolated in Ar matrix, and also obtained as a side-product of the reaction between potassium xanthate salts, ROC(S)SK, and ethyl chloroformate, ClC(O)OCH2CH3.

  15. Thermal decomposition of ethanol. 4. Ab initio chemical kinetics for reactions of H atoms with CH3CH2O and CH3CHOH radicals.

    PubMed

    Xu, Z F; Xu, Kun; Lin, M C

    2011-04-21

    The potential energy surfaces of H-atom reactions with CH(3)CH(2)O and CH(3)CHOH, two major radicals in the decomposition and oxidation of ethanol, have been studied at the CCSD(T)/6-311+G(3df,2p) level of theory with geometric optimization carried out at the BH&HLYP/6-311+G(3df,2p) level. The direct hydrogen abstraction channels and the indirect association/decomposition channels from the chemically activated ethanol molecule have been considered for both reactions. The rate constants for both reactions have been calculated at 100-3000 K and 10(-4) Torr to 10(3) atm Ar pressure by microcanonical VTST/RRKM theory with master equation solution for all accessible product channels. The results show that the major product channel of the CH(3)CH(2)O + H reaction is CH(3) + CH(2)OH under atmospheric pressure conditions. Only at high pressure and low temperature, the rate constant for CH(3)CH(2)OH formation by collisonal deactivation becomes dominant. For CH(3)CHOH + H, there are three major product channels; at high temperatures, CH(3)+CH(2)OH production predominates at low pressures (P < 100 Torr), while the formation of CH(3)CH(2)OH by collisional deactivation becomes competitive at high pressures and low temperatures (T < 500 K). At high temperatures, the direct hydrogen abstraction reaction producing CH(2)CHOH + H(2) becomes dominant. Rate constants for all accessible product channels in both systems have been predicted and tabulated for modeling applications. The predicted value for CH(3)CHOH + H at 295 K and 1 Torr pressure agrees closely with available experimental data. For practical modeling applications, the rate constants for the thermal unimolecular decomposition of ethanol giving key accessible products have been predicted; those for the two major product channels taking place by dehydration and C-C breaking agree closely with available literature data.

  16. Ab Initio Chemical Kinetics for the CH3 + O((3)P) Reaction and Related Isomerization-Decomposition of CH3O and CH2OH Radicals.

    PubMed

    Xu, Z F; Raghunath, P; Lin, M C

    2015-07-16

    The kinetics and mechanism of the CH3 + O reaction and related isomerization-decomposition of CH3O and CH2OH radicals have been studied by ab initio molecular orbital theory based on the CCSD(T)/aug-cc-pVTZ//CCSD/aug-cc-pVTZ, CCSD/aug-cc-pVDZ, and G2M//B3LYP/6-311+G(3df,2p) levels of theory. The predicted potential energy surface of the CH3 + O reaction shows that the CHO + H2 products can be directly generated from CH3O by the TS3 → LM1 → TS7 → LM2 → TS4 path, in which both LM1 and LM2 are very loose and TS7 is roaming-like. The result for the CH2O + H reaction shows that there are three low-energy barrier processes including CH2O + H → CHO + H2 via H-abstraction and CH2O + H → CH2OH and CH2O + H → CH3O by addition reactions. The predicted enthalpies of formation of the CH2OH and CH3O radicals at 0 K are in good agreement with available experimental data. Furthermore, the rate constants for the forward and some key reverse reactions have been predicted at 200-3000 K under various pressures. Based on the new reaction pathway for CH3 + O, the rate constants for the CH2O + H and CHO + H2 reactions were predicted with the microcanonical variational transition-state/Rice-Ramsperger-Kassel-Marcus (VTST/RRKM) theory. The predicted total and individual product branching ratios (i.e., CO versus CH2O) are in good agreement with experimental data. The rate constant for the hydrogen abstraction reaction of CH2O + H has been calculated by the canonical variational transition-state theory with quantum tunneling and small-curvature corrections to be k(CH2O + H → CHO + H2) = 2.28 × 10(-19) T(2.65) exp(-766.5/T) cm(3) molecule(-1) s(-1) for the 200-3000 K temperature range. The rate constants for the addition giving CH3O and CH2OH and the decomposition of the two radicals have been calculated by the microcanonical RRKM theory with the time-dependent master equation solution of the multiple quantum well system in the 200-3000 K temperature range at 1 Torr to

  17. Electron spin resonance of (CO 2 H)CH 2 CH 2 CH(CO 2 H) in irradiated glutaric acid

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Horsfield, A.; Morton, J. R.; Whiffen, D. H.

    It is concluded from electron spin resonance spectra that the radical (CO 2 H)CH 2 CH 2 CH(CO 2 H) remains trapped in a glutaric acid crystal after gamma -irradiation. This radical is found in two different conformations. Approximate hyperfine coupling constants are given for each, although exact interpretation is hindered by the overlapping of spectra. Reasons for the formation of the two forms of the radical are discussed.

  18. On the formation of the ·CH 2CH 2CH=NH 2+ distonic radical cation upon ionization of cyclopropylamine and allylamine

    NASA Astrophysics Data System (ADS)

    Nguyen, Minh Tho; Creve, Steven; Ha, Tae-Kyu

    1998-08-01

    Ab initio molecular orbital and density functional theory calculations have been applied to determine the relative stability of the cyclopropylamine 1 and allylamine (CH 2=CHCH 2NH 2+·2) radical cations and their isomers. It is confirmed that, upon ionization, 1 undergoes barrier-free ring-opening giving the distonic species ·CH 2CH 2CH=NH 2+3. 2 also rearranges by a 1,2-H-shift to the more stable 3 (by 70 kJ/mol) which is, however, less stable than the 1-aminopropene ion (CH 3-CH=CH-NH 2+·4) by 60 kJ/mol. The transition structure TS 2/3 lies 40 kJ/mol higher in energy than TS 3/4. Although QCISD and B3LYP calculations of isotropic hyperfine coupling constants agree reasonably with observed values, supporting the presence of the distonic 3 in ESR matrix experiments, the exclusive observation of 3, but not 4, is intriguing. This emphasizes the role of the matrix in stabilizing 3.

  19. Rate Constants for the Reactions of OH with CH(sub 3)Cl, CH(sub 2) C1(sub 2), CHC1(sub 3)and CH(sub 3)Br

    NASA Technical Reports Server (NTRS)

    Hsu, H-J.; DeMore, W.

    1994-01-01

    Rate constants for the reactions of OH with CH3C1, CH2Cl2, CHCl3 and CH3Br have been measured by a relative rate technique in which the reaction rate of each compound was compared to that of HFC-152a (CH3CHF2)and for CH2Cl2, HFC-161 (CH3CH2F).

  20. Low-Temperature Hydrocarbon Photochemistry: CH3 + CH3 Recombination in Giant Planet Atmospheres

    NASA Technical Reports Server (NTRS)

    Smith, Gregory P.; Huestis, David L.

    2002-01-01

    Planetary emissions of the methyl radical CH3 were observed for the first time in 1998 on Saturn and Neptune by the ISO (Infrared Space Observatory) mission satellite. CH3 is produced by VUV photolysis of CH4 and is the key photochemical intermediate leading complex organic molecules on the giant planets and moons. The CH3 emissions from Saturn were unexpectedly weak. A suggested remedy is to increase the rate of the recombination reaction CH3 + CH3 + H2 --> C2H6 + H2 at 140 K to a value at least 10 times that measured at room temperature in rare gases, but within the range of disagreeing theoretical expressions at low temperature. We are performing laboratory experiments at low temperature and very low pressure. The experiments are supported by RRKM theoretical modeling that is calibrated using the extensive combustion literature.

  1. Unusual reaction paths of SN2 nucleophile substitution reactions CH4 + H- → CH4 + H- and CH4 + F- → CH3F + H-: Quantum chemical calculations

    NASA Astrophysics Data System (ADS)

    Minyaev, Ruslan M.; Quapp, Wolfgang; Schmidt, Benjamin; Getmanskii, Ilya V.; Koval, Vitaliy V.

    2013-11-01

    Quantum chemical (CCSD(full)/6-311++G(3df,3pd), CCSD(T)(full)/6-311++G(3df,3pd)) and density function theory (B3LYP/6-311++G(3df,3pd)) calculations were performed for the SN2 nucleophile substitution reactions CH4 + H- → CH4 + H- and CH4 + F- → CH3F + H-. The calculated gradient reaction pathways for both reactions have an unusual behavior. An unusual stationary point of index 2 lies on the gradient reaction path. Using Newton trajectories for the reaction path, we can detect VRI point at which the reaction path branches.

  2. Reflected shock tube studies of high-temperature rate constants for OH + CH4 --> CH3 + H2O and CH3 + NO2 --> CH3O + NO.

    PubMed

    Srinivasan, N K; Su, M-C; Sutherland, J W; Michael, J V

    2005-03-10

    The reflected shock tube technique with multipass absorption spectrometric detection of OH radicals at 308 nm has been used to study the reactions OH + CH(4) --> CH(3) + H(2)O and CH(3) + NO(2) --> CH(3)O + NO. Over the temperature range 840-2025 K, the rate constants for the first reaction can be represented by the Arrhenius expression k = (9.52 +/- 1.62) x 10(-11) exp[(-4134 +/- 222 K)/T] cm(3) molecule(-1) s(-1). Since this reaction is important in both combustion and atmospheric chemistry, there have been many prior investigations with a variety of techniques. The present results extend the temperature range by 500 K and have been combined with the most accurate earlier studies to derive an evaluation over the extended temperature range 195-2025 K. A three-parameter expression describes the rate behavior over this temperature range, k = (1.66 x 10(-18))T(2.182) exp[(-1231 K)/T] cm(3) molecule(-1) s(-1). Previous theoretical studies are discussed, and the present evaluation is compared to earlier theoretical estimates. Since CH(3) radicals are a product of the reaction and could cause secondary perturbations in rate constant determinations, the second reaction was studied by OH radical production from the fast reactions CH(3)O --> CH(2)O + H and H + NO(2) --> OH + NO. The measured rate constant is 2.26 x 10(-11) cm(3) molecule(-1) s(-1) and is not dependent on temperature from 233 to 1700 K within experimental error.

  3. Total cross sections of electron scattering by molecules NF3, PF3, N(CH3)3, P(CH3)3, NH(CH3)2, PH(CH3)2, NH2CH3 and PH2CH3 at 30-5000 eV

    NASA Astrophysics Data System (ADS)

    Shi, D. H.; Sun, J. F.; Zhu, Z. L.; Liu, Y. F.

    2010-04-01

    Total cross sections of electron scattering by eight molecules NF3, PF3, N(CH3)3, P(CH3)3, NH(CH3)2, PH(CH3)2, NH2CH3 and PH2CH3, which have some structural similarities, are calculated at the Hartree-Fork level by the modified additivity rule approach [D.H. Shi, J.F. Sun, Z.L. Zhu, H. Ma, Y.F. Liu, Eur. Phys. J. D 45, 253 (2007); D.H. Shi, J.F. Sun, Y.F. Liu, Z.L. Zhu, X.D. Yang, Chin. Opt. Lett. 4, 192 (2006)]. The modified additivity rule approach takes into considerations that the contributions of the geometric shielding effect vary as the energy of incident electrons, the dimension of target molecule, the number of electrons in the molecule and the number of atoms constituting the molecule. The present investigations cover the impact energy range from 30 to 5000 eV. The quantitative total cross sections are compared with those obtained by experiments and other theories. Excellent agreement is observed even at energies of several tens of eV. It shows that the modified additivity rule approach is applicable to carry out the total cross section calculations of electron scattering by these molecules at intermediate and high energies, in particular over the energy range above 80 eV or so. It proves that the microscopic molecular properties, such as the geometrical size of the target and the number of atoms constituting the molecule, are of crucial importance in the TCS calculations. The new results for PH(CH3)2 and PH2CH3 are also presented at energies from 30 to 5000 eV, although no experimental and theoretical data are available for comparison. In the present calculations, the atoms are still represented by the spherical complex optical potential, which is composed of static, exchange, polarization and absorption terms.

  4. Two-wavelength single laser CH and CH(4) imaging in a lifted turbulent diffusion flame.

    PubMed

    Namazian, M; Schmitt, R L; Long, M B

    1988-09-01

    A new technique has been developed which allows simultaneous 2-D mapping of CH and CH 4 in a turbulent methane flame. A flashlamp-pumped dye laser using two back mirrors produces output at 431.5 and 444 nm simultaneously. The 431.5-nm line is used to excite the (0, 0) band of the A(2)Delta-X(2)Pi system of CH, and the fluorescence of the (0, 1) transition is observed at 489 nm. Coincidentally, the spontaneous Raman scattering from CH(4) also occurs near 489 nm for a 431.5-nm excitation. To separate the CH(4) and CH contributions, the 444-nm line is used to produce a spontaneous Raman signal from CH(4) that is spectrally separated from the CH fluorescence. Subtraction of the signals generated by the 431.5- and 444-nm wavelength beams yields separate measurements of CH(4) and CH. Raman-scattered light records the instantaneous distribution of the fuel, and simultaneously the CH fluorescence indicates the location of the flame zone. The resulting composite images provide important insight on the interrelationship between fuel-air mixing and subsequent combustion.M. Namazian is with Altex Technologies Corporation, 109 Via De Tesoros, Los Gatos, California 95030; R. L. Schmitt is with Sandia National Laboratories, Combustion Research Facility, Livermore, California 94550; and M. B. Long is with Yale University, Department of Mechanical Engineering, New Haven, Connecticut 06520.

  5. Electron driven processes in sulphur containing compounds CH3SCH3 and CH3SSCH3

    NASA Astrophysics Data System (ADS)

    Kopyra, Janina; Władziński, Jakub

    2015-06-01

    Dissociative electron attachment to gas phase dimethyl sulphide (CH3SCH3) and dimethyl disulphide (CH3SSCH3) has been studied by means of a crossed beams apparatus. Cleavage of the C-S bond within CH3SCH3 and the S-S bond within CH3SSCH3 is observed within a resonance in the energy range below 2 eV and visible preferentially via the appearance of the fragment CH2S-. The striking finding is that the intensity of CH2S- generated from CH3SSCH3 is more than two orders of magnitude higher than the intensity of the respective anionic fragment generated from CH3SCH3. Our results clearly demonstrate that the CH3SSCH3 molecule, which contains disulphide bridge is substantially more sensitive towards electron attachment resulting mainly in dissociation along the S-S bridge.

  6. Scaled Hartree-Fock force field calculations for organothallium compounds: Normal-mode analysis for TlCH sub 3 Tl(CH sub 3 ) sub 2 sup + , Tl(CH sub 3 ) sub 3 , Tl(CH sub 3 ) sub 2 Br, and Tl(CH sub 3 ) sub 4 sup minus

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Schwerdtfeger, P.; Bowmaker, G.A.; Boyd, P.D.W.

    1990-02-01

    In a recent paper we presented Hartree-Fock (HF) calculations for aliphatic organothallium compounds. The diagonal HF force constants obtained from a Fletcher-Powell geometry optimization are now used for a normal-mode analysis of TlCH{sub 3}, Tl(CH{sub 3}){sub 2}{sup +}, Tl(CH{sub 3}){sub 3}, Tl(CH{sub 3}){sub 2}Br, and Tl(CH{sub 3}){sub 4}{sup {minus}}. In order to calculate frequencies comparable to experimental values, the HF force field has been scaled by using scaling factors obtained from experimental infrared and Raman measurements on Tl(CH{sub 3}){sub 2}{sup +} and TlBr. The vibrational spectra of Tl(CH{sub 3}){sub 2}{sup +} were remeasured (infrared and Raman) in order to obtainmore » an accurate force field. Predictions are made for the vibrational spectrum of the as yet undetected TlCH{sub 3} molecule. Experimental infrared and Raman results for Tl(CH{sub 3}){sub 3} compare reasonably well with our calculated frequencies. Relativistic and correlation effects are analyzed for the vibrational frequencies of Tl(CH{sub 3}){sub 2}{sup +}.« less

  7. CH-TRU Waste Content Codes

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Washington TRU Solutions LLC

    2008-01-16

    The CH-TRU Waste Content Codes (CH-TRUCON) document describes the inventory of the U.S. Department of Energy (DOE) CH-TRU waste within the transportation parameters specified by the Contact-Handled Transuranic Waste Authorized Methods for Payload Control (CH-TRAMPAC). The CH-TRAMPAC defines the allowable payload for the Transuranic Package Transporter-II (TRUPACT-II) and HalfPACT packagings. This document is a catalog of TRUPACT-II and HalfPACT authorized contents and a description of the methods utilized to demonstrate compliance with the CH-TRAMPAC. A summary of currently approved content codes by site is presented in Table 1. The CH-TRAMPAC describes "shipping categories" that are assigned to each payload container.more » Multiple shipping categories may be assigned to a single content code. A summary of approved content codes and corresponding shipping categories is provided in Table 2, which consists of Tables 2A, 2B, and 2C. Table 2A provides a summary of approved content codes and corresponding shipping categories for the "General Case," which reflects the assumption of a 60-day shipping period as described in the CH-TRAMPAC and Appendix 3.4 of the CH-TRU Payload Appendices. For shipments to be completed within an approximately 1,000-mile radius, a shorter shipping period of 20 days is applicable as described in the CH-TRAMPAC and Appendix 3.5 of the CH-TRU Payload Appendices. For shipments to WIPP from Los Alamos National Laboratory (LANL), Nevada Test Site, and Rocky Flats Environmental Technology Site, a 20-day shipping period is applicable. Table 2B provides a summary of approved content codes and corresponding shipping categories for "Close-Proximity Shipments" (20-day shipping period). For shipments implementing the controls specified in the CH-TRAMPAC and Appendix 3.6 of the CH-TRU Payload Appendices, a 10-day shipping period is applicable. Table 2C provides a summary of approved content codes and corresponding shipping categories for "Controlled

  8. Formation of unexpected silicon- and disiloxane-bridged multiferrocenyl derivatives bearing Si-O-CH[double bond, length as m-dash]CH2 and Si-(CH2)2C(CH3)3 substituents via cleavage of tetrahydrofuran and trapping of its ring fragments.

    PubMed

    Bruña, Sonia; González-Vadillo, Ana Mª; Ferrández, Marta; Perles, Josefina; Montero-Campillo, M Merced; Mó, Otilia; Cuadrado, Isabel

    2017-09-12

    The formation of a family of silicon- and siloxane-bridged multiferrocenyl derivatives carrying different functional groups attached to silicon, including Fc 2 (CH 3 ) 3 C(CH 2 ) 2 SiCH[double bond, length as m-dash]CH 2 (5), Fc 2 (CH 2 [double bond, length as m-dash]CH-O)SiCH[double bond, length as m-dash]CH 2 (6), Fc 2 (OH)SiCH[double bond, length as m-dash]CH 2 (7), Fc 2 (CH 2 [double bond, length as m-dash]CH-O)Si-O-Si(O-CH[double bond, length as m-dash]CH 2 )Fc 2 (8) and Fc 2 (CH 2 [double bond, length as m-dash]CH-O)Si-O-SiFc 3 (9) is described. Silyl vinyl ether molecules 6, 8 and 9 and the heteroleptic vinylsilane 5 resulted from the competing metathesis reaction of lithioferrocene (FcLi), CH 2 [double bond, length as m-dash]CH-OLi or (CH 3 ) 3 C(CH 2 ) 2 Li with the corresponding multifunctional chlorosilane, Cl 3 SiCH[double bond, length as m-dash]CH 2 or Cl 3 Si-O-SiCl 3 . The last two organolithium species have been likely formed in situ by fragmentation of the tetrahydrofuran solvent. Diferrocenylvinyloxyvinylsilane 6 is noteworthy since it represents a rare example of a redox-active silyl mononomer in which two different C[double bond, length as m-dash]C polymerisable groups are directly connected to silicon. The molecular structures of the silicon-containing multiferrocenyl species 5, 6, 8 and 9 have been investigated by single-crystal X-ray diffraction studies, demonstrating the capture and storage processes of two ring fragments resulting from the cleavage of cyclic THF in redox-active and stable crystalline organometallic compounds. From electrochemical studies we found that by changing the anion of the supporting electrolyte from [PF 6 ] - to [B(C 6 F 5 ) 4 ] - , the redox behaviour of tetrametallic disiloxane 8 can be switched from a poorly resolved multistep redox process to four consecutive well-separated one-electron oxidations, corresponding to the sequential oxidation of the four ferrocenyl moieties.

  9. Direct observation of unimolecular decay of CH 3 CH 2 CHOO Criegee intermediates to OH radical products

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Fang, Yi; Liu, Fang; Klippenstein, Stephen J.

    2016-07-28

    The unimolecular decay of carbonyl oxide intermediates, known as Criegee intermediates, produced in alkene ozonolysis is a significant source of OH radicals in the troposphere. Here, the rate of appearance of OH radical products is examined directly in the time-domain for a prototypical alkyl-substituted Criegee intermediate, CH3CH2CHOO, following vibrational activation under collision-free conditions. Complementary statistical Rice-Ramsperger-Kassel-Marcus calculations of the microcanonical unimolecular decay rate for CH3CH2CHOO are also carried out at energies in the vicinity of the barrier for 1,4 hydrogen atom transfer that leads to OH products. Tunneling through the barrier, derived from high level electronic structure calculations, contributes significantlymore » to the decay rate. Infrared transitions of CH3CH2CHOO are identified in the CH stretch overtone region, which are detected by ultraviolet laser-induced fluorescence of the resultant OH products. The features observed are attributed to CH vibrational excitations and conformational forms utilizing insights from theory. Both experiment and theory yield unimolecular decay rates for CH3CH2CHOO of ca. 10(7) s(-1), which are slower than those obtained for syn-CH3CHOO or (CH3)(2)COO reported previously [Fang et al., J. Chem. Phys. 144, 061102 (2016)] at similar energies. Master equation modeling is also utilized to predict the thermal decay rate of CH3CH2CHOO under atmospheric conditions, giving a rate of 279 s(-1) at 298 K.« less

  10. Nuclear Hyperfine Structure in the Donor – Acceptor Complexes (CH3)3N-BF3 and (CH)33N-B(CH3)3

    EPA Science Inventory

    The donor-acceptor complexes (CH3)3N-BF3 and (CH3)3N-B(CH3)3 have been reinvestigated at high resolution by rotational spectroscopy in a supersonic jet. Nuclear hyperfine structure resulting from both nitrogen and boron has been resolved and quadrupole coupling constants have bee...

  11. ChIP-chip versus ChIP-seq: Lessons for experimental design and data analysis

    PubMed Central

    2011-01-01

    Background Chromatin immunoprecipitation (ChIP) followed by microarray hybridization (ChIP-chip) or high-throughput sequencing (ChIP-seq) allows genome-wide discovery of protein-DNA interactions such as transcription factor bindings and histone modifications. Previous reports only compared a small number of profiles, and little has been done to compare histone modification profiles generated by the two technologies or to assess the impact of input DNA libraries in ChIP-seq analysis. Here, we performed a systematic analysis of a modENCODE dataset consisting of 31 pairs of ChIP-chip/ChIP-seq profiles of the coactivator CBP, RNA polymerase II (RNA PolII), and six histone modifications across four developmental stages of Drosophila melanogaster. Results Both technologies produce highly reproducible profiles within each platform, ChIP-seq generally produces profiles with a better signal-to-noise ratio, and allows detection of more peaks and narrower peaks. The set of peaks identified by the two technologies can be significantly different, but the extent to which they differ varies depending on the factor and the analysis algorithm. Importantly, we found that there is a significant variation among multiple sequencing profiles of input DNA libraries and that this variation most likely arises from both differences in experimental condition and sequencing depth. We further show that using an inappropriate input DNA profile can impact the average signal profiles around genomic features and peak calling results, highlighting the importance of having high quality input DNA data for normalization in ChIP-seq analysis. Conclusions Our findings highlight the biases present in each of the platforms, show the variability that can arise from both technology and analysis methods, and emphasize the importance of obtaining high quality and deeply sequenced input DNA libraries for ChIP-seq analysis. PMID:21356108

  12. Resolved 12CH2D2 and 13CH3D in CH4 as Sensitive Indicators of Disequilibrium and Equilibrium during Microbial Methane Cycling

    NASA Astrophysics Data System (ADS)

    Ash, J. L.; Egger, M.; Slomp, C. P.; Kohl, I. E.; Treude, T.; Rumble, D.; Young, E. D.

    2016-12-01

    The ability to measure the relative concentrations of at least two doubly-substituted rare isotopologues of gases with biogeochemical relevance provides new constraints on sources and sinks of these gases. In particular, as shown recently for O2, the use of two independent, rare isotopologues allows for detection of thermodynamic intra-species equilibrium and disequilibrium. Here, we report the first measurements of fully resolved 13CH3D and 12CH2D2 from natural samples of microbial methane gas. A suite of sedimentary methane samples from the Bornholm Basin in the Baltic Sea was collected during IODP Exp. 347. Sample depths range from 2-20 meters below seafloor (mbsf). Methane concentrations decrease with depth, and mcrA (a marker for methanogenesis and methanotropy) is present throughout. See Figure. Both Δ13CH3D and Δ12CH2D2 increase with depth as methane concentrations decrease with the shallowest samples exhibiting disequilibrium by up to 2‰ in Δ13CH3D and 13‰ in Δ12CH2D2 while the deepest samples approach isotopic thermodynamic equilibrium (marked by grey bars in Figure). The Fe-mediated anaerobic oxidation of methane (Fe-AOM) has been inferred in these sediments by geochemical modeling . Slow methane cycling by methanogensis and methanotrophy is likely responsible for the approach to isotopic bond order equilibrium in CH4 with depth, consistent with Fe-AOM. While axenic culturing experiments generate methane with large deficits in 12CH2D2 (reported at this meeting), these data from the Baltic Sea demonstrate that isotopic equilibrium can be achieved during microbial recycling of methane. In the absence of Δ12CH2D2, the Δ13CH3D values alone could be misinterpreted as representing gradients in temperature due perhaps to exothermic organic matter degradation. The combination of both mass-18 rare isotopologues of methane provides the means to distinguish equilibrium from disequilibrium and probe microbial methane cycling even where Δ13CH3D suggests

  13. Diminished CAGE Effect in {p}-H2: Infrared Spectra of CH3S Observed from Photolysis of CH3SH, CH3SCH3, and CH3SSCH3 Isolated in {p}-H2

    NASA Astrophysics Data System (ADS)

    Lee, Yuan-Pern; Bahou, Mohammed

    2010-06-01

    We report infrared absorption spectrum of the methylthio (or thiomethoxy) radical, CH3S, isolated in solid {p}-H2. CH3S was produced by in situ UV photodissociation of three precursors: CH3SH, CH3SH3, and CH3SSCH3 isolated in solid {p}-H2. New absorption features commonly observed with similar intensity ratios in experiments using these precursors are assigned as absorption of CH3S. In Addition to the previously assigned transitions of ν 3 (a1) at 727.1 cm-1, fundamental transitions ν 6 (a1) at 771.1, ν 6 (e) at 1056.6, ν 5 (a1) at 1400.0, and &nu 4 (a1) at 2898.0 cm-1 were observed. The wavenumbers of these features agree satisfactorily with those predicted with a spin-vibronic Hamiltonian accounting for the anharmonic effects and the Jahn-Teller effects to the qu rtic term; the corresponding wavenumbers predicted from theory are ν 6 (a1) at 793, ν 6 (e) at 1105, ν 5 (a1) at 1436, and ν 4 (a1) at 2938 cm-1, with deviations of 14-4.6 % from experiments. Previous attempts of UV photolysis of CH3SCH3 and CH3SSCH3 isolated in an Ar matrix failed to produce CH3S. These results serve as an excellent example that the diminished cae effect of solid {p}-H2 makes production of free radicals via photolysis in situ feasible. If time permits, other examples will be discussed. A. V. Marenich and J. E. Boggs, J. Chem. Theory Comput., 1, 1162 (2005).

  14. Effects of Boreal Lake Wetlands on Atmospheric 13CH3D and 12CH2D2

    NASA Astrophysics Data System (ADS)

    Haghnegahdar, M. A.; Kohl, I. E.; Schauble, E. A.; Walter Anthony, K. M.; Young, E. D.

    2017-12-01

    Recently, we developed a theoretical model to investigate the potential use of 13CH3D and 12CH2D2 as tools for tracking atmospheric methane budget. We used electronic structure methods to estimate kinetic isotope fractionations associated with the major sink reactions of CH4 in air (reactions with •OH and Cl•), and literature data with reconnaissance measurements of the relative abundances of 13CH3D and 12CH2D2 to estimate the compositions of the largest atmospheric sources. Here we present new methane rare isotopologue data from boreal wetlands, comprising one of the most important sources, in order to evaluate the robustness of the model. Boreal wetlands (>55° N) account for more than half of the wetland area in the Northern hemisphere. We analyzed methane samples from high latitude lakes representing different geographical regions, geological and ecological contexts, methane fluxes, and isotopic signatures. Using clumped isotopes of CH4 we are able to determine the likely production mechanism for natural CH4 samples. So far, all of our analyzed samples except one plot in the microbial pure-culture methanogenesis field (Young et al. 2017) with ranges of -0.2‰ to +1.2‰ for Δ13CH3D, and -29.6‰ to -18.2‰ for Δ12CH2D2. These compositions are far from equilibrium. The one exception, from Lake Doughnut, Alaska, exhibits Δ13CH3D and Δ12CH2D2 values of +5.2‰ and +18.7‰, respectively, which fall near ambient thermodynamic equilibrium values. This may be an effect of methanotrophy. Mean Δ13CH3D and Δ12CH2D2 for all lake samples are +1.7‰ and -15.4‰ respectively, compared to our original estimate of +6.1‰ and +21.2‰ for the wetland methane source based on an assumption of equilibrium. If we assume that these samples are representative of the overall wetland source, Δ13CH3D decreases by 0.8‰ and Δ12CH2D2 decreases by 0.6‰ in our model of bulk atmospheric methane. Δ13CH3D and Δ12CH2D2 values of air (including •OH and Cl• sink

  15. ChIPWig: a random access-enabling lossless and lossy compression method for ChIP-seq data.

    PubMed

    Ravanmehr, Vida; Kim, Minji; Wang, Zhiying; Milenkovic, Olgica

    2018-03-15

    Chromatin immunoprecipitation sequencing (ChIP-seq) experiments are inexpensive and time-efficient, and result in massive datasets that introduce significant storage and maintenance challenges. To address the resulting Big Data problems, we propose a lossless and lossy compression framework specifically designed for ChIP-seq Wig data, termed ChIPWig. ChIPWig enables random access, summary statistics lookups and it is based on the asymptotic theory of optimal point density design for nonuniform quantizers. We tested the ChIPWig compressor on 10 ChIP-seq datasets generated by the ENCODE consortium. On average, lossless ChIPWig reduced the file sizes to merely 6% of the original, and offered 6-fold compression rate improvement compared to bigWig. The lossy feature further reduced file sizes 2-fold compared to the lossless mode, with little or no effects on peak calling and motif discovery using specialized NarrowPeaks methods. The compression and decompression speed rates are of the order of 0.2 sec/MB using general purpose computers. The source code and binaries are freely available for download at https://github.com/vidarmehr/ChIPWig-v2, implemented in C ++. milenkov@illinois.edu. Supplementary data are available at Bioinformatics online.

  16. Martian CH(4): sources, flux, and detection.

    PubMed

    Onstott, T C; McGown, D; Kessler, J; Lollar, B Sherwood; Lehmann, K K; Clifford, S M

    2006-04-01

    Recent observations have detected trace amounts of CH(4) heterogeneously distributed in the martian atmosphere, which indicated a subsurface CH(4) flux of ~2 x 10(5) to 2 x 10(9) cm(2) s(1). Four different origins for this CH(4) were considered: (1) volcanogenic; (2) sublimation of hydrate- rich ice; (3) diffusive transport through hydrate-saturated cryosphere; and (4) microbial CH(4) generation above the cryosphere. A diffusive flux model of the martian crust for He, H(2), and CH(4) was developed based upon measurements of deep fracture water samples from South Africa. This model distinguishes between abiogenic and microbial CH(4) sources based upon their isotopic composition, and couples microbial CH(4) production to H(2) generation by H(2)O radiolysis. For a He flux of approximately 10(5) cm(2) s(1) this model yields an abiogenic CH(4) flux and a microbial CH(4) flux of approximately 10(6) and approximately 10(9) cm(2) s(1), respectively. This flux will only reach the martian surface if CH(4) hydrate is saturated in the cryosphere; otherwise it will be captured within the cryosphere. The sublimation of a hydrate-rich cryosphere could generate the observed CH(4) flux, whereas microbial CH(4) production in a hypersaline environment above the hydrate stability zone only seems capable of supplying approximately 10(5) cm(2) s(1) of CH(4). The model predicts that He/H(2)/CH(4)/C(2)H(6) abundances and the C and H isotopic values of CH(4) and the C isotopic composition of C(2)H(6) could reveal the different sources. Cavity ring-down spectrometers represent the instrument type that would be most capable of performing the C and H measurements of CH(4) on near future rover missions and pinpointing the cause and source of the CH(4) emissions.

  17. Contrast between the mechanisms for dissociative electron attachment to CH3SCN and CH3NCS.

    PubMed

    Miller, Thomas M; Viggiano, Albert A; Shuman, Nicholas S

    2018-05-14

    The kinetics of thermal electron attachment to methyl thiocyanate (CH 3 SCN), methyl isothiocyanate (CH 3 NCS), and ethyl thiocyanate (C 2 H 5 SCN) were measured using flowing afterglow-Langmuir probe apparatuses at temperatures between 300 and 1000 K. CH 3 SCN and C 2 H 5 SCN undergo inefficient dissociative attachment to yield primarily SCN - at 300 K (k = 2 × 10 -10 cm 3 s -1 ), with increasing efficiency as temperature increases. The increase is well described by activation energies of 0.17 eV (CH 3 SCN) and 0.14 eV (C 2 H 5 SCN). CN - product is formed at <1% branching at 300 K, increasing to ∼30% branching at 1000 K. Attachment to CH 3 NCS yields exclusively SCN - ionic product but at a rate at 300 K that is below our detection threshold (k < 10 -12 cm 3 s -1 ). The rate coefficient increases rapidly with increasing temperature (k = 6 × 10 -11 cm 3 s -1 at 600 K), in a manner well described by an activation energy of 0.51 eV. Calculations at the B3LYP/def2-TZVPPD level suggest that attachment to CH 3 SCN proceeds through a dissociative state of CH 3 SCN - , while attachment to CH 3 NCS initially forms a weakly bound transient anion CH 3 NCS -* that isomerizes over an energetic barrier to yield SCN - . Kinetic modeling of the two systems is performed in an attempt to identify a kinetic signature differentiating the two mechanisms. The kinetic modeling reproduces the CH 3 NCS data only if dissociation through the transient anion is considered.

  18. Contrast between the mechanisms for dissociative electron attachment to CH3SCN and CH3NCS

    NASA Astrophysics Data System (ADS)

    Miller, Thomas M.; Viggiano, Albert A.; Shuman, Nicholas S.

    2018-05-01

    The kinetics of thermal electron attachment to methyl thiocyanate (CH3SCN), methyl isothiocyanate (CH3NCS), and ethyl thiocyanate (C2H5SCN) were measured using flowing afterglow-Langmuir probe apparatuses at temperatures between 300 and 1000 K. CH3SCN and C2H5SCN undergo inefficient dissociative attachment to yield primarily SCN- at 300 K (k = 2 × 10-10 cm3 s-1), with increasing efficiency as temperature increases. The increase is well described by activation energies of 0.17 eV (CH3SCN) and 0.14 eV (C2H5SCN). CN- product is formed at <1% branching at 300 K, increasing to ˜30% branching at 1000 K. Attachment to CH3NCS yields exclusively SCN- ionic product but at a rate at 300 K that is below our detection threshold (k < 10-12 cm3 s-1). The rate coefficient increases rapidly with increasing temperature (k = 6 × 10-11 cm3 s-1 at 600 K), in a manner well described by an activation energy of 0.51 eV. Calculations at the B3LYP/def2-TZVPPD level suggest that attachment to CH3SCN proceeds through a dissociative state of CH3SCN-, while attachment to CH3NCS initially forms a weakly bound transient anion CH3NCS-* that isomerizes over an energetic barrier to yield SCN-. Kinetic modeling of the two systems is performed in an attempt to identify a kinetic signature differentiating the two mechanisms. The kinetic modeling reproduces the CH3NCS data only if dissociation through the transient anion is considered.

  19. Sequential ChIP Protocol for Profiling Bivalent Epigenetic Modifications (ReChIP).

    PubMed

    Desvoyes, Bénédicte; Sequeira-Mendes, Joana; Vergara, Zaida; Madeira, Sofia; Gutierrez, Crisanto

    2018-01-01

    Identification of chromatin modifications, e.g., histone acetylation and methylation, among others, is widely carried out by using a chromatin immunoprecipitation (ChIP) strategy. The information obtained with these procedures is useful to gain an overall picture of modifications present in all cells of the population under study. It also serves as a basis to figure out the mechanisms of chromatin organization and gene regulation at the population level. However, the ultimate goal is to understand gene regulation at the level of single chromatin fibers. This requires the identification of chromatin modifications that occur at a given genomic location and within the same chromatin fiber. This is achieved by following a sequential ChIP strategy using two antibodies to distinguish different chromatin modifications. Here, we describe a sequential ChIP protocol (Re-ChIP), paying special attention to the controls needed and the required steps to obtain meaningful and reproducible results. The protocol is developed for young Arabidopsis seedlings but could be adapted to other plant materials.

  20. In-plane chemical pressure essential for superconductivity in BiCh2-based (Ch: S, Se) layered structure

    PubMed Central

    Mizuguchi, Yoshikazu; Miura, Akira; Kajitani, Joe; Hiroi, Takafumi; Miura, Osuke; Tadanaga, Kiyoharu; Kumada, Nobuhiro; Magome, Eisuke; Moriyoshi, Chikako; Kuroiwa, Yoshihiro

    2015-01-01

    BiCh2-based compounds (Ch: S, Se) are a new series of layered superconductors, and the mechanisms for the emergence of superconductivity in these materials have not yet been elucidated. In this study, we investigate the relationship between crystal structure and superconducting properties of the BiCh2-based superconductor family, specifically, optimally doped Ce1−xNdxO0.5F0.5BiS2 and LaO0.5F0.5Bi(S1−ySey)2. We use powder synchrotron X-ray diffraction to determine the crystal structures. We show that the structure parameter essential for the emergence of bulk superconductivity in both systems is the in-plane chemical pressure, rather than Bi-Ch bond lengths or in-plane Ch-Bi-Ch bond angle. Furthermore, we show that the superconducting transition temperature for all REO0.5F0.5BiCh2 superconductors can be determined from the in-plane chemical pressure. PMID:26447333

  1. Direct observation of unimolecular decay of CH{sub 3}CH{sub 2}CHOO Criegee intermediates to OH radical products

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Fang, Yi; Liu, Fang; Lester, Marsha I., E-mail: milester@sas.upenn.edu

    2016-07-28

    The unimolecular decay of carbonyl oxide intermediates, known as Criegee intermediates, produced in alkene ozonolysis is a significant source of OH radicals in the troposphere. Here, the rate of appearance of OH radical products is examined directly in the time-domain for a prototypical alkyl-substituted Criegee intermediate, CH{sub 3}CH{sub 2}CHOO, following vibrational activation under collision-free conditions. Complementary statistical Rice–Ramsperger–Kassel–Marcus calculations of the microcanonical unimolecular decay rate for CH{sub 3}CH{sub 2}CHOO are also carried out at energies in the vicinity of the barrier for 1,4 hydrogen atom transfer that leads to OH products. Tunneling through the barrier, derived from high level electronicmore » structure calculations, contributes significantly to the decay rate. Infrared transitions of CH{sub 3}CH{sub 2}CHOO are identified in the CH stretch overtone region, which are detected by ultraviolet laser-induced fluorescence of the resultant OH products. The features observed are attributed to CH vibrational excitations and conformational forms utilizing insights from theory. Both experiment and theory yield unimolecular decay rates for CH{sub 3}CH{sub 2}CHOO of ca. 10{sup 7} s{sup −1}, which are slower than those obtained for syn-CH{sub 3}CHOO or (CH{sub 3}){sub 2}COO reported previously [Fang et al., J. Chem. Phys. 144, 061102 (2016)] at similar energies. Master equation modeling is also utilized to predict the thermal decay rate of CH{sub 3}CH{sub 2}CHOO under atmospheric conditions, giving a rate of 279 s{sup −1} at 298 K.« less

  2. Thermochemistry and kinetics for 2-butanone-1-yl radical (CH2·C(═O)CH2CH3) reactions with O2.

    PubMed

    Sebbar, N; Bozzelli, J W; Bockhorn, H

    2014-01-09

    Thermochemistry of reactants, intermediates, transition state structures, and products along with kinetics on the association of CH2·C(═O)CH2CH3 (2-butanone-1-yl) with O2 and dissociation of the peroxy adduct isomers are studied. Thermochemical properties are determined using ab initio (G3MP2B3 and G3) composite methods along with density functional theory (B3LYP/6-311g(d,p)). Entropy and heat capacity contributions versus temperature are determined from structures, vibration frequencies, and internal rotor potentials. The CH2·C(═O)CH2CH3 radical + O2 association results in a chemically activated peroxy radical with 27 kcal mol(-1) excess of energy. The chemically activated adduct can react to stabilized peroxy or hydroperoxide alkyl radical adducts, further react to lactones plus hydroxyl radical, or form olefinic ketones and a hydroperoxy radical. Kinetic parameters are determined from the G3 composite methods derived thermochemical parameters, and quantum Rice-Ramsperger-Kassel (QRRK) analysis to calculate k(E) with master equation analysis to evaluate falloff in the chemically activated and dissociation reactions. One new, not previously reported, peroxy chemistry reaction is presented. It has a low barrier path and involves a concerted reaction resulting in olefin formation, H2O elimination, and an alkoxy radical.

  3. Computing energy levels of CH4, CHD3, CH3D, and CH3F with a direct product basis and coordinates based on the methyl subsystem.

    PubMed

    Zhao, Zhiqiang; Chen, Jun; Zhang, Zhaojun; Zhang, Dong H; Wang, Xiao-Gang; Carrington, Tucker; Gatti, Fabien

    2018-02-21

    Quantum mechanical calculations of ro-vibrational energies of CH 4 , CHD 3 , CH 3 D, and CH 3 F were made with two different numerical approaches. Both use polyspherical coordinates. The computed energy levels agree, confirming the accuracy of the methods. In the first approach, for all the molecules, the coordinates are defined using three Radau vectors for the CH 3 subsystem and a Jacobi vector between the remaining atom and the centre of mass of CH 3 . Euler angles specifying the orientation of a frame attached to CH 3 with respect to a frame attached to the Jacobi vector are used as vibrational coordinates. A direct product potential-optimized discrete variable vibrational basis is used to build a Hamiltonian matrix. Ro-vibrational energies are computed using a re-started Arnoldi eigensolver. In the second approach, the coordinates are the spherical coordinates associated with four Radau vectors or three Radau vectors and a Jacobi vector, and the frame is an Eckart frame. Vibrational basis functions are products of contracted stretch and bend functions, and eigenvalues are computed with the Lanczos algorithm. For CH 4 , CHD 3 , and CH 3 D, we report the first J > 0 energy levels computed on the Wang-Carrington potential energy surface [X.-G. Wang and T. Carrington, J. Chem. Phys. 141(15), 154106 (2014)]. For CH 3 F, the potential energy surface of Zhao et al. [J. Chem. Phys. 144, 204302 (2016)] was used. All the results are in good agreement with experimental data.

  4. Computing energy levels of CH4, CHD3, CH3D, and CH3F with a direct product basis and coordinates based on the methyl subsystem

    NASA Astrophysics Data System (ADS)

    Zhao, Zhiqiang; Chen, Jun; Zhang, Zhaojun; Zhang, Dong H.; Wang, Xiao-Gang; Carrington, Tucker; Gatti, Fabien

    2018-02-01

    Quantum mechanical calculations of ro-vibrational energies of CH4, CHD3, CH3D, and CH3F were made with two different numerical approaches. Both use polyspherical coordinates. The computed energy levels agree, confirming the accuracy of the methods. In the first approach, for all the molecules, the coordinates are defined using three Radau vectors for the CH3 subsystem and a Jacobi vector between the remaining atom and the centre of mass of CH3. Euler angles specifying the orientation of a frame attached to CH3 with respect to a frame attached to the Jacobi vector are used as vibrational coordinates. A direct product potential-optimized discrete variable vibrational basis is used to build a Hamiltonian matrix. Ro-vibrational energies are computed using a re-started Arnoldi eigensolver. In the second approach, the coordinates are the spherical coordinates associated with four Radau vectors or three Radau vectors and a Jacobi vector, and the frame is an Eckart frame. Vibrational basis functions are products of contracted stretch and bend functions, and eigenvalues are computed with the Lanczos algorithm. For CH4, CHD3, and CH3D, we report the first J > 0 energy levels computed on the Wang-Carrington potential energy surface [X.-G. Wang and T. Carrington, J. Chem. Phys. 141(15), 154106 (2014)]. For CH3F, the potential energy surface of Zhao et al. [J. Chem. Phys. 144, 204302 (2016)] was used. All the results are in good agreement with experimental data.

  5. CH_{4} production in the deep soil as a source of stem CH_{4} emission in Fagus sylvatica}

    NASA Astrophysics Data System (ADS)

    Maier, Martin; Machacova, Katerina; Urban, Otmar; Lang, Friederike

    2017-04-01

    Predicting greenhouse gas (GHG) fluxes on a global scale requires understanding fluxes on the local scale. Understanding GHG processes in soil-plant-atmosphere systems is essential to understand and mitigate GHG fluxes on the local scale. Forests are known to act as carbon sink. Yet, trees at waterlogged sites are known to emit large amounts of CH4, what can offset the positive GHG balance due the CO2 that is sequestered as wood. Generally, upland trees like European beech (Fagus sylvatica L.) are assumed not to emit CH4, and the upland forest soils are regarded as CH4 sinks. Soil-atmosphere fluxes and stem-atmosphere fluxes of CH4 were studied together with soil gas profiles at two upland beech forest sites in Germany and Czech Republic. Soil was a net CH4 sink at both sites. While most trees showed no or low emissions, one beech tree had exorbitant CH4 emissions that were higher than the CH4 sink capacity of the soil. A soil survey showed strong redoximorphic color patterns in the soil adjacent to this tree. Although the soil around the tree was taking up CH4, the soil gas profiles around this tree showed CH4 production at a soil depth >0.3 m. We interpret the coincidence of the production of CH4 in the deep soil below the beech with the large stem emissions as strong hint that there is a transport link between the soil and stem. We think that the root system represents a preferential transport system for CH4 despite the fact that beech roots usually do not have a special gas transport tissue. The observed CH4 stem emissions represent an important CH4 flux in this ecosystem, and, thus, should be considered in future research. Acknowledgement This research was supported by the Czech Academy of Sciences and the German Academic Exchange Service within the project "Methane (CH4) and nitrous oxide (N2O) emissions from Fagus sylvatica trees" (DAAD-15-03), the Czech Science Foundation (17-18112Y), National Programme for Sustainability I (LO1415) and project DFG (MA 5826

  6. Experimental and Computational Study fo CH, CH*, and OH* in an Axisymmetric Laminar Diffusion Flame

    NASA Technical Reports Server (NTRS)

    Walsh, K. T.

    1998-01-01

    In this study, we extend the results of previous combined numerical and experimental investigations of an axisymmetric laminar diffusion flame in which difference Raman spectroscopy, laser-induced fluorescence (LIF), and a multidimensional flame model were used to generate profiles of the temperature and major and minor species. A procedure is outlined by which the number densities of ground-state CH (X(sup 2)II) excited-state CH (A(sup 2)Delta, denoted CH*), and excited-state OH (A(sup 2)Sigma, denoted OH*) are measured and modeled. CH* and OH* number densities are deconvoluted from line-of-sight flame-emission measurements. Ground-state CH is measured using linear LIF. The computations are done with GRI Mech 2.11 as well as an alternate hydrocarbon mechanism. In both cases, additional reactions for the production and consumption of CH* and OH* are added from recent kinetic studies. Collisional quenching and spontaneous emission are responsible for the de-excitation of the excited-state radicals. As with our previous investigations, GRI Mech 2.11 continues to produce very good agreement with the overall flame length observed in the experiments, while significantly under predicting the flame lift-off height. The alternate kinetic scheme is much more accurate in predicting lift-off height but overpredicts the over-all flame length. Ground-state CH profiles predicted with GRI Mech 2.11 are in excellent agreement with the corresponding measurements, regarding both spatial distribution and absolute concentration (measured at 4 ppm) of the CH radical. Calculations of the excited-state species show reasonable agreement with the measurements as far as spatial distribution and overall characteristics are concerned. For OH*, the measured peak mole fraction, 1.3 x 10(exp -8), compared well with computed peaks, while the measured peak level for CH*, 2 x 10(exp -9), was severely underpredicted by both kinetic schemes, indicating that the formation and destruction kinetics

  7. Infrared-Terahertz Double-Resonance Spectroscopy of CH3F and CH3Cl at Atmospheric Pressure

    DTIC Science & Technology

    2012-05-16

    coincidence with the RQ3(6) rovibrational transition in CH3 35Cl [Fig. 4(b)]. At atmospheric pressure, nine more P -, Q-, and R-branch rovibrational...the double-resonance signatures of all IR-THz pump-probe coincidences at atmospheric pressure for 12CH3F and CH3 35Cl 052507-11050-2947/2012/85(5...were calculated using the rotational constants listed in Tables I and II. For CH3F, the standard P - type (J = − 1), Q-type (J = 0), and R-type (J

  8. ChIP-PIT: Enhancing the Analysis of ChIP-Seq Data Using Convex-Relaxed Pair-Wise Interaction Tensor Decomposition.

    PubMed

    Zhu, Lin; Guo, Wei-Li; Deng, Su-Ping; Huang, De-Shuang

    2016-01-01

    In recent years, thanks to the efforts of individual scientists and research consortiums, a huge amount of chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) experimental data have been accumulated. Instead of investigating them independently, several recent studies have convincingly demonstrated that a wealth of scientific insights can be gained by integrative analysis of these ChIP-seq data. However, when used for the purpose of integrative analysis, a serious drawback of current ChIP-seq technique is that it is still expensive and time-consuming to generate ChIP-seq datasets of high standard. Most researchers are therefore unable to obtain complete ChIP-seq data for several TFs in a wide variety of cell lines, which considerably limits the understanding of transcriptional regulation pattern. In this paper, we propose a novel method called ChIP-PIT to overcome the aforementioned limitation. In ChIP-PIT, ChIP-seq data corresponding to a diverse collection of cell types, TFs and genes are fused together using the three-mode pair-wise interaction tensor (PIT) model, and the prediction of unperformed ChIP-seq experimental results is formulated as a tensor completion problem. Computationally, we propose efficient first-order method based on extensions of coordinate descent method to learn the optimal solution of ChIP-PIT, which makes it particularly suitable for the analysis of massive scale ChIP-seq data. Experimental evaluation the ENCODE data illustrate the usefulness of the proposed model.

  9. The photolysis of CH3ONO

    NASA Technical Reports Server (NTRS)

    Wiebe, H. A.; Heicklen, J.

    1972-01-01

    The photolysis of CH3ONO, alone and in the presence of NO, NO-N2 mixtures, and NO-CO mixtures was studied between 25 and 150 C. The major products are CH2O, N2O, and H2O. The quantum yields of N2O were measured. The N2O yield is large at low pressures but approaches a high-pressure limiting value of 0.055 at all temperatures as the excited CH3O produced in the primary step is stabilized by collision. In the presence of excess CO, and N2O yield drops, and CO2 is produced (though not in sufficient amounts to account for the drop in N2O). When pure CH2ONO is photolyzed, CO is produced and NO accumulates in the system. Both products are formed in related processes and result from CH3O attack on CH2O.

  10. Spatial distribution of CH3 and CH2 radicals in a methane rf discharge

    NASA Astrophysics Data System (ADS)

    Sugai, H.; Kojima, H.; Ishida, A.; Toyoda, H.

    1990-06-01

    Spatial distributions of neutral radicals CH3 and CH2 in a capacitively coupled rf glow discharge of methane were measured by threshold ionization mass spectrometry. A strong asymmetry of the density profile was found for the CH2 radical in the high-pressure (˜100 mTorr) discharge. In addition, comprehensive measurements of electron energy distribution, ionic composition, and radical sticking coefficient were made to use as inputs to theoretical modeling of radicals in the methane plasma. The model predictions agree substantially with the measured radical distributions.

  11. Thz Spectroscopy of 12CH^+, 13CH^+, and 12CD^+

    NASA Astrophysics Data System (ADS)

    Yu, Shanshan; Drouin, Brian; Pearson, John; Amano, Takayoshi

    2015-06-01

    In 1937, Dunham detected a couple of unidentified lines in near-UV, and later Douglas and Herzberg identified them based on their laboratory observations to be low-J electronic transitions of CH^+. The electronic spectra, in particular the A^1Π-X^1σ^+ band, have been investigated extensively. On the other hand, the pure rotational transitions have not been studied so extensively. Only the lowest rotational transition, J=1-0, was observed in the laboratory for the normal species, 13CH^+, and CD^+. Based on the laboratory frequency, CH^+ was detected in star forming regions with the Hershel space observatory. Cernicharo et al identified pure rotational transitions from J=2-1 to J=6-5 in the far-infrared region in the ISO spectrum of the planetary nebula NGC 7027. The ISO spectra, however, were of low-resolution, so high-resolution spectroscopic observation is highly desirable. In this presentation, we have extended the measurements to higher-J lines up to 2 THz. For production of CH^+, an extended negative glow discharge in a gas mixture of CH_4 (˜ 0.5 mTorr) diluted in He (˜ 60 mTorr) was used. The optimum discharge current was about 15 mA and the axial magnetic filed to 160 Gauss was applied up. The discharge cell was cooled down to liquid nitrogen temperature. Several frequency multiplier chains, developed at JPL and purchased from Virginia Diodes, were used as THz radiation sources. New THz measurements are not only useful for providing better characterization of spectroscopic properties but also will serve as starting point for astronomical observations. T. Dunham, Publ. Astron. Soc. Pac., 49,~26 (1937) A. E. Douglas and G. Herzberg, Ap. J. 94,~381 (1941) T. Amano, Ap.J.Lett., 716, L1 (2010) T. Amano, J. Chem. Phys., 133, 244305 (2010) J. Cernicharo et al., Ap. J. Lett., 483, L65 (1997)

  12. BariumCopperChFluorine (Ch = Sulfur, Selenium, Tellurium) p-type transparent conductors

    NASA Astrophysics Data System (ADS)

    Zakutayev, Andriy

    BaCuChF (Ch = S, Se, Te) materials are chalcogen-based transparent conductors with wide optical band gaps (2.9 -- 3.5 eV) and a high concentration of free holes (1018 -- 1020 cm-3 ) caused by the presence of copper vacancies. Chalcogen vacancies compensate copper vacancies in these materials, setting the Fermi level close to the valence band maximum. BaCuChF thin film solid solutions prepared by pulsed laser deposition (PLD) have tunable properties, such as lattice constants, conductivity and optical band gaps. BaCuSF and BaCuSeF materials also feature room-temperature stable 3D excitons with spin-orbit-split levels. BaCuTeF has forbidden lowest-energy optical transitions which extends its transparency range. BaCuChF surfaces oxidize when exposed to air, but can be protected using Ch capping layers. Polycrystalline BaCuSeF thin films have a 4.85 eV work function, a 0.11 eV hole injection barrier into ZnPc, and 0.00 eV valence band offset with ZnTe. BaCuSeF should have s similar band offset and similar interfacial properties with CdTe and Cu(InGa)Se2, and BaCuSF should have no valence band offset with Cu2ZnSnS4, according to the transitivity rule. Therefore, BaCuSeF is suitable for applications as a p-layer in organic light-emitting diodes, p-i-n double-heterojunction and tandem chalcogenide solar cells.

  13. Carbon-Hydrogen (C-H) Bond Activation at PdIV: A Frontier in C-H Functionalization Catalysis.

    PubMed

    Topczewski, Joseph J; Sanford, Melanie S

    2015-01-01

    The direct functionalization of carbon-hydrogen (C-H) bonds has emerged as a versatile strategy for the synthesis and derivatization of organic molecules. Among the methods for C-H bond activation, catalytic processes that utilize a Pd II /Pd IV redox cycle are increasingly common. The C-H activation step in most of these catalytic cycles is thought to occur at a Pd II centre. However, a number of recent reports have suggested the feasibility of C-H cleavage occurring at Pd IV complexes. Importantly, these latter processes often result in complementary reactivity and selectivity relative to analogous transformations at Pd II . This Mini Review highlights proposed examples of C-H activation at Pd IV centres. Applications of this transformation in catalysis as well as mechanistic details obtained from stoichiometric model studies are discussed. Furthermore, challenges and future perspectives for the field are reviewed.

  14. Methane Provenance Determined by CH2D2 and 13CH3D Abundances

    NASA Astrophysics Data System (ADS)

    Kohl, I. E.; Giunta, T.; Warr, O.; Ash, J. L.; Ruffine, L.; Sherwood Lollar, B.; Young, E. D.

    2017-12-01

    Determining the provenance of naturally occurring methane gases is of major interest to energy companies and atmospheric climate modelers, among others. Bulk isotopic compositions and other geochemical tracers sometimes fail to provide definitive determinations of sources of methane due to complications from mixing and complicated chemical pathways of origin. Recent measurements of doubly-substituted isotopologues of methane, CH2D2 (UCLA) and 13CH3D (UCLA, CalTech, and MIT) have allowed for major improvements in sourcing natural methane gases. Early work has focused on formation temperatures obtained when the relative abundances of both doubly-substituted mass-18 species are consistent with internal equilibrium. When methane gases do not plot on the thermodynamic equilibrium curve in D12CH2D2 vs D13CH3D space, temperatures determined from D13CH3D values alone are usually spurious, even when appearing reasonable. We find that the equilibrium case is actually rare and almost exclusive to thermogenic gases produced at temperatures exceeding 100°C. All other relevant methane production processes appear to generate gases that are not in isotopologue-temperature equilibrium. When gases show departures from equilibrium as determined by the relationship between CH2D2 and 13CH3D abundances, data fall within empirically defined fields representing formation pathways. These fields are thus far consistent between different geological settings and and between lab experiments and natural samples. We have now defined fields for thermogenic gas production, microbial methanogenesis, low temperature abiotic (Sabatier) synthesis and higher temperature FTT synthesis. The majority of our natural methane data can be explained by mixing between end members originating within these production fields. Mixing can appear complex, resulting in both hyper-clumped and anti-clumped isotopologue abundances. In systems where mixtures dominate and end-members are difficult to sample, mixing models

  15. The catalytic effects of H2CO3, CH3COOH, HCOOH and H2O on the addition reaction of CH2OO + H2O → CH2(OH)OOH

    NASA Astrophysics Data System (ADS)

    Zhang, Tianlei; Lan, Xinguang; Wang, Rui; Roy, Soumendra; Qiao, Zhangyu; Lu, Yousong; Wang, Zhuqing

    2018-07-01

    The addition reaction of CH2OO + H2O → CH2(OH)OOH without and with X (X = H2CO3, CH3COOH and HCOOH) and H2O was studied at CCSD(T)/6-311+ G(3df,2dp)//B3LYP/6-311+G(2d,2p) level of theory. Our results show that X can catalyse CH2OO + H2O → CH2(OH)OOH reaction both by increasing the number of rings, and by adding the size of the ring in which ring enlargement by COOH moiety of X inserting into CH2OO...H2O is favourable one. Water-assisted CH2OO + H2O → CH2(OH)OOH can occur by H2O moiety of (H2O)2 or the whole (H2O)2 forming cyclic structure with CH2OO, where the latter form is more favourable. Because the concentration of H2CO3 is unknown, the influence of CH3COOH, HCOOH and H2O were calculated within 0-30 km altitude of the Earth's atmosphere. The results calculated within 0-5 km altitude show that H2O and HCOOH have obvious effect on enhancing the rate with the enhancement factors are, respectively, 62.47%-77.26% and 0.04%-1.76%. Within 5-30 km altitude, HCOOH has obvious effect on enhancing the title rate with the enhancement factor of 2.69%-98.28%. However, compared with the reaction of CH2OO + HCOOH, the rate of CH2OO...H2O + HCOOH is much slower.

  16. Training Management in the CH-46E Community After MAWTS-1 Stands Down Its CH-46E Division

    DTIC Science & Technology

    2012-04-23

    SHOULD INCLUDE THE FOREGOING STATEMENT. QUOTATION FROM, ABSTRACTION FROM, OR REPRODUCTION OF ALL OR ANY PART OF THIS DOCUMENT IS PERMITTED...HMH) currently fly either the CH-53D Sea Stallion or the CH-53E Super Stallion helicopters. Those units that fly the CH-53D Sea Stallion are in the...process of converting to the CH-53E Super Stallion or will transition the squadrons to medium lift assault support platforms.5 The HMHs currently

  17. Degraded Land Restoration in Reinstating CH4 Sink

    PubMed Central

    Singh, Jay Shankar; Gupta, Vijai K.

    2016-01-01

    Methane (CH4), a potent greenhouse gas, contributes about one third to the global green house gas emissions. CH4-assimilating microbes (mostly methanotrophs) in upland soils play very crucial role in mitigating the CH4 release into the atmosphere. Agricultural, environmental, and climatic shifts can alter CH4 sink profiles of soils, likely through shifts in CH4-assimilating microbial community structure and function. Landuse change, as forest and grassland ecosystems altered to agro-ecosystems, has already attenuated the soil CH4 sink potential, and are expected to be continued in the future. We hypothesized that variations in CH4 uptake rates in soils under different landuse practices could be an indicative of alterations in the abundance and/or type of methanotrophic communities in such soils. However, only a few studies have addressed to number and methanotrophs diversity and their correlation with the CH4 sink potential in soils of rehabilitated/restored lands. We focus on landuse practices that can potentially mitigate CH4 gas emissions, the most prominent of which are improved cropland, grazing land management, use of bio-fertilizers, and restoration of degraded lands. In this perspective paper, it is proposed that restoration of degraded lands can contribute considerably to improved soil CH4 sink strength by retrieving/conserving abundance and assortment of efficient methanotrophic communities. We believe that this report can assist in identifying future experimental directions to the relationships between landuse changes, methane-assimilating microbial communities and soil CH4 sinks. The exploitation of microbial communities other than methanotrophs can contribute significantly to the global CH4 sink potential and can add value in mitigating the CH4 problems. PMID:27379053

  18. Degraded Land Restoration in Reinstating CH4 Sink.

    PubMed

    Singh, Jay Shankar; Gupta, Vijai K

    2016-01-01

    Methane (CH4), a potent greenhouse gas, contributes about one third to the global green house gas emissions. CH4-assimilating microbes (mostly methanotrophs) in upland soils play very crucial role in mitigating the CH4 release into the atmosphere. Agricultural, environmental, and climatic shifts can alter CH4 sink profiles of soils, likely through shifts in CH4-assimilating microbial community structure and function. Landuse change, as forest and grassland ecosystems altered to agro-ecosystems, has already attenuated the soil CH4 sink potential, and are expected to be continued in the future. We hypothesized that variations in CH4 uptake rates in soils under different landuse practices could be an indicative of alterations in the abundance and/or type of methanotrophic communities in such soils. However, only a few studies have addressed to number and methanotrophs diversity and their correlation with the CH4 sink potential in soils of rehabilitated/restored lands. We focus on landuse practices that can potentially mitigate CH4 gas emissions, the most prominent of which are improved cropland, grazing land management, use of bio-fertilizers, and restoration of degraded lands. In this perspective paper, it is proposed that restoration of degraded lands can contribute considerably to improved soil CH4 sink strength by retrieving/conserving abundance and assortment of efficient methanotrophic communities. We believe that this report can assist in identifying future experimental directions to the relationships between landuse changes, methane-assimilating microbial communities and soil CH4 sinks. The exploitation of microbial communities other than methanotrophs can contribute significantly to the global CH4 sink potential and can add value in mitigating the CH4 problems.

  19. Constraining the sources of CH4 emissions during past abrupt climate change using CH4 triple isotopes mass balance from the ice core records

    NASA Astrophysics Data System (ADS)

    Dyonisius, M.; Petrenko, V. V.; Smith, A. W.; Hmiel, B.; Beck, J.; Seth, B.; Bock, M.; Hua, Q.; Yang, B.; Harth, C. M.; Beaudette, R.; Lee, J.; Erhardt, T.; Schmitt, J.; Brook, E.; Weiss, R. F.; Fischer, H.; Severinghaus, J. P.

    2017-12-01

    Methane (CH4) is the third most important greenhouse gas in the atmosphere after water vapor and CO2. Understanding how the natural CH4 budget has changed in response to changing climate in the past can provide insights on the sensitivity of the natural CH4 emissions to the current anthropogenic warming. CH4 isotopes (Δ14CH4, δ13C-CH4, and δD-CH4) from ice cores can be used to fingerprint the sources of CH4 increases in the past. We have successfully extracted 6 large volume (>1000kg) ice core samples from Taylor Glacier, Antarctica spanning the Oldest Dryas-Bølling transition ( 14.7ka) - the first abrupt warming and CH4 rise since the Last Glacial Maximum. Among the CH4 isotopes, our Δ 14CH4 data are unique in their ability to unambiguously distinguish between "old" CH4 sources (e.g. marine clathrate, geologic sources, old permafrost) and "modern" CH4 sources (e.g. tropical and boreal wetlands). Our Δ14CH4 data unambiguously rule out marine clathrate and old permafrost as the sources of the abrupt CH4 rise. Preliminary CH4 stable isotopes box modeling combined with interpolar CH4 concentration gradient from existing ice core records suggest that tropical wetlands were the dominant driver for the Oldest Dryas-Bølling CH4 rise.

  20. A Mechanistical Study on the Formation of Dimethyl Ether (CH3OCH3) and Ethanol (CH3CH2OH) in Methanol-containing Ices and Implications for the Chemistry of Star-forming Regions

    NASA Astrophysics Data System (ADS)

    Bergantini, Alexandre; Góbi, Sándor; Abplanalp, Matthew J.; Kaiser, Ralf I.

    2018-01-01

    The underlying formation mechanisms of complex organic molecules (COMs)—in particular, structural isomers—in the interstellar medium (ISM) are largely elusive. Here, we report new experimental findings on the role of methanol (CH3OH) and methane (CH4) ices in the synthesis of two C2H6O isomers upon interaction with ionizing radiation: ethanol (CH3CH2OH) and dimethyl ether (CH3OCH3). The present study reproduces the interstellar abundance ratios of both species with ethanol to dimethyl ether branching ratios of (2.33 ± 0.14):1 suggesting that methanol and methane represents the key precursor to both isomers within interstellar ices. Exploiting isotopic labeling combined with reflectron time-of-flight mass spectrometry (Re-TOF-MS) after isomer selective vacuum ultra-violet (VUV) photoionization of the neutral molecules, we also determine the formation mechanisms of both isomers via radical–radical recombination versus carbene (CH2) insertion with the former pathway being predominant. Formation routes to higher molecular weight reaction products such as ethylene glycol (HOCH2CH2OH), dimethyl peroxide (CH3OOCH3), and methoxymethanol (CH3OCH2OH) are discussed briefly as well.

  1. Interannual Variability and Trends of CH4, CO and OH Using the Computationally-Efficient CH4-CO-OH (ECCOH) Module

    NASA Technical Reports Server (NTRS)

    Elshorbany, Yasin F.; Duncan, Bryan N.; Strode, Sarah A.; Wang, James S.; Kouatchou, Jules

    2015-01-01

    Methane (CH4) is the second most important anthropogenic greenhouse gas (GHG). Its 100-year global warming potential (GWP) is 34 times larger than that for carbon dioxide. The 100-year integrated GWPof CH4 is sensitive to changes in hydroxyl radical (OH) levels.Oxidation of CH4 and carbon monoxide (CO) by OH is the main loss process, thus affecting the oxidizing capacity of the atmosphere and contributing to the global ozone background. Limitations of using archived, monthly OH fields for studies of methane's and COs evolution are that feedbacks of the CH4-CO-OH system on methane, CO and OH are not captured. In this study, we employ the computationally Efficient CH4-CO-OH (ECCOH) module (Elshorbany et al., 2015) to investigate the nonlinear feedbacks of the CH4-CO-OH system on the interannual variability and trends of the CH4, CO, OH system.

  2. Inverse Modeling of Surface CH4 and δ13C-CH4 Measurements to Understand Recent Trends in Global Methane Emissions

    NASA Astrophysics Data System (ADS)

    Karmakar, S.; Butenhoff, C. L.; Rice, A. L.; Lofdahl, D. B.; Khalil, A. K.

    2016-12-01

    Methane (CH4) is the second most important greenhouse gas with a radiative forcing of 0.97 W/m2 including both direct and indirect effects and a global warming potential of 28 over a 100-year time horizon. Unlike CO2 whose rate of growth in the atmosphere has remained positive and increased in recent decades, the behavior of atmospheric methane is considerably more complex and is much less understood on account of the spatiotemporal variability of its emissions which include biogenic (e.g. wetlands, ruminants, rice agriculture), thermogenic (fossil fuels), and pyrogenic (i.e. biomass burning) sources. After sustained growth during most of the 20th century, the CH4 growth rate declined falling from 15 ppbv/yr during the 1980s to 6 ppbv/yr in the 1990s to near-zero and even negative values in the early 2000s. With some surprise however, the growth rate rebounded in 2007 and has been on average 6 ppbv/yr during the past 10 years. During this same period the 13CH4/12CH4 ratio of atmospheric CH4 also declined suggesting the recent CH4 growth was caused by an increase in 13CH4-depleted biogenic emissions. Here, we provide additional insight into the recent behavior of atmospheric methane by performing a global three-dimensional Bayesian inversion of surface CH4 and 13CH4/12CH4 ratios over the period 1985-2015 using NOAA Global Monitoring Division (GMD) CH4 measurements and the GEOS-Chem chemical-transport model (CTM) at a horizontal grid resolution of 2ox2.5o. The use of the 3-D model allows us to exploit spatial patterns in the global CH4 and 13CH4/12CH4 fields that provide additional constraints on the retrieval of the time-dependent CH4 fluxes. This work follows up on our previous CH4 inversion where we used a 4ox5o horizontal grid for GEOS-Chem to retrieve fluxes from 1985 to 2009. At higher resolution more information is extracted from the observations due to improved model skill and a smaller number of stations aggregated within model grid cells. This increases the

  3. Thermal decomposition and oxidation of CH3OH.

    PubMed

    Lee, Pei-Fang; Matsui, Hiroyuki; Xu, Ding-Wei; Wang, Niann-Shiah

    2013-01-24

    Thermal decomposition of CH(3)OH diluted in Ar has been studied by monitoring H atoms behind reflected shock waves of 100 ppm CH(3)OH + Ar. The total decomposition rate k(1) for CH(3)OH + M → products obtained in this study is expressed as, ln(k(1)/cm(3) molecule(-1) s(-1)) = -(14.81 ± 1.22) - (38.86 ± 1.82) × 10(3)/T, over 1359-1644 K. The present result on k(1) is indicated to be substantially smaller than the extrapolation of the most of the previous experimental data but consistent with the published theoretical results [Faraday Discuss. 2002, 119, 191-205 and J. Phys. Chem. A 2007, 111, 3932-3950]. Oxidation of CH(3)OH has been studied also by monitoring H atoms behind shock waves of (0.35-100) ppm CH(3)OH + (100-400) ppm O(2) + Ar. For the low concentration CH(3)OH (below 10 ppm) + O(2) mixtures, the initial concentration of CH(3)OH is evaluated by comparing evolutions of H atoms in the same concentration of CH(3)OH with addition of 300 ppm H(2) diluted in Ar. The branching fraction for CH(3)OH + Ar → (1)CH(2) + H(2)O + Ar has been quantitatively evaluated from this comparative measurements with using recent experimental result on the yield of H atoms in the reaction of (1,3)CH(2) + O(2) [J. Phys. Chem. A 2012, 116, 9245-9254]; i.e., the branching fraction for the above reaction is evaluated as, φ(1a) = 0.20 ± 0.04 at T = 1880-2050 K, in the 1.3 and 3.5 ppm CH(3)OH + 100 ppm O(2) samples. An extended reaction mechanism for the pyrolysis and oxidation of CH(3)OH is constructed based on the results of the present study combined with the oxidation mechanism of natural gas [GRI-Mech 3.0]; evolution of H atoms can be predicted very well with this new reaction scheme over a wide concentration range for the pyrolysis (0.36-100 ppm CH(3)OH), and oxidation (0.36-100 ppm CH(3)OH + 100/400 ppm O(2)) of methanol.

  4. Subsoil methanogenesis as source of stem CH4 emission in upland forest trees: preferential CH4 transport via the root system?

    NASA Astrophysics Data System (ADS)

    Maier, M.; Machacova, K.; Urban, O.; Friederike, L.

    2016-12-01

    Quantifying and understanding green house gas fluxes in natural soil-plant-atmosphere systems are crucial to predicting global climate change. Wetland species or trees at waterlogged sites are known to emit large amounts of CH4. Yet upland forest soils are regarded as CH4 sinks and tree species like upland European beech (Fagus sylvatica, L.) are assumed not to emit CH4. We studied the soil-atmosphere and stem-atmosphere fluxes of CH4, and soil gas profiles at two upland beech forest sites in Central Europe. Soil was a net CH4 sink at both. Unusually there was one beech tree with substantial CH4 emissions that were higher than the CH4 sink of the soil. The soil gas profile at this tree indicated CH4 production at a soil depth >0.3 m, despite the net uptake of CH4 observed at the soil surface adjacent to the tree. Field soil assessment showed strong redoximorphic color patterns in the adjacent soil. We think that there is a transport link between the soil and stem via the root system representing a preferential transport mechanism for CH4 despite the fact that beech roots usually do not bear aerenchyma. The gas transport process , either via dissolved CH4 in the xylem water or in the root gas phase, is not yet clear. The observed CH4 stem emissions represent an important CH4flux in this ecosystem, und thus should be considered in future research. AcknowledgementThis research was financially supported by the Czech Academy of Sciences and the German Academic Exchange Service within the project "Methane (CH4) and nitrous oxide (N2O) emissions from Fagus sylvatica trees" (DAAD-15-03), National Programme for Sustainability I (LO1415) and project DFG (MA 5826/2-1). We would like to thank Marek Jakubik, Katerina Svobodova, Sinikka Paulus, Ellen Halaburt and Sally Haddad for technical support.

  5. Direct formation of (CH sub 3 ) sub 2 HSiCl from silicon and CH sub 3 Cl

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Magrini, K.A.; Falconer, J.L.; Koel, B.E.

    1989-07-13

    A Cu-catalyzed reaction procedure was found for the selective formation of dimethylchlorosilane ((CH{sub 3}){sub 2}HSiCl) from the direct reaction of CH{sub 3}Cl with solid Si. The new procedure is a two-step process. A Cu/Si sample is prepared by evaporating Cu onto clean polycrystalline Si under ultrahigh vacuum, and the Cu/Si surface is first activated by exposure to 10% HSiCl{sub 3}/CH{sub 3}Cl at 598 K. After the HSiCl{sub 3}CH{sub 3}Cl mixture is evacuated from the reactor, the activated Cu/Si surface is reacted in fresh CH{sub 3}Cl. For low surface concentrations of Cu, the partially hydrogenated silane, (CH{sub 3}){sub 2}HSiCl, is selectivelymore » produced. Trichlorosilane was also found to activate polycrystalline Si (in the absence of Cu) for production of highly chlorinated methylchlorosilanes at a much higher rate than on the Cu/Si surface but with poor selectively to (CH{sub 3}){sub 2}HSiCl. All reactions are carried out at atmospheric pressure in a reactor that is attached to an ultrahigh-vacuum chamber. This allows surface analysis of Auger electron spectroscopy, which detected SiCl{sub x} on reacted surfaces. These SiCl{sub x} sites, which appear necessary for methylchlorosilane formation, are apparently formed during activation by HSiCl{sub 3}.« less

  6. Photodissociation of the CH3O and CH3S radical molecules: An ab initio electronic structure study

    PubMed Central

    Bouallagui, A.; Zanchet, A.; Yazidi, O.; Jaïdane, N.; Bañares, L.; Senent, M.L.; García-Vela, A.

    2018-01-01

    The electronic states and the spin-orbit couplings between them involved in the photodissociation process of the radical molecules CH3X, CH3X → CH3 + X(X = O, S), taking place after the Ā(2A1) ← X̄(2E) transition, have been investigated using highly correlated ab initio techniques. A two-dimensional representation of both the potential-energy surfaces (PESs) and the couplings is generated. This description includes the C-X dissociative mode and the CH3 umbrella mode. Spin-orbit effects are found to play a relevant role on the shape of the excited state potential-energy surfaces, particularly in the CH3S case where the spin-orbit couplings are more than twice more intense than in CH3O. The potential surfaces and couplings reported here for the present set of electronic states allow for the first complete description of the above photodissociation process. The different photodissociation mechanisms are analyzed and discussed in the light of the results obtained. PMID:29143005

  7. A DFT-Elucidated Comparison of the Solution-Phase and SAM Electrochemical Properties of Short-Chain Mercaptoalkylferrocenes: Synthetic and Spectroscopic Aspects, and the Structure of Fc-CH2CH2-S-S-CH2CH2-Fc.

    PubMed

    Lewtak, Jan P; Landman, Marilé; Fernández, Israel; Swarts, Jannie C

    2016-03-07

    Facile synthetic procedures to synthesize a series of difficult-to-obtain mercaptoalkylferrocenes, namely, Fc(CH2)nSH, where n = 1 (1), 2 (2), 3 (3), or 4 (4) and Fc = Fe(η(5)-C5H5)(η(5)-C5H4), are reported. Dimerization of 1-4 to the corresponding disulfides 19-22 was observed in air. Dimer 20 (Z = 2) crystallized in the triclinic space group P1̅. Dimers 20-22 could be reduced back to the original Fc(CH2)nSH derivatives with LiAlH4 in refluxing tetrahydrofuran. Density functional theory (DFT) calculations showed that the highest occupied molecular orbital of 1-4 lies exclusively on the ferrocenyl group implying that the electrochemical oxidation observed at ca. -15 < Epa < 76 mV versus FcH/FcH(+) involves exclusively an Fe(II) to Fe(III) process. Further DFT calculations showed this one-electron oxidation is followed by proton loss on the thiol group to generate a radical, Fc(CH2)nS(•), with spin density mainly located on the sulfur. Rapid exothermic dimerization leads to the observed dimers, Fc(CH2)n-S-S-(CH 2)nFc. Reduction of the ferrocenium groups on the dimer occurs at potentials that still showed the ferrocenyl group ΔE = Epa,monomer - Epc,dimer ≤ 78 mV, indicating that the redox properties of the ferrocenyl group on the mercaptans are very similar to those of the dimer. (1)H NMR measurements showed that, like ferrocenyl oxidation, the resonance position of the sulfhydryl proton, SH, and others, are dependent on -(CH2)n- chain length. Self-assembled monolayers (SAMs) on gold were generated to investigate the electrochemical behavior of 1-4 in the absence of diffusion. Under these conditions, ΔE approached 0 mV for the longer chain derivatives at slow scan rates. The surface-bound ferrocenyl group of the metal-thioether, Fc(CH2)n -S-Au, is oxidized at approximately equal potentials as the equivalent CH2Cl2-dissolved ferrocenyl species 1-4. Surface coverage by the SAMs is dependent on alkyl chain length with the largest coverage obtained for 4, while

  8. Infrared spectroscopy of solid normal hydrogen doped with CH3F and O2 at 4.2 K: CH3F:O2 complex and CH3F migration

    NASA Astrophysics Data System (ADS)

    Abouaf-Marguin, L.; Vasserot, A.-M.

    2011-04-01

    Double doping of solid normal hydrogen with CH3F and O2 at about 4.2 K gives evidence of (ortho-H2)n:CH3F clusters and of O2:CH3F complex formation. FTIR analysis of the time evolution of the spectra in the region of the v3 C-F stretching mode indicates that these clusters behave very differently from (ortho-H2)n:H2O clusters. The main point is the observed migration of CH3F molecules in solid para-H2 at 4.2 K which differs from that of H2O under identical experimental conditions. This is confirmed by an increase over time of the integrated intensity of the CH3F:O2 complex with a rate constant K = 2.7(2) . 10-4 s-1.

  9. InChIKey collision resistance: an experimental testing

    PubMed Central

    2012-01-01

    InChIKey is a 27-character compacted (hashed) version of InChI which is intended for Internet and database searching/indexing and is based on an SHA-256 hash of the InChI character string. The first block of InChIKey encodes molecular skeleton while the second block represents various kinds of isomerism (stereo, tautomeric, etc.). InChIKey is designed to be a nearly unique substitute for the parent InChI. However, a single InChIKey may occasionally map to two or more InChI strings (collision). The appearance of collision itself does not compromise the signature as collision-free hashing is impossible; the only viable approach is to set and keep a reasonable level of collision resistance which is sufficient for typical applications. We tested, in computational experiments, how well the real-life InChIKey collision resistance corresponds to the theoretical estimates expected by design. For this purpose, we analyzed the statistical characteristics of InChIKey for datasets of variable size in comparison to the theoretical statistical frequencies. For the relatively short second block, an exhaustive direct testing was performed. We computed and compared to theory the numbers of collisions for the stereoisomers of Spongistatin I (using the whole set of 67,108,864 isomers and its subsets). For the longer first block, we generated, using custom-made software, InChIKeys for more than 3 × 1010 chemical structures. The statistical behavior of this block was tested by comparison of experimental and theoretical frequencies for the various four-letter sequences which may appear in the first block body. From the results of our computational experiments we conclude that the observed characteristics of InChIKey collision resistance are in good agreement with theoretical expectations. PMID:23256896

  10. InChIKey collision resistance: an experimental testing.

    PubMed

    Pletnev, Igor; Erin, Andrey; McNaught, Alan; Blinov, Kirill; Tchekhovskoi, Dmitrii; Heller, Steve

    2012-12-20

    InChIKey is a 27-character compacted (hashed) version of InChI which is intended for Internet and database searching/indexing and is based on an SHA-256 hash of the InChI character string. The first block of InChIKey encodes molecular skeleton while the second block represents various kinds of isomerism (stereo, tautomeric, etc.). InChIKey is designed to be a nearly unique substitute for the parent InChI. However, a single InChIKey may occasionally map to two or more InChI strings (collision). The appearance of collision itself does not compromise the signature as collision-free hashing is impossible; the only viable approach is to set and keep a reasonable level of collision resistance which is sufficient for typical applications.We tested, in computational experiments, how well the real-life InChIKey collision resistance corresponds to the theoretical estimates expected by design. For this purpose, we analyzed the statistical characteristics of InChIKey for datasets of variable size in comparison to the theoretical statistical frequencies. For the relatively short second block, an exhaustive direct testing was performed. We computed and compared to theory the numbers of collisions for the stereoisomers of Spongistatin I (using the whole set of 67,108,864 isomers and its subsets). For the longer first block, we generated, using custom-made software, InChIKeys for more than 3 × 1010 chemical structures. The statistical behavior of this block was tested by comparison of experimental and theoretical frequencies for the various four-letter sequences which may appear in the first block body.From the results of our computational experiments we conclude that the observed characteristics of InChIKey collision resistance are in good agreement with theoretical expectations.

  11. High Resolution CH4 Emissions and Dissolved CH4 Measurements Elucidate Surface Gas Exchange Processes in Toolik Lake, Arctic Alaska

    NASA Astrophysics Data System (ADS)

    Del Sontro, T.; Sollberger, S.; Kling, G. W.; Shaver, G. R.; Eugster, W.

    2013-12-01

    Approximately 14% of the Alaskan North Slope is covered in lakes of various sizes and depths. Diffusive carbon emissions (CH4 and CO2) from these lakes offset the tundra sink by ~20 %, but the offset would substantially increase if ebullitive CH4 emissions were also considered. Ultimately, arctic lake CH4 emissions are not insignificant in the global CH4 budget and their contribution is bound to increase due to impacts from climate change. Here we present high resolution CH4 emission data as measured via eddy covariance and a Los Gatos gas analyzer during the ice free period from Toolik Lake, a deep (20 m) Arctic lake located on the Alaskan North Slope, over the last few summers. Emissions are relatively low (< 25 mg CH4 m-2 d-1) with little variation over the summer. Diurnal variations regularly occur, however, with up to 3 times higher fluxes at night. Gas exchange is a relatively difficult process to estimate, but is normally done so as the product of the CH4 gradient across the air-water interface and the gas transfer velocity, k. Typically, k is determined based on the turbulence on the water side of the interface, which is most commonly approximated by wind speed; however, it has become increasingly apparent that this assumption does not remain valid across all water bodies. Dissolved CH4 profiles in Toolik revealed a subsurface peak in CH4 at the thermocline of up to 3 times as much CH4 as in the surface water. We hypothesize that convective mixing at night due to cooling surface waters brings the subsurface CH4 to the surface and causes the higher night fluxes. In addition to high resolution flux emission estimates, we also acquired high resolution data for dissolved CH4 in surface waters of Toolik Lake during the last two summers using a CH4 equilibrator system connected to a Los Gatos gas analyzer. Thus, having both the flux and the CH4 gradient across the air-water interface measured directly, we can calculate k and investigate the processes influencing

  12. Global Inverse Modeling of CH4 and δ13C-CH4 Measurements to Understand Recent Trends in Methane Emissions

    NASA Astrophysics Data System (ADS)

    Karmakar, S.; Butenhoff, C. L.; Rice, A. L.; Khalil, A. K.

    2017-12-01

    Methane (CH4) is the second most important greenhouse gas with a radiative forcing of 0.97 W/m2 including both direct and indirect effects and a global warming potential of 28 over a 100-year time horizon. After a decades-long period of decline beginning in the 1980s, the methane growth rate rebounded in 2007 for reasons that are of current debate. During this same growth period atmospheric methane became less enriched in the 13CH4 isotope suggesting the recent CH4 growth was caused by an increase in 13CH4-depleted biogenic emissions. Recent papers have attributed this growth to increasing emissions from wetlands, rice agriculture, and ruminants. In this work we provide additional insight into the recent behavior of atmospheric methane and global wetland emissions by performing a three-dimensional Bayesian inversion of surface CH4 and 13CH4/12CH4 ratios using NOAA Global Monitoring Division (GMD) "event-level" CH4 measurements and the GEOS-Chem chemical-transport model (CTM) at a horizontal grid resolution of 2ox2.5o. The spatial pattern of wetland emissions was prescribed using soil moisture and temperature from GEOS-5 meteorology fields and soil carbon pools from the Lund-Potsdam-Jena global vegetation model. In order to reduce the aggregation error caused by a potentially flawed distribution and to account for isotopic measurements that indicate northern high latitude wetlands are isotopically depleted in 13CH4 relative to tropical wetlands we separated our pattern into three latitudinal bands (90-30°N, 30°N-0, 0-90°S). Our preliminary results support previous claims that the recent increase in atmospheric methane is driven by increases in biogenic CH4 emissions. We find that while wetland emissions from northern high latitudes (90-30°N) remained relatively constant during this time, southern hemisphere wetland emissions rebounded from a decade-long decline and began to rise again in 2007 and have remained elevated to the present. Emissions from rice

  13. ChIP-nexus: a novel ChIP-exo protocol for improved detection of in vivo transcription factor binding footprints

    PubMed Central

    He, Qiye; Johnston, Jeff; Zeitlinger, Julia

    2014-01-01

    Understanding how eukaryotic enhancers are bound and regulated by specific combinations of transcription factors is still a major challenge. To better map transcription factor binding genome-wide at nucleotide resolution in vivo, we have developed a robust ChIP-exo protocol called ChIP experiments with nucleotide resolution through exonuclease, unique barcode and single ligation (ChIP-nexus), which utilizes an efficient DNA self-circularization step during library preparation. Application of ChIP-nexus to four proteins—human TBP and Drosophila NFkB, Twist and Max— demonstrates that it outperforms existing ChIP protocols in resolution and specificity, pinpoints relevant binding sites within enhancers containing multiple binding motifs and allows the analysis of in vivo binding specificities. Notably, we show that Max frequently interacts with DNA sequences next to its motif, and that this binding pattern correlates with local DNA sequence features such as DNA shape. ChIP-nexus will be broadly applicable to studying in vivo transcription factor binding specificity and its relationship to cis-regulatory changes in humans and model organisms. PMID:25751057

  14. Additional Value of CH4 Measurement in a Combined 13C/H2 Lactose Malabsorption Breath Test: A Retrospective Analysis

    PubMed Central

    Houben, Els; De Preter, Vicky; Billen, Jaak; Van Ranst, Marc; Verbeke, Kristin

    2015-01-01

    The lactose hydrogen breath test is a commonly used, non-invasive method for the detection of lactose malabsorption and is based on an abnormal increase in breath hydrogen (H2) excretion after an oral dose of lactose. We use a combined 13C/H2 lactose breath test that measures breath 13CO2 as a measure of lactose digestion in addition to H2 and that has a better sensitivity and specificity than the standard test. The present retrospective study evaluated the results of 1051 13C/H2 lactose breath tests to assess the impact on the diagnostic accuracy of measuring breath CH4 in addition to H2 and 13CO2. Based on the 13C/H2 breath test, 314 patients were diagnosed with lactase deficiency, 138 with lactose malabsorption or small bowel bacterial overgrowth (SIBO), and 599 with normal lactose digestion. Additional measurement of CH4 further improved the accuracy of the test as 16% subjects with normal lactose digestion and no H2-excretion were found to excrete CH4. These subjects should have been classified as subjects with lactose malabsorption or SIBO. In conclusion, measuring CH4-concentrations has an added value to the 13C/H2 breath test to identify methanogenic subjects with lactose malabsorption or SIBO. PMID:26371034

  15. Electron-spin-resonance studies of 12CH3F + , 13CH3F + , and 12CH2DF + in neon matrices at 4 K: Comparison with theoretical calculations

    NASA Astrophysics Data System (ADS)

    Knight, Lon B., Jr.; Gregory, Brian W.; Hill, Devon W.; Arrington, C. A.; Momose, Takamasa; Shida, Tadamasa

    1991-01-01

    Various isotopic forms of the methyl fluoride cation 12CH3F+, 13CH3F+, and 12CH2DF+ have been generated by photoionization at 16.8 eV and separately by electron bombardment at 50 eV. The first electron-spin-resonance (ESR) results are reported for this radical cation which was isolated in neon matrices at 4 K. The measured A tensors or nuclear hyperfine parameters were compared with the results obtained from various computational approaches. Surprising observations were the large amounts of spin density on the methyl group, especially the hydrogen atoms, and the extreme differences in the deuterated spectra compared to the nondeuterated case. The presence of a single D atom apparently acts to prevent dynamic Jahn-Teller averaging which makes the methyl hydrogens equivalent on the ESR time scale. Such a dramatic Jahn-Teller effect has been previously observed for the similar methane cations CH+4 and CH2D+2. The magnetic parameters for CH2DF+ in neon at 4 K are gX=2.0032(5), gY=2.0106(8), and gZ=2.0120(5); for H: AX = 483(1), AY=476(1), and AZ=483(1) MHz; for D: ‖AX‖=5.0(3), ‖AY‖<3, and ‖AZ‖=7.1(3) MHz; for 19F : AX=965(1), AY=-130(2), and AZ=-166(1) MHz. For CH3F+, the g tensor and 19F A tensor were similar to those above but the H atoms were equivalent with values of AX=317(1), AY=323(2), and AZ=312 MHz.

  16. Recent Developments in C-H Activation for Materials Science in the Center for Selective C-H Activation.

    PubMed

    Zhang, Junxiang; Kang, Lauren J; Parker, Timothy C; Blakey, Simon B; Luscombe, Christine K; Marder, Seth R

    2018-04-16

    Abstract : Organic electronics is a rapidly growing field driven in large part by the synthesis of ∏-conjugated molecules and polymers. Traditional aryl cross-coupling reactions such as the Stille and Suzuki have been used extensively in the synthesis of ∏-conjugated molecules and polymers, but the synthesis of intermediates necessary for traditional cross-couplings can include multiple steps with toxic and hazardous reagents. Direct arylation through C-H bond activation has the potential to reduce the number of steps and hazards while being more atom-economical. Within the Center for Selective C-H Functionalization (CCHF), we have been developing C-H activation methodology for the synthesis of ∏-conjugated materials of interest, including direct arylation of difficult-to-functionalize electron acceptor intermediates and living polymerization of ∏-conjugated polymers through C-H activation.

  17. Calculations on the orientation of the CH fragment in Co 3(CO) 9(μ 3-CH): Implications for metal surfaces

    NASA Astrophysics Data System (ADS)

    DeKock, Roger L.; Fehlner, Thomas P.

    1982-07-01

    A series of molecular orbital calculations using the Fenske-Hall method have been carried out on Co 3(CO) 9(μ 3-CH), in which the orientation of the CH fragment is varied with respect to the triangular plane of the three Co atoms. The calculations show that the energy differences between the orbitals that are predominantly CH in character are affected very little by the orientation of the CH fragment. These calculated differences are Δ(2 σ-1 σ)≅7 eV and Δ(1 π-1 σ)≅ 10.5 eV. The calculated splitting of the degenerate 1π orbitals for geometries with tilted CH fragments never amounted to more than 0.46 eV. Mixing of CH orbitals into the predominantly Co 3d manifold was extensive in all of the calculations. These calculations provide no support for the interpretation of energy loss and photoemission electron spectroscopy experiments in terms of CH fragments that are tilted with respect to the metal surface, but such an interpretation cannot be eliminated due to the diffuse nature of the spectral bands in the photoemission experiments.

  18. ChIP-PaM: an algorithm to identify protein-DNA interaction using ChIP-Seq data.

    PubMed

    Wu, Song; Wang, Jianmin; Zhao, Wei; Pounds, Stanley; Cheng, Cheng

    2010-06-03

    ChIP-Seq is a powerful tool for identifying the interaction between genomic regulators and their bound DNAs, especially for locating transcription factor binding sites. However, high cost and high rate of false discovery of transcription factor binding sites identified from ChIP-Seq data significantly limit its application. Here we report a new algorithm, ChIP-PaM, for identifying transcription factor target regions in ChIP-Seq datasets. This algorithm makes full use of a protein-DNA binding pattern by capitalizing on three lines of evidence: 1) the tag count modelling at the peak position, 2) pattern matching of a specific tag count distribution, and 3) motif searching along the genome. A novel data-based two-step eFDR procedure is proposed to integrate the three lines of evidence to determine significantly enriched regions. Our algorithm requires no technical controls and efficiently discriminates falsely enriched regions from regions enriched by true transcription factor (TF) binding on the basis of ChIP-Seq data only. An analysis of real genomic data is presented to demonstrate our method. In a comparison with other existing methods, we found that our algorithm provides more accurate binding site discovery while maintaining comparable statistical power.

  19. The ChArMEx database

    NASA Astrophysics Data System (ADS)

    Ferré, Hélène; Belmahfoud, Nizar; Boichard, Jean-Luc; Brissebrat, Guillaume; Cloché, Sophie; Descloitres, Jacques; Fleury, Laurence; Focsa, Loredana; Henriot, Nicolas; Mière, Arnaud; Ramage, Karim; Vermeulen, Anne; Boulanger, Damien

    2015-04-01

    The Chemistry-Aerosol Mediterranean Experiment (ChArMEx, http://charmex.lsce.ipsl.fr/) aims at a scientific assessment of the present and future state of the atmospheric environment in the Mediterranean Basin, and of its impacts on the regional climate, air quality, and marine biogeochemistry. The project includes long term monitoring of environmental parameters , intensive field campaigns, use of satellite data and modelling studies. Therefore ChARMEx scientists produce and need to access a wide diversity of data. In this context, the objective of the database task is to organize data management, distribution system and services, such as facilitating the exchange of information and stimulating the collaboration between researchers within the ChArMEx community, and beyond. The database relies on a strong collaboration between ICARE, IPSL and OMP data centers and has been set up in the framework of the Mediterranean Integrated Studies at Regional And Locals Scales (MISTRALS) program data portal. ChArMEx data, either produced or used by the project, are documented and accessible through the database website: http://mistrals.sedoo.fr/ChArMEx. The website offers the usual but user-friendly functionalities: data catalog, user registration procedure, search tool to select and access data... The metadata (data description) are standardized, and comply with international standards (ISO 19115-19139; INSPIRE European Directive; Global Change Master Directory Thesaurus). A Digital Object Identifier (DOI) assignement procedure allows to automatically register the datasets, in order to make them easier to access, cite, reuse and verify. At present, the ChArMEx database contains about 120 datasets, including more than 80 in situ datasets (2012, 2013 and 2014 summer campaigns, background monitoring station of Ersa...), 25 model output sets (dust model intercomparison, MEDCORDEX scenarios...), a high resolution emission inventory over the Mediterranean... Many in situ datasets

  20. The CH/π hydrogen bond: Implication in chemistry

    NASA Astrophysics Data System (ADS)

    Nishio, M.

    2012-06-01

    The CH/π hydrogen bond is the weakest extreme of hydrogen bonds that occurs between a soft acid CH and a soft base π-system. Implication in chemistry of the CH/π hydrogen bond includes issues of conformation, crystal packing, and specificity in host/guest complexes. The result obtained by analyzing the Cambridge Structural Database is reviewed. The peculiar axial preference of isopropyl group in α-phellandrene and folded conformation of levopimaric acid have been explained in terms of the CH/π hydrogen bond, by high-level ab initio MO calculations. Implication of the CH/π hydrogen bond in structural biology is also discussed, briefly.

  1. The products of the thermal decomposition of CH{sub 3}CHO

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Vasiliou, AnGayle; National Renewable Energy Laboratory, 1617 Cole Blvd., Golden, Colorado 80401; Piech, Krzysztof M.

    2011-07-07

    We have used a heated 2 cm x 1 mm SiC microtubular ({mu}tubular) reactor to decompose acetaldehyde: CH{sub 3}CHO +{Delta}{yields} products. Thermal decomposition is followed at pressures of 75-150 Torr and at temperatures up to 1675 K, conditions that correspond to residence times of roughly 50-100 {mu}s in the {mu}tubular reactor. The acetaldehyde decomposition products are identified by two independent techniques: vacuum ultraviolet photoionization mass spectroscopy (PIMS) and infrared (IR) absorption spectroscopy after isolation in a cryogenic matrix. Besides CH{sub 3}CHO, we have studied three isotopologues, CH{sub 3}CDO, CD{sub 3}CHO, and CD{sub 3}CDO. We have identified the thermal decomposition productsmore » CH{sub 3} (PIMS), CO (IR, PIMS), H (PIMS), H{sub 2} (PIMS), CH{sub 2}CO (IR, PIMS), CH{sub 2}=CHOH (IR, PIMS), H{sub 2}O (IR, PIMS), and HC{identical_to}CH (IR, PIMS). Plausible evidence has been found to support the idea that there are at least three different thermal decomposition pathways for CH{sub 3}CHO; namely, radical decomposition: CH{sub 3}CHO +{Delta}{yields} CH{sub 3}+[HCO]{yields} CH{sub 3}+ H + CO; elimination: CH{sub 3}CHO +{Delta}{yields} H{sub 2}+ CH{sub 2}=C=O; isomerization/elimination: CH{sub 3}CHO +{Delta}{yields}[CH{sub 2}=CH-OH]{yields} HC{identical_to}CH + H{sub 2}O. An interesting result is that both PIMS and IR spectroscopy show compelling evidence for the participation of vinylidene, CH{sub 2}=C:, as an intermediate in the decomposition of vinyl alcohol: CH{sub 2}=CH-OH +{Delta}{yields}[CH{sub 2}=C:]+ H{sub 2}O {yields} HC{identical_to}CH + H{sub 2}O.« less

  2. Electrochemical Cobalt-Catalyzed C-H Activation.

    PubMed

    Sauermann, Nicolas; Meyer, Tjark H; Ackermann, Lutz

    2018-06-19

    Carbon-heteroatom bonds represent omnipresent structural motifs of the vast majority of functionalized materials and bioactive compounds. C-H activation has emerged as arguably the most efficient strategy to construct C-Het bonds. Despite of major advances, these C-H transformations were largely dominated by precious transition metal catalysts, in combination with stoichiometric, toxic metal oxidants. Herein, we discuss the recent evolution of cobalt-catalyzed C-H activations that enable C-Het formations with electricity as the sole sustainable oxidant until May 2018. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. Ice core δD(CH4) record precludes marine hydrate CH4 emissions at the onset of Dansgaard-Oeschger events

    NASA Astrophysics Data System (ADS)

    Bock, M.; Schmitt, J.; Möller, L.; Spahni, R.; Blunier, T.; Fischer, H.

    2010-12-01

    Air enclosures in polar ice cores represent the only direct paleoatmospheric archive (besides firn air) and show that atmospheric CH4 concentrations changed in concert with northern hemisphere temperature during both glacial/interglacial transitions as well as rapid climate changes (Dansgaard-Oeschger events). For stadials and interstadials during Marine Isotope Stage 3 concentration jumps of 100 - 200 ppbv within a few decades are observed. A concentration gradient with higher values in the northern versus the southern hemisphere during warm stages was reconstructed from ice core methane data from Greenland and Antarctica. This gradient indicates additional methane emissions during warm periods located in the northern hemisphere. However, the underlying processes for these changes are still not well understood. With tropical and boreal wetlands, biomass burning, thermokarst lakes, ruminants, termites, UV-induced emissions from organic matter and marine gas hydrates all contributing to the natural atmospheric CH4 level, an unambiguous source attribution remains difficult. Also changes in the methane sinks can modify the tropospheric CH4 budget, as trace gases like volatile organic compounds are competing for the major reactant - the OH radical. Additionally, the changing global atmospheric methane concentration itself feeds back on its lifetime. Together with the CH4 interhemispheric gradient, stable hydrogen and carbon isotopic studies on methane (δD(CH4) and δ13CH4) in ice cores allow to constrain individual CH4 source/sink changes. Here we present clear evidence from the North Greenland Ice Core Project ice core based on the hydrogen isotopic composition of methane δD(CH4) that clathrates did not cause atmospheric methane concentration to rise at the onset of Dansgaard-Oeschger (DO) events 7 and 8 (34 - 41 kilo years before present), however, we can not exclude that they played a minor role during and at the end of an interstadial. Box modeling supports

  4. Rate Coefficient Measurements of the Reaction CH3 + O2 = CH3O + O

    NASA Technical Reports Server (NTRS)

    Hwang, S. M.; Ryu, Si-Ok; DeWitt, K. J.; Rabinowitz, M. J.

    1999-01-01

    Rate coefficients for the reaction CH3 + O2 = CH3O + O were measured behind reflected shock waves in a series of lean CH4-O2-Ar mixtures using hydroxyl and methyl radical diagnostics. The rate coefficients are well represented by an Arrhenius expression given as k = (1.60(sup +0.67, sub -0.47 ) x 10(exp 13) e(-15813 +/- 587 K/T)/cubic cm.mol.s. This expression, which is valid in the temperature range 1575-1822 K, supports the downward trend in the rate coefficients that has been reported in recent determinations. All measurements to date, including the present study, have been to some extent affected by secondary reactions. The complications due to secondary reactions, choice of thermochemical data, and shock-boundary layer interactions that affect the determination of the rate coefficients are examined.

  5. Rate Coefficient Measurements of the Reaction CH3+O2+CH3O+O

    NASA Technical Reports Server (NTRS)

    Hwang, S. M.; Ryu, Si-Ok; DeWitt, K. J.; Rabinowitz, M. J.

    1999-01-01

    Rate coefficients for the reaction CH3 + O2 = CH3O + O were measured behind reflected shock waves in a series of lean CH4-O2-Ar mixtures using hydroxyl and methyl radical diagnostics. The rate coefficients are well represented by an Arrhenius expression given as k = (1.60(sup +0.67, -0.47)) X 10(exp 13) exp(- 15813 +/- 587 K/T)cc/mol s. This expression, which is valid in the temperature range 1575-1822 K, supports the downward trend in the rate coefficients that has been reported in recent determinations. All measurements to date, including the present study, have been to some extent affected by secondary reactions. The complications due to secondary reactions, choice of thermochemical data, and shock-boundary layer interactions that affect the determination of the rate coefficients are examined.

  6. Tropospheric photooxidation of CF3CH2CHO and CF3(CH2)2CHO initiated by Cl atoms and OH radicals

    NASA Astrophysics Data System (ADS)

    Antiñolo, M.; Jiménez, E.; Notario, A.; Martínez, E.; Albaladejo, J.

    2009-11-01

    The absolute rate coefficients for the tropospheric reactions of chlorine (Cl) atoms and hydroxyl (OH) radicals with CF3CH2CHO and CF3(CH2)2CHO were measured as a function of temperature (263-371 K) and pressure (50-215 Torr of He) by pulsed UV laser photolysis techniques. Vacuum UV resonance fluorescence was employed to detect and monitor the time evolution of Cl atoms. Laser induced fluorescence was used in this work as a detection of OH radicals as a function of reaction time. No pressure dependence of the bimolecular rate coefficients, kCl and kOH, was found at all temperatures. At room temperature kCl and kOH were (in 10-11 cm3 molecule-1 s-1): kCl(CF3CH2CHO) = (1.55±0.53); kCl(CF3(CH2)2CHO) = (3.39±1.38); kOH(CF3CH2CHO) = (0.259±0.050); kOH(CF3(CH2)2CHO) = (1.28±0.24). A slightly negative temperature dependence of kCl was observed for CF3CH2CHO and CF3(CH2)2CHO, and kOH(CF3CH2CHO). In contrast, kOH(CF3(CH2)2CHO) did not exhibit a temperature dependence in the studied ranged. Arrhenius expressions for these reactions were: kCl(CF3CH2CHO) =(4.4±1.0) × 10-11 exp{-(316±68)/T} cm3 molecule-1 s-1, kCl(CF3(CH2)2CHO) = (2.9±0.7) × 10-10 exp{-625±80)/T} cm3 molecule-1 s-1, kOH(CF3CH2CHO) = (7.8±2.2) × 10-12 exp{-(314±90)/T} cm3 molecule-1 s-1. The atmospheric impact of the homogeneous removal by OH radicals and Cl atoms of these fluorinated aldehydes is discussed in terms of the global atmospheric lifetimes, taking into account different degradation pathways. The calculated lifetimes show that atmospheric oxidation of CF3(CH2)xCHO are globally dominated by OH radicals, however reactions initiated by Cl atoms can act as a source of free radicals at dawn in the troposphere.

  7. Tropospheric photooxidation of CF3CH2CHO and CF3(CH2)2CHO initiated by Cl atoms and OH radicals

    NASA Astrophysics Data System (ADS)

    Antiñolo, M.; Jiménez, E.; Notario, A.; Martínez, E.; Albaladejo, J.

    2010-02-01

    The absolute rate coefficients for the tropospheric reactions of chlorine (Cl) atoms and hydroxyl (OH) radicals with CF3CH2CHO and CF3(CH2)2CHO were measured as a function of temperature (263-371 K) and pressure (50-215 Torr of He) by pulsed UV laser photolysis techniques. Vacuum UV resonance fluorescence was employed to detect and monitor the time evolution of Cl atoms. Laser induced fluorescence was used in this work for the detection of OH radicals as a function of reaction time. No pressure dependence of the bimolecular rate coefficients, kCl and kOH, was found at all temperatures. At room temperature kCl and kOH were (in 10-11 cm3 molecule-1 s-1): kCl(CF3CH2CHO) = (1.55±0.53); kCl(CF3(CH2)2CHO) = (3.39±1.38); kCl(CF3CH2CHO) = (0.259±0.050); kCl(CF3(CH2)2CHO) = (1.28±0.24). A slightly positive temperature dependence of kCl was observed for CF3CH2CHO and CF3(CH2)2CHO, and kOH(CF3CH2CHO). In contrast, kOH(CF3(CH2)2CHO) did not exhibit a temperature dependence over the range investigated. Arrhenius expressions for these reactions were: kCl(CF3CH2CHO) = (4.4±1.0)×10-11 exp{-(316±68)/T} cm3 molecule-1 s-1 kCl(CF3(CH2)2CHO) = (2.9±0.7)×10-10 exp{-(625±80)/T} cm3 molecule-1 s-1 kOH(CF3CH2CHO) = (7.8±2.2)×10-12 exp{-(314±90)/T} cm3 molecule-1 s-1 The atmospheric impact of the homogeneous removal by OH radicals and Cl atoms of these fluorinated aldehydes is discussed in terms of the global atmospheric lifetimes, taking into account different degradation pathways. The calculated lifetimes show that atmospheric oxidation of CF3(CH2)x CHO are globally dominated by OH radicals, however reactions initiated by Cl atoms can act as a source of free radicals at dawn in the troposphere.

  8. Shipboard measurements and modeling of the distribution of CH4 and 13CH4 in the western Pacific

    NASA Astrophysics Data System (ADS)

    Bromley, T.; Allan, W.; Martin, R.; Mikaloff Fletcher, S. E.; Lowe, D. C.; Struthers, H.; Moss, R.

    2012-02-01

    We present observations of methane (CH4) mixing ratio and 13C/12C isotopic ratios in CH4 (δ13C) data from a collaborative shipboard project using bulk carrier ships sailing between Nelson, New Zealand, and Osaka, Japan, in the western Pacific Ocean. Measurements of the CH4 mixing ratio and δ13C in CH4were obtained from large clean-air samples collected in each 2.5° to 5° of latitude between 30°S and 30°N on eight voyages from 2004 to 2007. The data show large variations in CH4 mixing ratio in the tropical western Pacific, and data analysis suggests that these large variations are related to the positions and strengths of the South Pacific Convergence Zone and the Intertropical Convergence Zone, with variability in the sources playing a much smaller role. These measurements are compared with results from a modified version of the Unified Model (UMeth) general circulation model along two transects, one similar to the ship transects and another 18.75° to the east. Although UMeth was run to a steady state with the same sources and sinks each year, the gradient structures varied considerably from year to year, supporting our conclusion that variability in transport is a major driver for the observed variations in CH4. Simulations forced with an idealized representation of the El Niño-Southern Oscillation (ENSO) suggest that a large component of the observed variability in latitudinal gradients of CH4 and its δ13C arises from intrinsic variability in the climate system that does not occur on ENSO time scales.

  9. The ChIP-Seq tools and web server: a resource for analyzing ChIP-seq and other types of genomic data.

    PubMed

    Ambrosini, Giovanna; Dreos, René; Kumar, Sunil; Bucher, Philipp

    2016-11-18

    ChIP-seq and related high-throughput chromatin profilig assays generate ever increasing volumes of highly valuable biological data. To make sense out of it, biologists need versatile, efficient and user-friendly tools for access, visualization and itegrative analysis of such data. Here we present the ChIP-Seq command line tools and web server, implementing basic algorithms for ChIP-seq data analysis starting with a read alignment file. The tools are optimized for memory-efficiency and speed thus allowing for processing of large data volumes on inexpensive hardware. The web interface provides access to a large database of public data. The ChIP-Seq tools have a modular and interoperable design in that the output from one application can serve as input to another one. Complex and innovative tasks can thus be achieved by running several tools in a cascade. The various ChIP-Seq command line tools and web services either complement or compare favorably to related bioinformatics resources in terms of computational efficiency, ease of access to public data and interoperability with other web-based tools. The ChIP-Seq server is accessible at http://ccg.vital-it.ch/chipseq/ .

  10. Anomalous torsional tripling in the ν9 and ν10 CH3-deformation modes of ethane 12CH313CH3

    NASA Astrophysics Data System (ADS)

    Lattanzi, F.; di Lauro, C.

    2017-12-01

    We have investigated the anomalous torsional behavior in the coupled ν9 and ν10 vibrational fundamentals of 12CH313CH3, both states exhibiting a splitting into three components, instead of two, only in those rotational levels which are very close to resonance. We conclude that the intrinsic additional splitting, which occurs in the E-torsional components, for these two vibrational states is too small to be detected in the high resolution infrared spectrum, but it is substantively enhanced by their coupling. It is shown that this effect requires the simultaneous action of torsion independent operators, such as Fermi-type and z-Coriolis, not allowed in the more symmetric isotopologue 12CH312CH3, and torsion dependent operators, such as torsional-Coriolis, connecting the two vibrational states. Our conclusions lead to a simple model for the coupling of ν9 and ν10, with effective Fermi-type matrix elements W for the A-torsional components, and W ± w for the two pairs of E-torsional components. This causes the additional splitting in the E-pairs. This model is consistent with the mechanism causing the Coriolis-dependent decrease of the A-E torsional splitting in degenerate vibrational states. Exploratory calculations were performed making use of results from a normal mode analysis, showing that the effects predictable by the proposed model are of the correct order of magnitude compared to the observed features, with coupling parameter values reasonably consistent with those determined by the least squares fit of the observed transition wavenumbers.

  11. Isotopic signatures of anthropogenic CH4 sources in Alberta, Canada

    NASA Astrophysics Data System (ADS)

    Lopez, M.; Sherwood, O. A.; Dlugokencky, E. J.; Kessler, R.; Giroux, L.; Worthy, D. E. J.

    2017-09-01

    A mobile system was used for continuous ambient measurements of stable CH4 isotopes (12CH4 and 13CH4) and ethane (C2H6). This system was used during a winter mobile campaign to investigate the CH4 isotopic signatures and the C2H6/CH4 ratios of the main anthropogenic sources of CH4 in the Canadian province of Alberta. Individual signatures were derived from δ13CH4 and C2H6 measurements in plumes arriving from identifiable single sources. Methane emissions from beef cattle feedlots (n = 2) and landfill (n = 1) had δ13CH4 signatures of -66.7 ± 2.4‰ and -55.3 ± 0.2‰, respectively. The CH4 emissions associated with the oil or gas industry had distinct δ13CH4 signatures, depending on the formation process. Emissions from oil storage tanks (n = 5) had δ13CH4 signatures ranging from -54.9 ± 2.9‰ to -60.6 ± 0.6‰ and non-detectable C2H6, characteristic of secondary microbial methanogenesis in oil-bearing reservoirs. In contrast, CH4 emissions associated with natural gas facilities (n = 8) had δ13CH4 signatures ranging from -41.7 ± 0.7‰ to -49.7 ± 0.7‰ and C2H6/CH4 molar ratios of 0.10 for raw natural gas to 0.04 for processed/refined natural gas, consistent with thermogenic origins. These isotopic signatures and C2H6/CH4 ratios have been used for source discrimination in the weekly atmospheric measurements of stable CH4 isotopes over a two-month winter period at the Lac La Biche (LLB) measurement station, located in Alberta, approximately 200 km northeast of Edmonton. The average signature of -59.5 ± 1.4‰ observed at LLB is likely associated with transport of air after passing over oil industry sources located south of the station.

  12. ChAT-ChR2-EYFP mice have enhanced motor endurance but show deficits in attention and several additional cognitive domains.

    PubMed

    Kolisnyk, Benjamin; Guzman, Monica S; Raulic, Sanda; Fan, Jue; Magalhães, Ana C; Feng, Guoping; Gros, Robert; Prado, Vania F; Prado, Marco A M

    2013-06-19

    Acetylcholine (ACh) is an important neuromodulator in the nervous system implicated in many forms of cognitive and motor processing. Recent studies have used bacterial artificial chromosome (BAC) transgenic mice expressing channelrhodopsin-2 (ChR2) protein under the control of the choline acetyltransferase (ChAT) promoter (ChAT-ChR2-EYFP) to dissect cholinergic circuit connectivity and function using optogenetic approaches. We report that a mouse line used for this purpose also carries several copies of the vesicular acetylcholine transporter gene (VAChT), which leads to overexpression of functional VAChT and consequently increased cholinergic tone. We demonstrate that these mice have marked improvement in motor endurance. However, they also present severe cognitive deficits, including attention deficits and dysfunction in working memory and spatial memory. These results suggest that increased VAChT expression may disrupt critical steps in information processing. Our studies demonstrate that ChAT-ChR2-EYFP mice show altered cholinergic tone that fundamentally differentiates them from wild-type mice.

  13. CH4 production via CO2 reduction in a temperate bog - A source of (C-13)-depleted CH4

    NASA Technical Reports Server (NTRS)

    Lansdown, J. M.; Quay, P. D.; King, S. L.

    1992-01-01

    The paper reports measurements, taken over two annual cycles, of the flux and delta(C-13) of CH4 released from an acidic peat bog located in the foothills of the Cascade Range in Washington state, U.S. Measurements of the rate of aceticlastic methanogenesis and CO2 reduction in peat soil, using (C-14)-labeled acetate and sodium bicarbonate, show that acetate was not an important CH4 precursor and that CO2 reduction could account for all of the CH4 production. The in situ kinetic isotope effect for CO2 reduction, calculated using the delta-(C-13) of soil water CO2 and CH4 flux, was 0.932 +/- 0.007.

  14. ChLae1 and ChVel1 Regulate T-toxin Production, Virulence, Oxidative Stress Response, and Development of the Maize Pathogen Cochliobolus heterostrophus

    PubMed Central

    Wu, Dongliang; Oide, Shinichi; Zhang, Ning; Choi, May Yee; Turgeon, B. Gillian

    2012-01-01

    LaeA and VeA coordinate secondary metabolism and differentiation in response to light signals in Aspergillus spp. Their orthologs, ChLae1 and ChVel1, were identified in the maize pathogen Cochliobolus heterostrophus, known to produce a wealth of secondary metabolites, including the host selective toxin, T-toxin. Produced by race T, T-toxin promotes high virulence to maize carrying Texas male sterile cytoplasm (T-cms). T-toxin production is significantly increased in the dark in wild type (WT), whereas Chvel1 and Chlae1 mutant toxin levels are much reduced in the dark compared to WT. Correspondingly, expression of T-toxin biosynthetic genes (Tox1) is up-regulated in the dark in WT, while dark-induced expression is much reduced/minimal in Chvel1 and Chlae1 mutants. Toxin production and Tox1 gene expression are increased in ChVEL1 overexpression (OE) strains grown in the dark and in ChLAE1 strains grown in either light or dark, compared to WT. These observations establish ChLae1 and ChVel1 as the first factors known to regulate host selective toxin production. Virulence of Chlae1 and Chvel1 mutants and OE strains is altered on both T-cms and normal cytoplasm maize, indicating that both T-toxin mediated super virulence and basic pathogenic ability are affected. Deletion of ChLAE1 or ChVEL1 reduces tolerance to H2O2. Expression of CAT3, one of the three catalase genes, is reduced in the Chvel1 mutant. Chlae1 and Chvel1 mutants also show decreased aerial hyphal growth, increased asexual sporulation and female sterility. ChLAE1 OE strains are female sterile, while ChVEL1 OE strains are more fertile than WT. ChLae1 and ChVel1 repress expression of 1,8-dihydroxynaphthalene (DHN) melanin biosynthesis genes, and, accordingly, melanization is enhanced in Chlae1 and Chvel1 mutants, and reduced in OE strains. Thus, ChLae1 and ChVel1 positively regulate T-toxin biosynthesis, pathogenicity and super virulence, oxidative stress responses, sexual development, and aerial hyphal

  15. Infrared absorption of 1-chloro-2-methyl-2-propyl [⋅C(CH3)2CH2Cl] and 2-chloro-2-methylpropyl [⋅CH2C(CH3)2Cl] radicals produced in the addition reactions of Cl with isobutene (i-C4H8) in solid para-hydrogen.

    PubMed

    Chou, Ching-Yin; Lee, Yuan-Pern

    2016-10-07

    The addition reactions of chlorine atom with isobutene (i-C 4 H 8 ) in solid para-hydrogen (p-H 2 ) were investigated with infrared (IR) absorption spectra. When a p-H 2 matrix containing Cl 2 and isobutene was irradiated with ultraviolet light at 365 nm, intense lines in a set at 534.5, 1001.0, 1212.9, 1366.0, 2961.6, and 2934.7 cm -1 , and several weaker others due to the 1-chloro-2-methyl-2-propyl radical, ⋅ C(CH 3 ) 2 CH 2 Cl, and those in a second set including intense ones at 642.7, 799.2, 1098.2, 1371.8, and 3027.3 cm -1 due to the 2-chloro-2-methylpropyl radical, ⋅ CH 2 C(CH 3 ) 2 Cl, appeared; the ratio of ⋅ C(CH 3 ) 2 CH 2 Cl to ⋅ CH 2 C(CH 3 ) 2 Cl was approximately (3 ± 1):1. The observed wavenumbers and relative intensities agree with the vibrational wavenumbers and IR intensities predicted with the B3PW91/aug-cc-pVTZ method. That the Cl atom adds to both carbons of the C=C bond of isobutene with the terminal site slightly favored is consistent with the energies of products predicted theoretically, but is in contrast to the reaction of Cl + propene in solid p-H 2 in which the addition of Cl to mainly the central C atom was previously reported. The role of the p-H 2 matrix in affecting the reaction paths is discussed. Absorption lines of the complex i-C 4 H 8 ⋅Cl 2 and the dichloro-product anti-1,2-dichloro-2-methylpropane, a-CH 2 ClCCl(CH 3 ) 2 , are also characterized.

  16. Landscape patterns of CH4 fluxes in an alpine tundra ecosystem

    USGS Publications Warehouse

    West, A.E.; Brooks, P.D.; Fisk, M.C.; Smith, Lesley K.; Holland, E.A.; Jaeger, C. H.; Babcock, S.; Lai, R.S.; Schmidt, S.K.

    1999-01-01

    We measured CH4 fluxes from three major plant communities characteristic of alpine tundra in the Colorado Front Range. Plant communities in this ecosystem are determined by soil moisture regimes induced by winter snowpack distribution. Spatial patterns of CH4 flux during the snow-free season corresponded roughly with these plant communities. In Carex-dominated meadows, which receive the most moisture from snowmelt, net CH4 production occurred. However, CH4 production in one Carex site (seasonal mean = +8.45 mg CH4 m-2 d-1) was significantly larger than in the other Carex sites (seasonal means = -0.06 and +0.05 mg CH4 m-2 d-1). This high CH4 flux may have resulted from shallower snowpack during the winter. In Acomastylis meadows, which have an intermediate moisture regime, CH4 oxidation dominated (seasonal mean = -0.43 mg CH4 m-2 d-1). In the windswept Kobresia meadow plant community, which receive the least amount of moisture from snowmelt, only CH4 oxidation was observed (seasonal mean = -0.77 mg CH4 m-2 d-1). Methane fluxes correlated with a different set of environmental factors within each plant community. In the Carex plant community, CH4 emission was limited by soil temperature. In the Acomastylis meadows, CH4 oxidation rates correlated positively with soil temperature and negatively with soil moisture. In the Kobresia community, CH4 oxidation was stimulated by precipitation. Thus, both snow-free season CH4 fluxes and the controls on those CH4 fluxes were related to the plant communities determined by winter snowpack.

  17. Parallel factor ChIP provides essential internal control for quantitative differential ChIP-seq.

    PubMed

    Guertin, Michael J; Cullen, Amy E; Markowetz, Florian; Holding, Andrew N

    2018-04-17

    A key challenge in quantitative ChIP combined with high-throughput sequencing (ChIP-seq) is the normalization of data in the presence of genome-wide changes in occupancy. Analysis-based normalization methods were developed for transcriptomic data and these are dependent on the underlying assumption that total transcription does not change between conditions. For genome-wide changes in transcription factor (TF) binding, these assumptions do not hold true. The challenges in normalization are confounded by experimental variability during sample preparation, processing and recovery. We present a novel normalization strategy utilizing an internal standard of unchanged peaks for reference. Our method can be readily applied to monitor genome-wide changes by ChIP-seq that are otherwise lost or misrepresented through analytical normalization. We compare our approach to normalization by total read depth and two alternative methods that utilize external experimental controls to study TF binding. We successfully resolve the key challenges in quantitative ChIP-seq analysis and demonstrate its application by monitoring the loss of Estrogen Receptor-alpha (ER) binding upon fulvestrant treatment, ER binding in response to estrodiol, ER mediated change in H4K12 acetylation and profiling ER binding in patient-derived xenographs. This is supported by an adaptable pipeline to normalize and quantify differential TF binding genome-wide and generate metrics for differential binding at individual sites.

  18. ChIPnorm: a statistical method for normalizing and identifying differential regions in histone modification ChIP-seq libraries.

    PubMed

    Nair, Nishanth Ulhas; Sahu, Avinash Das; Bucher, Philipp; Moret, Bernard M E

    2012-01-01

    The advent of high-throughput technologies such as ChIP-seq has made possible the study of histone modifications. A problem of particular interest is the identification of regions of the genome where different cell types from the same organism exhibit different patterns of histone enrichment. This problem turns out to be surprisingly difficult, even in simple pairwise comparisons, because of the significant level of noise in ChIP-seq data. In this paper we propose a two-stage statistical method, called ChIPnorm, to normalize ChIP-seq data, and to find differential regions in the genome, given two libraries of histone modifications of different cell types. We show that the ChIPnorm method removes most of the noise and bias in the data and outperforms other normalization methods. We correlate the histone marks with gene expression data and confirm that histone modifications H3K27me3 and H3K4me3 act as respectively a repressor and an activator of genes. Compared to what was previously reported in the literature, we find that a substantially higher fraction of bivalent marks in ES cells for H3K27me3 and H3K4me3 move into a K27-only state. We find that most of the promoter regions in protein-coding genes have differential histone-modification sites. The software for this work can be downloaded from http://lcbb.epfl.ch/software.html.

  19. Room-temperature enantioselective C-H iodination via kinetic resolution.

    PubMed

    Chu, Ling; Xiao, Kai-Jiong; Yu, Jin-Quan

    2014-10-24

    Asymmetric carbon-hydrogen (C-H) activation reactions often rely on desymmetrization of prochiral C-H bonds on the same achiral molecule, using a chiral catalyst. Here, we report a kinetic resolution via palladium-catalyzed enantioselective C-H iodination in which one of the enantiomers of a racemic benzylic amine substrates undergoes faster aryl C-H insertion with the chiral catalysts than the other. The resulting enantioenriched C-H functionalization products would not be accessible through desymmetrization of prochiral C-H bonds. The exceedingly high relative rate ratio (k(fast)/k(slow) up to 244), coupled with the subsequent iodination of the remaining enantiomerically enriched starting material using a chiral ligand with the opposite configuration, enables conversion of both substrate enantiomers into enantiomerically pure iodinated products. Copyright © 2014, American Association for the Advancement of Science.

  20. Direct dynamics simulation of dioxetane formation and decomposition via the singlet .O-O-CH2-CH2. biradical: Non-RRKM dynamics

    NASA Astrophysics Data System (ADS)

    Sun, Rui; Park, Kyoyeon; de Jong, Wibe A.; Lischka, Hans; Windus, Theresa L.; Hase, William L.

    2012-07-01

    Electronic structure calculations and direct chemical dynamics simulations are used to study the formation and decomposition of dioxetane on its ground state singlet potential energy surface. The stationary points for 1O2 + C2H4, the singlet .O-O-CH2-CH2. biradical, the transition state (TS) connecting this biradical with dioxetane, and the two transition states and gauche .O-CH2-CH2-O. biradical connecting dioxetane with the formaldehyde product molecules are investigated at different levels of electronic structure theory including UB3LYP, UMP2, MRMP2, and CASSCF and a range of basis sets. The UB3LYP/6-31G* method was found to give representative energies for the reactive system and was used as a model for the simulations. UB3LYP/6-31G* direct dynamics trajectories were initiated at the TS connecting the .O-O-CH2-CH2. biradical and dioxetane by sampling the TS's vibrational energy levels, and rotational and reaction coordinate energies, with Boltzmann distributions at 300, 1000, and 1500 K. This corresponds to the transition state theory model for trajectories that pass the TS. The trajectories were directed randomly towards both the biradical and dioxetane. A small fraction of the trajectories directed towards the biradical recrossed the TS and formed dioxetane. The remainder formed 1O2 + C2H4 and of these ˜ 40% went directly from the TS to 1O2 + C2H4 without getting trapped and forming an intermediate in the .O-O-CH2-CH2. biradical potential energy minimum, a non-statistical result. The dioxetane molecules which are formed dissociate to two formaldehyde molecules with a rate constant two orders of magnitude smaller than that predicted by Rice-Ramsperger-Kassel-Marcus theory. The reaction dynamics from dioxetane to the formaldehyde molecules do not follow the intrinsic reaction coordinate or involve trapping in the gauche .O-CH2-CH2-O. biradical potential energy minimum. Important non-statistical dynamics are exhibited for this reactive system.

  1. C-H bond activation of hydrocarbons by an imidozirconocene complex.

    PubMed

    Hoyt, Helen M; Michael, Forrest E; Bergman, Robert G

    2004-02-04

    Monomeric imidozirconocene complexes of the type Cp2(L)Zr=NCMe3 (Cp = cyclopentadienyl, L = Lewis base) have been shown to activate the carbon-hydrogen bonds of benzene, but not the C-H bonds of saturated hydrocarbons. To our knowledge, this singularly important class of C-H activation reactions has heretofore not been observed in imidometallocene systems. The M=NR bond formed on heating the racemic ethylenebis(tetrahydro)indenyl methyl tert-butyl amide complex, however, cleanly and quantitatively activates a wide range of n-alkane, alkene, and arene C-H bonds. Mechanistic experiments support the proposal of intramolecular elimination of methane followed by a concerted addition of the hydrocarbon C-H bond. Products formed by activation of sp2 C-H bonds are generally more thermodynamically stable than those formed by activation of sp3 C-H bonds, and those resulting from reaction at primary C-H bonds are preferred over secondary sp3 C-H activation products. There is also evidence that thermodynamic selectivity among C-H bonds is sterically rather than electronically controlled.

  2. Mapping pan-Arctic CH4 emissions using an adjoint method by integrating process-based wetland and lake biogeochemical models and atmospheric CH4 concentrations

    NASA Astrophysics Data System (ADS)

    Tan, Z.; Zhuang, Q.; Henze, D. K.; Frankenberg, C.; Dlugokencky, E. J.; Sweeney, C.; Turner, A. J.

    2015-12-01

    Understanding CH4 emissions from wetlands and lakes are critical for the estimation of Arctic carbon balance under fast warming climatic conditions. To date, our knowledge about these two CH4 sources is almost solely built on the upscaling of discontinuous measurements in limited areas to the whole region. Many studies indicated that, the controls of CH4 emissions from wetlands and lakes including soil moisture, lake morphology and substrate content and quality are notoriously heterogeneous, thus the accuracy of those simple estimates could be questionable. Here we apply a high spatial resolution atmospheric inverse model (nested-grid GEOS-Chem Adjoint) over the Arctic by integrating SCIAMACHY and NOAA/ESRL CH4 measurements to constrain the CH4 emissions estimated with process-based wetland and lake biogeochemical models. Our modeling experiments using different wetland CH4 emission schemes and satellite and surface measurements show that the total amount of CH4 emitted from the Arctic wetlands is well constrained, but the spatial distribution of CH4 emissions is sensitive to priors. For CH4 emissions from lakes, our high-resolution inversion shows that the models overestimate CH4 emissions in Alaskan costal lowlands and East Siberian lowlands. Our study also indicates that the precision and coverage of measurements need to be improved to achieve more accurate high-resolution estimates.

  3. Thermodynamic and hydrochemical controls on CH4 in a coal seam gas and overlying alluvial aquifer: new insights into CH4 origins

    PubMed Central

    Owen, D. Des. R.; Shouakar-Stash, O.; Morgenstern, U.; Aravena, R.

    2016-01-01

    Using a comprehensive data set (dissolved CH4, δ13C-CH4, δ2H-CH4, δ13C-DIC, δ37Cl, δ2H-H2O, δ18O-H2O, Na, K, Ca, Mg, HCO3, Cl, Br, SO4, NO3 and DO), in combination with a novel application of isometric log ratios, this study describes hydrochemical and thermodynamic controls on dissolved CH4 from a coal seam gas reservoir and an alluvial aquifer in the Condamine catchment, eastern Surat/north-western Clarence-Moreton basins, Australia. δ13C-CH4 data in the gas reservoir (−58‰ to −49‰) and shallow coal measures underlying the alluvium (−80‰ to −65‰) are distinct. CO2 reduction is the dominant methanogenic pathway in all aquifers, and it is controlled by SO4 concentrations and competition for reactants such as H2. At isolated, brackish sites in the shallow coal measures and alluvium, highly depleted δ2H-CH4 (<310‰) indicate acetoclastic methanogenesis where SO4 concentrations inhibit CO2 reduction. Evidence of CH4 migration from the deep gas reservoir (200–500 m) to the shallow coal measures (<200 m) or the alluvium was not observed. The study demonstrates the importance of understanding CH4 at different depth profiles within and between aquifers. Further research, including culturing studies of microbial consortia, will improve our understanding of the occurrence of CH4 within and between aquifers in these basins. PMID:27578542

  4. A vacuum ultraviolet laser pulsed field ionization-photoion study of methane (CH 4): Determination of the appearance energy of methylium from methane with unprecedented precision and the resulting impact on the bond dissociation energies of CH 4 and CH 4 +

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Chang, Yih -Chung; Xiong, Bo; Bross, David H.

    Here, we report on the successful implementation of a high-resolution vacuum ultraviolet (VUV) laser pulsed field ionization-photoion (PFI-PI) detection method for the study of unimolecular dissociation of quantum-state- or energy-selected molecular ions. As a test case, we have determined the 0 K appearance energy (AE 0) for the formation of methylium, CH 3 +, from methane, CH 4, as AE 0 (CH 3 +/CH 4) = 14.32271 ± 0.00013 eV. This value has a significantly smaller error limit, but is otherwise consistent with previous laboratory and/or synchrotron-based studies of this dissociative photoionization onset. Furthermore, the sum of the VUV lasermore » PFI-PI spectra obtained for the parent CH 4 + ion and the fragment CH 3 + ions of methane is found to agree with the earlier VUV pulsed field ionization-photoelectron (VUV-PFI-PE) spectrum of methane, providing unambiguous validation of the previous interpretation that the sharp VUV-PFI-PE step observed at the AE 0 (CH 3 +/CH 4) threshold ensues because of higher PFI detection efficiency for fragment CH 3 + than for parent CH 4 +. This, in turn, is a consequence of the underlying high- n Rydberg dissociation mechanism for the dissociative photoionization of CH 4, which was proposed in previous synchrotron-based VUV-PFI-PE and VUV-PFI-PEPICO studies of CH 4. The present highly accurate 0 K dissociative ionization threshold for CH 4 can be utilized to derive accurate values for the bond dissociation energies of methane and methane cation. For methane, the straightforward application of sequential thermochemistry via the positive ion cycle leads to some ambiguity because of two competing VUV-PFI-PE literature values for the ionization energy of methyl radical. The ambiguity is successfully resolved by applying the Active Thermochemical Tables (ATcT) approach, resulting in D 0 (H-CH 3) = 432.463 ± 0.027 kJ/mol and D 0(H-CH 3 +) = 164.701 ± 0.038 kJ/mol.« less

  5. A vacuum ultraviolet laser pulsed field ionization-photoion study of methane (CH 4): Determination of the appearance energy of methylium from methane with unprecedented precision and the resulting impact on the bond dissociation energies of CH 4 and CH 4 +

    DOE PAGES

    Chang, Yih -Chung; Xiong, Bo; Bross, David H.; ...

    2017-03-27

    Here, we report on the successful implementation of a high-resolution vacuum ultraviolet (VUV) laser pulsed field ionization-photoion (PFI-PI) detection method for the study of unimolecular dissociation of quantum-state- or energy-selected molecular ions. As a test case, we have determined the 0 K appearance energy (AE 0) for the formation of methylium, CH 3 +, from methane, CH 4, as AE 0 (CH 3 +/CH 4) = 14.32271 ± 0.00013 eV. This value has a significantly smaller error limit, but is otherwise consistent with previous laboratory and/or synchrotron-based studies of this dissociative photoionization onset. Furthermore, the sum of the VUV lasermore » PFI-PI spectra obtained for the parent CH 4 + ion and the fragment CH 3 + ions of methane is found to agree with the earlier VUV pulsed field ionization-photoelectron (VUV-PFI-PE) spectrum of methane, providing unambiguous validation of the previous interpretation that the sharp VUV-PFI-PE step observed at the AE 0 (CH 3 +/CH 4) threshold ensues because of higher PFI detection efficiency for fragment CH 3 + than for parent CH 4 +. This, in turn, is a consequence of the underlying high- n Rydberg dissociation mechanism for the dissociative photoionization of CH 4, which was proposed in previous synchrotron-based VUV-PFI-PE and VUV-PFI-PEPICO studies of CH 4. The present highly accurate 0 K dissociative ionization threshold for CH 4 can be utilized to derive accurate values for the bond dissociation energies of methane and methane cation. For methane, the straightforward application of sequential thermochemistry via the positive ion cycle leads to some ambiguity because of two competing VUV-PFI-PE literature values for the ionization energy of methyl radical. The ambiguity is successfully resolved by applying the Active Thermochemical Tables (ATcT) approach, resulting in D 0 (H-CH 3) = 432.463 ± 0.027 kJ/mol and D 0(H-CH 3 +) = 164.701 ± 0.038 kJ/mol.« less

  6. FunChIP: an R/Bioconductor package for functional classification of ChIP-seq shapes.

    PubMed

    Parodi, Alice C L; Sangalli, Laura M; Vantini, Simone; Amati, Bruno; Secchi, Piercesare; Morelli, Marco J

    2017-08-15

    Chromatin Immunoprecipitation followed by sequencing (ChIP-seq) generates local accumulations of sequencing reads on the genome ("peaks"), which correspond to specific protein-DNA interactions or chromatin modifications. Peaks are detected by considering their total area above a background signal, usually neglecting their shapes, which instead may convey additional biological information. We present FunChIP, an R/Bioconductor package for clustering peaks according to a functional representation of their shapes: after approximating their profiles with cubic B-splines, FunChIP minimizes their functional distance and classifies the peaks applying a k-mean alignment and clustering algorithm. The whole pipeline is user-friendly and provides visualization functions for a quick inspection of the results. An application to the transcription factor Myc in 3T9 murine fibroblasts shows that clusters of peaks with different shapes are associated with different genomic locations and different transcriptional regulatory activity. The package is implemented in R and is available under Artistic Licence 2.0 from the Bioconductor website (http://bioconductor.org/packages/FunChIP). marco.morelli@iit.it. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

  7. A laser flash photolysis-resonance fluorescence kinetics study of the reaction Cl/2P/ + CH4 yields CH3 + HCl

    NASA Technical Reports Server (NTRS)

    Ravishankara, A. R.; Wine, P. H.

    1980-01-01

    The technique of laser flash photolysis-resonance fluorescence is employed to study the kinetics of the reaction Cl(2P) + CH4 yields CH3 + HCl over the temperature range 221-375 K. At temperatures less than or equal to 241 K the apparent bimolecular rate constant is found to be dependent upon the identity of the chemically inert gases in the reaction mixture. For Cl2/CH4/He reaction mixtures (total pressure = 50 torr) different bimolecular rate constants are measured at low and high methane concentrations. For Cl2/CH4/CCl/He and Cl2/CH4/Ar reaction mixtures, the bimolecular rate constant is independent of methane concentration, being approximately equal to the rate constant measured at low methane concentrations for Cl2/CH4/He mixtures. These rate constants are in good agreement with previous results obtained using the discharge flow-resonance fluorescence and competitive chlorination techniques. At 298 K the measured bimolecular rate constant is independent of the identity of the chemically inert gases in the reaction mixture and in good agreement with all previous investigations. The low-temperature results obtained in this investigation and all previous investigations can be rationalized in terms of a model which assumes that the Cl(2P 1/2) state reacts with CH4 much faster than the Cl(2P 3/2) state. Extrapolation of this model to higher temperatures, however, is not straightforward.

  8. The ChArMEx database

    NASA Astrophysics Data System (ADS)

    Ferré, Hélène; Descloitres, Jacques; Fleury, Laurence; Boichard, Jean-Luc; Brissebrat, Guillaume; Focsa, Loredana; Henriot, Nicolas; Mastrorillo, Laurence; Mière, Arnaud; Vermeulen, Anne

    2013-04-01

    The Chemistry-Aerosol Mediterranean Experiment (ChArMEx, http://charmex.lsce.ipsl.fr/) aims at a scientific assessment of the present and future state of the atmospheric environment in the Mediterranean Basin, and of its impacts on the regional climate, air quality, and marine biogeochemistry. The project includes long term monitoring of environmental parameters, intensive field campaigns, use of satellite data and modelling studies. Therefore ChARMEx scientists produce and need to access a wide diversity of data. In this context, the objective of the database task is to organize data management, distribution system and services such as facilitating the exchange of information and stimulating the collaboration between researchers within the ChArMEx community, and beyond. The database relies on a strong collaboration between OMP and ICARE data centres and falls within the scope of the Mediterranean Integrated Studies at Regional And Locals Scales (MISTRALS) program data portal. All the data produced by or of interest for the ChArMEx community will be documented in the data catalogue and accessible through the database website: http://mistrals.sedoo.fr/ChArMEx. The database website offers different tools: - A registration procedure which enables any scientist to accept the data policy and apply for a user database account. - Forms to document observations or products that will be provided to the database in compliance with metadata international standards (ISO 19115-19139; INSPIRE; Global Change Master Directory Thesaurus). - A search tool to browse the catalogue using thematic, geographic and/or temporal criteria. - Sorted lists of the datasets by thematic keywords, by measured parameters, by instruments or by platform type. - A shopping-cart web interface to order in situ data files. At present datasets from the background monitoring station of Ersa, Cape Corsica and from the 2012 ChArMEx pre-campaign are available. - A user-friendly access to satellite products

  9. Photolysis of CH{sub 3}CHO at 248 nm: Evidence of triple fragmentation from primary quantum yield of CH{sub 3} and HCO radicals and H atoms

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Morajkar, Pranay; Schoemaecker, Coralie; Fittschen, Christa, E-mail: christa.fittschen@univ-lille1.fr

    2014-06-07

    Radical quantum yields have been measured following the 248 nm photolysis of acetaldehyde, CH{sub 3}CHO. HCO radical and H atom yields have been quantified by time resolved continuous wave Cavity Ring Down Spectroscopy in the near infrared following their conversion to HO{sub 2} radicals by reaction with O{sub 2}. The CH{sub 3} radical yield has been determined using the same technique following their conversion into CH{sub 3}O{sub 2}. Absolute yields have been deduced for HCO radicals and H atoms through fitting of time resolved HO{sub 2} profiles, obtained under various O{sub 2} concentrations, to a complex model, while the CH{submore » 3} yield has been determined relative to the CH{sub 3} yield from 248 nm photolysis of CH{sub 3}I. Time resolved HO{sub 2} profiles under very low O{sub 2} concentrations suggest that another unknown HO{sub 2} forming reaction path exists in this reaction system besides the conversion of HCO radicals and H atoms by reaction with O{sub 2}. HO{sub 2} profiles can be well reproduced under a large range of experimental conditions with the following quantum yields: CH{sub 3}CHO + hν{sub 248nm} → CH{sub 3}CHO{sup *}, CH{sub 3}CHO{sup *} → CH{sub 3} + HCO ϕ{sub 1a} = 0.125 ± 0.03, CH{sub 3}CHO{sup *} → CH{sub 3} + H + CO ϕ{sub 1e} = 0.205 ± 0.04, CH{sub 3}CHO{sup *}→{sup o{sub 2}}CH{sub 3}CO + HO{sub 2} ϕ{sub 1f} = 0.07 ± 0.01. The CH{sub 3}O{sub 2} quantum yield has been determined in separate experiments as ϕ{sub CH{sub 3}} = 0.33 ± 0.03 and is in excellent agreement with the CH{sub 3} yields derived from the HO{sub 2} measurements considering that the triple fragmentation (R1e) is an important reaction path in the 248 nm photolysis of CH{sub 3}CHO. From arithmetic considerations taking into account the HO{sub 2} and CH{sub 3} measurements we deduce a remaining quantum yield for the molecular pathway: CH{sub 3}CHO{sup *} → CH{sub 4} + CO ϕ{sub 1b} = 0.6. All experiments

  10. Atmospheric lifetimes and ozone depletion potentials of methyl bromide (CH3Br) and dibromomethane (CH2Br2)

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Mellouki, A.; Talukdar, R.K.; Schmoltner, A.

    The rate coefficients for the reactions of OH radical with CH3Br and CH2Br2 were measured as functions of temperature using the laser photolysis - laser induced fluorescence method. This data was incorporated into a semiempirical model (Solomon et al., 1992) and a 2D model to calculate the steady-state ozone depletion potentials (ODP) and atmospheri lifetimes, tau, with greatly improved accuracy as compared to earlier studies. The calculated ODPs and tau are 0.65 and 1.7 years and 0.17 and 0.41 years for CH3Br and CH2Br2, respectively, using the semiempirical model. These lifetimes agree well with those calculated using a 2D model.more » This study better quantifies the ODPs and tau of these species which are needed inputs for discussion of possible regulation of human emissions currently under international considerations. 29 refs.« less

  11. Methanesulfonates of high-valent metals: syntheses and structural features of MoO2(CH3SO3)2, UO2(CH3SO3)2, ReO3(CH3SO3), VO(CH3SO3)2, and V2O3(CH3SO3)4 and their thermal decomposition under N2 and O2 atmosphere.

    PubMed

    Betke, Ulf; Neuschulz, Kai; Wickleder, Mathias S

    2011-11-04

    Oxide methanesulfonates of Mo, U, Re, and V have been prepared by reaction of MoO(3), UO(2)(CH(3)COO)(2)·2H(2)O, Re(2)O(7)(H(2)O)(2), and V(2)O(5) with CH(3)SO(3)H or mixtures thereof with its anhydride. These compounds are the first examples of solvent-free oxide methanesulfonates of these elements. MoO(2)(CH(3)SO(3))(2) (Pbca, a=1487.05(4), b=752.55(2), c=1549.61(5) pm, V=1.73414(9) nm(3), Z=8) contains [MoO(2)] moieties connected by [CH(3)SO(3)] ions to form layers parallel to (100). UO(2)(CH(3)SO(3))(2) (P2(1)/c, a=1320.4(1), b=1014.41(6), c=1533.7(1) pm, β=112.80(1)°, V=1.8937(3) nm(3), Z=8) consists of linear UO(2)(2+) ions coordinated by five [CH(3)SO(3)] ions, forming a layer structure. VO(CH(3)SO(3))(2) (P2(1)/c, a=1136.5(1), b=869.87(7), c=915.5(1) pm, β=113.66(1)°, V=0.8290(2) nm(3), Z=4) contains [VO] units connected by methanesulfonate anions to form corrugated layers parallel to (100). In ReO(3)(CH(3)SO(3)) (P1, a=574.0(1), b=1279.6(3), c=1641.9(3) pm, α=102.08(2), β=96.11(2), γ=99.04(2)°, V=1.1523(4) nm(3), Z=8) a chain structure exhibiting infinite O-[ReO(2)]-O-[ReO(2)]-O chains is formed. Each [ReO(2)]-O-[ReO(2)] unit is coordinated by two bidentate [CH(3)SO(3)] ions. V(2)O(3)(CH(3)SO(3))(4) (I2/a, a=1645.2(3), b=583.1(1), c=1670.2(3) pm, β=102.58(3), V=1.5637(5) pm(3), Z=4) adopts a chain structure, too, but contains discrete [VO]-O-[VO] moieties, each coordinated by two bidentate [CH(3)SO(3)] ligands. Additional methanesulfonate ions connect the [V(2)O(3)] groups along [001]. Thermal decomposition of the compounds was monitored under N(2) and O(2) atmosphere by thermogravimetric/differential thermal analysis and XRD measurements. Under N(2) the decomposition proceeds with reduction of the metal leading to the oxides MoO(2), U(3)O(7), V(4)O(7), and VO(2); for MoO(2)(CH(3)SO(3))(2), a small amount of MoS(2) is formed. If the thermal decomposition is carried out in a atmosphere of O(2) the oxides MoO(3) and V(2)O(5) are formed. Copyright

  12. Analysis of the heat capacity for pure CH4 and CH4/CCl4 on graphite near the melting point and calculation of the T-X phase diagram for (CH3)CCl3 + CCl4

    NASA Astrophysics Data System (ADS)

    Yurtseven, Hamit; Yılmaz, Aygül

    2016-06-01

    We study the temperature dependence of the heat capacity Cp for the pure CH4 and the coadsorbed CH4/CCl4 on graphite near the melting point. The heat capacity peaks are analyzed using the experimental data from the literature by means of the power-law formula. The critical exponents for the heat capacity are deduced below and above the melting point for CH4 (Tm = 104.8 K) and CH4/CCl4 (Tm = 99.2 K). Our exponent values are larger as compared with the predicted values of some theoretical models exhibiting second order transition. Our analyses indicate that the pure methane shows a nearly second order (weak discontinuity in the heat capacity peak), whereas the transition in coadsorbed CH4/CCl4 is of first order (apparent discontinuity in Cp). We also study the T - X phase diagram of a two-component system of CH3CCl3+CCl4 using the Landau phenomenological model. Phase lines of the R+L (rhombohedral+liquid) and FCC+L (face-centred cubic + liquid) are calculated using the observed T - X phase diagram of this binary mixture. Our results show that the Landau mean field theory describes the observed behavior of CH3CCl3+CCl4 adequately. From the calculated T - X phase diagram, critical behavior of some thermodynamic quantities can be predicted at various temperatures and concentrations (CCl4) for a binary mixture of CH3CCl3+CCl4.

  13. Computational Studies Of Chemical Reactions: The Hnc-Hcn And Ch[subscript3]Nc-Ch[subscript3]Cn Isomerizations

    ERIC Educational Resources Information Center

    Halpern, Arthur M.

    2006-01-01

    The application of computational methods to the isomerization of hydrogen isocyanide to hydrogen cyanide, HNC-HCN is described. The logical extension to the exercise is presented to the isomerization of the methyl-substituted compounds, methylisocyanide and methylcyanide, Ch[subscript 3]NC-CH[subscript3]CN.

  14. Synthesis, characterization, structural and biological aspects of copper(II) dithiocarbamate complexes - Part II, [Cu{S2CN(Me)(R1)}2], [Cu{S2CN(Me)(R2)}2] and [Cu{S2CN(R3)(R4)}2] {R1 = CH2CH(OMe)2, R2 = 2-methyl-1,3-dioxolane, R3 = CH2(CH2)2NCHPhOCH2Ph and R4 = CH2CH2OH}

    NASA Astrophysics Data System (ADS)

    Ferreira, Isabella P.; de Lima, Geraldo M.; Paniago, Eucler B.; Takahashi, Jacqueline A.; Krambrock, Klaus; Pinheiro, Carlos B.; Wardell, James L.; Visentin, Lorenzo C.

    2013-09-01

    Three new copper(II) dithiocarbamates (DTC), [Cu{S2CN(Me)(R1)}2] (1), [Cu{S2CN(Me)(R2)}2] (2) and [Cu{S2CN(R3)(R4)}2] (3) with R1 = CH2CH(OMe)2, R2 = 2-methyl-1,3-dioxolane, R3 = CH2(CH2)2NCHPhOCH2Ph and R4 = CH2CH2OH, have been synthesized and characterized by different spectroscopic techniques. Complexes (1) and (2) display typical EPR spectra for separated Cu(II) centers, and the spectrum of (3) is characteristic of two magnetically coupled Cu(II) ions with S = 1. The X-ray crystallographic determination has shown that complexes (1) and (2) crystallise in the triclinic and monoclinic systems. In addition both complexes are monomers in which the geometry at each Cu(II) is square planar. The in vitro antimicrobial activity of the sodium salts of ligands, and of the Cu(II)-DTC complexes have been screened against Aspergillus flavus, Aspergillus niger, Aspergillus parasiticus, Penicillium citrinum and Curvularia senegalensis, as well as Gram positive and Gram negative bacteria. Finally, the toxic effects of complexes (1)-(3) were performed using Chlorella vulgaris.

  15. The Relative Abundances of Resolved 12CH2D2 and 13CH3D and Mechanisms Controlling Isotopic Bond Ordering in Abiotic and Biotic Methane Gases

    NASA Astrophysics Data System (ADS)

    Young, E. D.; Kohl, I. E.; Sherwood Lollar, B.; Etiope, G.; Rumble, D.; Li, S.; Haghnegahdar, M. A.; Schauble, E. A.; McCain, K.; Foustoukos, D.; Sutcliffe, C. N.; Warr, O.; Ballentine, C. J.; Onstott, T. C.; Hosgormez, H.; Neubeck, A.; Marques, J. M.; Perez-Rodriguez, I. M.; Rowe, A. R.; LaRowe, D.; Magnabosco, C.; Bryndzia, T.

    2016-12-01

    We report measurements of resolved 12CH2D2 and 13CH3D at natural abundances in a variety of methane gases produced naturally and in the laboratory. The ability to resolve 12CH2D2 from 13CH3D provides unprecedented insights into the origin and evolution of CH4. The results identify conditions under which either isotopic bond order disequilibrium or equilibrium are expected. Where equilibrium obtains, concordant Δ12CH2D2 and Δ13CH3D temperatures can be used reliably for thermometry. We find that concordant temperatures do not always match previous hypotheses based on indirect estimates of temperature of formation nor temperatures derived from CH4/H2 D/H exchange, underscoring the importance of reliable thermometry based on the CH4 molecules themselves. Where Δ12CH2D2 and Δ13CH3D values are inconsistent with thermodynamic equilibrium, temperatures of formation derived from these species are spurious. In such situations, while formation temperatures are unavailable, disequilibrium isotopologue ratios nonetheless provide important information about the formation mechanism of the gas and the presence or absence of multiple sources or sinks. In particular, disequilibrium isotopologue ratios may provide the means for differentiating between methane produced by abiotic synthesis versus biological processes. Deficits in 12CH2D2 compared with equilibrium values in CH4 gas made by surface-catalyzed abiotic reactions are so large as to point towards a quantum tunneling origin. Tunneling also accounts for the more moderate depletions in 13CH3D that accompany the low 12CH2D2 abundances produced by abiotic reactions. The tunneling signature of abiotic CH4 formation may prove to be an important tracer of abiotic methane formation, especially where it is preserved by dissolution of gas in cool hydrothermal systems (e.g., Mars). Isotopologue signatures of abiotic methane production can be erased by infiltration of microbial communities, and Δ12CH2D2 values are a key tracer of

  16. iTAR: a web server for identifying target genes of transcription factors using ChIP-seq or ChIP-chip data.

    PubMed

    Yang, Chia-Chun; Andrews, Erik H; Chen, Min-Hsuan; Wang, Wan-Yu; Chen, Jeremy J W; Gerstein, Mark; Liu, Chun-Chi; Cheng, Chao

    2016-08-12

    Chromatin immunoprecipitation followed by massively parallel DNA sequencing (ChIP-seq) or microarray hybridization (ChIP-chip) has been widely used to determine the genomic occupation of transcription factors (TFs). We have previously developed a probabilistic method, called TIP (Target Identification from Profiles), to identify TF target genes using ChIP-seq/ChIP-chip data. To achieve high specificity, TIP applies a conservative method to estimate significance of target genes, with the trade-off being a relatively low sensitivity of target gene identification compared to other methods. Additionally, TIP's output does not render binding-peak locations or intensity, information highly useful for visualization and general experimental biological use, while the variability of ChIP-seq/ChIP-chip file formats has made input into TIP more difficult than desired. To improve upon these facets, here we present are fined TIP with key extensions. First, it implements a Gaussian mixture model for p-value estimation, increasing target gene identification sensitivity and more accurately capturing the shape of TF binding profile distributions. Second, it enables the incorporation of TF binding-peak data by identifying their locations in significant target gene promoter regions and quantifies their strengths. Finally, for full ease of implementation we have incorporated it into a web server ( http://syslab3.nchu.edu.tw/iTAR/ ) that enables flexibility of input file format, can be used across multiple species and genome assembly versions, and is freely available for public use. The web server additionally performs GO enrichment analysis for the identified target genes to reveal the potential function of the corresponding TF. The iTAR web server provides a user-friendly interface and supports target gene identification in seven species, ranging from yeast to human. To facilitate investigating the quality of ChIP-seq/ChIP-chip data, the web server generates the chart of the

  17. a Theoretical Characterization of Electronic States of CH2IOO and CH2OO Radicals Relevant to the Near IR Region

    NASA Astrophysics Data System (ADS)

    Dawes, Richard; Lolur, Phalgun; Huang, Meng; Kline, Neal; Miller, Terry A.

    2015-06-01

    Criegee intermediates (R1R2COO or CIs) arise from ozonolysis of biogenic and anthropogenic alkenes, which is an important process in the atmosphere. Recent breakthroughs in producing them in the gas phase have resulted in a flurry of experimental and theoretical studies. Producing the simplest CI (CH2OO) in the lab via photolysis of CH2I2 in the presence of O2 yields both CH2OO and CH2IOO with pressure dependent branching. As discussed in the preceding talk, both species might be expected to have electronic transitions in the near IR (NIR). Here we discuss electronic structure calculations used to characterize the electronic states of both systems in the relevant energy range. Using explicitly-correlated multireference configuration interaction (MRCI-F12) and coupled-cluster (UCCSD(T)-F12b) calculations we were first able to exclude CH2OO as the carrier of the observed NIR spectrum. Next, by computing frequencies and relaxed full torsional scans for the ~A and ~X states, we were able to aid in analysis and assignment of the NIR spectrum attributed to CH2IOO.

  18. Theoretical study on the reaction mechanism of CH 4 with CaO

    NASA Astrophysics Data System (ADS)

    Yang, Hua-Qing; Hu, Chang-Wei; Qin, Song

    2006-11-01

    The reaction pathways and energetics for the reaction of methane with CaO are discussed on the singlet spin state potential energy surface at the B3LYP/6-311+G(2df,2p) and QCISD/6-311++G(3df,3pd)//B3LYP/6-311+G(2df,2p) levels of theory. The reaction of methane with CaO is proposed to proceed in the following reaction pathways: CaO + CH 4 → CaOCH 4 → [TS] → CaOH + CH 3, CaO + CH 4 → OCaCH 4 → [TS] → HOCaCH 3 → CaOH + CH 3 or [TS] → CaCH 3OH → Ca + CH 3OH, and OCaCH 4 → [TS] → HCaOCH 3 → CaOCH 3 + H or [TS] → CaCH 3OH → Ca + CH 3OH. The gas-phase methane-methanol conversion by CaO is suggested to proceed via two kinds of important reaction intermediates, HOCaCH 3 and HCaOCH 3, and the reaction pathway via the hydroxy intermediate (HOCaCH 3) is energetically more favorable than the other one via the methoxy intermediate (HCaOCH 3). The hydroxy intermediate HOCaCH 3 is predicted to be the energetically most preferred configuration in the reaction of CaO + CH 4. Meanwhile, these three product channels (CaOH + CH 3, CaOCH 3 + H and Ca + CH 3OH) are expected to compete with each other, and the formation of methyl radical is the most preferable pathway energetically. On the other hand, the intermediates HCaOCH 3 and HOCaCH 3 are predicted to be the energetically preferred configuration in the reaction of Ca + CH 3OH, which is precisely the reverse reaction of methane hydroxylation.

  19. Tree CH4 fluxes in forestry drained peatland in southern Finland

    NASA Astrophysics Data System (ADS)

    Haikarainen, Iikka; Putkinen, Anuliina; Pyykkö, Petteri; Halmeenmäki, Elisa; Pihlatie, Mari

    2017-04-01

    Methane (CH4) is among the most important greenhouse gases and its atmospheric concentration is increasing. Boreal forests are commonly considered a net sink of atmospheric CH4 due to CH4 consuming bacteria in aerated soil layers. Recent studies have, however, demonstrated that trees are capable of emitting CH4 from their stems and shoots by transporting anaerobically produced CH4 from deeper soil layers to the atmosphere. Furthermore, trees may act as independent sources of CH4. We have measured tree stem CH4 exchange of boreal tree species at Lettosuo, a nutrient rich peatland forest in Tammela, southern Finland (60˚ 38' N, 23˚ 57' E), using the static chamber technique. Three species, downy birch (Betula pubescens), Norway spruce (Picea abies) and Scots pine (Pinus sylvestris), were selected under investigation as they represent common boreal tree species. Fluxes of CH4 were measured during 7.6.2016 - 17.10.2016 from in total 25 sample trees growing on two different plots: a treatment plot where all the pines were removed to raise the water table level (WTL) and a control plot. Three birches from the treatment plot were selected to measure CH4 flux variation within vertical profile of the trees. Characterization of microbial communities, quantification of methanogenic and methanotrophic functional genes, and measurements of potential CH4 production and consumption from peat profile and forest floor moss samples were also carried out to obtain insight to the CH4 flux dynamics at the studied sites. The pine removal treatment did not markedly change the average WTL, but it made the WTL more variable with frequently 10-15 cm closer to soil surface compared to the WTL on the control plot. We found small and variable CH4 emissions from the stems of trees on both of the plots, while occasional consumption of CH4 was also present. Generally the CH4 emissions were higher and more dominant at the treatment plot compared to the control plot, and the fluxes were

  20. Raman spectroscopy measurement of CH4 gas and CH4 dissolved in water for laser remote sensing in water

    NASA Astrophysics Data System (ADS)

    Somekawa, Toshihiro; Fujita, Masayuki

    2018-04-01

    We examined the applicability of Raman spectroscopy as a laser remote sensing tool for monitoring CH4 in water. The Raman technique has already been used successfully for measurements of CO2 gas in water. In this paper, considering the spectral transmittance of water, third harmonics of Q-switched Nd:YAG laser at 355 nm (UV region) was used for detection of CH4 Raman signals. The Raman signal at 2892 cm-1 from CH4 dissolved in water was detected at a tail of water Raman signal.

  1. Changing concentrations of CO, CH(4), C(5)H(8), CH(3)Br, CH(3)I, and dimethyl sulfide during the Southern Ocean Iron Enrichment Experiments.

    PubMed

    Wingenter, Oliver W; Haase, Karl B; Strutton, Peter; Friederich, Gernot; Meinardi, Simone; Blake, Donald R; Rowland, F Sherwood

    2004-06-08

    Oceanic iron (Fe) fertilization experiments have advanced the understanding of how Fe regulates biological productivity and air-sea carbon dioxide (CO(2)) exchange. However, little is known about the production and consumption of halocarbons and other gases as a result of Fe addition. Besides metabolizing inorganic carbon, marine microorganisms produce and consume many other trace gases. Several of these gases, which individually impact global climate, stratospheric ozone concentration, or local photochemistry, have not been previously quantified during an Fe-enrichment experiment. We describe results for selected dissolved trace gases including methane (CH(4)), isoprene (C(5)H(8)), methyl bromide (CH(3)Br), dimethyl sulfide, and oxygen (O(2)), which increased subsequent to Fe fertilization, and the associated decreases in concentrations of carbon monoxide (CO), methyl iodide (CH(3)I), and CO(2) observed during the Southern Ocean Iron Enrichment Experiments.

  2. The Drivers of the CH4 Seasonal Cycle in the Arctic and What Long-Term Observations of CH4 Imply About Trends in Arctic CH4 Fluxes

    NASA Astrophysics Data System (ADS)

    Sweeney, C.; Karion, A.; Bruhwiler, L.; Miller, J. B.; Wofsy, S. C.; Miller, C. E.; Chang, R. Y.; Dlugokencky, E. J.; Daube, B.; Pittman, J. V.; Dinardo, S. J.

    2012-12-01

    The large seasonal change in the atmospheric column for CH4 in the Arctic is driven by two dominant processes: transport of CH4 from low latitudes and surface emissions throughout the Arctic region. The NOAA ESRL Carbon Cycle Group Aircraft Program along with the NASA funded Carbon in Arctic Reservoirs Vulnerability Experiment (CARVE) have initiated an effort to better understand the factors controlling the seasonal changes in the mole fraction of CH4 in the Arctic with a multi-scale aircraft observing network in Alaska. The backbone of this network is multi-species flask sampling from 500 to 8000 masl that has been conducted every two weeks for the last 10 years over Poker Flat, AK. In addition regular profiles at the interior Alaska site at Poker Flat, NOAA has teamed up with the United States Coast Guard to make profiling flights with continuous observations of CO2, CO, CH4 and Ozone between Kodiak and Barrow every 2 weeks. More recently, CARVE has significantly added to this observational network with targeted flights focused on exploring the variability of CO2, CH4 and CO in the boundary layer both in the interior and the North Slope regions of Alaska. Taken together with the profiling of HIAPER Pole-to-Pole Observations (HIPPO), ground sites at Barrow and a new CARVE interior Alaska surface site just north of Fairbanks, AK, we now have the ability to investigate the full evolution of the seasonal cycle in the Arctic using both the multi-scale sampling offered by the different aircraft platforms as well as the multi-species sampling offered by in-situ and flask sampling. The flasks also provide a valuable tie-point between different platforms so that spatial and temporal gradients can be properly interpreted. In the context of the seasonal cycle observed by the aircraft platforms we will look at long term ground observations over the last 20 years to assess changes in Arctic CH4 emissions which have occurred as a result of 0.6C/decade changes in mean surface

  3. How to Combine ChIP with qPCR.

    PubMed

    Asp, Patrik

    2018-01-01

    Chromatin immunoprecipitation (ChIP) coupled with quantitative PCR (qPCR) has in the last 15 years become a basic mainstream tool in genomic research. Numerous commercially available ChIP kits, qPCR kits, and real-time PCR systems allow for quick and easy analysis of virtually anything chromatin-related as long as there is an available antibody. However, the highly accurate quantitative dimension added by using qPCR to analyze ChIP samples significantly raises the bar in terms of experimental accuracy, appropriate controls, data analysis, and data presentation. This chapter will address these potential pitfalls by providing protocols and procedures that address the difficulties inherent in ChIP-qPCR assays.

  4. The ChArMEx database

    NASA Astrophysics Data System (ADS)

    Ferré, Helene; Belmahfoud, Nizar; Boichard, Jean-Luc; Brissebrat, Guillaume; Descloitres, Jacques; Fleury, Laurence; Focsa, Loredana; Henriot, Nicolas; Mastrorillo, Laurence; Mière, Arnaud; Vermeulen, Anne

    2014-05-01

    The Chemistry-Aerosol Mediterranean Experiment (ChArMEx, http://charmex.lsce.ipsl.fr/) aims at a scientific assessment of the present and future state of the atmospheric environment in the Mediterranean Basin, and of its impacts on the regional climate, air quality, and marine biogeochemistry. The project includes long term monitoring of environmental parameters, intensive field campaigns, use of satellite data and modelling studies. Therefore ChARMEx scientists produce and need to access a wide diversity of data. In this context, the objective of the database task is to organize data management, distribution system and services, such as facilitating the exchange of information and stimulating the collaboration between researchers within the ChArMEx community, and beyond. The database relies on a strong collaboration between OMP and ICARE data centres and has been set up in the framework of the Mediterranean Integrated Studies at Regional And Locals Scales (MISTRALS) program data portal. All the data produced by or of interest for the ChArMEx community will be documented in the data catalogue and accessible through the database website: http://mistrals.sedoo.fr/ChArMEx. At present, the ChArMEx database contains about 75 datasets, including 50 in situ datasets (2012 and 2013 campaigns, Ersa background monitoring station), 25 model outputs (dust model intercomparison, MEDCORDEX scenarios), and a high resolution emission inventory over the Mediterranean. Many in situ datasets have been inserted in a relational database, in order to enable more accurate data selection and download of different datasets in a shared format. The database website offers different tools: - A registration procedure which enables any scientist to accept the data policy and apply for a user database account. - A data catalogue that complies with metadata international standards (ISO 19115-19139; INSPIRE European Directive; Global Change Master Directory Thesaurus). - Metadata forms to document

  5. Rate coefficients for the gas-phase reaction of the hydroxyl radical with CH2=CHF and CH2=CF2.

    PubMed

    Baasandorj, Munkhbayar; Knight, Gary; Papadimitriou, Vassileios C; Talukdar, Ranajit K; Ravishankara, A R; Burkholder, James B

    2010-04-08

    Rate coefficients, k, for the gas-phase reaction of the OH radical with CH(2)=CHF (k(1)) and CH(2)=CF(2) (k(2)) were measured under pseudo-first-order conditions in OH using pulsed laser photolysis to produce OH and laser-induced fluorescence (PLP-LIF) to detect it. Rate coefficients were measured over a range of temperature (220-373 K) and bath gas pressure (20-600 Torr; He, N(2)). The rate coefficients were found to be independent of pressure. The measured rate coefficient for reaction 1 at room temperature was k(1)(296 K) = (5.18 +/- 0.50) x 10(-12) cm(3) molecule(-1) s(-1), independent of pressure, and the temperature dependence is given by the Arrhenius expression k(1)(T) = (1.75 +/- 0.20) x 10(-12) exp[(316 +/- 25)/T] cm(3) molecule(-1) s(-1); the rate coefficients for reaction 2 were k(2)(296 K) = (2.79 +/- 0.25) x 10(-12) cm(3) molecule(-1) s(-1) and k(2)(T) = (1.75 +/- 0.20) x 10(-12) exp[(140 +/- 20)/T] cm(3) molecule(-1) s(-1). The quoted uncertainties are 2sigma (95% confidence level) and include estimated systematic errors. The fall-off parameters for reaction 2 of k(infinity) = 3 x 10(-12) cm(3) molecule(-1) s(-1) and k(0)(296 K) = 1.8 x 10(-28) cm(6) molecule(-2) s(-1) with F(c) = 0.6 reproduce the room temperature data obtained in this study combined with the low pressure rate coefficient data from Howard (J. Chem. Phys. 1976, 65, 4771). OH radical formation was observed for reactions 1 and 2 in the presence of O(2), and the mechanism was investigated using (18)OH and OD rate coefficient measurements with CH(2)=CHF and CH(2)=CF(2) over a range of temperature (260-373 K) and pressure (20-100 Torr, He). Quantum chemical calculations using density functional theory (DFT) were used to determine the geometries and energies of the reactants and adducts formed in reactions 1 and 2 and the peroxy radicals formed following the addition of O(2). The atmospheric lifetimes of CH(2)=CHF and CH(2)=CF(2) due to loss by reaction with OH are approximately 2 and 4

  6. Chemical and isotopic equilibrium between CO 2 and CH 4 in fumarolic gas discharges: Generation of CH 4 in arc magmatic-hydrothermal systems

    NASA Astrophysics Data System (ADS)

    Fiebig, Jens; Chiodini, Giovanni; Caliro, Stefano; Rizzo, Andrea; Spangenberg, Jorge; Hunziker, Johannes C.

    2004-05-01

    The chemical and isotopic composition of fumarolic gases emitted from Nisyros Volcano, Greece, and of a single gas sample from Vesuvio, Italy, was investigated in order to determine the origin of methane (CH 4) within two subduction-related magmatic-hydrothermal environments. Apparent temperatures derived from carbon isotope partitioning between CH 4 and CO 2 of around 340°C for Nisyros and 470°C for Vesuvio correlate well with aquifer temperatures as measured directly and/or inferred from compositional data using the H 2O-H 2-CO 2-CO-CH 4 geothermometer. Thermodynamic modeling reveals chemical equilibrium between CH 4, CO 2 and H 2O implying that carbon isotope partitioning between CO 2 and CH 4 in both systems is controlled by aquifer temperature. N 2/ 3He and CH 4/ 3He ratios of Nisyros fumarolic gases are unusually low for subduction zone gases and correspond to those of midoceanic ridge environments. Accordingly, CH 4 may have been primarily generated through the reduction of CO 2 by H 2 in the absence of any organic matter following a Fischer-Tropsch-type reaction. However, primary occurrence of minor amounts of thermogenic CH 4 and subsequent re-equilibration with co-existing CO 2 cannot be ruled out entirely. CO 2/ 3He ratios and δ 13C CO 2 values imply that the evolved CO 2 either derives from a metasomatized mantle or is a mixture between two components, one outgassing from an unaltered mantle and the other released by thermal breakdown of marine carbonates. The latter may contain traces of organic matter possibly decomposing to CH 4 during thermometamorphism.

  7. The First Laboratory Detection of Vibration-rotation Transitions of 12CH+ and 13CH+ and Improved Measurement of Their Rotational Transition Frequencies

    NASA Astrophysics Data System (ADS)

    Doménech, José L.; Jusko, Pavol; Schlemmer, Stephan; Asvany, Oskar

    2018-04-01

    C–H stretches of the fundamental ions CH+ and 13CH+, which have long been searched for, have been observed for the first time in the laboratory. The state-dependent attachment of He atoms to these ions at cryogenic temperatures has been exploited to obtain high-resolution rovibrational data. In addition, the lowest rotational transitions of CH+, 13CH+ and CD+ have been revisited and their rest frequency values have improved substantially.

  8. G331.512–0.103: An Interstellar Laboratory for Molecular Synthesis. I. The Ortho-to-para Ratios for CH3OH and CH3CN

    NASA Astrophysics Data System (ADS)

    Mendoza, Edgar; Bronfman, Leonardo; Duronea, Nicolas U.; Lépine, Jacques R. D.; Finger, Ricardo; Merello, Manuel; Hervías-Caimapo, Carlos; Gama, Diana R. G.; Reyes, Nicolas; Åke-Nyman, Lars

    2018-02-01

    Spectral line surveys reveal rich molecular reservoirs in G331.512–0.103, a compact radio source in the center of an energetic molecular outflow. In this first work, we analyze the physical conditions of the source by means of CH3OH and CH3CN. The observations were performed with the APEX Telescope. Six different system configurations were defined to cover most of the band within (292–356) GHz as a consequence, we detected a forest of lines toward the central core. A total of 70 lines of A/E–CH3OH and A/E–CH3CN were analyzed, including torsionally excited transitions of CH3OH ({ν }t=1). In a search for all the isotopologues, we identified transitions of 13CH3OH. The physical conditions were derived considering collisional and radiative processes. We found common temperatures for each A and E symmetry of CH3OH and CH3CN; the derived column densities indicate an A/E equilibrated ratio for both tracers. The results reveal that CH3CN and CH3OH trace a hot and cold component with {T}k∼ 141 K and {T}k∼ 74 K, respectively. In agreement with previous ALMA observations, the models show that the emission region is compact (≲ 5\\buildrel{\\prime\\prime}\\over{.} 5) with gas density n(H2) = (0.7–1)×107 cm‑3. The CH3OH/CH3CN abundance ratio and the evidences for prebiotic and complex organic molecules suggest a rich and active chemistry toward G331.512–0.103.

  9. A new method for speciated CH3O2 radical detection and HIRAC (Highly Instrumented Reactor for Atmospheric Chemistry) studies of the CH3O2 self-reaction

    NASA Astrophysics Data System (ADS)

    Onel, Lavinia; Brennan, Alexander; Seakins, Paul W.; Whalley, Lisa; Heard, Dwayne

    2016-04-01

    A new method has been developed for the speciated detection of CH3O2 radicals by FAGE (Fluorescence Assay by Gas Expansion) by titrating CH3O2 to CH3O by reaction with added NO and then detecting the resultant CH3O by LIF (laser induced fluorescence). The limit of detection of the technique is ˜108 cm-3 CH3O2 for a unity signal-to-noise ratio and 5 min averaging time. The method has been used for time monitoring of CH3O2 during its self-reaction within HIRAC at 1 bar and room temperature to determine a preliminary value of the rate coefficient of 4.2 × 10-13 cm3 s-1, which lies in the range of the previous results, (2.7 - 5.2) × 10-13 cm3 s-1.1 In addition to detection of CH3O2, products of the CH3O2 self-reaction were also observed for the two reaction channels over a range of temperatures from 260 - 320 K: (a) 2CH3O2 → CH2O + CH3OH; (b) 2CH3O2 → 2CH3O + O2, namely HO2 radicals (from reaction of CH3O + O2) and formaldehyde monitored by FAGE and formaldehyde and methanol observed by FTIR. A good agreement has been obtained between the FTIR and FAGE measurements of CH2O which increased to ˜ 2 ppmv over the experiments. Using the concentrations of CH3OH and CH2O, the branching ratio for channel (a) at room temperature has been determined as ra = 0.66 ± 0.06. The result is in very good agreement with the value recommended in the review of Tyndall et al.2 of ra = 0.63 ± 0.06. No temperature dependence of ra has been observed from 296 K to 321 K. 1. http://iupac.pole-ether.fr/ 2. G. S. Tyndall et al., J. Geophys. Res. 106, 12157 (2001).

  10. Crystal and molecular structure of the first dibino non-geminal macrocyclic dicyclophosphazene, & {;N 3P 3Cl 4[HN(CH 2) 3O(CH 2) 2O(CH 2) 3NH]&}; 2

    NASA Astrophysics Data System (ADS)

    Enjalbert, Renée; Galy, Jean; Sournies, François; Labarre, Jean-François

    1990-04-01

    Reaction of N 3P 3Cl 6 with the 4,7-dioxadecane-1,10-diamine (coded as 3O2O3) using an Et 2O/Na 2CO 3 water interface process leads to the DIBINO non-geminal 30-membered macrocyclic dicyclophosphazene &{;N 3P 3Cl 4[HN(CH 2) 3O(CH 2) 2O(CH 2) 3NH]&}; 2. This 30-crown-ether-like architecture crystallizes in the triclinic system, P1, a=9.019(6), b=9.224(5), c=11.542(8) Å, α=94.87(4), β=95.97(4), γ=99.68(3)°, V=936(1) Å 3, Dx=1.599 Mg m -3, R=0.049 for 2862 unique reflections and 199 variable parameters. The structure exhibits a spatial arrangement of two N 3P 3Cl 4 with two [HN(CH 2) 3O(CH 2) 3O(CH 2) 3NH] as bridges on different P atoms of N 3P 3 rings. Moreover, the two N 3P 3 rings are trans to the average plane of the 30-membered macrocycle ("chair" conformation).

  11. Coupled potential energy surface for the F(2P)+CH4→HF+CH3 entrance channel and quantum dynamics of the CH4·F- photodetachment.

    PubMed

    Westermann, Till; Eisfeld, Wolfgang; Manthe, Uwe

    2013-07-07

    An approach to construct vibronically and spin-orbit coupled diabatic potential energy surfaces (PESs) which describe all three relevant electronic states in the entrance channels of the X(P) + CH4 →HX + CH3 reactions (with X=F((2)P), Cl((2)P), or O((3)P)) is introduced. The diabatization relies on the permutational symmetry present in the methane molecule and results in diabatic states which transform as the three p orbitals of the X atom. Spin-orbit coupling is easily and accurately included using the atomic spin-orbit coupling matrix of the isolated X atom. The method is applied to the F + CH4 system obtaining an accurate PES for the entrance channel based on ab initio multi-reference configuration interaction (MRCI) calculations. Comparing the resulting PESs with spin-orbit MRCI calculations, excellent agreement is found for the excited electronic states at all relevant geometries. The photodetachment spectrum of CH4·F(-) is investigated via full-dimensional (12D) quantum dynamics calculations on the coupled PESs using the multi-layer multi-configurational time-dependent Hartree approach. Extending previous work [J. Palma and U. Manthe, J. Chem. Phys. 137, 044306 (2012)], which was restricted to the dynamics on a single adiabatic PES, the contributions of the electronically excited states to the photodetachment spectrum are calculated and compared to experiment. Considering different experimental setups, good agreement between experiment and theory is found. Addressing questions raised in the previous work, the present dynamical calculations show that the main contribution to the second peak in the photodetachment spectrum results from electron detachment into the electronically excited states of the CH4F complex.

  12. Reactivity of OH and CH3OH Between 22 and 64 K: Modelling the Gas Phase Production of CH3O in Barnard 1B

    PubMed Central

    Antiñolo, M.; Agúndez, M.; Jiménez, E.; Ballesteros, B.; Canosa, A.; Dib, G. El; Albaladejo, J.; Cernicharo, J.

    2016-01-01

    In the last years, ultra-low temperature chemical kinetic experiments have demonstrated that some gas-phase reactions are much faster than previously thought. One example is the reaction between OH and CH3OH, which has been recently found to be accelerated at low temperatures yielding CH3O as main product. This finding opened the question of whether the CH3O observed in the dense core Barnard 1b could be formed by the gas-phase reaction of CH3OH and OH. Several chemical models including this reaction and grain-surface processes have been developed to explain the observed abundance of CH3O with little success. Here we report for the first time rate coefficients for the gas-phase reaction of OH and CH3OH down to a temperature of 22 K, very close to those in cold interstellar clouds. Two independent experimental set-ups based on the supersonic gas expansion technique coupled to the pulsed laser photolysis-laser induced fluorescence technique were used to determine rate coefficients in the temperature range 22-64 K. The temperature dependence obtained in this work can be expressed as k(22-64 K) = (3.6 ± 0.1) × 10−12(T/300 K)−(1.0±0.2) cm3 molecule−1 s−1. Implementing this expression in a chemical model of a cold dense cloud results in CH3O/CH3OH abundance ratios similar or slightly lower than the value of ∼ 3 × 10−3 observed in Barnard 1b. This finding confirms that the gas-phase reaction between OH and CH3OH is an important contributor to the formation of interstellar CH3O. The role of grain-surface processes in the formation of CH3O, although it cannot be fully neglected, remains controversial. PMID:27279655

  13. Reactivity of OH and CH3OH Between 22 and 64 K: Modelling the Gas Phase Production of CH3O in Barnard 1B.

    PubMed

    Antiñolo, M; Agúndez, M; Jiménez, E; Ballesteros, B; Canosa, A; Dib, G El; Albaladejo, J; Cernicharo, J

    2016-05-20

    In the last years, ultra-low temperature chemical kinetic experiments have demonstrated that some gas-phase reactions are much faster than previously thought. One example is the reaction between OH and CH 3 OH, which has been recently found to be accelerated at low temperatures yielding CH 3 O as main product. This finding opened the question of whether the CH 3 O observed in the dense core Barnard 1b could be formed by the gas-phase reaction of CH 3 OH and OH. Several chemical models including this reaction and grain-surface processes have been developed to explain the observed abundance of CH 3 O with little success. Here we report for the first time rate coefficients for the gas-phase reaction of OH and CH 3 OH down to a temperature of 22 K, very close to those in cold interstellar clouds. Two independent experimental set-ups based on the supersonic gas expansion technique coupled to the pulsed laser photolysis-laser induced fluorescence technique were used to determine rate coefficients in the temperature range 22-64 K. The temperature dependence obtained in this work can be expressed as k (22-64 K) = (3.6 ± 0.1) × 10 -12 ( T/ 300 K) -(1.0±0.2) cm 3 molecule -1 s -1 . Implementing this expression in a chemical model of a cold dense cloud results in CH 3 O/CH 3 OH abundance ratios similar or slightly lower than the value of ∼ 3 × 10 -3 observed in Barnard 1b. This finding confirms that the gas-phase reaction between OH and CH 3 OH is an important contributor to the formation of interstellar CH 3 O. The role of grain-surface processes in the formation of CH 3 O, although it cannot be fully neglected, remains controversial.

  14. The Structure of Titan’s N2 and CH4 Coronae

    NASA Astrophysics Data System (ADS)

    Jiang, Fayu; Cui, Jun; Xu, Jiyao

    2017-12-01

    In this study, we analyze the structures of Titan’s N2 and CH4 coronae using a large data set acquired by the Ion Neutral Mass Spectrometer (INMS) instrument on board Cassini. The N2 and CH4 densities measured from the exobase up to 2000 km imply a mean exobase temperature of 146 K and 143 K, respectively, which is lower than the mean upper atmospheric temperature by 4 and 7 K. This indicates that on average, Titan possesses a subthermal rather than suprathermal corona. A careful examination reveals that the variability in corona structure is not very likely to be solar driven. Within the framework of the collisionless kinetic model, we investigate how the CH4 energy distribution near the exobase could be constrained if strong CH4 escape occurs on Titan. Several functional forms for the CH4 energy distribution are attempted, assuming two representative CH4 escape rates of 1.2× {10}25 s-1 and 2.2× {10}27 s-1. We find that the double Maxwellian and power-law distributions can reproduce the shape of the CH4 corona structure as well as the imposed CH4 escape rate. In both cases, the escape rate is contributed by a suprathermal CH4 population on the high-energy tail, with a number fraction below 5% and a characteristic energy of 0.1-0.6 eV per suprathermal CH4 molecule. The coexistence of the subthermal CH4 corona revealed by the INMS data and substantial CH4 escape suggested by some previous works could be reconciled by a significant departure in the exobase CH4 energy distribution from ideal Maxwellian that enhances escape and causes a noticeable redistribution of the corona structure.

  15. The relative abundances of resolved l2CH2D2 and 13CH3D and mechanisms controlling isotopic bond ordering in abiotic and biotic methane gases

    NASA Astrophysics Data System (ADS)

    Young, E. D.; Kohl, I. E.; Lollar, B. Sherwood; Etiope, G.; Rumble, D.; Li, S.; Haghnegahdar, M. A.; Schauble, E. A.; McCain, K. A.; Foustoukos, D. I.; Sutclife, C.; Warr, O.; Ballentine, C. J.; Onstott, T. C.; Hosgormez, H.; Neubeck, A.; Marques, J. M.; Pérez-Rodríguez, I.; Rowe, A. R.; LaRowe, D. E.; Magnabosco, C.; Yeung, L. Y.; Ash, J. L.; Bryndzia, L. T.

    2017-04-01

    We report measurements of resolved 12CH2D2 and 13CH3D at natural abundances in a variety of methane gases produced naturally and in the laboratory. The ability to resolve 12CH2D2 from 13CH3D provides unprecedented insights into the origin and evolution of CH4. The results identify conditions under which either isotopic bond order disequilibrium or equilibrium are expected. Where equilibrium obtains, concordant Δ12CH2D2 and Δ13CH3D temperatures can be used reliably for thermometry. We find that concordant temperatures do not always match previous hypotheses based on indirect estimates of temperature of formation nor temperatures derived from CH4/H2 D/H exchange, underscoring the importance of reliable thermometry based on the CH4 molecules themselves. Where Δ12CH2D2 and Δ13CH3D values are inconsistent with thermodynamic equilibrium, temperatures of formation derived from these species are spurious. In such situations, while formation temperatures are unavailable, disequilibrium isotopologue ratios nonetheless provide novel information about the formation mechanism of the gas and the presence or absence of multiple sources or sinks. In particular, disequilibrium isotopologue ratios may provide the means for differentiating between methane produced by abiotic synthesis vs. biological processes. Deficits in 12CH2D2 compared with equilibrium values in CH4 gas made by surface-catalyzed abiotic reactions are so large as to point towards a quantum tunneling origin. Tunneling also accounts for the more moderate depletions in 13CH3D that accompany the low 12CH2D2 abundances produced by abiotic reactions. The tunneling signature may prove to be an important tracer of abiotic methane formation, especially where it is preserved by dissolution of gas in cool hydrothermal systems (e.g., Mars). Isotopologue signatures of abiotic methane production can be erased by infiltration of microbial communities, and Δ12CH2D2 values are a key tracer of microbial recycling.

  16. Chromatin Immunoprecipitation (ChIP) Protocol for Low-abundance Embryonic Samples.

    PubMed

    Rehimi, Rizwan; Bartusel, Michaela; Solinas, Francesca; Altmüller, Janine; Rada-Iglesias, Alvaro

    2017-08-29

    Chromatin immunoprecipitation (ChIP) is a widely-used technique for mapping the localization of post-translationally modified histones, histone variants, transcription factors, or chromatin-modifying enzymes at a given locus or on a genome-wide scale. The combination of ChIP assays with next-generation sequencing (i.e., ChIP-Seq) is a powerful approach to globally uncover gene regulatory networks and to improve the functional annotation of genomes, especially of non-coding regulatory sequences. ChIP protocols normally require large amounts of cellular material, thus precluding the applicability of this method to investigating rare cell types or small tissue biopsies. In order to make the ChIP assay compatible with the amount of biological material that can typically be obtained in vivo during early vertebrate embryogenesis, we describe here a simplified ChIP protocol in which the number of steps required to complete the assay were reduced to minimize sample loss. This ChIP protocol has been successfully used to investigate different histone modifications in various embryonic chicken and adult mouse tissues using low to medium cell numbers (5 x 10 4 - 5 x 10 5 cells). Importantly, this protocol is compatible with ChIP-seq technology using standard library preparation methods, thus providing global epigenomic maps in highly relevant embryonic tissues.

  17. Temperature-Dependent Kinetics Studies of the Reactions Br((sup 2)P(sub 3/2)) + CH3SCH3 reversible reaction CH3SCH2 + HBr. Heat of Formation of the CH3SCH2 Radical

    NASA Technical Reports Server (NTRS)

    Jefferson, A.; Nicovich, J. M.; Wine, P. H.

    1997-01-01

    Time-resolved resonance fluorescence detection of Br((sup 2)P(sub 3/2)) atom disappearance or appearance 266 nm laser flash photolysis of CF2Br2/CH3SCH3/H2/N2 and Cl2CO/CH2SCH3/HBr/H2/N2 mixtures has been employed to study the kinetics of the reactions Br((sup 2)P(sub 3/2)) + CH3SCH3 reversible reaction HBr + CH3SCH2 (1,-1) as a function of temperature over the range 386-604 K. Arrhenius expressions in units of cu cm/molecule which describe the results are k3= (9.0 +/- 2.9) x 10 (exp -11) exp[(-2386 +/- 151)/T]; errors are 2 sigma and represent precision only. To our knowledge, these are the first kinetic data reported for each of the two reactions studied. Second and third law analyses of the equilibrium data for reactions 1 and -1 have been employed to obtain the following enthalpies of reaction in units of kcal/mol: Delta-H(298) = 6.11 +/- 1.37 and Delta-H(0) = 5.37 +/- 1.38. Combining the above enthalpies of reaction with the well-known heats of formation of Br, HBr, CH3SCH3 gives the following heats of formation of the CH3SCH2 radical in units of kcal/mol: Delta-H(sub(f,298)) = 32.7 +/- 1.4 and Delta-H(sub (f,0)) = 35.3 +/- 1.4; errors are 2 sigma and represent estimates of absolute accuracy. The C-H bond dissociation energy in CH3SCH3 obtained from our data, 93.7 +/- 1.4 kcal/mol at 298 K and 92.0 +/- 1.4 kcal at 0 k, agrees well with a recent molecular beam photofragmentaion study but is 3 kcal/mol lower than the value obtained from an iodination kinetics study.

  18. Enhanced Performance of Perovskite CH3NH3PbI3 Solar Cell by Using CH3NH3I as Additive in Sequential Deposition.

    PubMed

    Xie, Yian; Shao, Feng; Wang, Yaoming; Xu, Tao; Wang, Deliang; Huang, Fuqiang

    2015-06-17

    Sequential deposition is a widely adopted method to prepare CH3NH3PbI3 on mesostructured TiO2 electrode for organic lead halide perovskite solar cells. However, this method often suffers from the uncontrollable crystal size, surface morphology, and residual PbI2 in the resulting CH3NH3PbI3, which are all detrimental to the device performance. We herein present an optimized sequential solution deposition method by introducing different amount of CH3NH3I in PbI2 precursor solution in the first step to prepare CH3NH3PbI3 absorber on mesoporous TiO2 substrates. The addition of CH3NH3I in PbI2 precursor solution can affect the crystallization and composition of PbI2 raw films, resulting in the variation of UV-vis absorption and surface morphology. Proper addition of CH3NH3I not only enhances the absorption but also improves the efficiency of CH3NH3PbI3 solar cells from 11.13% to 13.37%. Photoluminescence spectra suggest that the improvement of device performance is attributed to the decrease of recombination rate of carriers in CH3NH3PbI3 absorber. This current method provides a highly repeatable route for enhancing the efficiency of CH3NH3PbI3 solar cell in the sequential solution deposition method.

  19. A comparative DFT study of interactions of Au and small gold clusters Aun (n = 2-4) with CH3S and CH2 radicals

    NASA Astrophysics Data System (ADS)

    Blaško, Martin; Rajský, Tomáš; Urban, Miroslav

    2017-03-01

    We compare DFT binding energies (BEs) of Au and small gold clusters interacting with CH3S and CH2 ligands (Aun-L complexes, n = 1-4). The spin state and the binding mechanism in Aun-L varies with the participation of singly occupied non-bonding orbitals or doubly occupied lone-pair orbitals of a ligand and on the number of atoms (even or odd) of Aun. The highest BE, 354 kJ/mol, exhibits the Au3-CH2 complex with the covalent bond in which participate two singly occupied orbitals of the triplet state of CH2. With CH3S the highest BE (277 kJ/mol) is calculated for Au3-SCH3 with the single Au-S bond.

  20. Relativistic GW calculations on CH3NH3PbI3 and CH3NH3SnI3 perovskites for solar cell applications.

    PubMed

    Umari, Paolo; Mosconi, Edoardo; De Angelis, Filippo

    2014-03-26

    Hybrid AMX3 perovskites (A = Cs, CH3NH3; M = Sn, Pb; X = halide) have revolutionized the scenario of emerging photovoltaic technologies, with very recent results demonstrating 15% efficient solar cells. The CH3NH3PbI3/MAPb(I(1-x)Cl(x))3 perovskites have dominated the field, while the similar CH3NH3SnI3 has not been exploited for photovoltaic applications. Replacement of Pb by Sn would facilitate the large uptake of perovskite-based photovoltaics. Despite the extremely fast progress, the materials electronic properties which are key to the photovoltaic performance are relatively little understood. Density Functional Theory electronic structure methods have so far delivered an unbalanced description of Pb- and Sn-based perovskites. Here we develop an effective GW method incorporating spin-orbit coupling which allows us to accurately model the electronic, optical and transport properties of CH3NH3SnI3 and CH3NH3PbI3, opening the way to new materials design. The different CH3NH3SnI3 and CH3NH3PbI3 electronic properties are discussed in light of their exploitation for solar cells, and found to be dominantly due to relativistic effects. These effects stabilize the CH3NH3PbI3 material towards oxidation, by inducing a deeper valence band edge. Relativistic effects, however, also increase the material band-gap compared to CH3NH3SnI3, due to the valence band energy downshift (~0.7 eV) being only partly compensated by the conduction band downshift (~0.2 eV).

  1. Relativistic GW calculations on CH3NH3PbI3 and CH3NH3SnI3 Perovskites for Solar Cell Applications

    PubMed Central

    Umari, Paolo; Mosconi, Edoardo; De Angelis, Filippo

    2014-01-01

    Hybrid AMX3 perovskites (A = Cs, CH3NH3; M = Sn, Pb; X = halide) have revolutionized the scenario of emerging photovoltaic technologies, with very recent results demonstrating 15% efficient solar cells. The CH3NH3PbI3/MAPb(I1−xClx)3 perovskites have dominated the field, while the similar CH3NH3SnI3 has not been exploited for photovoltaic applications. Replacement of Pb by Sn would facilitate the large uptake of perovskite-based photovoltaics. Despite the extremely fast progress, the materials electronic properties which are key to the photovoltaic performance are relatively little understood. Density Functional Theory electronic structure methods have so far delivered an unbalanced description of Pb- and Sn-based perovskites. Here we develop an effective GW method incorporating spin-orbit coupling which allows us to accurately model the electronic, optical and transport properties of CH3NH3SnI3 and CH3NH3PbI3, opening the way to new materials design. The different CH3NH3SnI3 and CH3NH3PbI3 electronic properties are discussed in light of their exploitation for solar cells, and found to be dominantly due to relativistic effects. These effects stabilize the CH3NH3PbI3 material towards oxidation, by inducing a deeper valence band edge. Relativistic effects, however, also increase the material band-gap compared to CH3NH3SnI3, due to the valence band energy downshift (~0.7 eV) being only partly compensated by the conduction band downshift (~0.2 eV). PMID:24667758

  2. Exploring the Reactivity Trends in the E2 and SN2 Reactions of X(-) + CH3CH2Cl (X = F, Cl, Br, HO, HS, HSe, NH2 PH2, AsH2, CH3, SiH3, and GeH3).

    PubMed

    Wu, Xiao-Peng; Sun, Xiao-Ming; Wei, Xi-Guang; Ren, Yi; Wong, Ning-Bew; Li, Wai-Kee

    2009-06-09

    The reactivity order of 12 anions toward ethyl chloride has been investigated by using the G2(+) method, and the competitive E2 and SN2 reactions are discussed and compared. The reactions studied are X(-) + CH3CH2Cl → HX + CH2═CH2 + Cl(-) and X(-) + CH3CH2Cl → CH3CH2X + Cl(-), with X = F, Cl, Br, HO, HS, HSe, NH2 PH2, AsH2, CH3, SiH3, and GeH3. Our results indicate that there is no general and straightforward relationship between the overall barriers and the proton affinity (PA) of X(-); instead, discernible linear correlations only exist for the X's within the same group of the periodic table. Similar correlations are also found with the electronegativity of central atoms in X, deformation energy of the E2 transition state (TS), and the overall enthalpy of reaction. It is revealed that the electronegativity will significantly affect the barrier height, and a more electronegative X will stabilize the E2 and SN2 transition states. Multiple linear regression analysis shows that there is a reasonable linear correlation between E2 (or SN2) overall barriers and the linear combination of PA of X(-) and electronegativity of the central atom.

  3. ALMA Detection of Interstellar Methoxymethanol (CH3OCH2OH)

    NASA Astrophysics Data System (ADS)

    McGuire, Brett A.; Shingledecker, Christopher N.; Willis, Eric R.; Burkhardt, Andrew M.; El-Abd, Samer; Motiyenko, Roman A.; Brogan, Crystal L.; Hunter, Todd R.; Margulès, Laurent; Guillemin, Jean-Claude; Garrod, Robin T.; Herbst, Eric; Remijan, Anthony J.

    2017-12-01

    We report the detection of interstellar methoxymethanol (CH3OCH2OH) in Atacama Large Millimeter/submillimeter Array (ALMA) Bands 6 and 7 toward the MM1 core in the high-mass star-forming region NGC 6334I at ∼0.″1–1″ spatial resolution. A column density of 4(2) × 1018 cm‑2 at T ex = 200 K is derived toward MM1, ∼34 times less abundant than methanol (CH3OH), and significantly higher than predicted by astrochemical models. Probable formation and destruction pathways are discussed, primarily through the reaction of the CH3OH photodissociation products, the methoxy (CH3O) and hydroxymethyl (CH2OH) radicals. Finally, we comment on the implications of these mechanisms on gas-phase versus grain-surface routes operative in the region, and the possibility of electron-induced dissociation of CH3OH rather than photodissociation.

  4. ChIP-seq: advantages and challenges of a maturing technology.

    PubMed

    Park, Peter J

    2009-10-01

    Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a technique for genome-wide profiling of DNA-binding proteins, histone modifications or nucleosomes. Owing to the tremendous progress in next-generation sequencing technology, ChIP-seq offers higher resolution, less noise and greater coverage than its array-based predecessor ChIP-chip. With the decreasing cost of sequencing, ChIP-seq has become an indispensable tool for studying gene regulation and epigenetic mechanisms. In this Review, I describe the benefits and challenges in harnessing this technique with an emphasis on issues related to experimental design and data analysis. ChIP-seq experiments generate large quantities of data, and effective computational analysis will be crucial for uncovering biological mechanisms.

  5. ChIPBase v2.0: decoding transcriptional regulatory networks of non-coding RNAs and protein-coding genes from ChIP-seq data.

    PubMed

    Zhou, Ke-Ren; Liu, Shun; Sun, Wen-Ju; Zheng, Ling-Ling; Zhou, Hui; Yang, Jian-Hua; Qu, Liang-Hu

    2017-01-04

    The abnormal transcriptional regulation of non-coding RNAs (ncRNAs) and protein-coding genes (PCGs) is contributed to various biological processes and linked with human diseases, but the underlying mechanisms remain elusive. In this study, we developed ChIPBase v2.0 (http://rna.sysu.edu.cn/chipbase/) to explore the transcriptional regulatory networks of ncRNAs and PCGs. ChIPBase v2.0 has been expanded with ∼10 200 curated ChIP-seq datasets, which represent about 20 times expansion when comparing to the previous released version. We identified thousands of binding motif matrices and their binding sites from ChIP-seq data of DNA-binding proteins and predicted millions of transcriptional regulatory relationships between transcription factors (TFs) and genes. We constructed 'Regulator' module to predict hundreds of TFs and histone modifications that were involved in or affected transcription of ncRNAs and PCGs. Moreover, we built a web-based tool, Co-Expression, to explore the co-expression patterns between DNA-binding proteins and various types of genes by integrating the gene expression profiles of ∼10 000 tumor samples and ∼9100 normal tissues and cell lines. ChIPBase also provides a ChIP-Function tool and a genome browser to predict functions of diverse genes and visualize various ChIP-seq data. This study will greatly expand our understanding of the transcriptional regulations of ncRNAs and PCGs. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  6. Photosynthates as dominant source of CH4 and CO2 in soil water and CH4 emitted to the atmosphere from paddy fields

    NASA Astrophysics Data System (ADS)

    Minoda, Tomomi; Kimura, Mamoto; Wada, Eitaro

    1996-09-01

    Emission rates of CH4 from paddy soil with and without rice straw applications were measured with pot experiments to estimate the contribution of rice straw to the total CH4 emission during the growth period of rice plants. The CH4 derived from rice straw was calculated to be 44% of the total emission. 13CO2 uptake experiments were also carried out four times from June 30 to September 13, 1994, to estimate the contribution of photosynthesized carbon to CH4 emission. The contribution percentages of photosynthesized carbon to the total CH4 emitted to the atmosphere were 3.8% around June 30, 31% around July 25, 30% around August 19, and 14% around September 13 in the treatment with rice straw applications, and 52% around July 25, 28% around August 19, and 15% around September 13 in the treatment without rice straw applications. They were calculated to be 22% and 29% for the entire growth period in the treatments with and without rice straw applications, respectively. The contribution percentages of photosynthesized carbon to the total CH4 and inorganic carbon (Σ CO2) dissolved in soil water were 1.3%, 30%, 29%, and 34% for dissolved CH4 and 3.0%, 36%, 30% and 28% for dissolved inorganic carbon around June 30, July 25, August l9, and September 13, respectively, in the treatment with rice straw applications. They were 70%, 23%, and 32% for dissolved CH4 and 31%, 16%, and 19% for dissolved inorganic carbon around July 25, August 19, and September 13, respectively, in the treatment without rice straw applications.

  7. Contribution of Anthropogenic and Natural Emissions to Global CH4 Balances by Utilizing δ13C-CH4 Observations in CarbonTracker Data Assimilation System (CTDAS)

    NASA Astrophysics Data System (ADS)

    Kangasaho, V. E.; Tsuruta, A.; Aalto, T.; Backman, L. B.; Houweling, S.; Krol, M. C.; Peters, W.; van der Laan-Luijkx, I. T.; Lienert, S.; Joos, F.; Dlugokencky, E. J.; Michael, S.; White, J. W. C.

    2017-12-01

    The atmospheric burden of CH4 has more than doubled since preindustrial time. Evaluating the contribution from anthropogenic and natural emissions to the global methane budget is of great importance to better understand the significance of different sources at the global scale, and their contribution to changes in growth rate of atmospheric CH4 before and after 2006. In addition, observations of δ13C-CH4 suggest an increase in natural sources after 2006, which matches the observed increase and variation of CH4 abudance. Methane emission sources can be identified using δ13C-CH4, because different sources produce methane with process-specific isotopic signatures. This study focuses on inversion model based estimates of global anthropogenic and natural methane emission rates to evaluate the existing methane emission estimates with a new δ13C-CH4 inversion system. In situ measurements of atmospheric methane and δ13C-CH4 isotopic signature, provided by the NOAA Global Monitoring Division and the Institute of Arctic and Alpine Research, will be assimilated into the CTDAS-13C-CH4. The system uses the TM5 atmospheric transport model as an observation operator, constrained by ECMWF ERA Interim meteorological fields, and off-line TM5 chemistry fields to account for the atmospheric methane sink. LPX-Bern DYPTOP ecosystem model is used for prior natural methane emissions from wetlands, peatlands and mineral soils, GFED v4 for prior fire emissions and EDGAR v4.2 FT2010 inventory for prior anthropogenic emissions. The EDGAR antropogenic emissions are re-divided into enteric fermentation and manure management, landfills and waste water, rice, coal, oil and gas, and residential emissions, and the trend of total emissions is scaled to match optimized anthropogenic emissions from CTE-CH4. In addition to these categories, emissions from termites and oceans are included. Process specific δ13C-CH4 isotopic signatures are assigned to each emission source to estimate 13CH4 fraction

  8. The Grammar of Ch'orti' Maya Folktales

    ERIC Educational Resources Information Center

    Dugan, James Timothy

    2014-01-01

    This study describes the grammar of the Ch'orti' Maya language as it appears in a collection of oral literature. I collected the stories that form the basis of this study in and around Jocotan, Guatemala, during 2004 and 2005. I worked with bilingual story-tellers to make audio recordings of the original Ch'orti'-language tales, produce textual…

  9. How Many Ch-Class NEOs Do We Expect?

    NASA Astrophysics Data System (ADS)

    Rivkin, A. S.; DeMeo, F. E.

    2017-09-01

    The Ch spectral class is thought to contain objects that have water in their minerals, and they are of great interest to scientists and the nascent asteroid mining industry. We use models of asteroid delivery to near-Earth space and measurements of the different compositions of asteroids to estimate there should be at least 20 Ch asteroids larger than 100 m that are more accessible than the Moon, though we note that there are some untested assumptions that lead to that number. Further work must be done to identify the specific Ch asteroids.

  10. Characterization of the Minimum Energy Paths for the Reactions of CH(X(sup 2 Pi) and (1)CH2 with C2H2

    NASA Technical Reports Server (NTRS)

    Walch, Stephen P.; Langhoff, S. R. (Technical Monitor)

    1994-01-01

    The reactions of CH(sup 2 Pi) and singlet methylene (1)CH2 with acetylene lead to intermediates which may be important in soot formation. CH(sup 2 Pi) + acetylene leads to CHCHCH (C3H3), CHCCH (C3H2), and propargyl (CH2CCH). (1)CH2 + acetylene leads to cyclopropene and propargyl. All of these reaction products are formed with no barrier. Miller and Melius have previously discussed the dimerization of propargyl to give benzene. C3H3 and C3H2 can dimerize with no barrier to give benzene and para-benzyne, respectively. C3H3 and C3H2 can also add to smaller polynuclear aromatic hydrocarbons (PAH), and may be important species in forming larger PAH or fullerenes.

  11. Microwave Spectroscopic Investigations of the C-H\\cdotsπ Containing Complexes CH_2F_2\\cdotsPROPYNE and CH_2ClF\\cdotsPROPYNE

    NASA Astrophysics Data System (ADS)

    Peebles, Rebecca A.; Peebles, Sean A.; Christenholz, Cori L.; Ernst, Anthony A.; Dhahir, Yasser J.

    2013-06-01

    The spectra of the CH_2F_2\\cdotspropyne and CH_2ClF\\cdotspropyne complexes have been studied by chirped-pulse and resonant cavity Fourier-transform microwave spectroscopy and by ab initio calculations at the MP2/6-311++G(2d,2p) level. Both complexes contain C-H\\cdotsπ contacts, with the halogen atoms angled towards the methyl group end of the propyne. While CH_2F_2\\cdotspropyne has C_s symmetry, CH_2ClF\\cdotspropyne has C_1 symmetry, with the fluorine and chlorine atoms straddling the propyne. Investigation of four single ^{13}C and the DC≡CCH_3 isotopologues in CH_2F_2\\cdotspropyne has allowed a detailed structural determination, while only the ^{35}Cl and ^{37}Cl isotopologues have so far been assigned for CH_2ClF\\cdotspropyne. Experimental data will be compared with ab initio results and with the analogous acetylene complexes, both of which have C_s symmetry structures, with double C-H\\cdotsπ interactions.

  12. (Phosphinoalkyl)silanes. 4.(1) Hydrozirconation as a Non-Photochemical Route to (Phosphinopropyl)silanes: Facile Assembly of the Bis(3-(diphenylphosphino)propyl)silyl ("biPSi") Ligand Framework. Access to the Related Poly(3-(dimethylsilyl)propyl)phosphines R(n)()P(CH(2)CH(2)CH(2)SiMe(2)H)(3)(-)(n)() (n = 1, R = Ph; n = 0).

    PubMed

    Zhou, Xiaobing; Stobart, Stephen R.; Gossage, Robert A.

    1997-08-13

    Treatment of SiEt(3)(CH=CH(2)) with ZrCp(2)HCl (Schwartz's reagent) followed by reaction with PPh(2)Cl provides a high-yield (75%) route to Ph(2)PCH(2)CH(2)SiEt(3), and accordingly hydrozirconation of CH(2)=CHCH(2)SiHMe(2) affords the intermediate ZrCp(2)(CH(2)CH(2)CH(2)SiHMe(2))Cl (2). The latter, which is very sensitive to hydrolysis and reacts with HCl forming SiHMe(2)Pr(n)() and with NBS or I(2) affording SiHMe(2)CH(2)CH(2)CH(2)X (X = Br (3), I (4)), behaves similarly with PPh(2)Cl, PPhCl(2), or PBr(3) undergoing cleavage to the known Ph(2)PCH(2)CH(2)CH(2)SiMe(2)H (i.e. chelH, A) and the novel bis- and tris(silylpropyl)phosphines PhP(CH(2)CH(2)CH(2)SiMe(2)H)(2) (5) and P(CH(2)CH(2)CH(2)SiMe(2)H)(3) (6), respectively, with concomitant formation of ZrCp(2)Cl(2). Corresponding hydroboration of allylsilanes is facile, but subsequent phosphine halide cleavage yields (phosphinoalkyl)silanes only as constituents of intractable mixtures. Hydrozirconation followed by phosphination with PPh(2)Cl also converts SiHMe(CH(2)CH=CH(2))(2) to SiHMe(CH(2)CH(2)CH(2)PPh(2))(2) (i.e. biPSiH, B) together with a propyl analogue Ph(2)PCH(2)CH(2)CH(2)SiMe(Pr(n)())H (7) of A (ca. 2:1 ratio), as well as SiH(CH(2)CH=CH(2))(3) to a mixture (ca. 5:2:1 ratio) of SiH(CH(2)CH(2)CH(2)PPh(2))(3) (i.e. triPSiH, C), a new analogue SiH(Pr(n)())(CH(2)CH(2)CH(2)PPh(2))(2) (8) of B, and a further analogue Ph(2)PCH(2)CH(2)CH(2)SiHPr(n)()(2) (9) of A. A further analogue SiH(2)(CH(2)CH(2)CH(2)PPh(2))(2) (10) of biPSiH (B) is obtained similarly starting from SiH(2)(CH(2)CH=CH(2))(2). Steric control of silylalkyl cleavage from 2 is indicated by the fact that, like PPh(2)Cl (which forms B), two further biPSiH analogues SiH(Me)[CH(2)CH(2)CH(2)P(n-hex)(2)](2) (11) and SiH(Me)(CH(2)CH(2)CH(2)PPhBz)(2) (12) were obtained using P(n-hex)(2)Cl (i.e. n-hex = CH(3)(CH(2))(4)CH(2)-) or PPhBzCl (i.e. Bz = -CH(2)C(6)H(5)), respectively, whereas neither PPr(i)(2)Cl nor PBu(t)(2)Cl led to (phosphinoalkyl)silane formation

  13. 40 CFR 1065.660 - THC, NMHC, and CH4 determination.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 33 2014-07-01 2014-07-01 false THC, NMHC, and CH4 determination. 1065... POLLUTION CONTROLS ENGINE-TESTING PROCEDURES Calculations and Data Requirements § 1065.660 THC, NMHC, and CH4 determination. (a) THC determination and initial THC/CH 4 contamination corrections. (1) If we...

  14. 40 CFR 1065.660 - THC, NMHC, and CH4 determination.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 34 2012-07-01 2012-07-01 false THC, NMHC, and CH4 determination. 1065... POLLUTION CONTROLS ENGINE-TESTING PROCEDURES Calculations and Data Requirements § 1065.660 THC, NMHC, and CH4 determination. (a) THC determination and initial THC/CH 4 contamination corrections. (1) If we...

  15. 40 CFR 1065.660 - THC, NMHC, and CH4 determination.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 34 2013-07-01 2013-07-01 false THC, NMHC, and CH4 determination. 1065... POLLUTION CONTROLS ENGINE-TESTING PROCEDURES Calculations and Data Requirements § 1065.660 THC, NMHC, and CH4 determination. (a) THC determination and initial THC/CH 4 contamination corrections. (1) If we...

  16. 40 CFR 1065.660 - THC, NMHC, and CH4 determination.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 33 2011-07-01 2011-07-01 false THC, NMHC, and CH4 determination. 1065... POLLUTION CONTROLS ENGINE-TESTING PROCEDURES Calculations and Data Requirements § 1065.660 THC, NMHC, and CH4 determination. (a) THC determination and THC/CH 4 initial contamination corrections. (1) If we...

  17. Gas-Phase Synthesis and Characterization of CH4-Loaded Hydroquinone Clathrates

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Lee, J.; Lee, Y; Takeya, S

    2010-01-01

    A CH{sub 4}-loaded hydroquinone (HQ) clathrate was synthesized via a gas-phase reaction using the {alpha}-form of crystalline HQ and CH{sub 4} gas at 12 MPa and room temperature. Solid-state {sup 13}C cross-polarization/magic angle spinning (CP/MAS) NMR and Raman spectroscopic measurements confirm the incorporation of CH{sub 4} molecules into the cages of the HQ clathrate framework. The chemical analysis indicates that about 69% of the cages are filled by CH{sub 4} molecules, that is, 0.69 CH{sub 4} per three HQ molecules. Rietveld refinement using synchrotron X-ray powder diffraction (XRD) data shows that the CH{sub 4}-loaded HQ clathrate adopts the {beta}-form ofmore » HQ clathrate in a hexagonal space group R3 with lattice parameters of a = 16.6191 {angstrom} and c = 5.5038 {angstrom}. Time-resolved synchrotron XRD and quadrupole mass spectroscopic measurements show that the CH{sub 4}-loaded HQ clathrate is stable up to 368 K and gradually transforms to the {alpha}-form by releasing the confined CH{sub 4} gases between 368-378 K. Using solid-state {sup 13}C CP/MAS NMR, the reaction kinetics between the {alpha}-form HQ and CH{sub 4} gas is qualitatively described in terms of the particle size of the crystalline HQ.« less

  18. Arctic tundra and mountain landscapes are persistent sinks of atmospheric CH4

    NASA Astrophysics Data System (ADS)

    Christiansen, Jesper; Winkler, Renato; Juncher Jørgensen, Christian

    2017-04-01

    Recent studies have shown significant rates of net uptake of atmospheric methane (CH4) in Arctic tundra soils. Oxidation of CH4 in these cold, dry soils in the Arctic region can counteract CH4 emissions from wetlands and play a potential important role for the net Arctic CH4 budget. However, significant knowledge gaps exist on the overall magnitude of the net CH4 sink in these cold, dry systems as the spatial and environmental limits for CH4 oxidation has not been determined. In particular, the extent, magnitude and drivers of CH4 oxidation in mountains and alpine landforms, which occupy large land areas in the Arctic and High Arctic has not yet been investigated leaving a potential vast CH4 sink unquantified with major potential implications for our conceptual view of Arctic CH4 budget in a changing climate. Here we present the results from two expeditions in the summers of 2015 and 2016 from Disko Bay and in the pro-glacial landscape in vicinity of the Russell Glacier, Kangerlussuaq, Greenland, respectively. The aim of our work is to determine the magnitude and extent of net uptake of atmospheric CH4 across a variety of previously unexplored dry tundra and post-glacial landforms in the Arctic, i.e. marginal moraines and other glacial features at the Greenland ice sheet as well as mountain tops and outwash plains. We used high-precision, mobile cavity-ring-down spectrometers (e.g. model G4301 GasScouter, Picarro Inc.) to achieve reliable flux estimates in sub-ambient CH4 concentration levels with a 4-minute enclosure time per chamber measurement. Our results show a persistent net uptake of CH4 uptake in these dry, extreme environments that rival the sink strength observed in temperate forest soils, otherwise considered the primary global terrestrial sink of atmospheric CH4. In this dynamic glacial landscape the magnitude of the net CH4 uptake is mainly constrained by recent landscape evolution along glacier margins and meltwater systems. Utilizing the high

  19. Coupled-cluster sum-frequency generation nonlinear susceptibilities of methyl (CH3) and methylene (CH2) groups.

    PubMed

    Tetsassi Feugmo, Conrard Giresse; Liégeois, Vincent; Champagne, Benoît

    2017-11-15

    The first vibrational sum frequency generation (SFG) spectra based on molecular properties calculated at the coupled cluster singles and doubles (CCSD) level of approximation have been simulated for interfacial model alkyl chains, providing benchmark data for comparisons with approximate methods, including density functional theory (DFT). The approach proceeds in three steps. In the first two steps, the molecular spectral properties are determined: the vibrational normal modes and frequencies and then the derivatives of the dipole moment and of the polarizability with respect to the normal coordinates. These derivatives are evaluated with a numerical differentiation approach, of which the accuracy was monitored using Romberg's procedure. Then, in the last step, a three-layer model is employed to evaluate the macroscopic second-order nonlinear optical responses and thereby the simulated SFG spectra of the alkyl interface. Results emphasize the following facts: (i) the dipole and polarizability derivatives calculated at the DFT level with the B3LYP exchange-correlation functional can differ, with respect to CCSD, by as much as ±10 to 20% and ±20 to 50% for the CH 3 and CH 2 vibrations, respectively; (ii) these differences are enhanced when considering the SFG intensities as well as their variations as a function of the experimental configuration (ppp versus ssp) and as a function of the tilt and rotation angles, defining the orientation of the alkyl chain at the interface; (iii) these differences originate from both the vibrational normal coordinates and the Cartesian derivatives of the dipole moment and polarizability; (iv) freezing the successive fragments of the alkyl chain strongly modifies the SFG spectrum and enables highlighting the delocalization effects between the terminal CH 3 group and its neighboring CH 2 units; and finally (v) going from the free chain to the free methyl model, and further to C 3v constraints on leads to large variations of two ratios

  20. Photochemical Modeling of CH3 Abundances in the Outer Solar System

    NASA Technical Reports Server (NTRS)

    Lee, Anthony Y. T.; Yung, Yuk L.; Moses, Julianne

    2000-01-01

    Recent measurements of methyl radicals (CH3) in the upper atmospheres of Saturn and Neptune by the Infrared Space Observatory (ISO) provide new constraints to photochemical models of hydrocarbon chemistry in the outer solar system. The derived column abundances of CH3 on Saturn above 10 mbar and Neptune above the 0.2 mbar pressure level are (2.5 - 6.0) x 10(exp 13) / sq cm and (0.7 - 2.8) x 10(exp 13) / sq cm, respectively. We use the updated Caltech/Jet Propulsion Laboratory photochemical model, which incorporates hydrocarbon photochemistry, vertical molecular and bulk atmospheric eddy diffusion, and realistic radiative transfer modeling, to study the CH3 abundances in the upper atmosphere of the giant planets and Titan. We identify the key reactions that control the concentrations of CH3 in the model, such as the three-body recombination reaction, CH3 + CH3 + M yields C2H6 + M. We evaluate and extrapolate the three-body rate constant of this reaction to the low-temperature limit (1.8 x 10(exp -16) T(sup -3.75) e(sup -300/T), T < 300 K) and compare methyl radical abundances in five atmospheres: Jupiter, Saturn, Uranus, Neptune, and Titan. The sensitivity of our models to the rate coefficients for the reactions H + CH3 + M yields CH4 + M, H + C2H3 yields C2H2 + H2, (sup 1)CH2 + H2 yields CH3 + H, and H + C2H5 yields 2CH3, the branching ratios of CH4 photolysis, vertical mixing in the five atmospheres, and Lyman alpha photon enhancement at the orbit of Neptune have all been tested. The results of our model CH3 abundances for both Saturn (5.1 x 10(exp 13) / sq cm) and Neptune (2.2 x 10(exp 13) / sq cm) show good agreement with ISO Short Wavelength Spectrometer measurements. Using the same chemical reaction set, our calculations also successfully generate vertical profiles of stable hydrocarbons consistent with Voyager and ground-based measurements in these outer solar system atmospheres. Predictions of CH3 column concentrations (for p <= 0.2 mbar) in the atmospheres

  1. Megafauna and frozen soil: the drivers of atmospheric CH4 dynamics

    NASA Astrophysics Data System (ADS)

    Zimov, N.; Zimov, S. A.

    2010-12-01

    During the last deglaciation (LD) a strong increase in atmospheric methane (CH4) concentrations occurred simultaneously with a rise in Greenland temperatures indicating that in the north, during this time period, strong CH4 sources “awakened”, as additionally documented by the appearance of a strong gradient between northern (Greenland) and southern (Antarctica) hemisphere atmospheric CH4 concentrations. This rise could not be caused by wetland expansion. A reconstruction of peatland formation dynamics has indicated that wetlands on Earth were few in LD and only actively expanded 10,000 yr BP, after atmospheric CH4 concentrations began to decline. Destabilization of methane clathrates also could not be the source for atmospheric CH4 increase. Geological CH4 (including methane clathrates) has the highest deuterium content (δD) among all of the known sources of CH4 while atmospheric CH4 δD values determined for the LD were record low. To explain recorded atmospheric CH4 and its isotopic dynamics required a strong northern source, which was active only during the LD and that provided very low δD CH4 values. Such a source is permafrost thawing under anaerobic conditions (or better stated soils of mammoth steppe-tundra ecosystems). Permafrost thawing is the strongest, among known, wetland sources (usually over 100g CH4/m2yr) and has a unique isotopic signature (δD = -400 per mil (-338 to -479 per mil), δ13C = -73 per mil (-58 to -99 per mil)). The main sources of atmospheric CH4 have different isotopic signatures (δ13C, δD). The isotopic content of atmospheric CH4 is a simple function of the weight average for all of the sources. Inclusion of permafrost source into a budget model of the atmospheric methane and its isotopes allowed us to reconstruct the dynamics of methane’s main sources. Model indicated geological source to be negligible as in LGM so and in LD and Holocene. During the glaciation, the largest methane source was megafauna, whose 1

  2. Spectroscopic properties of morin in various CH3OH-H2O and CH3CN-H2O mixed solvents.

    PubMed

    Park, Hyoung-Ryun; Im, Seo-Eun; Seo, Jung-Ja; Kim, Bong-Gon; Yoon, Jin Ah; Bark, Ki-Min

    2015-01-01

    The specific fluorescence properties of morin (3,2',4',5,7-pentahydroxyflavone) were studied in various CH3OH-H2O and CH3CN-H2O mixed solvents. Although the dihedral angle is large in the S0 state, morin has an almost planar molecular structure in the S1 state owing to the very low rotational energy barrier around the interring bond between B and the A, C ring. The excited state intramolecular proton transfer (ESIPT) at the S1 state cannot occur immediately after excitation, S1 → S0 fluorescence can be observed. Two conformers, Morin A and B have been known. At the CH3OH-H2O, Morin B will be the principal species but at the CH3CN-H2O, Morin A is the principal species. At the CH3OH-H2O, owing to the large Franck-Condon (FC) factor for S2 → S1 internal convernal (IC) and flexible molecular structure, only S1 → S0 fluorescence was exhibited. At the CH3CN-H2O, as the FC factor for S2 → S1 IC is small and molecular structure is rigid, S2 → S0 and S1 → S0 dual fluorescence was observed. This abnormal fluorescence property was further supported by the small pK1 value, effective delocalization of the lone pair electrons of C(2')-OH to the A, C ring, and a theoretical calculation. © 2014 The American Society of Photobiology.

  3. Hot filament-dissociation of (CH3)3SiH and (CH3)4Si, probed by vacuum ultra violet laser time of flight mass spectroscopy.

    PubMed

    Sharma, Ramesh C; Koshi, Mitsuo

    2006-11-01

    The decomposition of trimethylsilane and tetramethylsilane has been investigated for the first time, using hot wire (catalytic) at various temperatures. Trimethylsilane is catalytic-dissociated in these species SiH(2), CH(3)SiH, CH(3), CH(2)Si. Time of flight mass spectroscopy signal of these species are linearly increasing with increasing catalytic-temperature. Time of flight mass spectroscopy (TOFMS) signals of (CH(3))(3)SiH and photodissociated into (CH(3))(2)SiH are decreasing with increasing hot filament temperature. TOFMS signal of (CH(3))(4)Si is decreasing with increasing hot wire temperature, but (CH(3))(3)Si signal is almost constant with increasing the temperature. We calculated activation energies of dissociated species of the parental molecules for fundamental information of reaction kinetics for the first time. Catalytic-dissociation of trimethylsilane, and tetramethylsilane single source time of flight coupled single photon VUV (118 nm) photoionization collisionless radicals at temperature range of tungsten filament 800-2360 K. The study is focused to understand the fundamental information on reaction kinetics of these molecules at hot wire temperature, and processes of catalytic-chemical vapour deposition (Cat-CVD) technique which could be implemented in amorphous and crystalline SiC semiconductors thin films.

  4. Le Châtelier reciprocal relations and the mechanical analog

    NASA Astrophysics Data System (ADS)

    Gilmore, Robert

    1983-08-01

    Le Châtelier's principle is discussed carefully in terms of two sets of simple thermodynamic examples. The principle is then formulated quantitatively for general thermodynamic systems. The formulation is in terms of a perturbation-response matrix, the Le Châtelier matrix [L]. Le Châtelier's principle is contained in the diagonal elements of this matrix, all of which exceed one. These matrix elements describe the response of a system to a perturbation of either its extensive or intensive variables. These response ratios are inverses of each other. The Le Châtelier matrix is symmetric, so that a new set of thermodynamic reciprocal relations is derived. This quantitative formulation is illustrated by a single simple example which includes the original examples and shows the reciprocities among them. The assumptions underlying this new quantitative formulation of Le Châtelier's principle are general and applicable to a wide variety of nonthermodynamic systems. Le Châtelier's principle is formulated quantitatively for mechanical systems in static equilibrium, and mechanical examples of this formulation are given.

  5. A brief overview of the Chemistry-Aerosol Mediterranean Experiment (ChArMEx) database and campaign operation centre (ChOC)

    NASA Astrophysics Data System (ADS)

    Ferré, Hélène; Dulac, François; Belmahfoud, Nizar; Brissebrat, Guillaume; Cloché, Sophie; Descloitres, Jacques; Fleury, Laurence; Focsa, Loredana; Henriot, Nicolas; Ramage, Karim; Vermeulen, Anne

    2016-04-01

    Initiated in 2010 in the framework of the multidisciplinary research programme MISTRALS (Mediterranean Integrated Studies at Regional and Local Scales; http:www.mistrals-home.org), the Chemistry-Aerosol Mediterranean Experiment (ChArMEx, http://charmex.lsce.ipsl.fr/) aims at federating the scientific community for an updated assessment of the present and future state of the atmospheric environment in the Mediterranean Basin, and of its impacts on the regional climate, air quality, and marine biogeochemistry. The project combines mid- and long-term monitoring, intensive field campaigns, use of satellite data, and modelling studies. In this presentation we provide an overview of the campaign operation centre (http://choc.sedoo.fr/) and project database (http://mistrals.sedoo.fr/ChArMEx), at the end of the first experimental phase of the project that included a series of large campaigns based on airborne means (including balloons and various aircraft) and a network of surface stations. Those campaigns were performed mainly in the western Mediterranean basin in the summer of 2012, 2013 and 2014 with the help of the ChArMEx Operation Centre (ChOC), an open web site that has the objective to gather and display daily quick-looks from model forecasts and near-real time in situ and remote sensing observations of physical and chemical weather conditions relevant for the everyday campaign operation decisions. The ChOC is also useful for post campaign analyses and can be completed with a number of quick-looks of campaign results obtained later in order to offer an easy access to, and comprehensive view of all available data during the campaign period. The items included are selected according to the objectives and location of the given campaigns. The second experimental phase of ChArMEx from 2015 on is more focused on the eastern basin. In addition, the project operation centre is planned to be adapted for a joint MERMEX-ChArMEx oceanographic cruise (PEACETIME) for a study at

  6. Ozone Depletion Potential of CH3Br

    NASA Technical Reports Server (NTRS)

    Sander, Stanley P.; Ko, Malcolm K. W.; Sze, Nien Dak; Scott, Courtney; Rodriquez, Jose M.; Weisenstein, Debra K.

    1998-01-01

    The ozone depletion potential (ODP) of methyl bromide (CH3Br) can be determined by combining the model-calculated bromine efficiency factor (BEF) for CH3Br and its atmospheric lifetime. This paper examines how changes in several key kinetic data affect BEF. The key reactions highlighted in this study include the reaction of BrO + H02, the absorption cross section of HOBr, the absorption cross section and the photolysis products of BrON02, and the heterogeneous conversion of BrON02 to HOBR and HN03 on aerosol particles. By combining the calculated BEF with the latest estimate of 0.7 year for the atmospheric lifetime of CH3Br, the likely value of ODP for CH3Br is 0.39. The model-calculated concentration of HBr (approximately 0.3 pptv) in the lower stratosphere is substantially smaller than the reported measured value of about I pptv. Recent publications suggested models can reproduce the measured value if one assumes a yield for HBr from the reaction of BrO + OH or from the reaction of BrO + H02. Although the DeAlore et al. evaluation concluded any substantial yield of HBr from BrO + HO2 is unlikely, for completeness, we calculate the effects of these assumed yields on BEF for CH3Br. Our calculations show that the effects are minimal: practically no impact for an assumed 1.3% yield of HBr from BrO + OH and 10% smaller for an assumed 0.6% yield from BrO + H02.

  7. Two-Photon Holographic Stimulation of ReaChR

    PubMed Central

    Chaigneau, Emmanuelle; Ronzitti, Emiliano; Gajowa, Marta A.; Soler-Llavina, Gilberto J.; Tanese, Dimitrii; Brureau, Anthony Y. B.; Papagiakoumou, Eirini; Zeng, Hongkui; Emiliani, Valentina

    2016-01-01

    Optogenetics provides a unique approach to remotely manipulate brain activity with light. Reaching the degree of spatiotemporal control necessary to dissect the role of individual cells in neuronal networks, some of which reside deep in the brain, requires joint progress in opsin engineering and light sculpting methods. Here we investigate for the first time two-photon stimulation of the red-shifted opsin ReaChR. We use two-photon (2P) holographic illumination to control the activation of individually chosen neurons expressing ReaChR in acute brain slices. We demonstrated reliable action potential generation in ReaChR-expressing neurons and studied holographic 2P-evoked spiking performances depending on illumination power and pulse width using an amplified laser and a standard femtosecond Ti:Sapphire oscillator laser. These findings provide detailed knowledge of ReaChR's behavior under 2P illumination paving the way for achieving in depth remote control of multiple cells with high spatiotemporal resolution deep within scattering tissue. PMID:27803649

  8. Mobilization of Selenite by Ralstonia metallidurans CH34

    PubMed Central

    Roux, Murielle; Sarret, Géraldine; Pignot-Paintrand, Isabelle; Fontecave, Marc; Coves, Jacques

    2001-01-01

    Ralstonia metallidurans CH34 (formerly Alcaligenes eutrophus CH34) is a soil bacterium characteristic of metal-contaminated biotopes, as it is able to grow in the presence of a variety of heavy metals. R. metallidurans CH34 is reported now to resist up to 6 mM selenite and to reduce selenite to elemental red selenium as shown by extended X-ray absorption fine-structure analysis. Growth kinetics analysis suggests an adaptation of the cells to the selenite stress during the lag-phase period. Depending on the culture conditions, the medium can be completely depleted of selenite. Selenium accumulates essentially in the cytoplasm as judged from electron microscopy and energy-dispersive X-ray analysis. Elemental selenium, highly insoluble, represents a nontoxic storage form for the bacterium. The ability of R. metallidurans CH34 to reduce large amounts of selenite may be of interest for bioremediation processes targeting selenite-polluted sites. PMID:11157242

  9. Data exploration, quality control and statistical analysis of ChIP-exo/nexus experiments

    PubMed Central

    Welch, Rene; Chung, Dongjun; Grass, Jeffrey; Landick, Robert

    2017-01-01

    Abstract ChIP-exo/nexus experiments rely on innovative modifications of the commonly used ChIP-seq protocol for high resolution mapping of transcription factor binding sites. Although many aspects of the ChIP-exo data analysis are similar to those of ChIP-seq, these high throughput experiments pose a number of unique quality control and analysis challenges. We develop a novel statistical quality control pipeline and accompanying R/Bioconductor package, ChIPexoQual, to enable exploration and analysis of ChIP-exo and related experiments. ChIPexoQual evaluates a number of key issues including strand imbalance, library complexity, and signal enrichment of data. Assessment of these features are facilitated through diagnostic plots and summary statistics computed over regions of the genome with varying levels of coverage. We evaluated our QC pipeline with both large collections of public ChIP-exo/nexus data and multiple, new ChIP-exo datasets from Escherichia coli. ChIPexoQual analysis of these datasets resulted in guidelines for using these QC metrics across a wide range of sequencing depths and provided further insights for modelling ChIP-exo data. PMID:28911122

  10. Kinetics of the Br2-CH3CHO Photochemical Chain Reaction

    NASA Technical Reports Server (NTRS)

    Nicovich, J. M.; Shackelford, C. J.; Wine, P. H.

    1997-01-01

    Time-resolved resonance fluorescence spectroscopy was employed in conjunction with laser flash photolysis of Br2 to study the kinetics of the two elementary steps in the photochemical chain reaction nBr2 + nCH3CHO + hv yields nCH3CBrO + nHBr. In the temperature range 255-400 K, the rate coefficient for the reaction Br((sup 2)P(sub 3/2)) + CH3CHO yields CH3CO + HBr is given by the Arrhenius expression k(sub 6)(T) = (1.51 +/- 0.20) x 10(exp -11) exp(-(364 +/- 41)/T)cu cm/(molecule.s). At 298 K, the reaction CH3CO + Br2 yields CH3CBrO + Br proceeds at a near gas kinetic rate, k(sub 7)(298 K) = (1.08 +/- 0.38) x 10(exp -10)cu cm/(molecule.s).

  11. Hyperfine excitation of CH in collisions with atomic and molecular hydrogen

    NASA Astrophysics Data System (ADS)

    Dagdigian, Paul J.

    2018-04-01

    We investigate here the excitation of methylidene (CH) induced by collisions with atomic and molecular hydrogen (H and H2). The hyperfine-resolved rate coefficients were obtained from close coupling nuclear-spin-free scattering calculations. The calculations are based upon recent, high-accuracy calculations of the CH(X2Π)-H(2S) and CH(X2Π)-H2 potential energy surfaces. Cross-sections and rate coefficients for collisions with atomic H, para-H2, and ortho-H2 were computed for all transitions between the 32 hyperfine levels for CH(X2Π) involving the n ≤ 4 rotational levels for temperatures between 10 and 300 K. These rate coefficients should significantly aid in the interpretation of astronomical observations of CH spectra. As a first application, the excitation of CH is simulated for conditions in typical molecular clouds.

  12. Communication: Photodissociation of CH3CHO at 308 nm: Observation of H-roaming, CH3-roaming, and transition state pathways together along the ground state surface

    NASA Astrophysics Data System (ADS)

    Li, Hou-Kuan; Tsai, Po-Yu; Hung, Kai-Chan; Kasai, Toshio; Lin, King-Chuen

    2015-01-01

    Following photodissociation of acetaldehyde (CH3CHO) at 308 nm, the CO(v = 1-4) fragment is acquired using time-resolved Fourier-transform infrared emission spectroscopy. The CO(v = 1) rotational distribution shows a bimodal feature; the low- and high-J components result from H-roaming around CH3CO core and CH3-roaming around CHO radical, respectively, in consistency with a recent assignment by Kable and co-workers (Lee et al., Chem. Sci. 5, 4633 (2014)). The H-roaming pathway disappears at the CO(v ≥ 2) states, because of insufficient available energy following bond-breaking of H + CH3CO. By analyzing the CH4 emission spectrum, we obtained a bimodal vibrational distribution; the low-energy component is ascribed to the transition state (TS) pathway, consistent with prediction by quasiclassical trajectory calculations, while the high-energy component results from H- and CH3-roamings. A branching fraction of H-roaming/CH3-roaming/TS contribution is evaluated to be (8% ± 3%)/(68% ± 10%)/(25% ± 5%), in which the TS pathway was observed for the first time. The three pathways proceed concomitantly along the electronic ground state surface.

  13. Radical routes to interstellar glycolaldehyde. The possibility of stereoselectivity in gas-phase polymerization reactions involving CH(2)O and ˙CH(2)OH.

    PubMed

    Wang, Tianfang; Bowie, John H

    2010-10-21

    A previous report that the interstellar molecule glycolaldehyde (HOCH(2)CHO) can be made from hydroxymethylene (HOCH:) and formaldehyde has been revisited at the CCSD(T)/6-311++G(3df,2p)//MP2/6-311++G(3df,2p) level of theory. This reaction competes with the formation of acetic acid and methylformate, molecules which have also been detected in interstellar clouds. Other possible modes of formation of glycolaldehyde by radical/radical reactions have been shown to be viable theoretically as follows: HO˙+˙CH2CHO -->HOCH2CHO [ΔG(Γ)(298K)=-303kJ mol⁻¹] HOCH2˙+˙CHO-->HOCH2CHO (-259kJ mol⁻¹). The species in these two processes are known interstellar molecules. Key radicals ˙CH(2)CHO and ˙CH(2)OH in these sequences have been shown to be stable for the microsecond duration of neutralization/reionization experiments in the dual collision cells of a VG ZAB 2HF mass spectrometer. The polymerization reaction HOCH(2)CH˙OH + nCH(2)O → HOCH(2)[CH(OH)](n)˙CHOH (n = 1 to 3) has been studied theoretically and shown to be energetically feasible, as is the cyclization reaction of HOCH(2)[(CH(2)OH)(4)]˙CHOH (in the presence of one molecule of water at the reacting centre) to form glucose. The probability of such a reaction sequence is small even if polymerization were to occur in interstellar ice containing a significant concentration of CH(2)O. The large number of stereoisomers produced by such a reaction sequence makes the formation of a particular sugar, again for example glucose, an inefficient synthesis. The possibility of stereoselectivity occurring during the polymerization was investigated for two diastereoisomers of HOCH(2)[(CHOH)](2)˙CHOH. No significant difference was found in the transition state energies for addition of CH(2)O to these two diastereoisomers, but a barrier difference of 12 kJ mol(-1) was found for the H transfer reactions ˙OCH(2)[(CHOH)](2)CH(2)OH → HOCH(2)[(CHOH)(2)˙CHOH of the two diastereoisomers.

  14. Energetics of the O-H bond and of intramolecular hydrogen bonding in HOC6H4C(O)Y (Y = H, CH3, CH2CH=CH2, C[triple bond]CH, CH2F, NH2, NHCH3, NO2, OH, OCH3, OCN, CN, F, Cl, SH, and SCH3) compounds.

    PubMed

    Bernardes, Carlos E S; Minas da Piedade, Manuel E

    2008-10-09

    The energetics of the phenolic O-H bond in a series of 2- and 4-HOC 6H 4C(O)Y (Y = H, CH3, CH 2CH=CH2, C[triple bond]CH, CH2F, NH2, NHCH 3, NO2, OH, OCH3, OCN, CN, F, Cl, SH, and SCH3) compounds and of the intramolecular O...H hydrogen bond in 2-HOC 6H 4C(O)Y, was investigated by using a combination of experimental and theoretical methods. The standard molar enthalpies of formation of 2-hydroxybenzaldehyde (2HBA), 4-hydroxybenzaldehyde (4HBA), 2'-hydroxyacetophenone (2HAP), 2-hydroxybenzamide (2HBM), and 4-hydroxybenzamide (4HBM), at 298.15 K, were determined by micro- or macrocombustion calorimetry. The corresponding enthalpies of vaporization or sublimation were also measured by Calvet drop-calorimetry and Knudsen effusion measurements. The combination of the obtained experimental data led to Delta f H m (o)(2HBA, g) = -238.3 +/- 2.5 kJ.mol (-1), DeltafHm(o)(4HBA, g) = -220.3 +/- 2.0 kJ.mol(-1), Delta f H m (o)(2HAP, g) = -291.8 +/- 2.1 kJ.mol(-1), DeltafHm(o)(2HBM, g) = -304.8 +/- 1.5 kJ.mol (-1), and DeltafHm(o) (4HBM, g) = -278.4 +/- 2.4 kJ.mol (-1). These values, were used to assess the predictions of the B3LYP/6-31G(d,p), B3LYP/6-311+G(d,p), B3LYP/aug-cc-pVDZ, B3P86/6-31G(d,p), B3P86/6-311+G(d,p), B3P86/aug-cc-pVDZ, and CBS-QB3 methods, for the enthalpies of a series of isodesmic gas phase reactions. In general, the CBS-QB3 method was able to reproduce the experimental enthalpies of reaction within their uncertainties. The B3LYP/6-311+G(d,p) method, with a slightly poorer accuracy than the CBS-QB3 approach, achieved the best performance of the tested DFT models. It was further used to analyze the trends of the intramolecular O...H hydrogen bond in 2-HOC 6H 4C(O)Y evaluated by the ortho-para method and to compare the energetics of the phenolic O-H bond in 2- and 4-HOC 6H 4C(O)Y compounds. It was concluded that the O-H bond "strength" is systematically larger for 2-hydroxybenzoyl than for the corresponding 4-hydroxybenzoyl isomers mainly due to the presence of

  15. RKR Franck-Condon factors for blue and ultraviolet transitions of some molecules of astrophysical interest and some comments on the interstellar abundance of CH, CH+ and SiH+.

    NASA Technical Reports Server (NTRS)

    Liszt, H. S.; Hayden Smith, W.

    1972-01-01

    RKR Franck-Condon factors for thirteen of the blue and ultraviolet transitions of AlF, AlO, BH, BD, CH, CD, CH(+), SiO and SiH(+) have been calculated. The interstellar abundances of CH, CH(+) and SiH(+) are discussed with regard to recent laboratory measurements, our Franck-Condon factors, and observations of the sun and the interstellar medium.

  16. CH functionalization of heteroaromatic compounds by transition metal catalysis

    NASA Astrophysics Data System (ADS)

    Tanba, Shunsuke; Fujiwara, Taiki; Monguchi, Daiki; Mori, Atsunori

    2010-06-01

    Transition metal-catalyzed CH functioanlization of thiazoles and thiophenes are carried out. The reaction of thiophene with aryl halide in the presence of a palladium catalyst underwent the CC bond forming reaction at the CH bond of thiophene. By employing the reaction head-to-tail-type oligothiophene is synthesized in a stepwise manner. When several azoles are treated with secondary amines and amides in the presence of a copper catalyst, oxidative CH-NH coupling took place to form the carbon-nitrogen bond.

  17. Towards the new CH2018 climate scenarios for Switzerland

    NASA Astrophysics Data System (ADS)

    Fischer, Andreas; Schär, Christoph; Croci-Maspoli, Mischa; Knutti, Reto; Liniger, Mark; Strassmann, Kuno

    2017-04-01

    There is a growing demand for regional assessments of future climate change and its impacts on society and ecosystems to inform and facilitate appropriate adaptation strategies. The basis for such assessments are consistent and up-to-date climate change scenarios on the local to regional scale. In Switzerland, an important step has been accomplished by the release of the climate scenarios in 2011 ("CH2011"). Since then, new climate model simulations have become available and the scientific understanding has improved. It is hence desirable to update these national scenarios. The new CH2018 scenarios are developed in the framework of the recently founded National Center for Climate Services (NCCS), a network consisting of several federal offices and academic partners. The CH2018 scenarios will build primarily upon the latest Euro-CORDEX regional climate model simulations assuming different pathways of future greenhouse gas concentrations. Compared to CH2011, more emphasis will be put on changes in extremes and in putting the projected changes in the context of observed variability. Results of a recently conducted survey on end-user needs in Switzerland will guide the development process toward the CH2018 scenarios. It ensures that the scenarios are presented and communicated in a user-oriented format and find a wide applicability across different sectors in Switzerland. In the presentation we will show the full methodological setup to generate the CH2018 scenarios and how consistency across the methods and products is maximized. First results on mean changes and selected indices will be presented. In terms of dissemination, the results of the user survey show the necessity to address all different user types of climate scenarios, especially the non-experts. Compared to CH2011, this implies a stronger focus on consulting, condensing complex information and providing tutorials. In the presentation, we will outline our plans on dissemination in order to adequately

  18. CH/π Interactions in Carbohydrate Recognition.

    PubMed

    Spiwok, Vojtěch

    2017-06-23

    Many carbohydrate-binding proteins contain aromatic amino acid residues in their binding sites. These residues interact with carbohydrates in a stacking geometry via CH/π interactions. These interactions can be found in carbohydrate-binding proteins, including lectins, enzymes and carbohydrate transporters. Besides this, many non-protein aromatic molecules (natural as well as artificial) can bind saccharides using these interactions. Recent computational and experimental studies have shown that carbohydrate-aromatic CH/π interactions are dispersion interactions, tuned by electrostatics and partially stabilized by a hydrophobic effect in solvated systems.

  19. Purification of nanogram-range immunoprecipitated DNA in ChIP-seq application.

    PubMed

    Zhong, Jian; Ye, Zhenqing; Lenz, Samuel W; Clark, Chad R; Bharucha, Adil; Farrugia, Gianrico; Robertson, Keith D; Zhang, Zhiguo; Ordog, Tamas; Lee, Jeong-Heon

    2017-12-21

    Chromatin immunoprecipitation-sequencing (ChIP-seq) is a widely used epigenetic approach for investigating genome-wide protein-DNA interactions in cells and tissues. The approach has been relatively well established but several key steps still require further improvement. As a part of the procedure, immnoprecipitated DNA must undergo purification and library preparation for subsequent high-throughput sequencing. Current ChIP protocols typically yield nanogram quantities of immunoprecipitated DNA mainly depending on the target of interest and starting chromatin input amount. However, little information exists on the performance of reagents used for the purification of such minute amounts of immunoprecipitated DNA in ChIP elution buffer and their effects on ChIP-seq data. Here, we compared DNA recovery, library preparation efficiency, and ChIP-seq results obtained with several commercial DNA purification reagents applied to 1 ng ChIP DNA and also investigated the impact of conditions under which ChIP DNA is stored. We compared DNA recovery of ten commercial DNA purification reagents and phenol/chloroform extraction from 1 to 50 ng of immunopreciptated DNA in ChIP elution buffer. The recovery yield was significantly different with 1 ng of DNA while similar in higher DNA amounts. We also observed that the low nanogram range of purified DNA is prone to loss during storage depending on the type of polypropylene tube used. The immunoprecipitated DNA equivalent to 1 ng of purified DNA was subject to DNA purification and library preparation to evaluate the performance of four better performing purification reagents in ChIP-seq applications. Quantification of library DNAs indicated the selected purification kits have a negligible impact on the efficiency of library preparation. The resulting ChIP-seq data were comparable with the dataset generated by ENCODE consortium and were highly correlated between the data from different purification reagents. This study provides

  20. Data exploration, quality control and statistical analysis of ChIP-exo/nexus experiments.

    PubMed

    Welch, Rene; Chung, Dongjun; Grass, Jeffrey; Landick, Robert; Keles, Sündüz

    2017-09-06

    ChIP-exo/nexus experiments rely on innovative modifications of the commonly used ChIP-seq protocol for high resolution mapping of transcription factor binding sites. Although many aspects of the ChIP-exo data analysis are similar to those of ChIP-seq, these high throughput experiments pose a number of unique quality control and analysis challenges. We develop a novel statistical quality control pipeline and accompanying R/Bioconductor package, ChIPexoQual, to enable exploration and analysis of ChIP-exo and related experiments. ChIPexoQual evaluates a number of key issues including strand imbalance, library complexity, and signal enrichment of data. Assessment of these features are facilitated through diagnostic plots and summary statistics computed over regions of the genome with varying levels of coverage. We evaluated our QC pipeline with both large collections of public ChIP-exo/nexus data and multiple, new ChIP-exo datasets from Escherichia coli. ChIPexoQual analysis of these datasets resulted in guidelines for using these QC metrics across a wide range of sequencing depths and provided further insights for modelling ChIP-exo data. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  1. Direct Dynamics Simulation of Dissociation of the [CH3--I--OH]- Ion-Molecule Complex

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Xie, Jing; McClellan, Miranda; Sun, Rui

    Direct dynamics simulations were used to study dissociation of the [CH3--I--OH]- complex ion, which was observed in a previous study of the OH- + CH3I gas phase reaction (J. Phys. Chem. A 2013, 117, 7162). Restricted B97-1 simulations were performed to study dissociation at 65, 75 and 100 kcal/mol and the [CH3--I--OH]- ion dissociated exponentially, in accord with RRKM theory. For these energies the major dissociation products are CH3I + OH-, CH2I- + H2O, and CH3OH + I-. Unrestricted B97-1 and restricted and unrestricted CAM-B3LYP simulations were also performed at 100 kcal/mol to compare with the restricted B97-1 results. Themore » {CH3I + OH-}:{CH2I- + H2O}:{CH3OH + I-} product ratio is 0.72 : 0.15 : 0.13, 0.81 : 0.05 : 0.14, 0.71 : 0.19 : 0.10 , and 0.83 : 0.13 : 0.04 for the restricted B97-1, unrestricted B97-1, restricted CAM-B3LYP, and unrestricted CAM-B3LYP simulations, respectively. Other product channels found are CH2 + I- + H2O, CH2 + I-(H2O), CH4 + IO-, CH3 - + IOH, and CH3 + IOH-. The CH3 - + IOH singlet products are only given by the restricted B97-1 simulation and the lower energy CH3 + IOH- doublet products are only formed by the unrestricted B97-1 simulation. Also studied were the direct and indirect atomic-level mechanisms for forming CH3I + OH-, CH2I- + H2O, and CH3OH + I-. The majority of CH3I + OH- were formed through a direct mechanism. For both CH2I- + H2O and CH3OH + I-, the direct mechanism is overall more important than the indirect mechanisms, with the round-about like mechanism the most important indirect mechanism at high excitation energies. Mechanism comparisons between the B97-1 and CAM-B3LYP simulations showed that formation of the CH3OH---I- complex is favored for the B97-1 simulations, while formation of the HO----HCH2I complex is favored for the CAM-B3LYP simulations. The unrestricted simulations give a higher percentage of indirect mechanisms than the restricted simulations. The possible role of the self-interaction error in

  2. Scalable and sustainable electrochemical allylic C-H oxidation

    NASA Astrophysics Data System (ADS)

    Horn, Evan J.; Rosen, Brandon R.; Chen, Yong; Tang, Jiaze; Chen, Ke; Eastgate, Martin D.; Baran, Phil S.

    2016-05-01

    New methods and strategies for the direct functionalization of C-H bonds are beginning to reshape the field of retrosynthetic analysis, affecting the synthesis of natural products, medicines and materials. The oxidation of allylic systems has played a prominent role in this context as possibly the most widely applied C-H functionalization, owing to the utility of enones and allylic alcohols as versatile intermediates, and their prevalence in natural and unnatural materials. Allylic oxidations have featured in hundreds of syntheses, including some natural product syntheses regarded as “classics”. Despite many attempts to improve the efficiency and practicality of this transformation, the majority of conditions still use highly toxic reagents (based around toxic elements such as chromium or selenium) or expensive catalysts (such as palladium or rhodium). These requirements are problematic in industrial settings; currently, no scalable and sustainable solution to allylic oxidation exists. This oxidation strategy is therefore rarely used for large-scale synthetic applications, limiting the adoption of this retrosynthetic strategy by industrial scientists. Here we describe an electrochemical C-H oxidation strategy that exhibits broad substrate scope, operational simplicity and high chemoselectivity. It uses inexpensive and readily available materials, and represents a scalable allylic C-H oxidation (demonstrated on 100 grams), enabling the adoption of this C-H oxidation strategy in large-scale industrial settings without substantial environmental impact.

  3. Valorization of CH4 emissions into high-added-value products: Assessing the production of ectoine coupled with CH4 abatement.

    PubMed

    Cantera, Sara; Lebrero, Raquel; Sadornil, Lidia; García-Encina, Pedro A; Muñoz, Raúl

    2016-11-01

    This study assessed an innovative strategy for the valorization of dilute methane emissions based on the bio-conversion of CH4 (the second most important greenhouse gas (GHG)) into ectoine by the methanotrophic ectoine-producing strain Methylomicrobium alcaliphilum 20 Z. The influence of CH4 (2-20%), Cu(2+) (0.05-50 μM) and NaCl (0-9%) concentration as well as temperature (25-35 °C) on ectoine synthesis and specific CH4 biodegradation rate was evaluated for the first time. Concentrations of 20% CH4 (at 3% NaCl, 0.05 μM Cu(2+), 25 °C) and 6% NaCl (at 4% CH4, 0.05 μM Cu(2+), 25 °C) supported the maximum intra-cellular ectoine production yield (31.0 ±1.7 and 66.9 ±4.2 mg g biomass(-1), respectively). On the other hand, extra-cellular ectoine concentrations of up to 4.7 ± 0.1 mg L(-1) were detected at high Cu(2+)concentrations (50 μM), despite this methanotroph has not been previously classified as an ectoine-excreting strain. This research demonstrated the feasibility of the bio-conversion of dilute emissions of methane into high-added value products in an attempt to develop a sustainable GHG bioeconomy. Copyright © 2016 Elsevier Ltd. All rights reserved.

  4. Satellite Boreal Measurements over Alaska and Canada During June-July 2004: Simultaneous Measurements of Upper Tropospheric CO, C2H6, HCN, CH3Cl, CH4, C2H2, CH2OH, HCOOH, OCS, and SF6 Mixing Ratios

    NASA Technical Reports Server (NTRS)

    Rinsland, Curtis P.; Dufour, Gaelle; Boone, Chris D.; Bernath, Peter F.; Chiou, Linda; Coheur, Pierre-Francois; Turquety, Solene; Clerbaux, Cathy

    2007-01-01

    Simultaneous ACE (Atmospheric Chemistry Experiment) upper tropospheric CO, C2H6, HCN, CH3Cl, CH4 , C2H2 , CH30H, HCOOH, and OCS measurements show plumes up to 185 ppbv (10 (exp -9) per unit volume) for CO, 1.36 ppbv for C2H6, 755 pptv (10(exp -12) per unit volume) for HCN, 1.12 ppbv for CH3C1, 1.82 ppmv, (10(exp -6) per unit volume) for CH4, 0.178 ppbv for C2H2, 3.89 ppbv for CH30H, 0.843 ppbv for HCOOH, and 0.48 ppbv for OCS in western Canada and Alaska at 50 deg N-68 deg N latitude between 29 June and 23 July 2004. Enhancement ratios and emission factors for HCOOH, CH30H, HCN, C2H6, and OCS relative to CO at 250-350 hPa are inferred from measurements of young plumes compared with lower mixing ratios assumed to represent background conditions based on a CO emission factor derived from boreal measurements. Results are generally consistent with the limited data reported for various vegetative types and emission phases measured in extratropical forests including boreal forests. The low correlation between fire product emission mixing ratios and the S176 mixing ratio is consistent with no significant SF6 emissions from the biomass fires.

  5. Hydrothermal plumes in the Gulf of Aden, as characterized by light transmission, Mn, Fe, CH4 and δ13C-CH4 anomalies

    NASA Astrophysics Data System (ADS)

    Gamo, Toshitaka; Okamura, Kei; Hatanaka, Hiroshi; Hasumoto, Hiroshi; Komatsu, Daisuke; Chinen, Masakazu; Mori, Mutsumi; Tanaka, Junya; Hirota, Akinari; Tsunogai, Urumu; Tamaki, Kensaku

    2015-11-01

    We conducted water column surveys to search for hydrothermal plumes over the spreading axes in the Gulf of Aden between 45°35‧E and 52°42‧E. We measured light transmission and chemical tracers Mn, Fe, CH4 and δ13C of CH4 in seawater taken using a CTD-Carrousel multi-sampling system at 12 locations including a control station in the Arabian Sea. We recognized three types of hydrothermal plumes at depths of 650 to 900 m (shallow plumes), 1000 to 1200 m (intermediate plumes), and >1500 m (deep plumes). The shallow plumes were apparently originated from newly discovered twin seamounts (12°03-06‧N and 45°35-41‧E) at the westernmost survey area, where two-dimensional distributions of light transmission and Mn were mapped by tow-yo observations of the CTD-sampling system with an in situ auto-analyzer GAMOS. The maximum concentrations of Mn, Fe, and CH4 of 46 nM, 251 nM, and 15 nM, respectively, were observed for collected seawater within the shallow plumes. The intermediate plumes were characterized by anomalies of light transmission, Mn, Fe, and δ13C of CH4, but by little CH4 anomalies, suggesting that CH4 had been consumed down to the background level during the aging of the plumes. Anomalies of δ3He already reported by the World Ocean Circulation Experiment (WOCE) program exhibited a hydrothermal plume-like peak at 2000 m depth in the Gulf of Aden, which seems to coincide with the deep plumes observed in this study. The endmember δ13C-CH4 values for the shallow and the deep plumes were estimated to be in a range between -10‰ and -15‰, demonstrating that the sources of CH4 are not biogenic but magmatic as similarly observed at sediment-starved mid-oceanic ridges.

  6. Hospital clinical trial: Homeopathy (Agraphis nutans 5CH, Thuya occidentalis 5CH, Kalium muriaticum 9CH and Arsenicum iodatum 9CH) as adjuvant, in children with otitis media with effusion.

    PubMed

    Pedrero-Escalas, M F; Jimenez-Antolin, J; Lassaletta, L; Diaz-Saez, G; Gavilán, J

    2016-09-01

    Otitis media with effusion (OME) is the most common cause of paediatric hearing loss. No single treatment has proved its effectiveness. There is a lack of evidence-based medicine studies in the area of homeopathy. A prospective randomized, double blinded interventional placebo control study was conducted. Patients, from 2 months to 12 years, with OME diagnosed by pneumatic otoscopy (PNO) and tympanometry, were randomized into two groups. Both groups received aerosol therapy (mucolytics and corticosteroids). In addition, the experimental group (EG) received homeopathy (Agraphis nutans 5CH, Thuya Occidentalis 5CH, Kalium muriaticum 9CH and Arsenicum iodatum), and the placebo group (PG) placebo, both of them for 3 months. Patients were evaluated by PNO examination and tympanometry at baseline, at 45 and 90 days. 97 patients were enrolled. In the EG, 61.9% of individuals were cured (PNO went from negative in the 1st visit to positive in the 3rd visit) compared with 56.8% of patients treated with placebo. 4.8% of patients in the EG suffered a recurrence (positive PNO in the 2nd visit changed to negative in the 3rd visit) while 11.4% did in the PG. No significant difference was found. Adverse events were distributed similarly, except in the case of upper respiratory tract infections, which were less frequent in EG (3 vs. 13, p: 0.009). The homeopathic scheme used as adjuvant treatment cannot be claimed to be an effective treatment in children with OME. EUDRACT number: 2011-006086-17, PROTOCOL code: 55005646. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  7. Electronic structure, transport, and phonons of SrAg ChF ( Ch = S,Se,Te): Bulk superlattice thermoelectrics

    DOE PAGES

    Gudelli, Vijay Kumar; Kanchana, V.; Vaitheeswaran, G.; ...

    2015-07-15

    Here, we report calculations of the electronic structure, vibrational properties, and transport for the p-type semiconductors, SrAg ChF ( Ch = S, Se, and Te). We find soft phonons with low frequency optical branches intersecting the acoustic modes below 50 cm –1, indicative of a material with low thermal conductivity. The bands at and near the valence-band maxima are highly two-dimensional, which leads to high thermopowers even at high carrier concentrations, which is a combination that suggests good thermoelectric performance. These materials may be regarded as bulk realizations of superlattice thermoelectrics.

  8. [CH(3)(CH(2))(11)NH(3)]SnI(3): a hybrid semiconductor with MoO(3)-type tin(II) iodide layers.

    PubMed

    Xu, Zhengtao; Mitzi, David B

    2003-10-20

    The organic-inorganic hybrid [CH(3)(CH(2))(11)NH(3)]SnI(3) presents a lamellar structure with a Sn-I framework isotypic to that of MoO(3). The SnI(3)(-) layer consists of edge and corner-sharing SnI(6) octahedra in which one of the six Sn-I bonds is distinctly elongated (e.g., 3.62 A), indicating lone-pair stereoactivity for the Sn(II) atom. The overall electronic character remains comparable with that of the well-studied SnI(4)(2)(-)-based perovskite semiconductors, such as [CH(3)(CH(2))(11)NH(3)](2)SnI(4), with a red-shifted and broadened exciton peak associated with the band gap, apparently due to the increased dimensionality of the Sn-I framework. The title compound offers, aside from the hybrid perovskites, a new type of solution-processable Sn-I network for potential applications in semiconductive devices.

  9. Biologic properties of a CH2 domain-deleted recombinant immunoglobulin.

    PubMed

    Slavin-Chiorini, D C; Horan Hand, P H; Kashmiri, S V; Calvo, B; Zaremba, S; Schlom, J

    1993-01-02

    Monoclonal antibody (MAb) B72.3 reacts with TAG-72, a high-molecular-weight mucin expressed on several types of human carcinoma, and is currently being used in clinical trials for the diagnosis and therapy of human carcinoma. An expression construct containing cDNA encoding an immunoglobulin (Ig) heavy chain, with the variable region of murine MAb B72.3 and a human Ig constant region with a deletion of the CH2 domain, was generated. Immunoglobulin from the transfectoma with the highest expression of the TAG-72 immunoreactive antibody was designated MAb chimeric (c) B72.3 delta CH2. The pharmacokinetics of serum clearance of iodine-labeled MAbs cB72.3 delta CH2 and the intact cB72.3 were compared in athymic mice. By 24 hr, less than 1% of the cB72.3 delta CH2 was left in the plasma, while 36% of the cB72.3 still remained. The T1/2 alpha values of the cB72.3 delta CH2 and cB72.3 MAbs were 1.7 and 2.4 hr, respectively. The T1/2 beta values were 7.8 hr for the domain-deleted cMAb and 48.9 hr for cB72.3. Biodistribution studies in athymic mice bearing LS-174T xenografts showed a reduction in the percentage of injected dose per gram in tumor with 131I-cB72.3 delta CH2; however, the 131I-cB72.3 delta CH2 both localized to tumors faster and cleared from the blood faster than the 125I-cB72.3 MAb. Only trace amounts of the 131I-cB72.3 delta CH2 were detected in normal tissues, including kidney. The faster clearance rate, more rapid tumor targeting and lack of metabolic uptake in normal tissues demonstrated with the iodine-labeled CH2 domain-deleted cMAb may be an advantage for certain clinical protocols.

  10. CH-47F Improved Cargo Helicopter (CH-47F)

    DTIC Science & Technology

    2015-12-01

    Confidence Level Confidence Level of cost estimate for current APB: 50% The Confidence Level of the CH-47F APB cost estimate, which was approved on April...M) Initial PAUC Development Estimate Changes PAUC Production Estimate Econ Qty Sch Eng Est Oth Spt Total 10.316 -0.491 3.003 -0.164 2.273 7.378...SAR Baseline to Current SAR Baseline (TY $M) Initial APUC Development Estimate Changes APUC Production Estimate Econ Qty Sch Eng Est Oth Spt Total

  11. Microheterogeneity in CH3OH/CD3OH mixture

    NASA Astrophysics Data System (ADS)

    Wrzeszcz, Władysław; Mazurek, Sylwester; Szostak, Roman; Tomza, Paweł; Czarnecki, Mirosław A.

    2018-01-01

    Recently, we demonstrated the presence of microheterogeneity in binary mixtures of unlike alcohols. [RSC Adv. 2016, 6, 37195-37202] The aim of this work was examination if this phenomenon occurs also in the mixture of very similar alcohols like CH3OH and CD3OH. Theoretical calculations suggest that the isotopic substitution in methyl group influences properties of the OH group. Hence, one can expect that this effect may lead to partial separation of CH3OH and CD3OH at a molecular level and it contributes to deviation from the ideal mixture. This work evidences that CH3OH/CD3OH mixture also deviates from the ideal one, but the extent of this deviation is much smaller as compared with the mixtures of other alcohols. It is of particular note that this deviation results mainly from the difference between the CH3 and CD3 groups, while the contribution from the OH groups is small. The structure of CH3OH/CD3OH mixture at a molecular level is similar to the structure of binary mixtures of other alcohols. The mixture is composed of the homoclusters of both alcohols and the mixed clusters. The homoclusters existing in the mixture are similar to those present in bulk alcohols. The highest population of the heteroclusters and the largest deviation from the ideal mixture were observed at equimolar mixture. Both the experimental and theoretical results reveal that in CH3OH/CD3OH mixture dominate the cyclic tetramers and larger clusters, while the population of the linear clusters is negligible. Though the extent and strength of hydrogen bonding in both alcohols are the same, the position and intensity of the 2ν(OH) band for CH3OH and CD3OH are different. We propose possible explanation of this observation.

  12. ChIP-seq and ChIP-exo profiling of Pol II, H2A.Z, and H3K4me3 in human K562 cells.

    PubMed

    Mchaourab, Zenab F; Perreault, Andrea A; Venters, Bryan J

    2018-03-06

    The human K562 chronic myeloid leukemia cell line has long served as an experimental paradigm for functional genomic studies. To systematically and functionally annotate the human genome, the ENCODE consortium generated hundreds of functional genomic data sets, such as chromatin immunoprecipitation coupled to sequencing (ChIP-seq). While ChIP-seq analyses have provided tremendous insights into gene regulation, spatiotemporal insights were limited by a resolution of several hundred base pairs. ChIP-exonuclease (ChIP-exo) is a refined version of ChIP-seq that overcomes this limitation by providing higher precision mapping of protein-DNA interactions. To study the interplay of transcription initiation and chromatin, we profiled the genome-wide locations for RNA polymerase II (Pol II), the histone variant H2A.Z, and the histone modification H3K4me3 using ChIP-seq and ChIP-exo. In this Data Descriptor, we present detailed information on parallel experimental design, data generation, quality control analysis, and data validation. We discuss how these data lay the foundation for future analysis to understand the relationship between the occupancy of Pol II and nucleosome positions at near base pair resolution.

  13. Experimental binding energies for the metal complexes [Mg(CH3OH)n](2+), [Ca(CH3OH)n](2+), and [Sr(CH3OH)n](2+) for n in the range 4-20.

    PubMed

    Bruzzi, E; Stace, A J

    2014-10-09

    A supersonic source of clusters has been used to prepare neutral complexes of methanol in association with an alkaline earth metal atom. From these complexes the following metal-containing dications have been generated through electron ionization: [Mg(CH3OH)n](2+), [Ca(CH3OH)n](2+), and [Sr(CH3OH)n](2+), and for n in the range 4-20, kinetic energy release measurements following the evaporation of a single molecule have been undertaken using a high resolution mass spectrometer. Using finite heat bath theory, these data have been transformed into binding energies for individual methanol molecules attached to each of the three cluster systems. In the larger complexes (n > 6) the results exhibit a consistent trend, whereby the experimental binding energy data for all three metal ions are similar, suggesting that the magnitude of the charge rather than charge density influences the strength of the interaction. From a comparison with data recorded previously for (CH3OH)nH(+) it is found that the 2+ charge on a metal ion has an effect on the binding energy of molecules in complexes containing up to 20 solvent molecules. The results recorded for [Ca(CH3OH)n](2+) show evidence of a very marked transition between n = 6 and 7, which is thought to coincide with the completion of a primary solvation shell and the onset of molecules starting to occupy a second and most probably a third shell.

  14. Chætognath transcriptome reveals ancestral and unique features among bilaterians

    PubMed Central

    Marlétaz, Ferdinand; Gilles, André; Caubit, Xavier; Perez, Yvan; Dossat, Carole; Samain, Sylvie; Gyapay, Gabor; Wincker, Patrick; Le Parco, Yannick

    2008-01-01

    Background The chætognaths (arrow worms) have puzzled zoologists for years because of their astonishing morphological and developmental characteristics. Despite their deuterostome-like development, phylogenomic studies recently positioned the chætognath phylum in protostomes, most likely in an early branching. This key phylogenetic position and the peculiar characteristics of chætognaths prompted further investigation of their genomic features. Results Transcriptomic and genomic data were collected from the chætognath Spadella cephaloptera through the sequencing of expressed sequence tags and genomic bacterial artificial chromosome clones. Transcript comparisons at various taxonomic scales emphasized the conservation of a core gene set and phylogenomic analysis confirmed the basal position of chætognaths among protostomes. A detailed survey of transcript diversity and individual genotyping revealed a past genome duplication event in the chætognath lineage, which was, surprisingly, followed by a high retention rate of duplicated genes. Moreover, striking genetic heterogeneity was detected within the sampled population at the nuclear and mitochondrial levels but cannot be explained by cryptic speciation. Finally, we found evidence for trans-splicing maturation of transcripts through splice-leader addition in the chætognath phylum and we further report that this processing is associated with operonic transcription. Conclusion These findings reveal both shared ancestral and unique derived characteristics of the chætognath genome, which suggests that this genome is likely the product of a very original evolutionary history. These features promote chætognaths as a pivotal model for comparative genomics, which could provide new clues for the investigation of the evolution of animal genomes. PMID:18533022

  15. High-resolution sub-Doppler infrared spectroscopy of atmospherically relevant Criegee precursor CH2I radicals: CH2 stretch vibrations and "charge-sloshing" dynamics

    NASA Astrophysics Data System (ADS)

    Kortyna, A.; Lesko, D. M. B.; Nesbitt, D. J.

    2018-05-01

    The combination of a pulsed supersonic slit-discharge source and single-mode difference frequency direct absorption infrared spectroscopy permit first high resolution infrared study of the iodomethyl (CH2I) radical, with the CH2I radical species generated in a slit jet Ne/He discharge and cooled to 16 K in the supersonic expansion. Dual laser beam detection and collisional collimation in the slit expansion yield sub-Doppler linewidths (60 MHz), an absolute frequency calibration of 13 MHz, and absorbance sensitivities within a factor of two of the shot-noise limit. Fully rovibrationally resolved direct absorption spectra of the CH2 symmetric stretch mode (ν2) are obtained and fitted to a Watson asymmetric top Hamiltonian with electron spin-rotation coupling, providing precision rotational constants and spin-rotation tensor elements for the vibrationally excited state. Analysis of the asymmetric top rotational constants confirms a vibrationally averaged planar geometry in both the ground- and first-excited vibrational levels. Sub-Doppler resolution permits additional nuclear spin hyperfine structures to be observed, with splittings in excellent agreement with microwave measurements on the ground state. Spectroscopic data on CH2I facilitate systematic comparison with previous studies of halogen-substituted methyl radicals, with the periodic trends strongly correlated with the electronegativity of the halogen atom. Interestingly, we do not observe any asymmetric CH2 stretch transitions, despite S/N ≈ 25:1 on strongest lines in the corresponding symmetric CH2 stretch manifold. This dramatic reversal of the more typical 3:1 antisymmetric/symmetric CH2 stretch intensity ratio signals a vibrational transition moment poorly described by simple "bond-dipole" models. Instead, the data suggest that this anomalous intensity ratio arises from "charge sloshing" dynamics in the highly polar carbon-iodine bond, as supported by ab initio electron differential density plots and

  16. Limitations and possibilities of low cell number ChIP-seq

    PubMed Central

    2012-01-01

    Background Chromatin immunoprecipitation coupled with high-throughput DNA sequencing (ChIP-seq) offers high resolution, genome-wide analysis of DNA-protein interactions. However, current standard methods require abundant starting material in the range of 1–20 million cells per immunoprecipitation, and remain a bottleneck to the acquisition of biologically relevant epigenetic data. Using a ChIP-seq protocol optimised for low cell numbers (down to 100,000 cells / IP), we examined the performance of the ChIP-seq technique on a series of decreasing cell numbers. Results We present an enhanced native ChIP-seq method tailored to low cell numbers that represents a 200-fold reduction in input requirements over existing protocols. The protocol was tested over a range of starting cell numbers covering three orders of magnitude, enabling determination of the lower limit of the technique. At low input cell numbers, increased levels of unmapped and duplicate reads reduce the number of unique reads generated, and can drive up sequencing costs and affect sensitivity if ChIP is attempted from too few cells. Conclusions The optimised method presented here considerably reduces the input requirements for performing native ChIP-seq. It extends the applicability of the technique to isolated primary cells and rare cell populations (e.g. biobank samples, stem cells), and in many cases will alleviate the need for cell culture and any associated alteration of epigenetic marks. However, this study highlights a challenge inherent to ChIP-seq from low cell numbers: as cell input numbers fall, levels of unmapped sequence reads and PCR-generated duplicate reads rise. We discuss a number of solutions to overcome the effects of reducing cell number that may aid further improvements to ChIP performance. PMID:23171294

  17. An eight-dimensional quantum dynamics study of the Cl + CH{sub 4}→ HCl + CH{sub 3} reaction

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Liu, Na; Yang, Minghui, E-mail: yangmh@wipm.ac.cn

    2015-10-07

    In this work, the later-barrier reaction Cl + CH{sub 4} → HCl + CH{sub 3} is investigated with an eight-dimensional quantum dynamics method [R. Liu et al., J. Chem. Phys. 137, 174113 (2012)] on the ab initio potential energy surface of Czakó and Bowman [J. Chem. Phys. 136, 044307 (2012)]. The reaction probabilities with CH{sub 4} initially in its ground and vibrationally excited states are calculated with a time-dependent wavepacket method. The theoretical integral cross sections (ICSs) are extensively compared with the available experimental measurements. For the ground state reaction, the theoretical ICSs excellently agree with the experimental ones. Themore » good agreements are also achieved for ratios between ICSs of excited reactions. For ICS ratios between various states, the theoretical values are also consistent with the experimental observations. The rate constants over 200-2000 K are calculated and the non-Arrhenius effect has been observed which is coincident with the previous experimental observations and theoretical calculations.« less

  18. ChIPBase: a database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data.

    PubMed

    Yang, Jian-Hua; Li, Jun-Hao; Jiang, Shan; Zhou, Hui; Qu, Liang-Hu

    2013-01-01

    Long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) represent two classes of important non-coding RNAs in eukaryotes. Although these non-coding RNAs have been implicated in organismal development and in various human diseases, surprisingly little is known about their transcriptional regulation. Recent advances in chromatin immunoprecipitation with next-generation DNA sequencing (ChIP-Seq) have provided methods of detecting transcription factor binding sites (TFBSs) with unprecedented sensitivity. In this study, we describe ChIPBase (http://deepbase.sysu.edu.cn/chipbase/), a novel database that we have developed to facilitate the comprehensive annotation and discovery of transcription factor binding maps and transcriptional regulatory relationships of lncRNAs and miRNAs from ChIP-Seq data. The current release of ChIPBase includes high-throughput sequencing data that were generated by 543 ChIP-Seq experiments in diverse tissues and cell lines from six organisms. By analysing millions of TFBSs, we identified tens of thousands of TF-lncRNA and TF-miRNA regulatory relationships. Furthermore, two web-based servers were developed to annotate and discover transcriptional regulatory relationships of lncRNAs and miRNAs from ChIP-Seq data. In addition, we developed two genome browsers, deepView and genomeView, to provide integrated views of multidimensional data. Moreover, our web implementation supports diverse query types and the exploration of TFs, lncRNAs, miRNAs, gene ontologies and pathways.

  19. Large CH4 production fueled by autochthonous OC in an anoxic sediment

    NASA Astrophysics Data System (ADS)

    Grasset, Charlotte; Mendonça, Raquel; Villamor Saucedo, Gabriella; Sobek, Sebastian

    2017-04-01

    River damming and human-induced eutrophication both affect river and lake functioning, increase organic carbon (OC) sedimentation rates and generate anoxic conditions in bottom waters. Under these conditions, OC in sediments is decomposed into CO2 and CH4, a high potential greenhouse gas. It has been shown that the decomposition of land-derived (allochthonous) OC is inhibited at anoxic conditions, compared to OC internally produced (autochthonous). However, the overall extent and end products (CO2 or CH4) of anoxic decomposition remain poorly known for different types of OC, making it difficult to judge the effect of river damming and eutrophication on greenhouse gas emissions from inland waters. We incubated different types of allochthonous OC (terrestrial plants) and autochthonous OC (phytoplankton and aquatic vascular plants) in an anoxic sediment during 130 days. We aimed to test 1) if this addition of relatively fresh OC resulted in an increase of CH4 production and 2) if autochthonous OC would produce more CH4 than allochthonous OC. We assessed the contribution to CH4 production of the different OC sources (i.e. sediment or added OC) with stable isotope measurements. We found that the addition of relatively fresh OC greatly increased CH4 production. Autochthonous OC generally produced more CH4 than allochthonous OC, but the overall extent of CH4 production was highly variable between the different autochthonous OC types. The d13C-CH4 measurements indicated that CH4 originated exclusively from the added OC. We conclude that the production of CH4 is likely to to be high in eutrophic as well as in artificial lakes, especially when these systems have anoxic bottom waters and high internal primary productivity and thus a high supply of autochthonous OC to the sediment. The current expansion of reservoir construction in concert with almost globally prevalent anthropogenic eutrophication are therefore likely to increase CH4 production in inland waters.

  20. Warming Early Mars With CH4

    NASA Astrophysics Data System (ADS)

    Justh, H. L.; Kasting, J. F.

    2002-12-01

    The nature of the ancient climate of Mars remains one of the fundamental unresolved problems in martian research. While the present environment is hostile to life, images from the Mariner, Viking and Mars Global Surveyor missions, have shown geologic features on the martian surface that seem to indicate an earlier period of hydrologic activity. The fact that ancient valley networks and degraded craters have been seen on the martian surface indicates that the early martian climate may have been more Earth-like, with a warmer surface temperature. The presence of liquid water would require a greenhouse effect much larger than needed at present, as the solar constant, S0, was 25% lower 3.8 billion years ago when the channels are thought to have formed (1,2). Previous calculations have shown that gaseous CO2 and H2O alone could not have warmed the martian surface to the temperature needed to account for the presence of liquid water (3). It has been hypothesized that a CO2-H2O atmosphere could keep early Mars warm if it was filled with CO2 ice clouds in the upper martian troposphere (4). Obtaining mean martian surface temperatures above 273 K would require nearly 100% cloud cover, a condition that is unrealistic for condensation clouds on early Mars. Any reduction in cloud cover makes it difficult to achieve warm martian surface temperatures except at high pressures and CO2 clouds could cool the martian surface if they were low and optically thick (5). CO2 and CH4 have been suggested as important greenhouse gases on the early Earth. Our research focuses on the effects of increased concentrations of atmospheric greenhouse gases on the surface temperature of early Mars, with emphasis on the reduced greenhouse gas, CH4. To investigate the possible warming effect of CH4, we modified a one-dimensional, radiative-convective climate model used in previous studies of the early martian climate (5). New cloud-free temperature profiles for various surface pressures and CH4 mixing

  1. Was Early Mars Warmed by CH4?

    NASA Astrophysics Data System (ADS)

    Justh, H. L.; Kasting, J. F.

    2001-12-01

    Images from the Mariner, Viking and Mars Global Surveyor missions have shown geologic features on the Martian surface that seem to indicate an earlier period of hydrologic activity. Many researchers have suggested that the early Martian climate was more Earth-like with a Ts of 273 K or higher. The presence of liquid water would require a greenhouse effect much larger than needed at present since S0 is 25% lower 3.8 billion years ago when the channels are thought to have formed. Research into the effects of CO2 clouds upon the climate of early Mars have yielded results that would not effectively warm the surface to the temperature needed to account for the presence of liquid water. Forget and Pierrehumbert (Science, 1997) showed that large crystals of CO2 ice in clouds that form in the upper troposphere would produce a strong warming effect. Obtaining mean surface temperatures above 273 K would require 100% cloud cover, a condition that is unrealistic for early Mars. It has also been shown that any reduction in cloud cover makes it difficult to achieve warm Martian surface temperatures except at high pressures. CO2 clouds could also cool the Martian surface if they were low and optically thick. CO2 ice may be hard to nucleate, leading to the formation of very large particles (Glandorf, private communication). CH4 has been suggested as an important greenhouse gas on the early Earth. This has led us to look at CH4 as a potential solution to the early Mars climate issue. To investigate the possible warming effect of CH4, we utilized a modified, one-dimensional, radiative-convective climate model that has been used in previous studies of the early Martian climate. New calculations of the effects of CH4 upon the early Martian climate will be presented. The use of CH4 to warm the surface of early Mars does not necessarily imply the presence of life on Mars. Abiotic sources of CH4, such as serpentinization of ultramafic rocks, could supply the concentrations needed to warm

  2. Cationic and Neutral Cp*M(NO)(κ2-Ph2PCH2CH2PPh2) Complexes of Molybdenum and Tungsten: Lewis-Acid-Induced Intramolecular C-H Activation.

    PubMed

    Handford, Rex C; Wakeham, Russell J; Patrick, Brian O; Legzdins, Peter

    2017-03-20

    Treatment of CH 2 Cl 2 solutions of Cp*M(NO)Cl 2 (Cp* = η 5 -C 5 (CH 3 ) 5 ; M = Mo, W) first with 2 equiv of AgSbF 6 in the presence of PhCN and then with 1 equiv of Ph 2 PCH 2 CH 2 PPh 2 affords the yellow-orange salts [Cp*M(NO)(PhCN)(κ 2 -Ph 2 PCH 2 CH 2 PPh 2 )](SbF 6 ) 2 in good yields (M = Mo, W). Reduction of [Cp*M(NO)(PhCN)(κ 2 -Ph 2 PCH 2 CH 2 PPh 2 )](SbF 6 ) 2 with 2 equiv of Cp 2 Co in C 6 H 6 at 80 °C produces the corresponding 18e neutral compounds, Cp*M(NO)(κ 2 -Ph 2 PCH 2 CH 2 PPh 2 ) which have been isolated as analytically pure orange-red solids. The addition of 1 equiv of the Lewis acid, Sc(OTf) 3 , to solutions of Cp*M(NO)(κ 2 -Ph 2 PCH 2 CH 2 PPh 2 ) at room temperature results in the immediate formation of thermally stable Cp*M(NO→Sc(OTf) 3 )(H)(κ 3 -(C 6 H 4 )PhPCH 2 CH 2 PPh 2 ) complexes in which one of the phenyl substituents of the Ph 2 PCH 2 CH 2 PPh 2 ligands has undergone intramolecular orthometalation. In a similar manner, addition of BF 3 produces the analogous Cp*M(NO→BF 3 )(H)(κ 3 -(C 6 H 4 )PhPCH 2 CH 2 PPh 2 ) complexes. In contrast, B(C 6 F 5 ) 3 forms the 1:1 Lewis acid-base adducts, Cp*M(NO→B(C 6 F 5 ) 3 )(κ 2 -Ph 2 PCH 2 CH 2 PPh 2 ) in CH 2 Cl 2 at room temperature. Upon warming to 80 °C, Cp*Mo(NO→B(C 6 F 5 ) 3 )(κ 2 -Ph 2 PCH 2 CH 2 PPh 2 ) converts cleanly to the orthometalated product Cp*Mo(NO→B(C 6 F 5 ) 3 )(H)(κ 3 -(C 6 H 4 )PhPCH 2 CH 2 PPh 2 ), but Cp*W(NO→B(C 6 F 5 ) 3 )(κ 2 -Ph 2 PCH 2 CH 2 PPh 2 ) generates a mixture of products whose identities remain to be ascertained. Attempts to extend this chemistry to include related Ph 2 PCH 2 PPh 2 compounds have had only limited success. All new complexes have been characterized by conventional spectroscopic and analytical methods, and the solid-state molecular structures of most of them have been established by single-crystal X-ray crystallographic analyses.

  3. Uncovering the CH-53E Doppler Myth

    DTIC Science & Technology

    2008-01-01

    The Corps’ Changing Super Stallion 8 Helicopter Night Vision System 9 Heads-Up Display (BUD) 9 The Infamous Doppler 12 )FUTURE SOLUTIONS 14 Universal...ABSTRACTION FROM, OR REPRODUCTION OF ALL OR ANY PART OF THIS DOCUMENT IS PERMITTED PROVIDED PROPER ACKNOWLEDGEMENT IT MADE. List ofIllustrations Page...remains intimately familiar to those flying the Marine Corps’ CH-53E "Super Stallion " today. Fortunately, the CH.-53Es flown throughout the world today

  4. Collisional excitation of CH2 rotational/fine-structure levels by helium

    NASA Astrophysics Data System (ADS)

    Dagdigian, P. J.; Lique, F.

    2018-02-01

    Accurate determination of the abundance of CH2 in interstellar media relies on both radiative and collisional rate coefficients. We investigate here the rotational/fine-structure excitation of CH2 induced by collisions with He. We employ a recoupling technique to generate fine-structure-resolved cross-sections and rate coefficients from close coupling spin-free scattering calculations. The calculations are based on a recent, high-accuracy CH2-He potential energy surface computed at the coupled clusters level of theory. The collisional cross-section calculations are performed for all fine-structure transitions among the first 22 and 24 energy levels of ortho- and para-CH2, respectively, and for temperatures up to 300 K. As a first application, we simulate the excitation of CH2 in typical molecular clouds. The excitation temperatures of the CH2 lines are found to be small at typical densities of molecular clouds, showing that the non-local thermodynamic equilibrium approach has to be used to analyse interstellar spectra. We also found that the fine-structure lines connected with the 404 - 313 and 505 - 414 rotational transitions show possible maser emissions so that they can be easily seen in emission. These calculations show that CH2 may have to be detected mainly through absorption spectra.

  5. WETTING STIMULATES ATMOSPHERIC CH4 OXIDATION BY ALPINE SOIL (R823442)

    EPA Science Inventory

    Studies were done to assess the effects of soil moisture manipulations on CH4 oxidation in soils from a dry alpine tundra site. When water was added to these soils there was a stimulation of CH4 oxidation. This stimulation of CH4 oxidation took ti...

  6. Above- and belowground fluxes of CH4 from boreal shrubs and Scots pine

    NASA Astrophysics Data System (ADS)

    Halmeenmäki, Elisa; Heinonsalo, Jussi; Santalahti, Minna; Putkinen, Anuliina; Fritze, Hannu; Pihlatie, Mari

    2016-04-01

    Boreal upland forests are considered as an important sink for the greenhouse gas methane (CH4) due to CH4 oxidizing microbes in the soil. However, recent evidence suggests that vegetation can act as a significant source of CH4. Also, preliminary measurements indicate occasional emissions of CH4 above the tree canopies of a boreal forest. Nevertheless, the sources and the mechanisms of the observed CH4 emissions are still mostly unknown. Furthermore, the majority of CH4 flux studies have been conducted with the soil chamber method, thus not considering the role of the vegetation itself. We conducted a laboratory experiment to study separately the above- and belowground CH4 fluxes of bilberry (Vaccinium myrtillus), lingonberry (Vaccinium vitis-idaea), heather (Calluna vulgaris), and Scots pine (Pinus sylvestris), which were grown in microcosms. The above- and belowground fluxes of the plants were measured separately, and these fluxes were compared to fluxes of microcosms containing only humus soil. In addition to the flux measurements, we analysed the CH4 producing archaea (methanogens) and the CH4 consuming bacteria (methanotrophs) with the qPCR method to discover whether these microbes contribute to the CH4 exchange from the plant material and the soil. The results of the flux measurements indicate that the humus soil with roots of lingonberry, heather, and Scots pine consume CH4 compared to bare humus soil. Simultaneously, the shoots of heather and Scots pine emit small amounts of CH4. We did not find detectable amounts of methanogens from any of the samples, suggesting the produced CH4 could be of non-microbial origin, or produced by very small population of methanogens. Based on the first preliminary results, methanotrophs were present in all the studied plant species, and especially in high amounts in the rooted soils, thus implying that the methanotrophs could be responsible of the CH4 uptake in the root-soil systems.

  7. A Time-Dependent Quantum Dynamics Study of the H2 + CH3 yields H + CH4 Reaction

    NASA Technical Reports Server (NTRS)

    Wang, Dunyou; Kwak, Dochan (Technical Monitor)

    2002-01-01

    We present a time-dependent wave-packet propagation calculation for the H2 + CH3 yields H + CH4 reaction in six degrees of freedom and for zero total angular momentum. Initial state selected reaction probability for different initial rotational-vibrational states are presented in this study. The cumulative reaction probability (CRP) is obtained by summing over initial-state-selected reaction probability. The energy-shift approximation to account for the contribution of degrees of freedom missing in the 6D calculation is employed to obtain an approximate full-dimensional CRP. Thermal rate constant is compared with different experiment results.

  8. High Resolution Direct Frequency Comb Spectroscopy of Vinyl Bromide (C_2H_3Br) and Nitromethane (CH_3NO_2) in the CH Stretch Region

    NASA Astrophysics Data System (ADS)

    Changala, Bryan; Spaun, Ben; Patterson, David; Ye, Jun

    2016-06-01

    We present high resolution rovibrational spectra of buffer gas cooled vinyl bromide (C_2H_3Br) and nitromethane (CH_3NO_2) in the 3 μm CH stretch region, acquired via cavity-enhanced direct frequency comb absorption spectroscopy. The ˜10 K translational and rotational temperatures of the molecular gas, as well as the narrow linewidth of the frequency comb, yield well resolved rotational structure, isotope shifts, and nuclear hyperfine splittings. Given the wide bandwidth of the light source and the long path length of the enhancement cavity, we measure entire vibrational bands in a single shot with high signal-to-noise ratios. We discuss spectra of the entire fundamental CH stretch manifolds of both C_2H_3Br and CH_3NO_2, which provide contrasting examples of rovibrational structure of rigid and non-rigid systems. C_2H_3Br is a relatively normal asymmetric top, exhibiting local perturbations to its rotational structure. Conversely, CH_3NO_2 contains an essentially unhindered methyl rotor. Of particular interest are its quasi-degenerate asymmetric CH stretch modes. Here, one must consider multiple couplings between torsional, rotational, and vibrational angular momentum, leading to qualitatively new level patterns and structure.

  9. Selective Generation of the Radical Cation Isomers [CH3CN](•+) and [CH2CNH](•+) via VUV Photoionization of Different Neutral Precursors and Their Reactivity with C2H4.

    PubMed

    Polášek, Miroslav; Zins, Emilie-Laure; Alcaraz, Christian; Žabka, Ján; Křížová, Věra; Giacomozzi, Linda; Tosi, Paolo; Ascenzi, Daniela

    2016-07-14

    Experimental and theoretical studies have been carried out to demonstrate the selective generation of two different C2H3N(+) isomers, namely, the acetonitrile [CH3CN](•+) and the ketenimine [CH2CNH](•+) radical cations. Photoionization and dissociative photoionization experiments from different neutral precursors (acetonitrile and butanenitrile) have been performed using vacuum ultraviolet (VUV) synchrotron radiation in the 10-15 eV energy range, delivered by the DESIRS beamline at the SOLEIL storage ring. For butanenitrile (CH3CH2CH2CN) an experimental ionization threshold of 11.29 ± 0.05 eV is obtained, whereas the appearance energy for the formation of [CH2CNH](•+) fragments is 11.52 ± 0.05 eV. Experimental findings are fully supported by theoretical calculations at the G4 level of theory (ZPVE corrected energies at 0 K), giving a value of 11.33 eV for the adiabatic ionization energy of butanenitrile and an exothermicity of 0.49 for fragmentation into [CH2CNH](•+) plus C2H4, hampered by an energy barrier of 0.29 eV. The energy difference between [CH3CN](•+) and [CH2CNH](•+) is 2.28 eV (with the latter being the lowest energy isomer), and the isomerization barrier is 0.84 eV. Reactive monitoring experiments of the [CH3CN](•+) and [CH2CNH](•+) isomers with C2H4 have been performed using the CERISES guided ion beam tandem mass spectrometer and exploiting the selectivity of ethylene that gives exothermic charge exchange and proton transfer reactions with [CH3CN](•+) but not with [CH2CNH](•+) isomers. In addition, minor reactive channels are observed leading to the formation of new C-C bonds upon reaction of [CH3CN](•+) with C2H4, and their astrochemical implications are briefly discussed.

  10. Interaction of antitumor drug Sn(CH 3) 2Cl 2 with DNA and RNA

    NASA Astrophysics Data System (ADS)

    Nafisi, Shohreh; Sobhanmanesh, Amir; Esm-Hosseini, Majid; Alimoghaddam, Kamran; Tajmir-Riahi, Heidar Ali

    2005-08-01

    Sn(CH3)2Cl2 exerts its antitumor activity in a specific way. Unlike anticancer cis-Pt(NH3)2Cl2 drug which binds strongly to the nitrogen atoms of DNA bases, Sn(CH3)2Cl2 shows no major affinity towards base binding. Thus, the mechanism of action by which tinorganometallic compounds exert antitumor activity would be different from that of the cisplatin drug. The aim of this study was to examine the binding of Sn(CH3)2Cl2 with calf thymus DNA and yeast RNA in aqueous solutions at pH 7.1-6.6 with constant concentrations of DNA and RNA and various molar ratios of Sn(CH3)2Cl2/DNA (phosphate) and Sn(CH3)2Cl2/RNA of 1/40, 1/20, 1/10, 1/5. Fourier transform infrared (FTIR) and UV-visible difference spectroscopic methods were used to determine the Sn(CH3)2Cl2 binding mode, binding constant, sequence selectivity and structural variations of Sn(CH3)2Cl2/DNA and Sn(CH3)2Cl2/RNA complexes in aqueous solution. Sn(CH3)2Cl2 hydrolyzes in water to give Sn(CH3)2(OH)2 and [Sn(CH3)2(OH)(H2O)n]+ species. Spectroscopic evidence showed that interaction occurred mainly through (CH3)2Sn(IV) hydroxide and polynucleotide backbone phosphate group with overall binding constant of K(Sn(CH3)2Cl2-DNA)=1.47×105 M-1 and K(Sn(CH3)2Cl2-RNA)=7.33×105 M-1. Sn(CH3)2Cl2 induced no biopolymer conformational changes with DNA remaining in the B-family structure and RNA in A-conformation upon drug complexation.

  11. Palladium-catalysed electrophilic aromatic C-H fluorination

    NASA Astrophysics Data System (ADS)

    Yamamoto, Kumiko; Li, Jiakun; Garber, Jeffrey A. O.; Rolfes, Julian D.; Boursalian, Gregory B.; Borghs, Jannik C.; Genicot, Christophe; Jacq, Jérôme; van Gastel, Maurice; Neese, Frank; Ritter, Tobias

    2018-02-01

    Aryl fluorides are widely used in the pharmaceutical and agrochemical industries, and recent advances have enabled their synthesis through the conversion of various functional groups. However, there is a lack of general methods for direct aromatic carbon-hydrogen (C-H) fluorination. Conventional methods require the use of either strong fluorinating reagents, which are often unselective and difficult to handle, such as elemental fluorine, or less reactive reagents that attack only the most activated arenes, which reduces the substrate scope. A method for the direct fluorination of aromatic C-H bonds could facilitate access to fluorinated derivatives of functional molecules that would otherwise be difficult to produce. For example, drug candidates with improved properties, such as increased metabolic stability or better blood-brain-barrier penetration, may become available. Here we describe an approach to catalysis and the resulting development of an undirected, palladium-catalysed method for aromatic C-H fluorination using mild electrophilic fluorinating reagents. The reaction involves a mode of catalysis that is unusual in aromatic C-H functionalization because no organometallic intermediate is formed; instead, a reactive transition-metal-fluoride electrophile is generated catalytically for the fluorination of arenes that do not otherwise react with mild fluorinating reagents. The scope and functional-group tolerance of this reaction could provide access to functional fluorinated molecules in pharmaceutical and agrochemical development that would otherwise not be readily accessible.

  12. E2 and SN2 Reactions of X(-) + CH3CH2X (X = F, Cl); an ab Initio and DFT Benchmark Study.

    PubMed

    Bento, A Patrícia; Solà, Miquel; Bickelhaupt, F Matthias

    2008-06-01

    We have computed consistent benchmark potential energy surfaces (PESs) for the anti-E2, syn-E2, and SN2 pathways of X(-) + CH3CH2X with X = F and Cl. This benchmark has been used to evaluate the performance of 31 popular density functionals, covering local-density approximation, generalized gradient approximation (GGA), meta-GGA, and hybrid density-functional theory (DFT). The ab initio benchmark has been obtained by exploring the PESs using a hierarchical series of ab initio methods [up to CCSD(T)] in combination with a hierarchical series of Gaussian-type basis sets (up to aug-cc-pVQZ). Our best CCSD(T) estimates show that the overall barriers for the various pathways increase in the order anti-E2 (X = F) < SN2 (X = F) < SN2 (X = Cl) ∼ syn-E2 (X = F) < anti-E2 (X = Cl) < syn-E2 (X = Cl). Thus, anti-E2 dominates for F(-) + CH3CH2F, and SN2 dominates for Cl(-) + CH3CH2Cl, while syn-E2 is in all cases the least favorable pathway. Best overall agreement with our ab initio benchmark is obtained by representatives from each of the three categories of functionals, GGA, meta-GGA, and hybrid DFT, with mean absolute errors in, for example, central barriers of 4.3 (OPBE), 2.2 (M06-L), and 2.0 kcal/mol (M06), respectively. Importantly, the hybrid functional BHandH and the meta-GGA M06-L yield incorrect trends and qualitative features of the PESs (in particular, an erroneous preference for SN2 over the anti-E2 in the case of F(-) + CH3CH2F) even though they are among the best functionals as measured by their small mean absolute errors of 3.3 and 2.2 kcal/mol in reaction barriers. OLYP and B3LYP have somewhat higher mean absolute errors in central barriers (5.6 and 4.8 kcal/mol, respectively), but the error distribution is somewhat more uniform, and as a consequence, the correct trends are reproduced.

  13. Rhodium-catalyzed C-H functionalization with N-acylsaccharins.

    PubMed

    Wu, Hongxiang; Liu, Tingting; Cui, Ming; Li, Yue; Jian, Junsheng; Wang, Hui; Zeng, Zhuo

    2017-01-18

    A rhodium-catalyzed C-H functionalization with activated amides by decarbonylation has been developed. Notably, this is the first C-H arylation employing N-acylsaccharins as coupling partners to give biaryls in good to excellent yields. The highlight of the work is the high tolerance of functional groups such as formyl, ester, and vinyl and the use of a removable directing group.

  14. Direct production of OH radicals upon CH overtone activation of (CH{sub 3}){sub 2}COO Criegee intermediates

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Liu, Fang; Beames, Joseph M.; Lester, Marsha I., E-mail: milester@sas.upenn.edu

    2014-12-21

    Ozonolysis of alkenes, a principle non-photolytic source of atmospheric OH radicals, proceeds through unimolecular decay of energized carbonyl oxide intermediates, known as Criegee intermediates. In this work, cold dimethyl-substituted Criegee intermediates are vibrationally activated in the CH stretch overtone region to drive the 1,4 hydrogen transfer reaction that leads to OH radical products. IR excitation of (CH{sub 3}){sub 2}COO reveals the vibrational states with sufficient oscillator strength, coupling to the reaction coordinate, and energy to surmount the effective barrier (≤ 16.0 kcal mol{sup −1}) to reaction. Insight on the dissociation dynamics is gleaned from homogeneous broadening of the spectral features,more » indicative of rapid intramolecular vibrational energy redistribution and/or reaction, as well as the quantum state distribution of the OH X{sup 2}Π (v = 0) products. The experimental results are compared with complementary electronic structure calculations, which provide the IR absorption spectrum and geometric changes along the intrinsic reaction coordinate. Additional theoretical analysis reveals the vibrational modes and couplings that permit (CH{sub 3}){sub 2}COO to access to the transition state region for reaction. The experimental and theoretical results are compared with an analogous recent study of the IR activation of syn-CH{sub 3}CHOO and its unimolecular decay to OH products [F. Liu, J. M. Beames, A. S. Petit, A. B. McCoy, and M. I. Lester, Science 345, 1596 (2014)].« less

  15. Towards mild metal-catalyzed C-H bond activation.

    PubMed

    Wencel-Delord, Joanna; Dröge, Thomas; Liu, Fan; Glorius, Frank

    2011-09-01

    Functionalizing traditionally inert carbon-hydrogen bonds represents a powerful transformation in organic synthesis, providing new entries to valuable structural motifs and improving the overall synthetic efficiency. C-H bond activation, however, often necessitates harsh reaction conditions that result in functional group incompatibilities and limited substrate scope. An understanding of the reaction mechanism and rational design of experimental conditions have led to significant improvement in both selectivity and applicability. This critical review summarizes and discusses endeavours towards the development of mild C-H activation methods and wishes to trigger more research towards this goal. In addition, we examine select examples in complex natural product synthesis to demonstrate the synthetic utility of mild C-H functionalization (84 references). This journal is © The Royal Society of Chemistry 2011

  16. ChEVAS: Combining Suprarenal EVAS with Chimney Technique

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Torella, Francesco, E-mail: f.torella@liverpool.ac.uk; Chan, Tze Y., E-mail: tze.chan@rlbuht.nhs.uk; Shaikh, Usman, E-mail: usman.shaikh@rlbuht.nhs.uk

    2015-10-15

    Endovascular sealing with the Nellix{sup ®} endoprosthesis (EVAS) is a new technique to treat infrarenal abdominal aortic aneurysms. We describe the use of endovascular sealing in conjunction with chimney stents for the renal arteries (chEVAS) in two patients, one with a refractory type Ia endoleak and an expanding aneurysm, and one with a large juxtarenal aneurysm unsuitable for fenestrated endovascular repair (EVAR). Both aneurysms were successfully excluded. Our report confirms the utility of chEVAS in challenging cases, where suprarenal seal is necessary. We suggest that, due to lack of knowledge on its durability, chEVAS should only been considered when moremore » conventional treatment modalities (open repair and fenestrated EVAR) are deemed difficult or unfeasible.« less

  17. Estudio del CH interestelar

    NASA Astrophysics Data System (ADS)

    Olano, C.; Lemarchand, G.; Sanz, A. J.; Bava, J. A.

    El objetivo principal de este proyecto consiste en el estudio de la distribución y abundancia del CH en nubes interestelares a través de la observación de las líneas hiperfinas del CH en 3,3 GHz. El CH es una molécula de amplia distribución en el espacio interestelar y una de las pocas especies que han sido observadas tanto con técnicas de radio como ópticas. Desde el punto de vista tecnológico se ha desarrollado un cabezal de receptor que permitirá la realización de observaciones polarimétricas en la frecuencia de 3,3 GHz, con una temperatura del sistema de 60 K y un ancho de banda de 140 MHz, y que será instalado en el foco primario de la antena parabólica del IAR. El cabezal del receptor es capaz de detectar señales polarizadas, separando las componentes de polarización circular derecha e izquierda. Para tal fin el cabezal consta de dos ramas receptoras que amplificarán la señal y la trasladarán a una frecuencia más baja (frecuencia intermedia), permitiendo de esa forma un mejor transporte de la señal a la sala de control para su posterior procesamiento. El receptor además de tener características polarimétricas, podrá ser usado en el continuo y en la línea, utilizando las ventajas observacionales y de procesamiento de señal que actualmente posee el IAR.

  18. Infrared absorption of CH3OSO and CD3OSO radicals produced upon photolysis of CH3OS(O)Cl and CD3OS(O)Cl in p-H2 matrices.

    PubMed

    Lee, Yu-Fang; Kong, Lin-Jun; Lee, Yuan-Pern

    2012-03-28

    Irradiation at 239 ± 20 nm of a p-H(2) matrix containing methoxysulfinyl chloride, CH(3)OS(O)Cl, at 3.2 K with filtered light from a medium-pressure mercury lamp produced infrared (IR) absorption lines at 3028.4 (attributable to ν(1), CH(2) antisymmetric stretching), 2999.5 (ν(2), CH(3) antisymmetric stretching), 2950.4 (ν(3), CH(3) symmetric stretching), 1465.2 (ν(4), CH(2) scissoring), 1452.0 (ν(5), CH(3) deformation), 1417.8 (ν(6), CH(3) umbrella), 1165.2 (ν(7), CH(3) wagging), 1152.1 (ν(8), S=O stretching mixed with CH(3) rocking), 1147.8 (ν(9), S=O stretching mixed with CH(3) wagging), 989.7 (ν(10), C-O stretching), and 714.5 cm(-1) (ν(11), S-O stretching) modes of syn-CH(3)OSO. When CD(3)OS(O)Cl in a p-H(2) matrix was used, lines at 2275.9 (ν(1)), 2251.9 (ν(2)), 2083.3 (ν(3)), 1070.3 (ν(4)), 1056.0 (ν(5)), 1085.5 (ν(6)), 1159.7 (ν(7)), 920.1 (ν(8)), 889.0 (ν(9)), 976.9 (ν(10)), and 688.9 (ν(11)) cm(-1) appeared and are assigned to syn-CD(3)OSO; the mode numbers correspond to those used for syn-CH(3)OSO. The assignments are based on the photolytic behavior and a comparison of observed vibrational wavenumbers, infrared intensities, and deuterium isotopic shifts with those predicted with the B3P86∕aug-cc-pVTZ method. Our results extend the previously reported four transient IR absorption bands of gaseous syn-CH(3)OSO near 2991, 2956, 1152, and 994 cm(-1) to 11 lines, including those associated with C-O, O-S, and S=O stretching modes. Vibrational wavenumbers of syn-CD(3)OSO are new. These results demonstrate the advantage of a diminished cage effect of solid p-H(2) such that the Cl atom, produced via UV photodissociation of CH(3)OS(O)Cl in situ, might escape from the original cage to yield isolated CH(3)OSO radicals.

  19. Helicopter Flying Qualities Characteristics-CH-46E. Volume 1

    DTIC Science & Technology

    1983-10-03

    STABILITY 54 6.0 CONTROL SENSITIVITY 61 . ° i CONTENTS (continued) Page 7.0 TIME HISTORY DATA 65 7.1 GENERAL 65 7.2 DYNAMIC STABILITY 65 7.3 CONTROL...The CH-46E meets these requirements by comfortable margins at the conditions tested. 61 NADC-81118-60 Volume 1 CH-46E (FRB, CONTROL IESPON!SE CH-46E...0 4.- ip L% t ,. _ 5" * ,.4 ••t, EFIGURE 7-5 I 7 ----- 1 FIU- - IA2 NADC-81118-6 Volume I-- .4 . > b in Zh. JI - ag4A 19-- O e t’ c 4 a I,- t

  20. Catalyst- and Reagent-free Electrochemical Azole C-H Amination.

    PubMed

    Qiu, Youai; Struwe, Julia; Meyer, Tjark H; Oliveira, Joao Carlos Agostinho Carlos Agostinho; Ackermann, Lutz

    2018-06-14

    Catalyst-, and chemical oxidant-free electrochemical azole C-H aminations were accomplished via cross-dehydrogenative C-H/N-H functionalization. The catalyst-free electrochemical C-H amination proved feasible on azoles with high levels of efficacy and selectivity, avoiding the use of stoichiometric oxidants under ambient conditions. Likewise, the C(sp3)-H nitrogenation proved viable under otherwise identical conditions. The dehydrogenative C-H amination featured ample scope, including cyclic and acyclic aliphatic amines as well as anilines, and employed sustainable electricity as the sole oxidant. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. Distinct transport properties of O2 and CH4 across a carbon nanotube

    NASA Astrophysics Data System (ADS)

    Meng, Xianwen; Wang, Yu; Zhao, Yanjiao; Huang, Jiping

    2013-04-01

    It is of fundamental importance to investigate either O2 or CH4 molecules across nanochannels in many areas such as breathing or separation. Thus, many researches have focused on such a single type of molecules across nanochannels. However, O2 and CH4 can often appear together and crucially affect human life, say, in a mine. On the basis of molecular dynamics simulations, here we attempt to investigate the mixture of O2 and CH4, in order to identify their different transport properties in a nanochannel. We take a single-walled carbon nanotube (SWCNT) as a model nanochannel, and find that their transport properties are distinctly different. As the concentration of O2 increases up to a high value of 0.8, it is always faster for CH4 molecules to transport across the SWCNT, and the total number of gas molecules transporting across the SWCNT is decreased. Meanwhile, CH4 molecules are always dominant in the SWCNT, and the total number of O2 or CH4 inside the SWCNT is a constant. By calculating the van der Waals interaction between the SWCNT and O2 or CH4, we find that the net interaction between CH4 and the SWCNT is much stronger. Our findings may offer some hints on how to separate CH4 from O2, and/or store CH4 efficiently.

  2. Ion energy distributions and the density of CH3 radicals in a low pressure inductively coupled CH4/H2 plasma used for nanocrystalline diamond deposition

    NASA Astrophysics Data System (ADS)

    Okada, Katsuyuki; Komatsu, Shojiro; Matsumoto, Seiichiro

    2003-11-01

    Ion energy distributions (IEDs) and the density of CH3 radicals (n) in a 13.56 MHz radio frequency (rf) low pressure inductively coupled CH4/H2 plasma used for nanocrystalline diamond deposition have been investigated with a quadrupole mass spectrometer. The energy distributions of positive ions were measured in a CH4/H2 plasma with 50 mTorr of the gas pressure at 500 W of the plasma input power, and were compared with those of an Ar plasma. We have found that the IEDs of Ar+, CH4+, and C2H5+ have a nearly monoenergetic peak, and a hump due to a small degree of capacitive coupling. The plasma potentials obtained from the peaks are consistent with the previously reported values measured with a Langmuir probe. On the other hand, the IEDs of H+, H2+, and H3+ have a clear asymmetric double peak due to the modulation of rf driven glow discharge. The n monotonously increases with increasing pressure. The n indicates that CH3 radicals are main precursors for the growth of nanocrystalline diamond. The estimated sticking coefficient of the CH3 radical is comparable with the reported value.

  3. Atmospheric chemistry of cyc-CF2CF2CF2CH=CH-: Kinetics, products, and mechanism of gas-phase reaction with OH radicals, and atmospheric implications

    NASA Astrophysics Data System (ADS)

    Guo, Qin; Zhang, Ni; Uchimaru, Tadafumi; Chen, Liang; Quan, Hengdao; Mizukado, Junji

    2018-04-01

    The rate constants for the gas-phase reactions of cyc-CF2CF2CF2CH=CH- with OH radicals were determined by a relative rate method between 253 and 328 K. The rate constant k1 at 298 K was measured to be (1.08 ± 0.04) × 10-13 cm3 molecule-1 s-1, and the Arrhenius expression was k1 = (3.72 ± 0.14) × 10-13 exp [(-370 ± 12)/T]. The atmospheric lifetime of cyc-CF2CF2CF2CH=CH- was calculated to be 107 d. The products and mechanism for the reaction of cyc-CF2CF2CF2CH=CH- with OH radicals were also investigated. CO, CO2, and COF2 were identified as the main carbon-containing products following the OH-initiated reaction. Moreover, the radiative efficiency (RE) was determined to be 0.143 W m-2 ppb-1, and the global warming potentials (GWPs) for 20, 100, and 500 yr were 54, 15, and 4, respectively. The photochemical ozone creation potential of the title compound was estimated to be 1.3.

  4. Replacing -CH2CH2- with -CONH- does not significantly change rates of charge transport through Ag(TS)-SAM//Ga2O3/EGaIn junctions.

    PubMed

    Thuo, Martin M; Reus, William F; Simeone, Felice C; Kim, Choongik; Schulz, Michael D; Yoon, Hyo Jae; Whitesides, George M

    2012-07-04

    This paper describes physical-organic studies of charge transport by tunneling through self-assembled monolayers (SAMs), based on systematic variations of the structure of the molecules constituting the SAM. Replacing a -CH(2)CH(2)- group with a -CONH- group changes the dipole moment and polarizability of a portion of the molecule and has, in principle, the potential to change the rate of charge transport through the SAM. In practice, this substitution produces no significant change in the rate of charge transport across junctions of the structure Ag(TS)-S(CH(2))(m)X(CH(2))(n)H//Ga(2)O(3)/EGaIn (TS = template stripped, X = -CH(2)CH(2)- or -CONH-, and EGaIn = eutectic alloy of gallium and indium). Incorporation of the amide group does, however, increase the yields of working (non-shorting) junctions (when compared to n-alkanethiolates of the same length). These results suggest that synthetic schemes that combine a thiol group on one end of a molecule with a group, R, to be tested, on the other (e.g., HS~CONH~R) using an amide-based coupling provide practical routes to molecules useful in studies of molecular electronics.

  5. Ligand-accelerated non-directed C-H functionalization of arenes.

    PubMed

    Wang, Peng; Verma, Pritha; Xia, Guoqin; Shi, Jun; Qiao, Jennifer X; Tao, Shiwei; Cheng, Peter T W; Poss, Michael A; Farmer, Marcus E; Yeung, Kap-Sun; Yu, Jin-Quan

    2017-11-22

    The directed activation of carbon-hydrogen bonds (C-H) is important in the development of synthetically useful reactions, owing to the proximity-induced reactivity and selectivity that is enabled by coordinating functional groups. Palladium-catalysed non-directed C-H activation could potentially enable further useful reactions, because it can reach more distant sites and be applied to substrates that do not contain appropriate directing groups; however, its development has faced substantial challenges associated with the lack of sufficiently active palladium catalysts. Currently used palladium catalysts are reactive only with electron-rich arenes, unless an excess of arene is used, which limits synthetic applications. Here we report a 2-pyridone ligand that binds to palladium and accelerates non-directed C-H functionalization with arene as the limiting reagent. This protocol is compatible with a broad range of aromatic substrates and we demonstrate direct functionalization of advanced synthetic intermediates, drug molecules and natural products that cannot be used in excessive quantities. We also developed C-H olefination and carboxylation protocols, demonstrating the applicability of our methodology to other transformations. The site selectivity in these transformations is governed by a combination of steric and electronic effects, with the pyridone ligand enhancing the influence of sterics on the selectivity, thus providing complementary selectivity to directed C-H functionalization.

  6. Ligand-accelerated non-directed C-H functionalization of arenes

    NASA Astrophysics Data System (ADS)

    Wang, Peng; Verma, Pritha; Xia, Guoqin; Shi, Jun; Qiao, Jennifer X.; Tao, Shiwei; Cheng, Peter T. W.; Poss, Michael A.; Farmer, Marcus E.; Yeung, Kap-Sun; Yu, Jin-Quan

    2017-11-01

    The directed activation of carbon-hydrogen bonds (C-H) is important in the development of synthetically useful reactions, owing to the proximity-induced reactivity and selectivity that is enabled by coordinating functional groups. Palladium-catalysed non-directed C-H activation could potentially enable further useful reactions, because it can reach more distant sites and be applied to substrates that do not contain appropriate directing groups; however, its development has faced substantial challenges associated with the lack of sufficiently active palladium catalysts. Currently used palladium catalysts are reactive only with electron-rich arenes, unless an excess of arene is used, which limits synthetic applications. Here we report a 2-pyridone ligand that binds to palladium and accelerates non-directed C-H functionalization with arene as the limiting reagent. This protocol is compatible with a broad range of aromatic substrates and we demonstrate direct functionalization of advanced synthetic intermediates, drug molecules and natural products that cannot be used in excessive quantities. We also developed C-H olefination and carboxylation protocols, demonstrating the applicability of our methodology to other transformations. The site selectivity in these transformations is governed by a combination of steric and electronic effects, with the pyridone ligand enhancing the influence of sterics on the selectivity, thus providing complementary selectivity to directed C-H functionalization.

  7. Competing E2 and SN2 Mechanisms for the F- + CH3CH2I Reaction.

    PubMed

    Yang, Li; Zhang, Jiaxu; Xie, Jing; Ma, Xinyou; Zhang, Linyao; Zhao, Chenyang; Hase, William L

    2017-02-09

    Anti-E2, syn-E2, inv-, and ret-S N 2 reaction channels for the gas-phase reaction of F - + CH 3 CH 2 I were characterized with a variety of electronic structure calculations. Geometrical analysis confirmed synchronous E2-type transition states for the elimination of the current reaction, instead of nonconcerted processes through E1cb-like and E1-like mechanisms. Importantly, the controversy concerning the reactant complex for anti-E2 and inv-S N 2 paths has been clarified in the present work. A positive barrier of +19.2 kcal/mol for ret-S N 2 shows the least feasibility to occur at room temperature. Negative activation energies (-16.9, -16.0, and -4.9 kcal/mol, respectively) for inv-S N 2, anti-E2, and syn-E2 indicate that inv-S N 2 and anti-E2 mechanisms significantly prevail over the eclipsed elimination. Varying the leaving group for a series of reactions F - + CH 3 CH 2 Y (Y = F, Cl, Br, and I) leads to monotonically decreasing barriers, which relates to the gradually looser TS structures following the order F > Cl > Br > I. The reactivity of each channel nearly holds unchanged except for the perturbation between anti-E2 and inv-S N 2. RRKM calculation reveals that the reaction of the fluorine ion with ethyl iodide occurs predominately via anti-E2 elimination, and the inv-S N 2 pathway is suppressed, although it is energetically favored. This phenomenon indicates that, in evaluating the competition between E2 and S N 2 processes, the kinetic or dynamical factors may play a significant role. By comparison with benchmark CCSD(T) energies, MP2, CAM-B3LYP, and M06 methods are recommended to perform dynamics simulations of the title reaction.

  8. Speciated Monitoring of Gas-Phase Organic Peroxy Radicals by Chemical Ionization Mass Spectrometry: Cross-Reactions between CH3O2, CH3(CO)O2, (CH3)3CO2, and c-C6H11O2.

    PubMed

    Nozière, Barbara; Hanson, David R

    2017-11-09

    Organic peroxy radicals ("RO 2 ", with R organic) are key intermediates in most oxygen-rich systems, where organic compounds are oxidized (natural environment, flames, combustion engines, living organisms, etc). But, until recently, techniques able to monitor simultaneously and distinguish between RO 2 species ("speciated" detection) have been scarce, which has limited the understanding of complex systems containing these radicals. Mass spectrometry using proton transfer ionization has been shown previously to detect individual gas-phase RO 2 separately. In this work, we illustrate its ability to speciate and monitor several RO 2 simultaneously by investigating reactions involving CH 3 O 2 , CH 3 C(O)O 2 , c-C 6 H 11 O 2 , and (CH 3 ) 3 CO 2 . The detection sensitivity of each of these radicals was estimated by titration with NO to between 50 and 1000 Hz/ppb, with a factor from 3 to 5 of uncertainties, mostly due to the uncertainties in knowing the amounts of added NO. With this, the RO 2 concentration in the reactor was estimated between 1 × 10 10 and 1 × 10 12 molecules cm -3 . When adding a second radical species to the reactor, the kinetics of the cross-reaction could be studied directly from the decay of the first radical. The time-evolution of two and sometimes three different RO 2 was followed simultaneously, as the CH 3 O 2 produced in further reaction steps was also detected in some systems. The rate coefficients obtained are (in molecule -1 cm 3 s -1 ): k CH3O2+CH3C(O)O2 = 1.2 × 10 -11 , k CH3O2+t-butylO2 = 3.0 × 10 -15 , k c-hexylO2+CH3O2 = 1.2 × 10 -13 , k t-butylO2+CH3C(O)O2 = 3.7 × 10 -14 , and k c-hexylO2+t-butylO2 = 1.5 × 10 -15 . In spite of their good comparison with the literature and good reproducibility, large uncertainties (×5/5) are recommended on these results because of those in the detection sensitivities. This work is a first illustration of the potential applications of this technique for the investigation of organic radicals in

  9. Synergistic Heterobimetallic Manifold for Expedient Manganese(I)-Catalyzed C-H Cyanation.

    PubMed

    Liu, Weiping; Richter, Sven C; Mei, Ruhuai; Feldt, Milica; Ackermann, Lutz

    2016-12-12

    The manganese-catalyzed cyanation of inert C-H bonds was achieved within a heterobimetallic catalysis regime. The manganese(I) catalysis proved widely applicable and enabled C-H cyanations on indoles, pyrroles and thiophenes by facile C-H manganesation. The robustness of the manganese catalyst set the stage for the racemization-free C-H cyanation of amino acids with excellent levels of positional and chemo selectivity by the new cyanating agent NCFS. Experimental and computational mechanistic studies provided strong support for a synergistic heterobimetallic activation mode, facilitating the key C-C formation. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. CH stretching overtone spectra of trimethyl amine and dimethyl sulfide

    NASA Astrophysics Data System (ADS)

    Billinghurst, Brant E.; Gough, Kathleen M.; Low, Geoffrey R.; Kjaergaard, Henrik G.

    2004-01-01

    Trimethyl amine (TMA) exhibits the largest known difference in CH bond lengths within a methyl group, due to what is known as the lone pair trans effect. Dimethyl sulfide also exhibits this effect, but to a far lesser extent, making it ideal for comparison to TMA. In this paper, the first through fourth overtone spectra of N(CH3)3, N(CD3)3, N(CD2H)(CD3)2, N(CH3)(CD3)2, N(CD3)(CH3)2 and S(CH3)2 are reported and all major bands are assigned. The intensities of the observed bands are compared to intensities predicted by the harmonically coupled anharmonic oscillator local mode model. Good correlation is found between the experimental intensities and those predicted with the local mode model and HF/6-311++G(2d,2p) calculated dipole moment functions. An increase in the ability to resolve peaks as methyl groups are deuterated suggests that the lone pair mediates increased coupling between methyl groups.

  11. CH(X2∏, a4∑-) ... OH2 and CH2(X˜3B1, ã1A1) ... OH2 interactions. A first principles investigation

    NASA Astrophysics Data System (ADS)

    Tzeli, Demeter; Mavridis, Aristides

    We have investigated the interaction of the methylidene, CH(X2∏, a4∑-) and methylene, CH2(X˜3B1, ã1A1) with H2O, employing the (P)MPn (n = 2, 4) techniques in conjunction with the sequence of correlation consistent basis sets aug-cc-pVxZ, x = 2, 3, and 4. For the CH ... OH2 system, we have located four minima (m) and three transition states (ts) and for the CH2 ... OH2, five minima and four transition states. All our results have been corrected for zero-point energy (ZPE) and basis set superposition errors (BSSE), while for the most important m_ structures, we report complete basis set (CBS) interaction limits. We also report fully optimized geometries, harmonic frequencies, dipole moments, Mulliken charges, and potential energy curves. The highest CH(X2∏) ... OH2 (m1_2∏) and CH2(ã1A1) ... OH2 (m1_1A1) interactions are the result of electron transfer from the oxygen atom to the empty pπ orbitals of CH(X2∏) and CH2(ã1A1), respectively (ylide-like structures). At the (P)MP4/AQZ//MP2/ATZ level, including ZPE, BSSE, and CBS extrapolation, we obtain ΔE0(BSSE)+CBS = -9.36 kcal/mol at rC ... O = 1.752 Å, and -9.73 kcal/mol at rC ... O = 1.741 Å for the m1_2∏ and m1_1A1, respectively.

  12. ChREBP regulates fructose-induced glucose production independently of insulin signaling

    PubMed Central

    Kim, Mi-Sung; Krawczyk, Sarah A.; Doridot, Ludivine; Fowler, Alan J.; Wang, Jennifer X.; Trauger, Sunia A.; Noh, Hye-Lim; Kang, Hee Joon; Meissen, John K.; Blatnik, Matthew; Kim, Jason K.; Lai, Michelle; Herman, Mark A.

    2016-01-01

    Obese, insulin-resistant states are characterized by a paradoxical pathogenic condition in which the liver appears to be selectively insulin resistant. Specifically, insulin fails to suppress glucose production, yet successfully stimulates de novo lipogenesis. The mechanisms underlying this dysregulation remain controversial. Here, we hypothesized that carbohydrate-responsive element-binding protein (ChREBP), a transcriptional activator of glycolytic and lipogenic genes, plays a central role in this paradox. Administration of fructose increased hepatic hexose-phosphate levels, activated ChREBP, and caused glucose intolerance, hyperinsulinemia, hypertriglyceridemia, and hepatic steatosis in mice. Activation of ChREBP was required for the increased expression of glycolytic and lipogenic genes as well as glucose-6-phosphatase (G6pc) that was associated with the effects of fructose administration. We found that fructose-induced G6PC activity is a major determinant of hepatic glucose production and reduces hepatic glucose-6-phosphate levels to complete a homeostatic loop. Moreover, fructose activated ChREBP and induced G6pc in the absence of Foxo1a, indicating that carbohydrate-induced activation of ChREBP and G6PC dominates over the suppressive effects of insulin to enhance glucose production. This ChREBP/G6PC signaling axis is conserved in humans. Together, these findings support a carbohydrate-mediated, ChREBP-driven mechanism that contributes to hepatic insulin resistance. PMID:27669460

  13. Microheterogeneity in CH3OH/CD3OH mixture.

    PubMed

    Wrzeszcz, Władysław; Mazurek, Sylwester; Szostak, Roman; Tomza, Paweł; Czarnecki, Mirosław A

    2018-01-05

    Recently, we demonstrated the presence of microheterogeneity in binary mixtures of unlike alcohols. [RSC Adv. 2016, 6, 37195-37202] The aim of this work was examination if this phenomenon occurs also in the mixture of very similar alcohols like CH 3 OH and CD 3 OH. Theoretical calculations suggest that the isotopic substitution in methyl group influences properties of the OH group. Hence, one can expect that this effect may lead to partial separation of CH 3 OH and CD 3 OH at a molecular level and it contributes to deviation from the ideal mixture. This work evidences that CH 3 OH/CD 3 OH mixture also deviates from the ideal one, but the extent of this deviation is much smaller as compared with the mixtures of other alcohols. It is of particular note that this deviation results mainly from the difference between the CH 3 and CD 3 groups, while the contribution from the OH groups is small. The structure of CH 3 OH/CD 3 OH mixture at a molecular level is similar to the structure of binary mixtures of other alcohols. The mixture is composed of the homoclusters of both alcohols and the mixed clusters. The homoclusters existing in the mixture are similar to those present in bulk alcohols. The highest population of the heteroclusters and the largest deviation from the ideal mixture were observed at equimolar mixture. Both the experimental and theoretical results reveal that in CH 3 OH/CD 3 OH mixture dominate the cyclic tetramers and larger clusters, while the population of the linear clusters is negligible. Though the extent and strength of hydrogen bonding in both alcohols are the same, the position and intensity of the 2ν(OH) band for CH 3 OH and CD 3 OH are different. We propose possible explanation of this observation. Copyright © 2017 Elsevier B.V. All rights reserved.

  14. Formation of doubly and triply bonded unsaturated compounds HCN, HNC, and CH2NH via N + CH4 low-temperature solid state reaction: from molecular clouds to solar system objects

    NASA Astrophysics Data System (ADS)

    Mencos, Alejandro; Krim, Lahouari

    2018-06-01

    We show in the current study carried out in solid phase at cryogenic temperatures that methane (CH4) ice exposed to nitrogen atoms is a source of two acids HCN, HNC, and their corresponding hydrogenated unsaturated species CH2NH, in addition to CH3, C2H6, CN-, and three nitrogen hydrides NH, NH2, and NH3. The solid state N + CH4 reaction taken in the ground state seems to be strongly temperature dependent. While at temperatures lower than 10 K only CH3, NH, NH2, and NH3 species formation is promoted due to CH bond dissociation and NH bond formation, stable compounds with CN bonds are formed at temperatures ranged between 10 and 40 K. Many of these reaction products, resulting from CH4 + N reaction, have already been observed in N2-rich regions such as the atmospheres of Titan, Kuiper belt objects, and molecular clouds of the interstellar medium. Our results show the power of the solid state N-atom chemistry in the transformation of simple astrochemical relevant species, such as CH4 molecules and N atoms into complex organic molecules which are also potentially prebiotic species.

  15. Endohedral complexes of fullerene-like silica molecules with H2O, CH4, and CH3NH2 molecules

    NASA Astrophysics Data System (ADS)

    Filonenko, O. V.; Lobanov, V. V.

    2013-07-01

    The possibility of formation of (SiO2)60@H2O, (SiO2)60@CH4, and (SiO2)60@CH3NH2 endohedral complexes was studied by the density functional (DFT) method (B3LYP exchange correlation functional, 6-31G** basis). The penetration of these molecules into the cavity of fullerene-like silica molecules is hindered by high activation barriers, which ensures the stability of the complexes formed during the synthesis of these molecules.

  16. Remote site-selective C-H activation directed by a catalytic bifunctional template

    NASA Astrophysics Data System (ADS)

    Zhang, Zhipeng; Tanaka, Keita; Yu, Jin-Quan

    2017-03-01

    In chemical syntheses, the activation of carbon-hydrogen (C-H) bonds converts them directly into carbon-carbon or carbon-heteroatom bonds without requiring any prior functionalization. C-H activation can thus substantially reduce the number of steps involved in a synthesis. A single specific C-H bond in a substrate can be activated by using a ‘directing’ (usually a functional) group to obtain the desired product selectively. The applicability of such a C-H activation reaction can be severely curtailed by the distance of the C-H bond in question from the directing group, and by the shape of the substrate, but several approaches have been developed to overcome these limitations. In one such approach, an understanding of the distal and geometric relationships between the functional groups and C-H bonds of a substrate has been exploited to achieve meta-selective C-H activation by using a covalently attached, U-shaped template. However, stoichiometric installation of this template has not been feasible in the absence of an appropriate functional group on which to attach it. Here we report the design of a catalytic, bifunctional nitrile template that binds a heterocyclic substrate via a reversible coordination instead of a covalent linkage. The two metal centres coordinated to this template have different roles: one reversibly anchors substrates near the catalyst, and the other cleaves remote C-H bonds. Using this strategy, we demonstrate remote, site-selective C-H olefination of heterocyclic substrates that do not have the necessary functional groups for covalently attaching templates.

  17. Remote site-selective C-H activation directed by a catalytic bifunctional template.

    PubMed

    Zhang, Zhipeng; Tanaka, Keita; Yu, Jin-Quan

    2017-03-23

    In chemical syntheses, the activation of carbon-hydrogen (C-H) bonds converts them directly into carbon-carbon or carbon-heteroatom bonds without requiring any prior functionalization. C-H activation can thus substantially reduce the number of steps involved in a synthesis. A single specific C-H bond in a substrate can be activated by using a 'directing' (usually a functional) group to obtain the desired product selectively. The applicability of such a C-H activation reaction can be severely curtailed by the distance of the C-H bond in question from the directing group, and by the shape of the substrate, but several approaches have been developed to overcome these limitations. In one such approach, an understanding of the distal and geometric relationships between the functional groups and C-H bonds of a substrate has been exploited to achieve meta-selective C-H activation by using a covalently attached, U-shaped template. However, stoichiometric installation of this template has not been feasible in the absence of an appropriate functional group on which to attach it. Here we report the design of a catalytic, bifunctional nitrile template that binds a heterocyclic substrate via a reversible coordination instead of a covalent linkage. The two metal centres coordinated to this template have different roles: one reversibly anchors substrates near the catalyst, and the other cleaves remote C-H bonds. Using this strategy, we demonstrate remote, site-selective C-H olefination of heterocyclic substrates that do not have the necessary functional groups for covalently attaching templates.

  18. The Rotation-Torsion Spectrum of CH_2DOH

    NASA Astrophysics Data System (ADS)

    Hilali, A. El; Coudert, L. H.; Margulès, L.; Motiyenko, R.; Klee, S.

    2010-06-01

    Due to the asymmetry of the CH_2D group, the internal rotation problem in the partially deuterated species of methanol CH_2DOH is a complicated one as, unlike in the normal species CH_3OH, the inertia tensor depends on the angle of internal rotation. The CH_2DOH species also displays a dense far infrared torsional spectrum difficult to assign. Recently 38 torsional subbands of CH_2DOH have been identified, but for most of them there is neither an assignment nor an analysis of their rotational structure. In this paper an analysis of the rotation-torsion spectrum of CH_2DOH will be presented. The rotational structure of 23 torsional subbands have been assigned. These subbands are Δ v_t &ge 1 perpendicular subbands with a value of v'_t up to 10b and values of K' and K'' ranging from 0 to 9. For all subbands, the Q-branch was assigned, for 3 subbands, the R- and P-branches could also be found. The results of the rotational analysis with an expansion in J(J+1) of the new subbands and of already observed ones will be presented. When available, microwave lines within the lower torsional level, recorded in this work or already measured, were added to the data set. A theoretical approach aimed at calculating the rotation-torsion energy levels has also been developed. It is based on an expansion in terms of rotation-torsion operators with C_s symmetry and accounts for the dependence of the inertia tensor on the angle of internal rotation. This approach will be used to carry out a preliminary global analyses of the wavenumbers and of the frequencies. Lauvergnat, Coudert, Klee, and Smirnov, J. Mol. Spec. 256 (2009) 204. Quade, Liu, Mukhopadhyay, and Su, J. Mol. Spec. 192 (1998) 378; Mukhopadhyay, J. Mol. Struct. 695-696 (2004) 357. Liu and Quade, J. Mol. Spec. 146 (1991) 252 Mukhopadhyay et al., J. Chem. Phys. 116 (2002) 3710.

  19. Accessing the Nitromethane (CH3NO2) Potential Energy Surface in Methanol (CH3OH)-Nitrogen Monoxide (NO) Ices Exposed to Ionizing Radiation: An FTIR and PI-ReTOF-MS Investigation.

    PubMed

    Góbi, Sándor; Crandall, Parker B; Maksyutenko, Pavlo; Förstel, Marko; Kaiser, Ralf I

    2018-03-08

    (D 3 -)Methanol-nitrogen monoxide (CH 3 OH/CD 3 OH-NO) ices were exposed to ionizing radiation to facilitate the eventual determination of the CH 3 NO 2 potential energy surface (PES) in the condensed phase. Reaction intermediates and products were monitored via infrared spectroscopy (FTIR) and photoionization reflectron time-of-flight mass spectrometry (PI-ReTOF-MS) during the irradiation and temperature controlled desorption (TPD) phase, respectively. Distinct photoionization energies were utilized to discriminate the isomer(s) formed in these processes. The primary methanol radiolysis products were the methoxy (CH 3 O) and hydroxymethyl (CH 2 OH) radicals along with atomic hydrogen. The former was found to react barrierlessly with nitrogen monoxide resulting in the formation of cis- and trans-methyl nitrite (CH 3 ONO), which is the most abundant product that can be observed in the irradiated samples. On the other hand, the self-recombination of hydroxymethyl radicals yielding ethylene glycol (HO(CH 2 ) 2 OH) and glycerol (HOCH 2 CH 2 (OH)CH 2 OH) is preferred over the recombination with nitrogen monoxide to nitrosomethanol (HOCH 2 NO).

  20. Infrared Spectra and Band Strengths of CH3SH, an Interstellar Molecule

    NASA Technical Reports Server (NTRS)

    Hudson, R. L.

    2016-01-01

    Three solid phases of CH3SH (methanethiol or methyl mercaptan) have been prepared and their mid-infrared spectra recorded at 10-110 degrees Kelvin, with an emphasis on the 17-100 degrees Kelvin region. Refractive indices have been measured at two temperatures and used to estimate ice densities and infrared band strengths. Vapor pressures for the two crystalline phases of CH3SH at 110 degrees Kelvin are estimated. The behavior of amorphous CH3SH on warming is presented and discussed in terms of Ostwald's step rule. Comparisons to CH3OH under similar conditions are made, and some inconsistencies and ambiguities in the CH3SH literature are examined and corrected.

  1. Stringent upper limit of CH4 on Mars based on SOFIA/EXES observations

    NASA Astrophysics Data System (ADS)

    Aoki, S.; Richter, M. J.; DeWitt, C.; Boogert, A.; Encrenaz, T.; Sagawa, H.; Nakagawa, H.; Vandaele, A. C.; Giuranna, M.; Greathouse, T. K.; Fouchet, T.; Geminale, A.; Sindoni, G.; McKelvey, M.; Case, M.; Kasaba, Y.

    2018-03-01

    Discovery of CH4 in the Martian atmosphere has led to much discussion since it could be a signature of biological and/or geological activities on Mars. However, the presence of CH4 and its temporal and spatial variations are still under discussion because of the large uncertainties embedded in the previous observations. We performed sensitive measurements of Martian CH4 by using the Echelon-Cross-Echelle Spectrograph (EXES) onboard the Stratospheric Observatory for Infrared Astronomy (SOFIA) on 16 March 2016, which corresponds to summer (Ls = 123.2∘) in the northern hemisphere on Mars. The high altitude of SOFIA ( 13.7 km) enables us to significantly reduce the effects of terrestrial atmosphere. Thanks to this, SOFIA/EXES improves our chances of detecting Martian CH4 lines because it reduces the impact of telluric CH4 on Martian CH4, and allows us to use CH4 lines in the 7.5 μm band which has less contamination. However, our results show no unambiguous detection of Martian CH4. The Martian disk was spatially resolved into 3 × 3 areas, and the upper limits on the CH4 volume mixing ratio range from 1 to 9 ppb across the Martian atmosphere, which is significantly less than detections in several other studies. These results emphasize that release of CH4 on Mars is sporadic and/or localized if the process is present.

  2. Glucose-6-phosphate mediates activation of the carbohydrate responsive binding protein (ChREBP)

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Li, Ming V.; Departments of Medicine and Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030; Chen, Weiqin

    2010-05-07

    Carbohydrate response element binding protein (ChREBP) is a Mondo family transcription factor that activates a number of glycolytic and lipogenic genes in response to glucose stimulation. We have previously reported that high glucose can activate the transcriptional activity of ChREBP independent of the protein phosphatase 2A (PP2A)-mediated increase in nuclear entry and DNA binding. Here, we found that formation of glucose-6-phosphate (G-6-P) is essential for glucose activation of ChREBP. The glucose response of GAL4-ChREBP is attenuated by D-mannoheptulose, a potent hexokinase inhibitor, as well as over-expression of glucose-6-phosphatase (G6Pase); kinetics of activation of GAL4-ChREBP can be modified by exogenously expressedmore » GCK. Further metabolism of G-6-P through the two major glucose metabolic pathways, glycolysis and pentose-phosphate pathway, is not required for activation of ChREBP; over-expression of glucose-6-phosphate dehydrogenase (G6PD) diminishes, whereas RNAi knockdown of the enzyme enhances, the glucose response of GAL4-ChREBP, respectively. Moreover, the glucose analogue 2-deoxyglucose (2-DG), which is phosphorylated by hexokinase, but not further metabolized, effectively upregulates the transcription activity of ChREBP. In addition, over-expression of phosphofructokinase (PFK) 1 and 2, synergistically diminishes the glucose response of GAL4-ChREBP. These multiple lines of evidence support the conclusion that G-6-P mediates the activation of ChREBP.« less

  3. Macromolecule simulation and CH4 adsorption mechanism of coal vitrinite

    NASA Astrophysics Data System (ADS)

    Yu, Song; Yan-ming, Zhu; Wu, Li

    2017-02-01

    The microscopic mechanism of interactions between CH4 and coal macromolecules is of significant practical and theoretical importance in CBM development and methane storage. Under periodic boundary conditions, the optimal energy configuration of coal vitrinite, which has a higher torsion degree and tighter arrangement, can be determined by the calculation of molecular mechanics (MM) and molecular dynamics (MD), and annealing kinetics simulation based on ultimate analysis, 13C NMR, FT IR and HRTEM. Macromolecular stabilization is primarily due to the van der Waals energy and covalent bond energy, mainly consisting of bond torsion energy and bond angle energy. Using the optimal configuration as the adsorbent, GCMC simulation of vitrinite adsorption of CH4 is conducted. A saturated state is reached after absorbing 17 CH4s per coal vitrinite molecule. CH4 is preferentially adsorbed on the edge, and inclined to gathering around the branched chains of the inner vitrinite sites. Finally, the adsorption parameters are calculated through first principle DFT. The adsorbability order is as follows: aromatic structure> heteroatom rings > oxygen functional groups. The adsorption energy order is as follows: Top < Bond < Center, Up < Down. The order of average RDF better reflects the adsorption ability and that of [-COOH] is lower than those of [sbnd Cdbnd O] and [Csbnd Osbnd C]. CH4 distributed in the distance of 0.99-16 Å to functional groups in the type of monolayer adsorption and the average distance order manifest as [sbnd Cdbnd O] (1.64 Å) < [Csbnd Osbnd C] (1.89 Å) < [sbnd COOH] (3.78 Å) < [-CH3] (4.11 Å) according to the average RDF curves. CH4 enriches around [sbnd Cdbnd O] and [Csbnd O-C] whereas is rather dispersed about [-COOH] and [CH3]. Simulation and experiment data are both in strong agreement with the Langmuir and D-A isothermal adsorption model and the D-A model fit better than Langmuir model. Preferential adsorption sites and orientations in vitrinite are

  4. Selective sp3 C-H alkylation via polarity-match-based cross-coupling.

    PubMed

    Le, Chip; Liang, Yufan; Evans, Ryan W; Li, Ximing; MacMillan, David W C

    2017-07-06

    The functionalization of carbon-hydrogen (C-H) bonds is one of the most attractive strategies for molecular construction in organic chemistry. The hydrogen atom is considered to be an ideal coupling handle, owing to its relative abundance in organic molecules and its availability for functionalization at almost any stage in a synthetic sequence. Although many C-H functionalization reactions involve C(sp 3 )-C(sp 2 ) coupling, there is a growing demand for C-H alkylation reactions, wherein sp 3 C-H bonds are replaced with sp 3 C-alkyl groups. Here we describe a polarity-match-based selective sp 3 C-H alkylation via the combination of photoredox, nickel and hydrogen-atom transfer catalysis. This methodology simultaneously uses three catalytic cycles to achieve hydridic C-H bond abstraction (enabled by polarity matching), alkyl halide oxidative addition, and reductive elimination to enable alkyl-alkyl fragment coupling. The sp 3 C-H alkylation is highly selective for the α-C-H of amines, ethers and sulphides, which are commonly found in pharmaceutically relevant architectures. This cross-coupling protocol should enable broad synthetic applications in de novo synthesis and late-stage functionalization chemistry.

  5. Selective sp3 C-H alkylation via polarity-match-based cross-coupling

    NASA Astrophysics Data System (ADS)

    Le, Chip; Liang, Yufan; Evans, Ryan W.; Li, Ximing; MacMillan, David W. C.

    2017-07-01

    The functionalization of carbon-hydrogen (C-H) bonds is one of the most attractive strategies for molecular construction in organic chemistry. The hydrogen atom is considered to be an ideal coupling handle, owing to its relative abundance in organic molecules and its availability for functionalization at almost any stage in a synthetic sequence. Although many C-H functionalization reactions involve C(sp3)-C(sp2) coupling, there is a growing demand for C-H alkylation reactions, wherein sp3 C-H bonds are replaced with sp3 C-alkyl groups. Here we describe a polarity-match-based selective sp3 C-H alkylation via the combination of photoredox, nickel and hydrogen-atom transfer catalysis. This methodology simultaneously uses three catalytic cycles to achieve hydridic C-H bond abstraction (enabled by polarity matching), alkyl halide oxidative addition, and reductive elimination to enable alkyl-alkyl fragment coupling. The sp3 C-H alkylation is highly selective for the α-C-H of amines, ethers and sulphides, which are commonly found in pharmaceutically relevant architectures. This cross-coupling protocol should enable broad synthetic applications in de novo synthesis and late-stage functionalization chemistry.

  6. Theoretical study of the mechanism of CH2CO + CN reaction

    NASA Astrophysics Data System (ADS)

    Sun, Hao; He, Hong-Qing; Hong, Bo; Chang, Ying-Fei; An, Zhe; Wang, Rong-Shun

    The potential energy surface information of the CH2CO + CN reaction is obtained at the B3LYP/6-311+G(d,p) level. To gain further mechanistic knowledge, higher-level single-point calculations for the stationary points are performed at the QCISD(T)/6-311++G(d,p) level. The CH2CO + CN reaction proceeds through four possible mechanisms: direct hydrogen abstraction, olefinic carbon addition-elimination, carbonyl carbon addition-elimination, and side oxygen addition-elimination. Our calculations demonstrate that R?IM1?TS3?P3: CH2CN + CO is the energetically favorable channel; however, channel R?IM2?TS4?P4: CH2NC + CO is considerably competitive, especially as the temperature increases (R, IM, TS, and P represent reactant, intermediate, transition state, and product, respectively). The present study may be helpful in probing the mechanism of the CH2CO + CN reaction.

  7. A ChIP-Seq Data Analysis Pipeline Based on Bioconductor Packages.

    PubMed

    Park, Seung-Jin; Kim, Jong-Hwan; Yoon, Byung-Ha; Kim, Seon-Young

    2017-03-01

    Nowadays, huge volumes of chromatin immunoprecipitation-sequencing (ChIP-Seq) data are generated to increase the knowledge on DNA-protein interactions in the cell, and accordingly, many tools have been developed for ChIP-Seq analysis. Here, we provide an example of a streamlined workflow for ChIP-Seq data analysis composed of only four packages in Bioconductor: dada2, QuasR, mosaics, and ChIPseeker. 'dada2' performs trimming of the high-throughput sequencing data. 'QuasR' and 'mosaics' perform quality control and mapping of the input reads to the reference genome and peak calling, respectively. Finally, 'ChIPseeker' performs annotation and visualization of the called peaks. This workflow runs well independently of operating systems (e.g., Windows, Mac, or Linux) and processes the input fastq files into various results in one run. R code is available at github: https://github.com/ddhb/Workflow_of_Chipseq.git.

  8. Communication: Photodissociation of CH{sub 3}CHO at 308 nm: Observation of H-roaming, CH{sub 3}-roaming, and transition state pathways together along the ground state surface

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Li, Hou-Kuan; Tsai, Po-Yu; Hung, Kai-Chan

    2015-01-28

    Following photodissociation of acetaldehyde (CH{sub 3}CHO) at 308 nm, the CO(v = 1–4) fragment is acquired using time-resolved Fourier-transform infrared emission spectroscopy. The CO(v = 1) rotational distribution shows a bimodal feature; the low- and high-J components result from H-roaming around CH{sub 3}CO core and CH{sub 3}-roaming around CHO radical, respectively, in consistency with a recent assignment by Kable and co-workers (Lee et al., Chem. Sci. 5, 4633 (2014)). The H-roaming pathway disappears at the CO(v ≥ 2) states, because of insufficient available energy following bond-breaking of H + CH{sub 3}CO. By analyzing the CH{sub 4} emission spectrum, we obtainedmore » a bimodal vibrational distribution; the low-energy component is ascribed to the transition state (TS) pathway, consistent with prediction by quasiclassical trajectory calculations, while the high-energy component results from H- and CH{sub 3}-roamings. A branching fraction of H-roaming/CH{sub 3}-roaming/TS contribution is evaluated to be (8% ± 3%)/(68% ± 10%)/(25% ± 5%), in which the TS pathway was observed for the first time. The three pathways proceed concomitantly along the electronic ground state surface.« less

  9. The ChIP-exo Method: Identifying Protein-DNA Interactions with Near Base Pair Precision.

    PubMed

    Perreault, Andrea A; Venters, Bryan J

    2016-12-23

    Chromatin immunoprecipitation (ChIP) is an indispensable tool in the fields of epigenetics and gene regulation that isolates specific protein-DNA interactions. ChIP coupled to high throughput sequencing (ChIP-seq) is commonly used to determine the genomic location of proteins that interact with chromatin. However, ChIP-seq is hampered by relatively low mapping resolution of several hundred base pairs and high background signal. The ChIP-exo method is a refined version of ChIP-seq that substantially improves upon both resolution and noise. The key distinction of the ChIP-exo methodology is the incorporation of lambda exonuclease digestion in the library preparation workflow to effectively footprint the left and right 5' DNA borders of the protein-DNA crosslink site. The ChIP-exo libraries are then subjected to high throughput sequencing. The resulting data can be leveraged to provide unique and ultra-high resolution insights into the functional organization of the genome. Here, we describe the ChIP-exo method that we have optimized and streamlined for mammalian systems and next-generation sequencing-by-synthesis platform.

  10. Measuring Sister Chromatid Cohesion Protein Genome Occupancy in Drosophila melanogaster by ChIP-seq.

    PubMed

    Dorsett, Dale; Misulovin, Ziva

    2017-01-01

    This chapter presents methods to conduct and analyze genome-wide chromatin immunoprecipitation of the cohesin complex and the Nipped-B cohesin loading factor in Drosophila cells using high-throughput DNA sequencing (ChIP-seq). Procedures for isolation of chromatin, immunoprecipitation, and construction of sequencing libraries for the Ion Torrent Proton high throughput sequencer are detailed, and computational methods to calculate occupancy as input-normalized fold-enrichment are described. The results obtained by ChIP-seq are compared to those obtained by ChIP-chip (genomic ChIP using tiling microarrays), and the effects of sequencing depth on the accuracy are analyzed. ChIP-seq provides similar sensitivity and reproducibility as ChIP-chip, and identifies the same broad regions of occupancy. The locations of enrichment peaks, however, can differ between ChIP-chip and ChIP-seq, and low sequencing depth can splinter broad regions of occupancy into distinct peaks.

  11. Metabolite Regulation of Nuclear Localization of Carbohydrate-response Element-binding Protein (ChREBP)

    PubMed Central

    Sato, Shogo; Jung, Hunmin; Nakagawa, Tsutomu; Pawlosky, Robert; Takeshima, Tomomi; Lee, Wan-Ru; Sakiyama, Haruhiko; Laxman, Sunil; Wynn, R. Max; Tu, Benjamin P.; MacMillan, John B.; De Brabander, Jef K.; Veech, Richard L.; Uyeda, Kosaku

    2016-01-01

    The carbohydrate-response element-binding protein (ChREBP) is a glucose-responsive transcription factor that plays an essential role in converting excess carbohydrate to fat storage in the liver. In response to glucose levels, ChREBP is regulated by nuclear/cytosol trafficking via interaction with 14-3-3 proteins, CRM-1 (exportin-1 or XPO-1), or importins. Nuclear localization of ChREBP was rapidly inhibited when incubated in branched-chain α-ketoacids, saturated and unsaturated fatty acids, or 5-aminoimidazole-4-carboxamide ribonucleotide. Here, we discovered that protein-free extracts of high fat-fed livers contained, in addition to ketone bodies, a new metabolite, identified as AMP, which specifically activates the interaction between ChREBP and 14-3-3. The crystal structure showed that AMP binds directly to the N terminus of ChREBP-α2 helix. Our results suggest that AMP inhibits the nuclear localization of ChREBP through an allosteric activation of ChREBP/14-3-3 interactions and not by activation of AMPK. AMP and ketone bodies together can therefore inhibit lipogenesis by restricting localization of ChREBP to the cytoplasm during periods of ketosis. PMID:26984404

  12. Method of preparing (CH.sub.3).sub.3 SiNSO and byproducts thereof

    DOEpatents

    Spicer, Leonard D.; Bennett, Dennis W.; Davis, Jon F.

    1984-01-01

    (CH.sub.3).sub.3 SiNSO is produced by the reaction of ((CH.sub.3).sub.3 Si).sub.2 NH with SO.sub.2. Also produced in the reaction are ((CH.sub.3).sub.3 Si).sub.2 O and a new solid compound [NH.sub.4 ][(CH.sub.3).sub.3 SiOSO.sub.2 ]. Both (CH.sub.3).sub.3 SiNSO and [NH.sub.4 ][(CH.sub.3).sub.3 SiOSO.sub.2 ] have fluorescent properties. The reaction of the subject invention is used in a method of measuring the concentration of SO.sub.2 pollutants in gases. By the method, a sample of gas is bubbled through a solution of ((CH.sub.3).sub.3 Si).sub.2 NH, whereby any SO.sub.2 present in the gas will react to produce the two fluorescent products. The measured fluorescence of these products can then be used to calculate the concentration of SO.sub.2 in the original gas sample. The solid product [NH.sub.4 ][(CH.sub.3).sub.3 SiOSO.sub.2 ] may be used as a standard in solid state NMR spectroscopy.

  13. Radiation-induced transformations of isolated CH3CN molecules in noble gas matrices

    NASA Astrophysics Data System (ADS)

    Kameneva, Svetlana V.; Volosatova, Anastasia D.; Feldman, Vladimir I.

    2017-12-01

    The transformations of isolated CH3CN molecules in various solid noble-gas matrices (Ne, Ar, Kr, and Xe) under the action of X-ray irradiation at 5 K were investigated by FTIR spectroscopy. The main products are CH3NC, CH2CNH and CH2NCH molecular isomers as well as CH2CN and CH2NC radicals. The matrix has a strong effect on the distribution of reaction channels. In particular, the highest relative yield of keteneimine (CH2CNH) was found in Ne matrix, whereas the formation of CH3NC predominates in xenon. It was explained by differences in the matrix ionization energy (IE) resulting in different distributions of hot ionic reactions. The reactions of neutral excited states are mainly involved in Xe matrix with low IE, while the isomerization of the primary acetonitrile positive ions may be quite effective in Ne and Ar. Annealing of the irradiated samples results in mobilization of trapped hydrogen atoms followed by their reactions with radicals to yield parent molecule and its isomers. The scheme of the radiation-induced processes and its implications for the acetonitrile chemistry in cosmic ices are discussed.

  14. The Rotational Spectrum of Anti-Ethylamine (CH3CH2NH2) from 10 to 270 GHz: A Laboratory Study and Astronomical Search in Sgr B2(N)

    NASA Astrophysics Data System (ADS)

    Apponi, A. J.; Sun, M.; Halfen, D. T.; Ziurys, L. M.; Müller, H. S. P.

    2008-02-01

    The pure rotational spectrum of the lowest energy (anti-) conformer of ethylamine (CH3CH2NH2) has been measured in the frequency range of 10-270 GHz. The spectrum was recorded using both millimeter-wave absorption spectroscopy and Fourier transform microwave (FTMW) techniques. Ten rotational transitions of this molecule were recorded in the frequency range of 10-40 GHz using FTMW methods, resulting in the assignment of 53 quadrupole-resolved hyperfine lines; in the millimeter-wave region (48-270 GHz), nearly 600 transitions were assigned to the ground (anti-) state. The amine group in CH3CH2NH2 undergoes inversion, resulting in a doubling that is frequently small and most apparent in the low-frequency K-doubling transitions. In addition, seemingly random rotational levels of this molecule were found to be significantly perturbed. The cause of these perturbations is presently uncertain, but torsion-rotation interactions with the higher lying gauche conformers seem to be a likely explanation. An astronomical search was conducted for ethylamine toward Sgr B2(N) using the Kitt Peak 12 m antenna and the Sub-Millimeter Telescope (SMT) of the Arizona Radio Observatory. Frequencies of 70 favorable rotational transitions were observed in this search, which covered the range 68-263 GHz. Ethylamine was not conclusively detected in Sgr B2(N), with an upper limit to the column density of (1-8) × 1013 cm-2 with f(CH3CH2NH2/H2) ~ (0.3-3) × 10-11, assuming a rotational temperature of 50-220 K. These observations indicate a gas-phase CH3CH2NH2/CH3NH2 ratio of <0.001-0.01, in contrast to the nearly equal ratio suggested by the acid hydrolysis of cometary solids from the Stardust mission.

  15. Chemoselective Aliphatic C-H Bond Oxidation Enabled by Polarity Reversal.

    PubMed

    Dantignana, Valeria; Milan, Michela; Cussó, Olaf; Company, Anna; Bietti, Massimo; Costas, Miquel

    2017-12-27

    Methods for selective oxidation of aliphatic C-H bonds are called on to revolutionize organic synthesis by providing novel and more efficient paths. Realization of this goal requires the discovery of mechanisms that can alter in a predictable manner the innate reactivity of these bonds. Ideally, these mechanisms need to make oxidation of aliphatic C-H bonds, which are recognized as relatively inert, compatible with the presence of electron rich functional groups that are highly susceptible to oxidation. Furthermore, predictable modification of the relative reactivity of different C-H bonds within a molecule would enable rapid diversification of the resulting oxidation products. Herein we show that by engaging in hydrogen bonding, fluorinated alcohols exert a polarity reversal on electron rich functional groups, directing iron and manganese catalyzed oxidation toward a priori stronger and unactivated C-H bonds. As a result, selective hydroxylation of methylenic sites in hydrocarbons and remote aliphatic C-H oxidation of otherwise sensitive alcohol, ether, amide, and amine substrates is achieved employing aqueous hydrogen peroxide as oxidant. Oxidations occur in a predictable manner, with outstanding levels of product chemoselectivity, preserving the first-formed hydroxylation product, thus representing an extremely valuable tool for synthetic planning and development.

  16. Diurnal variability of CO2 and CH4 emissions from tropical reservoirs

    NASA Astrophysics Data System (ADS)

    Linkhorst, Annika; Reinaldo Paranaíba, José; Barros, Nathan; DelSontro, Tonya; Isidorova, Anastasija; Mendonça, Raquel; Sobek, Sebastian

    2017-04-01

    Reservoirs are important atmospheric sources of carbon dioxide (CO2) and methane (CH4) with CH4 being a greenhouse gas (GHG) at least 28 times more potent than CO2. Reservoir GHG emissions tend to be heterogeneous, however, and thus current emission estimates are likely conservative since they often overlook emission hot spots and hot moments, especially for CH4 ebullition. For CO2, diffusion is the dominant flux pathway, and diurnal patterns in CO2 emissions can largely be linked to photosynthesis. In contrast, ebullition, the release of gases through bubbles that are formed in the sediments and travel through the water column, is a major emission pathway for CH4 in shallow waters. We visually observed a change in quantity and size of bubbles at different times of the day, and therefore conducted a diurnal study in four different Brazilian reservoirs of different size, age, climatic and geographic characteristics. We hypothesized that sub-daily trends in CH4 ebullition occur in Brazilian reservoirs as bubble release depends on physical factors such as turbulence and hydrostatic pressure, which can exhibit sub-daily patterns in large, managed reservoirs. In each reservoir, we performed measurements of CO2 and CH4 fluxes at one location over 24 hours. CH4 ebullition was tracked continuously by an echosounder, and 13 anchored bubble traps per reservoir were sampled every three hours. Further, a custom-built equilibrator monitored dissolved CH4 and CO2 concentrations, and diffusive and total fluxes of CO2 and CH4 were measured using floating chambers in triplicates every 30 minutes during the same period. We observed that CH4 ebullition as well as CH4 and CO2 diffusion peaked during the day, with peak fluxes being up to four times higher than low fluxes. However, the exact timing and magnitude varied for the different sampling events, and could in part be linked to biological and physical properties of the respective reservoir. This study combined different state

  17. A ChIP-Seq Data Analysis Pipeline Based on Bioconductor Packages

    PubMed Central

    Park, Seung-Jin; Kim, Jong-Hwan; Yoon, Byung-Ha; Kim, Seon-Young

    2017-01-01

    Nowadays, huge volumes of chromatin immunoprecipitation-sequencing (ChIP-Seq) data are generated to increase the knowledge on DNA-protein interactions in the cell, and accordingly, many tools have been developed for ChIP-Seq analysis. Here, we provide an example of a streamlined workflow for ChIP-Seq data analysis composed of only four packages in Bioconductor: dada2, QuasR, mosaics, and ChIPseeker. ‘dada2’ performs trimming of the high-throughput sequencing data. ‘QuasR’ and ‘mosaics’ perform quality control and mapping of the input reads to the reference genome and peak calling, respectively. Finally, ‘ChIPseeker’ performs annotation and visualization of the called peaks. This workflow runs well independently of operating systems (e.g., Windows, Mac, or Linux) and processes the input fastq files into various results in one run. R code is available at github: https://github.com/ddhb/Workflow_of_Chipseq.git. PMID:28416945

  18. The ChEMBL database as linked open data

    PubMed Central

    2013-01-01

    Background Making data available as Linked Data using Resource Description Framework (RDF) promotes integration with other web resources. RDF documents can natively link to related data, and others can link back using Uniform Resource Identifiers (URIs). RDF makes the data machine-readable and uses extensible vocabularies for additional information, making it easier to scale up inference and data analysis. Results This paper describes recent developments in an ongoing project converting data from the ChEMBL database into RDF triples. Relative to earlier versions, this updated version of ChEMBL-RDF uses recently introduced ontologies, including CHEMINF and CiTO; exposes more information from the database; and is now available as dereferencable, linked data. To demonstrate these new features, we present novel use cases showing further integration with other web resources, including Bio2RDF, Chem2Bio2RDF, and ChemSpider, and showing the use of standard ontologies for querying. Conclusions We have illustrated the advantages of using open standards and ontologies to link the ChEMBL database to other databases. Using those links and the knowledge encoded in standards and ontologies, the ChEMBL-RDF resource creates a foundation for integrated semantic web cheminformatics applications, such as the presented decision support. PMID:23657106

  19. Site-selective and stereoselective functionalization of non-activated tertiary C-H bonds

    NASA Astrophysics Data System (ADS)

    Liao, Kuangbiao; Pickel, Thomas C.; Boyarskikh, Vyacheslav; Bacsa, John; Musaev, Djamaladdin G.; Davies, Huw M. L.

    2017-11-01

    The synthesis of complex organic compounds usually relies on controlling the reactions of the functional groups. In recent years, it has become possible to carry out reactions directly on the C-H bonds, previously considered to be unreactive. One of the major challenges is to control the site-selectivity because most organic compounds have many similar C-H bonds. The most well developed procedures so far rely on the use of substrate control, in which the substrate has one inherently more reactive C-H bond or contains a directing group or the reaction is conducted intramolecularly so that a specific C-H bond is favoured. A more versatile but more challenging approach is to use catalysts to control which site in the substrate is functionalized. p450 enzymes exhibit C-H oxidation site-selectivity, in which the enzyme scaffold causes a specific C-H bond to be functionalized by placing it close to the iron-oxo haem complex. Several studies have aimed to emulate this enzymatic site-selectivity with designed transition-metal catalysts but it is difficult to achieve exceptionally high levels of site-selectivity. Recently, we reported a dirhodium catalyst for the site-selective functionalization of the most accessible non-activated (that is, not next to a functional group) secondary C-H bonds by means of rhodium-carbene-induced C-H insertion. Here we describe another dirhodium catalyst that has a very different reactivity profile. Instead of the secondary C-H bond, the new catalyst is capable of precise site-selectivity at the most accessible tertiary C-H bonds. Using this catalyst, we modify several natural products, including steroids and a vitamin E derivative, indicating the applicability of this method of synthesis to the late-stage functionalization of complex molecules. These studies show it is possible to achieve site-selectivity at different positions within a substrate simply by selecting the appropriate catalyst. We hope that this work will inspire the design of

  20. Using a modified Marcus model to analyze the Brønsted correlation of gas-phase reactions of the deprotonation of para-substituted toluenes by CH2Cl-, H(O)C-, CH3O-, H(F)N-, NH2C≡C-, and CH3C≡C- anions

    NASA Astrophysics Data System (ADS)

    Romanskii, I. A.

    2017-10-01

    Ab initio calculations of the energy parameters for a series of gas-phase reactions of the deprotonation of para-substituted toluenes (OH, CH3, H, Cl, NC, CN, and NO2 substituents) by CH2Cl-, H(O)C-, CH3O-, H(F)N-, NH2C≡C-, and CH3C≡C- anions (the conjugated acids are chloromethane (CH3Cl), formaldehyde (H2CO), methanol (CH3OH), fluoroamine (NH2F), aminoacetylene (NH2C≡CH), and methylacetylene (CH3C≡CH), respectively) is performed using a technique of intramolecular reorganization proposed earlier. The equilibrium ( E a eq) and nonequilibrium ( E a neq ) contributions to energy of activation E a are found for distance Q(C…B) = 3.0 Å (where C and B are the central atoms of the acid and base). At this value of Q, the tunneling mechanism of proton transfer predominates. The results from calculations, together with similar data obtained earlier for reactions of the deprotonation of toluenes by CH2CN- anions, are considered from the viewpoint of the harmonic Marcus model. It is found that in the graph Δ E 0 - E a neq (where Δ E 0 is the internal energy of the reaction (for a collision complex)), the points for five reaction series with C-bases fall on the same quadratic (within the -11 to 12 kcal/mol range of Δ E 0) curve; the second curve, which includes points for the series with N- and O-bases (OCH3 - and H(F)N-) is shifted below the first curve by 1.5 kcal/mol. For most reaction series (except the one with the strongest bases, CH2Cl- and H(O)C-), the curvature and slope of graph Δ E 0 - E a neq are in agreement with the theory. The correlations of energies E a neq , E a eq, E a, and Δ E 0 with the energy of reaction Δ E 00 are satisfactorily described by quadratic equations as well. Differences between the structures of bases are reflected most by energy E a eq and the height of the proton tunneling barrier in the activated complex (AC) E b. For the series of reactions of toluene with a set of bases, graphs Δ E 00 - E a eq and Δ E 0 - E b show

  1. Palladium-catalysed transannular C-H functionalization of alicyclic amines

    NASA Astrophysics Data System (ADS)

    Topczewski, Joseph J.; Cabrera, Pablo J.; Saper, Noam I.; Sanford, Melanie S.

    2016-03-01

    Discovering pharmaceutical candidates is a resource-intensive enterprise that frequently requires the parallel synthesis of hundreds or even thousands of molecules. C-H bonds are present in almost all pharmaceutical agents. Consequently, the development of selective, rapid and efficient methods for converting these bonds into new chemical entities has the potential to streamline pharmaceutical development. Saturated nitrogen-containing heterocycles (alicyclic amines) feature prominently in pharmaceuticals, such as treatments for depression (paroxetine, amitifadine), diabetes (gliclazide), leukaemia (alvocidib), schizophrenia (risperidone, belaperidone), malaria (mefloquine) and nicotine addiction (cytisine, varenicline). However, existing methods for the C-H functionalization of saturated nitrogen heterocycles, particularly at sites remote to nitrogen, remain extremely limited. Here we report a transannular approach to selectively manipulate the C-H bonds of alicyclic amines at sites remote to nitrogen. Our reaction uses the boat conformation of the substrates to achieve palladium-catalysed amine-directed conversion of C-H bonds to C-C bonds on various alicyclic amine scaffolds. We demonstrate this approach by synthesizing new derivatives of several bioactive molecules, including varenicline.

  2. Application of one-dimensional semiclassical transition state theory to the CH3OH + H ⇌ CH2OH/CH3O + H2 reactions.

    PubMed

    Shan, Xiao; Clary, David C

    2018-03-13

    The rate constants of the two branches of H-abstractions from CH 3 OH by the H-atom and the corresponding reactions in the reverse direction are calculated using the one-dimensional semiclassical transition state theory (1D SCTST). In this method, only the reaction mode vibration of the transition state (TS) is treated anharmonically, while the remaining internal degrees of freedom are treated as they would have been in a standard TS theory calculation. A total of eight ab initio single-point energy calculations are performed in addition to the computational cost of a standard TS theory calculation. This allows a second-order Richardson extrapolation method to be employed to improve the numerical estimation of the third- and fourth-order derivatives, which in turn are used in the calculation of the anharmonic constant. Hindered-rotor (HR) vibrations are identified in the equilibrium states of CH 3 OH and CH 2 OH, and the TSs of the reactions. The partition function of the HRs are calculated using both a simple harmonic oscillator model and a more sophisticated one-dimensional torsional eigenvalue summation (1D TES) method. The 1D TES method can be easily adapted in 1D SCTST computation. The resulting 1D SCTST with 1D TES rate constants show good agreement to previous theoretical and experimental works. The effects of the HR on rate constants for different reactions are also investigated.This article is part of the theme issue 'Modern theoretical chemistry'. © 2018 The Author(s).

  3. Mechanistic and kinetic study of the CH3CO + O2 reaction.

    PubMed

    Hou, Hua; Li, Aixiao; Hu, Hongyi; Li, Yuzhen; Li, Hui; Wang, Baoshan

    2005-06-08

    Potential-energy surface of the CH3CO + O2 reaction has been calculated by ab initio quantum chemistry methods. The geometries were optimized using the second-order Moller-Plesset theory (MP2) with the 6-311G(d,p) basis set and the coupled-cluster theory with single and double excitations (CCSD) with the correlation consistent polarized valence double zeta (cc-pVDZ) basis set. The relative energies were calculated using the Gaussian-3 second-order Moller-Plesset theory with the CCSD/cc-pVDZ geometries. Multireference self-consistent-field and MP2 methods were also employed using the 6-311G(d,p) and 6-311++G(3df,2p) basis sets. Both addition/elimination and direct abstraction mechanisms have been investigated. It was revealed that acetylperoxy radical [CH3C(O)OO] is the initial adduct and the formation of OH and alpha-lactone [CH2CO2(1A')] is the only energetically accessible decomposition channel. The other channels, e.g., abstraction, HO2 + CH2CO, O + CH3CO2, CO + CH3O2, and CO2 + CH3O, are negligible. Multichannel Rice-Ramsperger-Kassel-Marcus theory and transition state theory (E-resolved) were employed to calculate the overall and individual rate coefficients and the temperature and pressure dependences. Fairly good agreement between theory and experiments has been obtained without any adjustable parameters. It was concluded that at pressures below 3 Torr, OH and CH2CO2(1A') are the major nascent products of the oxidation of acetyl radicals, although CH2CO2(1A') might either undergo unimolecular decomposition to form the final products of CH2O + CO or react with OH and Cl to generate H2O and HCl. The acetylperoxy radicals formed by collisional stabilization are the major products at the elevated pressures. In atmosphere, the yield of acetylperoxy is nearly unity and the contribution of OH is only marginal.

  4. Spectrally-resolved UV photodesorption of CH4 in pure and layered ices

    NASA Astrophysics Data System (ADS)

    Dupuy, R.; Bertin, M.; Féraud, G.; Michaut, X.; Jeseck, P.; Doronin, M.; Philippe, L.; Romanzin, C.; Fillion, J.-H.

    2017-07-01

    Context. Methane is among the main components of the ice mantles of interstellar dust grains, where it is at the start of a rich solid-phase chemical network. Quantification of the photon-induced desorption yield of these frozen molecules and understanding of the underlying processes is necessary to accurately model the observations and the chemical evolution of various regions of the interstellar medium. Aims: This study aims at experimentally determining absolute photodesorption yields for the CH4 molecule as a function of photon energy. The influence of the ice composition is also investigated. By studying the methane desorption from layered CH4:CO ice, indirect desorption processes triggered by the excitation of the CO molecules are monitored and quantified. Methods: Tunable monochromatic vacuum ultraviolet light (VUV) light from the DESIRS beamline of the SOLEIL synchrotron is used in the 7-13.6 eV (177-91 nm) range to irradiate pure CH4 or layers of CH4 deposited on top of CO ice samples. The release of species in the gas phase is monitored by quadrupole mass spectrometry, and absolute photodesorption yields of intact CH4 are deduced. Results: CH4 photodesorbs for photon energies higher than 9.1 eV ( 136 nm). The photodesorption spectrum follows the absorption spectrum of CH4, which confirms a desorption mechanism mediated by electronic transitions in the ice. When it is deposited on top of CO, CH4 desorbs between 8 and 9 eV with a pattern characteristic of CO absorption, indicating desorption induced by energy transfer from CO molecules. Conclusions: The photodesorption of CH4 from pure ice in various interstellar environments is around 2.0 ± 1.0 × 10-3 molecules per incident photon. Results on CO-induced indirect desorption of CH4 provide useful insights for the generalization of this process to other molecules co-existing with CO in ice mantles.

  5. A high level computational study of the CH4/CF4 dimer: how does it compare with the CH4/CH4 and CF4/CF4 dimers?

    NASA Astrophysics Data System (ADS)

    Biller, Matthew J.; Mecozzi, Sandro

    2012-04-01

    The interaction within the methane-methane (CH4/CH4), perfluoromethane-perfluoromethane (CF4/CF4) methane-perfluoromethane dimers (CH4/CF4) was calculated using the Hartree-Fock (HF) method, multiple orders of Møller-Plesset perturbation theory [MP2, MP3, MP4(DQ), MP4(SDQ), MP4(SDTQ)], and coupled cluster theory [CCSD, CCSD(T)], as well as the PW91, B97D, and M06-2X density functional theory (DFT) functionals. The basis sets of Dunning and coworkers (aug-cc-pVxZ, x = D, T, Q), Krishnan and coworkers [6-311++G(d,p), 6-311++G(2d,2p)], and Tsuzuki and coworkers [aug(df, pd)-6-311G(d,p)] were used. Basis set superposition error (BSSE) was corrected via the counterpoise method in all cases. Interaction energies obtained with the MP2 method do not fit with the experimental finding that the methane-perfluoromethane system phase separates at 94.5 K. It was not until the CCSD(T) method was considered that the interaction energy of the methane-perfluoromethane dimer (-0.69 kcal mol-1) was found to be intermediate between the methane (-0.51 kcal mol-1) and perfluoromethane (-0.78 kcal mol-1) dimers. This suggests that a perfluoromethane molecule interacts preferentially with another perfluoromethane (by about 0.09 kcal mol-1) than with a methane molecule. At temperatures much lower than the CH4/CF4 critical solution temperature of 94.5 K, this energy difference becomes significant and leads perfluoromethane molecules to associate with themselves, forming a phase separation. The DFT functionals yielded erratic results for the three dimers. Further development of DFT is needed in order to model dispersion interactions in hydrocarbon/perfluorocarbon systems.

  6. Windrow composting mitigated CH4 emissions: characterization of methanogenic and methanotrophic communities in manure management.

    PubMed

    Chen, Ruirui; Wang, Yiming; Wei, Shiping; Wang, Wei; Lin, Xiangui

    2014-12-01

    With increasing livestock breeding, methane (CH4 ) emissions from manure management will increasingly contribute more to atmospheric CH4 concentration. The dynamics of methanogens and methanotrophs have not yet been studied in the manure environment. The current study combines surface CH4 emissions with methanogenic and methanotrophic community analyses from two management practices, windrow composting (WCOM) and solid storage (SSTO). Our results showed that there was an c. 50% reduction of CH4 emissions with WCOM compared with SSTO over a 50-day period. A sharp decrease in the quantities of both methanogens and methanotrophs in WCOM suggested that CH4 mitigation was mainly due to decreased CH4 production rather than increased CH4 oxidation. Pyrosequencing analysis demonstrated that aeration caused a clear shift of dominant methanogens in the manure, with specifically a significant decrease in Methanosarcina and increase in Methanobrevibacter. The composition of methanogenic community was influenced by manure management and regulated CH4 production. A sharp increase in the quantity of methanotrophs in SSTO suggested that microbial CH4 oxidation is an important sink for the CH4 produced. The increased abundance of Methylococcaceae in SSTO suggested that Type I methanotrophs have an advantage in CH4 oxidation in occupying niches under low CH4 and high O2 conditions. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

  7. Resonant two-photon ionization and ab initio conformational analysis of haloethyl benzenes (PhCH(2)CH(2)X,X=Cl,F).

    PubMed

    Martin, Danielle E; Robertson, Evan G; Morrison, Richard J S; Dobney, Bruce

    2007-10-07

    The S(1) <-- S(0) transitions of the gaseous (2-fluoroethyl)-benzene (FEB) and (2-chloroethyl)-benzene (CEB) have been investigated using a combination of two-color resonant two-photon ionization and UV-UV hole burning spectroscopy. Both anti and gauche conformers have been identified on the basis of rotational band contour analysis supported by ab initio calculations on the ground and electronically excited states. The gauche origin band of FEB at 37,673 cm(-1) is redshifted 50 cm(-1) relative to the corresponding anti origin, while CEB origin bands overlap at 37,646 cm(-1). Relative conformational stability and populations in the jet have been estimated for both molecules, based on the intensity ratio of S(1) <-- S(0) band origin transitions. These are compared with a range of related molecules with the structural motif PhCH(2)CH(2)X (X=CH(3),CH(2)CH(3),NH(2),OH,COOH,CCH,CN). Theory and experimental results for FEB and CEB show repulsive interactions between the halogen substituents and the pi cloud of the phenyl rings destabilizing the gauche conformers, but the preference for the anti conformers is relatively modest. The gauche conformer origins show very different hybrid character: FEB is largely b type, while CEB is an ac hybrid in keeping with theoretically computed TM "rotations" (theta(elec)) of -7 degrees and -56 degrees , respectively. This difference is attributed largely to rotation of the side chain in opposite directions about the C(1)C(alpha) bond. Spectra of FEB(H(2)O) and CEB(H(2)O) single water clusters show evidence of an anti conformation in the host molecule.

  8. Thermodynamic properties of seven gaseous halogenated hydrocarbons from acoustic measurements: CHClFCF3, CHF2 CF3, CF3 CH3, CHF2CH3, CF3CHFCHF2, CF3CH2CF3, and CHF2CF2CH2F

    NASA Astrophysics Data System (ADS)

    Gillis, K. A.

    1997-01-01

    Measurements of the speed of sound in seven halogenated hydrocarbons are presented. The compounds in this study are 1-chloro-1,2,2,2-tetrafluoroethane (CHClFCF3 or HCFC-124), pentafluoroethane (CHF2 CF3 or HFC-125), 1,1,1-trifluoroethane (CF3CH3 or HFC-143a), 1,1-difluoroethane (CHF2CH3 or HFC-152a), 1,1,1,2,3,3-hexafluoropropane (CF3CHFCHF2 or HFC-236ea), 1,1,1,3,3,3-hexafluoropropane (CF3CH2CF3 or HFC-236fa), and 1,1,2,2,3-pentafluoropropane (CHF2CF2CH2F or HFC-245ca). The measurements were performed with a cylindrical resonator at temperatures between 240 and 400 K and at pressures up to 1.0 MPa. Ideal-gas heat capacities and acoustic virial coefficients were directly deduced from the data. The ideal-gas heat capacity of HFC-125 from this work differs from spectroscopic calculations by less than 0.2% over the measurement range. The coefficients for virial equations of state were obtained from the acoustic data and hard-core square-well intermolecular potentials. Gas densities that were calculated from the virial equations of state for HCFC-124 and HFC-125 differ from independent density measurements by at most 0.15%, for the ranges of temperature and pressure over which both acoustic and Burnett data exist. The uncertainties in the derived properties for the other five compounds are comparable to those for HCFC-124 and HFC-125.

  9. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.

    PubMed

    Landt, Stephen G; Marinov, Georgi K; Kundaje, Anshul; Kheradpour, Pouya; Pauli, Florencia; Batzoglou, Serafim; Bernstein, Bradley E; Bickel, Peter; Brown, James B; Cayting, Philip; Chen, Yiwen; DeSalvo, Gilberto; Epstein, Charles; Fisher-Aylor, Katherine I; Euskirchen, Ghia; Gerstein, Mark; Gertz, Jason; Hartemink, Alexander J; Hoffman, Michael M; Iyer, Vishwanath R; Jung, Youngsook L; Karmakar, Subhradip; Kellis, Manolis; Kharchenko, Peter V; Li, Qunhua; Liu, Tao; Liu, X Shirley; Ma, Lijia; Milosavljevic, Aleksandar; Myers, Richard M; Park, Peter J; Pazin, Michael J; Perry, Marc D; Raha, Debasish; Reddy, Timothy E; Rozowsky, Joel; Shoresh, Noam; Sidow, Arend; Slattery, Matthew; Stamatoyannopoulos, John A; Tolstorukov, Michael Y; White, Kevin P; Xi, Simon; Farnham, Peggy J; Lieb, Jason D; Wold, Barbara J; Snyder, Michael

    2012-09-01

    Chromatin immunoprecipitation (ChIP) followed by high-throughput DNA sequencing (ChIP-seq) has become a valuable and widely used approach for mapping the genomic location of transcription-factor binding and histone modifications in living cells. Despite its widespread use, there are considerable differences in how these experiments are conducted, how the results are scored and evaluated for quality, and how the data and metadata are archived for public use. These practices affect the quality and utility of any global ChIP experiment. Through our experience in performing ChIP-seq experiments, the ENCODE and modENCODE consortia have developed a set of working standards and guidelines for ChIP experiments that are updated routinely. The current guidelines address antibody validation, experimental replication, sequencing depth, data and metadata reporting, and data quality assessment. We discuss how ChIP quality, assessed in these ways, affects different uses of ChIP-seq data. All data sets used in the analysis have been deposited for public viewing and downloading at the ENCODE (http://encodeproject.org/ENCODE/) and modENCODE (http://www.modencode.org/) portals.

  10. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

    PubMed Central

    Landt, Stephen G.; Marinov, Georgi K.; Kundaje, Anshul; Kheradpour, Pouya; Pauli, Florencia; Batzoglou, Serafim; Bernstein, Bradley E.; Bickel, Peter; Brown, James B.; Cayting, Philip; Chen, Yiwen; DeSalvo, Gilberto; Epstein, Charles; Fisher-Aylor, Katherine I.; Euskirchen, Ghia; Gerstein, Mark; Gertz, Jason; Hartemink, Alexander J.; Hoffman, Michael M.; Iyer, Vishwanath R.; Jung, Youngsook L.; Karmakar, Subhradip; Kellis, Manolis; Kharchenko, Peter V.; Li, Qunhua; Liu, Tao; Liu, X. Shirley; Ma, Lijia; Milosavljevic, Aleksandar; Myers, Richard M.; Park, Peter J.; Pazin, Michael J.; Perry, Marc D.; Raha, Debasish; Reddy, Timothy E.; Rozowsky, Joel; Shoresh, Noam; Sidow, Arend; Slattery, Matthew; Stamatoyannopoulos, John A.; Tolstorukov, Michael Y.; White, Kevin P.; Xi, Simon; Farnham, Peggy J.; Lieb, Jason D.; Wold, Barbara J.; Snyder, Michael

    2012-01-01

    Chromatin immunoprecipitation (ChIP) followed by high-throughput DNA sequencing (ChIP-seq) has become a valuable and widely used approach for mapping the genomic location of transcription-factor binding and histone modifications in living cells. Despite its widespread use, there are considerable differences in how these experiments are conducted, how the results are scored and evaluated for quality, and how the data and metadata are archived for public use. These practices affect the quality and utility of any global ChIP experiment. Through our experience in performing ChIP-seq experiments, the ENCODE and modENCODE consortia have developed a set of working standards and guidelines for ChIP experiments that are updated routinely. The current guidelines address antibody validation, experimental replication, sequencing depth, data and metadata reporting, and data quality assessment. We discuss how ChIP quality, assessed in these ways, affects different uses of ChIP-seq data. All data sets used in the analysis have been deposited for public viewing and downloading at the ENCODE (http://encodeproject.org/ENCODE/) and modENCODE (http://www.modencode.org/) portals. PMID:22955991

  11. myChEMBL: a virtual machine implementation of open data and cheminformatics tools.

    PubMed

    Ochoa, Rodrigo; Davies, Mark; Papadatos, George; Atkinson, Francis; Overington, John P

    2014-01-15

    myChEMBL is a completely open platform, which combines public domain bioactivity data with open source database and cheminformatics technologies. myChEMBL consists of a Linux (Ubuntu) Virtual Machine featuring a PostgreSQL schema with the latest version of the ChEMBL database, as well as the latest RDKit cheminformatics libraries. In addition, a self-contained web interface is available, which can be modified and improved according to user specifications. The VM is available at: ftp://ftp.ebi.ac.uk/pub/databases/chembl/VM/myChEMBL/current. The web interface and web services code is available at: https://github.com/rochoa85/myChEMBL.

  12. Observing and modeling links between soil moisture, microbes and CH4 fluxes from forest soils

    NASA Astrophysics Data System (ADS)

    Christiansen, Jesper; Levy-Booth, David; Barker, Jason; Prescott, Cindy; Grayston, Sue

    2017-04-01

    Soil moisture is a key driver of methane (CH4) fluxes in forest soils, both of the net uptake of atmospheric CH4 and emission from the soil. Climate and land use change will alter spatial patterns of soil moisture as well as temporal variability impacting the net CH4 exchange. The impact on the resultant net CH4 exchange however is linked to the underlying spatial and temporal distribution of the soil microbial communities involved in CH4 cycling as well as the response of the soil microbial community to environmental changes. Significant progress has been made to target specific CH4 consuming and producing soil organisms, which is invaluable in order to understand the microbial regulation of the CH4 cycle in forest soils. However, it is not clear as to which extent soil moisture shapes the structure, function and abundance of CH4 specific microorganisms and how this is linked to observed net CH4 exchange under contrasting soil moisture regimes. Here we report on the results from a research project aiming to understand how the CH4 net exchange is shaped by the interactive effects soil moisture and the spatial distribution CH4 consuming (methanotrophs) and producing (methanogens). We studied the growing season variations of in situ CH4 fluxes, microbial gene abundances of methanotrophs and methanogens, soil hydrology, and nutrient availability in three typical forest types across a soil moisture gradient in a temperate rainforest on the Canadian Pacific coast. Furthermore, we conducted laboratory experiments to determine whether the net CH4 exchange from hydrologically contrasting forest soils responded differently to changes in soil moisture. Lastly, we modelled the microbial mediation of net CH4 exchange along the soil moisture gradient using structural equation modeling. Our study shows that it is possible to link spatial patterns of in situ net exchange of CH4 to microbial abundance of CH4 consuming and producing organisms. We also show that the microbial

  13. CuMnOS Nanoflowers with Different Cu+/Cu2+ Ratios for the CO2-to-CH3OH and the CH3OH-to-H2 Redox Reactions

    NASA Astrophysics Data System (ADS)

    Chen, Xiaoyun; Abdullah, Hairus; Kuo, Dong-Hau

    2017-01-01

    A conservative CO2-Methanol (CH3OH) regeneration cycle, to capture and reutilize the greenhouse gas of CO2 by aqueous hydrogenation for industry-useful CH3OH and to convert aqueous CH3OH solution by dehydrogenation for the clean energy of hydrogen (H2), is demonstrated at normal temperature and pressure (NTP) with two kinds of CuMnOS nanoflower catalysts. The [Cu+]-high CuMnOS led to a CH3OH yield of 21.1 mmol·g-1catal.·h-1 in the CuMnOS-CO2-H2O system and the other [Cu+]-low one had a H2 yield of 7.65 mmol·g-1catal.·h-1 in the CuMnOS-CH3OH-H2O system. The successful redox reactions at NTP rely on active lattice oxygen of CuMnOS catalysts and its charge (hole or electron) transfer ability between Cu+ and Cu2+. The CO2-hydrogenated CH3OH in aqueous solution is not only a fuel but also an ideal liquid hydrogen storage system for transportation application.

  14. CuMnOS Nanoflowers with Different Cu+/Cu2+ Ratios for the CO2-to-CH3OH and the CH3OH-to-H2 Redox Reactions

    PubMed Central

    Chen, Xiaoyun; Abdullah, Hairus; Kuo, Dong-Hau

    2017-01-01

    A conservative CO2-Methanol (CH3OH) regeneration cycle, to capture and reutilize the greenhouse gas of CO2 by aqueous hydrogenation for industry-useful CH3OH and to convert aqueous CH3OH solution by dehydrogenation for the clean energy of hydrogen (H2), is demonstrated at normal temperature and pressure (NTP) with two kinds of CuMnOS nanoflower catalysts. The [Cu+]-high CuMnOS led to a CH3OH yield of 21.1 mmol·g−1catal.·h−1 in the CuMnOS-CO2-H2O system and the other [Cu+]-low one had a H2 yield of 7.65 mmol·g−1catal.·h−1 in the CuMnOS-CH3OH-H2O system. The successful redox reactions at NTP rely on active lattice oxygen of CuMnOS catalysts and its charge (hole or electron) transfer ability between Cu+ and Cu2+. The CO2-hydrogenated CH3OH in aqueous solution is not only a fuel but also an ideal liquid hydrogen storage system for transportation application. PMID:28117456

  15. CuMnOS Nanoflowers with Different Cu+/Cu2+ Ratios for the CO2-to-CH3OH and the CH3OH-to-H2 Redox Reactions.

    PubMed

    Chen, Xiaoyun; Abdullah, Hairus; Kuo, Dong-Hau

    2017-01-24

    A conservative CO 2 -Methanol (CH 3 OH) regeneration cycle, to capture and reutilize the greenhouse gas of CO 2 by aqueous hydrogenation for industry-useful CH 3 OH and to convert aqueous CH 3 OH solution by dehydrogenation for the clean energy of hydrogen (H 2 ), is demonstrated at normal temperature and pressure (NTP) with two kinds of CuMnOS nanoflower catalysts. The [Cu + ]-high CuMnOS led to a CH 3 OH yield of 21.1 mmol·g -1 catal.·h -1 in the CuMnOS-CO 2 -H 2 O system and the other [Cu + ]-low one had a H 2 yield of 7.65 mmol·g -1 catal.·h -1 in the CuMnOS-CH 3 OH-H 2 O system. The successful redox reactions at NTP rely on active lattice oxygen of CuMnOS catalysts and its charge (hole or electron) transfer ability between Cu + and Cu 2+ . The CO 2 -hydrogenated CH 3 OH in aqueous solution is not only a fuel but also an ideal liquid hydrogen storage system for transportation application.

  16. Thermal Decomposition of Methyl Acetate (CH_3COOCH_3) in a Flash-Pyrolysis Micro-Reactor

    NASA Astrophysics Data System (ADS)

    Porterfield, Jessica P.; Bross, David H.; Ruscic, Branko; Thorpe, James H.; Nguyen, Thanh Lam; Baraban, Joshua H.; Stanton, John F.; Daily, John W.; Ellison, Barney

    2017-06-01

    The thermal decomposition of methyl acetate (CH_3COOCH_3) has been studied in a set of flash pyrolysis micro-reactors. Samples were diluted to (0.06 - 0.13%) in carrier gases (He, Ar) and subjected to temperatures of 300 - 1600 K at roughly 20 Torr. After residence times of approximately 25 - 150 μseconds, the unimolecular pyrolysis products were detected by vacuum ultraviolet photoionization mass spectrometry at 10.487 eV (118.2 nm). Complementary product identification was provided by matrix isolation infrared spectroscopy. Decomposition began at 1000 K with the observation of (CH_2=C=O, CH_3OH), products of a four centered rearrangement with a Δ_{rxn}H_{298} = 39.1 ± 0.2 kcal mol^{-1}. As the micro-reactor was heated to 1300 K, a mixture of (CH_2=C=O, CH_3OH, CH_3, CH_2=O, H, CO, CO_2) appeared. A new novel pathway is calculated in which both methyl groups leave behind CO_2 simultaneously, Δ_{rxn}H_{298} = 74.5 ± 0.4 kcal mol^{-1}. This pathway is in contrast to step-wise loss of methyl radical, which can go in two ways: Δ_{rxn}H_{298} (CH_3COOCH_3 → CH_3 + COOCH_3) = 95.4 ± 0.4 kcal mol^{-1}, Δ_{rxn}H_{298} (CH_3COOCH_3 → CH_3COO + CH_3) = 88.0 ± 0.3 kcal mol^{-1}.

  17. High pressure Raman spectroscopy of H2O-CH3OH mixtures.

    PubMed

    Hsieh, Wen-Pin; Chien, Yu-Hsiang

    2015-02-23

    Complex intra-molecular interactions and the hydrogen-bonding network in H2O-volatile mixtures play critical roles in many dynamics processes in physical chemistry, biology, and Earth and planetary sciences. We used high pressure Raman spectroscopy to study the pressure evolution of vibrational frequencies and bonding behavior in H2O-CH3OH mixtures. We found that the presence of low CH3OH content in H2O increases the transition pressure where water crystallizes to ice VI, but does not significantly change the pressure where ice VI transforms to ice VII. Furthermore, the stiffening rates of C-H stretching frequencies dω/dP in CH3OH significantly decrease upon the crystallization of water, and the softening rates of the O-H stretching frequencies of ice VII are suppressed over a narrow pressure range, after which the frequencies of these modes shift with pressure in ways similar to pure CH3OH and ice VII, respectively. Such complex pressure evolution of Raman frequencies along with pronounced variations in Raman intensities of CH3OH within the sample, and the hysteresis of the water-ice VI phase transition suggest pressure-induced segregation of low content CH3OH from ice VII. These findings indicate the significant influence of volatiles on the crystallization of sub-surface ocean and thermal evolution within large icy planets and satellites.

  18. 2,2‧,2″-Thiotris(acetic acid) betaine, S(CH2COOH)2(CH2COO), and 2,2‧,2″-selenotris(acetic acid) betaine, Se(CH2COOH)2(CH2COO)

    NASA Astrophysics Data System (ADS)

    Doudin, Khalid; Törnroos, Karl W.

    2017-04-01

    The title compounds, X(CH2COOH)2(CH2COO), X = S, 1, and X = Se, 2, have been characterised by FTIR, NMR and MS and by their crystal structures at 123(2) K. The FTIR spectra show two major peaks, at 1396 and 1731 cm-1 in 1 and at 1390 and 1721 cm-1 in 2. The 77Se NMR signal of 2 at 325.5 ppm is 83.4 ppm downfield from the signal of Se(CH2COOH)2 indicating a substantial selenonium character of 2. The two compounds are isostructural and have a pyramidal configuration. The C-X-C bond angles range from 99.29 to 103.14° in 1 and from 97.56 to 99.87° in 2. The Xsbnd Csbnd Cdbnd O torsion angles for the three substituents are most different; one of the carboxylic acid groups attains the anti-conformation with rather short S⋯O(H) and Se⋯O(H) distances, 2.744 and 2.750 Å, the other acid group is synclinal and with longer S⋯Odbnd C and Se⋯Odbnd C distances, 3.063 and 3.090 Å, whereas the carboxylate group is in the Xsbnd Csbnd C plane with X⋯Osbnd C distances of 2.869 and 2.908 Å in 1 and 2. The presence of these strong X⋯O interactions is suggested to be the cause for the very low Bronsted basicity of this class of betaines preventing salts of the corresponding acids, the presently unknown [X(CH2COOH)3]+ - cations, to be isolated. The molecules are linked together with two fairly strong but different hydrogen bonds to the carboxylate oxygen atoms with O⋯O distances of 2.493 and 2.580 Å in 1 and 2.489 and 2.581 Å in 2 and with one X⋯Odbnd C contact, 3.244 Å in 1 and 3.209 Å in 2. The carbonyl oxygen atoms do not participate significantly in intermolecular hydrogen bonding and there are no contacts between the heteroatoms.

  19. CH-π Interaction Driven Macroscopic Property Transition on Smart Polymer Surface

    NASA Astrophysics Data System (ADS)

    Li, Minmin; Qing, Guangyan; Xiong, Yuting; Lai, Yuekun; Sun, Taolei

    2015-10-01

    Life systems have evolved to utilize weak noncovalent interactions, particularly CH-π interaction, to achieve various biofunctions, for example cellular communication, immune response, and protein folding. However, for artificial materials, it remains a great challenge to recognize such weak interaction, further transform it into tunable macroscopic properties and realize special functions. Here we integrate monosaccharide-based CH-π receptor capable of recognizing aromatic peptides into a smart polymer with three-component “Recognition-Mediating-Function” design, and report the CH-π interaction driven surface property switching on smart polymer film, including wettability, adhesion, viscoelasticity and stiffness. Detailed studies indicate that, the CH-π interaction induces the complexation between saccharide unit and aromatic peptide, which breaks the initial amphiphilic balance of the polymer network, resulting in contraction-swelling conformational transition for polymer chains and subsequent dramatic switching in surface properties. This work not only presents a new approach to control the surface property of materials, but also points to a broader research prospect on CH-π interaction at a macroscopic level.

  20. CH-π Interaction Driven Macroscopic Property Transition on Smart Polymer Surface.

    PubMed

    Li, Minmin; Qing, Guangyan; Xiong, Yuting; Lai, Yuekun; Sun, Taolei

    2015-10-29

    Life systems have evolved to utilize weak noncovalent interactions, particularly CH-π interaction, to achieve various biofunctions, for example cellular communication, immune response, and protein folding. However, for artificial materials, it remains a great challenge to recognize such weak interaction, further transform it into tunable macroscopic properties and realize special functions. Here we integrate monosaccharide-based CH-π receptor capable of recognizing aromatic peptides into a smart polymer with three-component "Recognition-Mediating-Function" design, and report the CH-π interaction driven surface property switching on smart polymer film, including wettability, adhesion, viscoelasticity and stiffness. Detailed studies indicate that, the CH-π interaction induces the complexation between saccharide unit and aromatic peptide, which breaks the initial amphiphilic balance of the polymer network, resulting in contraction-swelling conformational transition for polymer chains and subsequent dramatic switching in surface properties. This work not only presents a new approach to control the surface property of materials, but also points to a broader research prospect on CH-π interaction at a macroscopic level.

  1. Optimal use of tandem biotin and V5 tags in ChIP assays

    PubMed Central

    Kolodziej, Katarzyna E; Pourfarzad, Farzin; de Boer, Ernie; Krpic, Sanja; Grosveld, Frank; Strouboulis, John

    2009-01-01

    Background Chromatin immunoprecipitation (ChIP) assays coupled to genome arrays (Chip-on-chip) or massive parallel sequencing (ChIP-seq) lead to the genome wide identification of binding sites of chromatin associated proteins. However, the highly variable quality of antibodies and the availability of epitopes in crosslinked chromatin can compromise genomic ChIP outcomes. Epitope tags have often been used as more reliable alternatives. In addition, we have employed protein in vivo biotinylation tagging as a very high affinity alternative to antibodies. In this paper we describe the optimization of biotinylation tagging for ChIP and its coupling to a known epitope tag in providing a reliable and efficient alternative to antibodies. Results Using the biotin tagged erythroid transcription factor GATA-1 as example, we describe several optimization steps for the application of the high affinity biotin streptavidin system in ChIP. We find that the omission of SDS during sonication, the use of fish skin gelatin as blocking agent and choice of streptavidin beads can lead to significantly improved ChIP enrichments and lower background compared to antibodies. We also show that the V5 epitope tag performs equally well under the conditions worked out for streptavidin ChIP and that it may suffer less from the effects of formaldehyde crosslinking. Conclusion The combined use of the very high affinity biotin tag with the less sensitive to crosslinking V5 tag provides for a flexible ChIP platform with potential implications in ChIP sequencing outcomes. PMID:19196479

  2. Evaluation of origins of CH4 carbon emitted from rice paddies

    NASA Astrophysics Data System (ADS)

    Watanabe, Akira; Takeda, Takuya; Kimura, Makoto

    1999-10-01

    Possible carbon sources for CH4 emitted from rice paddies are organic matter applied to the fields, such as rice straw (RS), soil organic matter (SOM), and carbon supplied from rice plants (RP), such as exudates and sloughed tissues. To estimate the contribution of each carbon source to CH4 emission, a pot experiment was conducted using 13C-enriched soil sample and 13C-enriched RS as tracers. The percentage contribution of RP carbon was estimated by subtraction. When RS was applied at a rate corresponding to 6 t ha-1, the percentage contributions of RS, SOM, and RP carbon to CH4 emission throughout the period of rice growth were 42%, 18-21%, and 37-40%, respectively. The values for SOM and RP carbon for the treatment in which RS was not applied were 15-20% and 80-85%, respectively. Seasonal variations in the percentage contribution of soil organic carbon to CH4 emission were small in the range between 13% and 30% for the pots with RS and between 15% and 24% for the pots without RS. In the RS-applied treatment, RS and SOM accounted for almost 100% of the CH4 carbon early in the period of rice growth, while 65-70% of the CH4 emission in the milky stage was derived from RP carbon.

  3. Periodic mesoporous organosilicas containing interconnected [Si(CH2)]3 rings.

    PubMed

    Landskron, Kai; Hatton, Benjamin D; Perovic, Doug D; Ozin, Geoffrey A

    2003-10-10

    A periodic mesoporous organosilica composed of interconnected three-ring [Si(CH2)]3 units built of three SiO2(CH2)2 tetrahedral subunits is reported. It represents the archetype of a previously unknown class of nanocomposite materials in which two bridging organic groups are bound to each silicon atom. It can be obtained with powder and oriented film morphologies. The nanocomposite is self-assembled from the cyclic three-ring silsesquioxane [(EtO)2Si(CH2)]3 precursor and a surfactant mesophase to give a well-ordered mesoporous framework. Low dielectric constants and good mechanical stability of the films were measured, making this material interesting for microelectronic applications. Methylene group reactivity of the three-ring precursor provides entry to a family of nanocomposites, exemplified by the synthesis and self-assembly of [(EtO)2Si(CHR)][(EtO)2Si(CH2)]2 (where R indicates iodine, bromine, or an ethyl group).

  4. Optical emission spectroscopic studies and comparisons of CH{sub 3}F/CO{sub 2} and CH{sub 3}F/O{sub 2} inductively coupled plasmas

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Lou, Qiaowei; Kaler, Sanbir; Donnelly, Vincent M., E-mail: vmdonnelly@uh.edu

    2015-03-15

    A CH{sub 3}F/CO{sub 2} inductively coupled plasma (ICP), sustained in a compact plasma reactor, was investigated as a function of power (5–400 W) and feed gas composition, at a pressure of 10 mTorr, using optical emission spectroscopy and rare gas actinometry. Number densities of H, F, and O increased rapidly between 74% and 80% CO{sub 2}, ascribed to the transition from polymer-covered to polymer-free reactor walls, similar to that found previously in CH{sub 3}F/O{sub 2} ICPs at 48% O{sub 2}. Below 40% O{sub 2} or CO{sub 2}, relative emission intensity ratios were almost identical for most key species in CH{sub 3}F/O{submore » 2} and CH{sub 3}F/CO{sub 2} ICPs except for higher OH/Xe (a qualitative measure of OH and H{sub 2}O densities) over the full range of CH{sub 3}F/O{sub 2} composition. The number density of H, F, and O increased with power in CH{sub 3}F/CO{sub 2} (20%/80%) plasmas (polymer-free walls), reaching 4.0, 0.34, and 1.6 × 10{sup 13}/cm{sup 3}, respectively, at 300 W. The CO number density increased with power and was estimated, based on self-actinometry, to be 8.8 × 10{sup 13}/cm{sup 3} at 300 W. The CO{sub 2} number density was independent of power below 40 W (where very little decomposition occurred), and then decreased rapidly with increasing power, reaching 2.8 × 10{sup 13}/cm{sup 3} at 300 W, corresponding to 83% dissociation. Films deposited on p-Si, 10 cm from the open, downstream end of the plasma reactor, were analyzed by x-ray photoelectron spectroscopy. Between 10% and 40% CO{sub 2} or O{sub 2} addition to CH{sub 3}F, film deposition rates fell and O content in the films increased. Faster deposition rates in CH{sub 3}F/CO{sub 2} plasmas were ascribed mainly to a larger thermodynamic driving force to form solid carbon, compared with CH{sub 3}F/O{sub 2} plasmas. Oxygen content in the films increased with increasing CO{sub 2} or O{sub 2} addition, but for the same deposition rate, no substantial differences

  5. CH3Cl, CH2Cl2, CHCl3, and CCl4: Infrared spectra, radiative efficiencies, and global warming potentials

    NASA Astrophysics Data System (ADS)

    Wallington, Timothy J.; Pivesso, Bruno Pasquini; Lira, Alane Moura; Anderson, James E.; Nielsen, Claus Jørgen; Andersen, Niels Højmark; Hodnebrog, Øivind

    2016-05-01

    Infrared spectra for the title compounds were measured experimentally in 700 Torr of air at 295 K and systematically modeled in B3LYP, M06-2X and MP2 calculations employing various basis sets. Calibrated infrared spectra over the wavenumber range 600-3500 cm-1 are reported and combined with literature data to provide spectra for use in experimental studies and radiative transfer calculations. Integrated absorption cross sections are (units of cm-1 molecule-1): CH3Cl, 660-780 cm-1, (3.89±0.19)×10-18; CH2Cl2, 650-800 cm-1, (2.16±0.11)×10-17; CHCl3, 720-810 cm-1, (4.08±0.20)×10-17; and CCl4, 730-825 cm-1, (6.30±0.31)×10-17. CH3Cl, CH2Cl2, CHCl3, and CCl4 have radiative efficiencies of 0.004, 0.028, 0.070, and 0.174 W m-2 ppb-1 and global warming potentials (100 year horizon) of 5, 8, 15, and 1775, respectively. Quantum chemistry calculations generally predict larger band intensities than the experimental values. The best agreement with experiments is obtained in MP2(Full) calculations employing basis sets of at least triple-zeta quality augmented by diffuse functions. The B3LYP functional is found ill-suited for calculating vibrational frequencies and infrared intensities of halocarbons.

  6. Molecular structure and conformational preferences of 1-bromo-1-silacyclohexane, CH2(CH2CH2)2SiH-Br, as studies by gas-phase electron diffraction and quantum chemistry

    NASA Astrophysics Data System (ADS)

    Belyakov, A. V.; Baskakov, A. A.; Naraev, V. N.; Rykov, A. N.; Oberhammer, H.; Arnason, I.; Wallevik, S. O.

    2012-10-01

    The molecular structure of axial and equatorial conformer of the 1-bromo-1-silacyclohexane molecule, CH2(CH2CH2)2SiH-Br, as well as thermodynamic equilibrium between these species are investigated by means of gas-phase electron diffraction and quantum chemistry on the MP2(full)/SDB-AUG-cc-PVTZ level of theory. It is revealed that according to electron diffraction data, the compound exists in the gasphase as a mixture of conformers possessing the chair conformation of the six-membered ring and C s symmetry and differing in the axial and equatorial position of the Si-Br bond (ax. = 80(5) mol %, eq. = 20(7) mol %) at 352 K, that corresponds to the value of A = ( G {ax/○} - G {eq/○}) = -0.82(32) kcal/mol. It is found that observed data agree well with theoretical ones. Using Natural Bond Orbital (NBO) analysis it is revealed that axial conformer of 1-bromo-1-silacyclohexane molecule is an example of the stabilization of the form that is unfavorable from the point of view of steric effects and effects of conjugations. It is concluded that stabilization is achieved due to electrostatic interactions.

  7. Further development of a global pollution model for CO, CH4, and CH2 O

    NASA Technical Reports Server (NTRS)

    Peters, L. K.

    1975-01-01

    Global tropospheric pollution models are developed that describe the transport and the physical and chemical processes occurring between the principal sources and sinks of CH4 and CO. Results are given of long term static chemical kinetic computer simulations and preliminary short term dynamic simulations.

  8. Analysis of ChIP-seq Data in R/Bioconductor.

    PubMed

    de Santiago, Ines; Carroll, Thomas

    2018-01-01

    The development of novel high-throughput sequencing methods for ChIP (chromatin immunoprecipitation) has provided a very powerful tool to study gene regulation in multiple conditions at unprecedented resolution and scale. Proactive quality-control and appropriate data analysis techniques are of critical importance to extract the most meaningful results from the data. Over the last years, an array of R/Bioconductor tools has been developed allowing researchers to process and analyze ChIP-seq data. This chapter provides an overview of the methods available to analyze ChIP-seq data based primarily on software packages from the open-source Bioconductor project. Protocols described in this chapter cover basic steps including data alignment, peak calling, quality control and data visualization, as well as more complex methods such as the identification of differentially bound regions and functional analyses to annotate regulatory regions. The steps in the data analysis process were demonstrated on publicly available data sets and will serve as a demonstration of the computational procedures routinely used for the analysis of ChIP-seq data in R/Bioconductor, from which readers can construct their own analysis pipelines.

  9. Assessing fugitive emissions of CH4 from high-pressure gas pipelines

    NASA Astrophysics Data System (ADS)

    Worrall, Fred; Boothroyd, Ian; Davies, Richard

    2017-04-01

    The impact of unconventional natural gas production using hydraulic fracturing methods from shale gas basins has been assessed using life-cycle emissions inventories, covering areas such as pre-production, production and transmission processes. The transmission of natural gas from well pad to processing plants and its transport to domestic sites is an important source of fugitive CH4, yet emissions factors and fluxes from transmission processes are often based upon ver out of date measurements. It is important to determine accurate measurements of natural gas losses when compressed and transported between production and processing facilities so as to accurately determine life-cycle CH4 emissions. This study considers CH4 emissions from the UK National Transmission System (NTS) of high pressure natural gas pipelines. Mobile surveys of CH4 emissions using a Picarro Surveyor cavity-ring-down spectrometer were conducted across four areas in the UK, with routes bisecting high pressure pipelines and separate control routes away from the pipelines. A manual survey of soil gas measurements was also conducted along one of the high pressure pipelines using a tunable diode laser. When wind adjusted 92 km of high pressure pipeline and 72 km of control route were drive over a 10 day period. When wind and distance adjusted CH4 fluxes were significantly greater on routes with a pipeline than those without. The smallest leak detectable was 3% above ambient (1.03 relative concentration) with any leaks below 3% above ambient assumed ambient. The number of leaks detected along the pipelines correlate to the estimated length of pipe joints, inferring that there are constant fugitive CH4 emissions from these joints. When scaled up to the UK's National Transmission System pipeline length of 7600 km gives a fugitive CH4 flux of 4700 ± 2864 kt CH4/yr - this fugitive emission from high pressure pipelines is 0.016% of the annual gas supply.

  10. Molecular Level Investigation of CH 4 and CO 2 Adsorption in Hydrated Calcium–Montmorillonite

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Lee, Mal-Soon; McGrail, B. Peter; Rousseau, Roger

    2017-11-17

    We have studied the mechanism of intercalation and methane adsorption from a H2O/CH4/CO2 mixture on a prototypical shale component, Ca-montmorillonite. We employed ab initio molecular dynamics simulations at 323 K and 90 bar to obtain molecular level information of adsorption energetics, speciation, and structural and thermodynamic properties. Interaction of CH4 with surface Lewis acidic sites (Ca2+, surface OH) results in large induced dipoles (~1 D) that lead to relatively strong adsorption energies that level off once a full CH4 layer is formed. Intercalated CH4, also exhibits induced dipoles at low hydration levels, when the interaction with Ca2+ cations are lessmore » hindered. CO2 displaces CH4 in the coordination sphere of the cations (in the interlayer) or in the surface, thereby driving CH4 extraction. Our simulations indicate that there is a Goldilocks pressure range (~60-100 bar) where scCO2 –facilitated CH4 extraction will be maximized.« less

  11. ChEMBL web services: streamlining access to drug discovery data and utilities

    PubMed Central

    Davies, Mark; Nowotka, Michał; Papadatos, George; Dedman, Nathan; Gaulton, Anna; Atkinson, Francis; Bellis, Louisa; Overington, John P.

    2015-01-01

    ChEMBL is now a well-established resource in the fields of drug discovery and medicinal chemistry research. The ChEMBL database curates and stores standardized bioactivity, molecule, target and drug data extracted from multiple sources, including the primary medicinal chemistry literature. Programmatic access to ChEMBL data has been improved by a recent update to the ChEMBL web services (version 2.0.x, https://www.ebi.ac.uk/chembl/api/data/docs), which exposes significantly more data from the underlying database and introduces new functionality. To complement the data-focused services, a utility service (version 1.0.x, https://www.ebi.ac.uk/chembl/api/utils/docs), which provides RESTful access to commonly used cheminformatics methods, has also been concurrently developed. The ChEMBL web services can be used together or independently to build applications and data processing workflows relevant to drug discovery and chemical biology. PMID:25883136

  12. Ozone Depletion Potential of CH3Br. Appendix H

    NASA Technical Reports Server (NTRS)

    Ko, Malcolm K. W.; Sze, Nien Dak; Scott, Courtney; Rodriguez, Jose M.; Weisenstein, Debra K.; Sander, Stanley P.

    1998-01-01

    The ozone depletion potential (ODP) of methyl bromide (CH3Br) can be determined by combining the model-calculated bromine efficiency factor (BEF) for CH3Br and its atmospheric lifetime. This paper examines how changes in several key kinetic data affect BEF. The key reactions highlighted in this study include the reaction of BrO + HO2, the absorption cross section of HOBr, the absorption cross section and the photolysis products of BrONO2, and the heterogeneous conversion of BrONO2 to HOBr and HNO3 on aerosol particles. By combining the calculated BEF with the latest estimate of 0.7 year for the atmospheric lifetime of CH3Br, the likely value of ODP for CH3Br is 0.39. The model-calculated concentration of HBr (approx. 0.3 pptv) in the lower stratosphere is substantially smaller than the reported measured value of about 1 pptv. Recent publications suggested models can reproduce the measured value if one assumes a yield for HBr from the reaction of BrO + OH or from the reaction of BrO + HO2. Although the evaluation concluded any substantial yield of HBr from BrO + HO2 is unlikely, for completeness, we calculate the effects of these assumed yields on BEF for CH3Br. Our calculations show that the effects are minimal: practically no impact for an assumed 1.3% yield of HBr from BrO + OH and 10% smaller for an assumed 0.6% yield from BrO + HO2.

  13. CH4 emissions from two floodplain fens of differing nutrient status

    NASA Astrophysics Data System (ADS)

    Stanley, Kieran; Heppell, Catherine; Belyea, Lisa; Baird, Andrew

    2014-05-01

    Floodplain fens emit large amounts of CH4 in comparison with ombrotrophic bogs. Little is known about the effect of fluvial nitrogen (N) and phosphorus (P) on CH4 dynamics in fens, although N and P affect carbon (C) dynamics indirectly in other environments by controlling plant growth and root exudate release, as well as by altering microbial biomass and decomposition rates. This study aimed to compare CH4 emissions from two floodplain fen sites which differ in nutrient status, Sutton Fen (52°45'N 001°30'E) and Strumpshaw Fen (52°36'N 001°27'E), in the Norfolk Broadland of England. Sutton and Strumpshaw Fen are under conservation management and both sites have water levels that vary within a few decimetres above and below the surface. The sites are dominated by reed (Phragmites australis). Areas within the fens where the reed was cut in 2009 were chosen for this study. Average plant height and mean aboveground biomass were significantly greater at Strumpshaw (107.2 ± 7.8 cm and 1578 ± 169 g m-2, respectively) than Sutton (56.5 ± 5.1 cm and 435 ± 42 g m-2) as were mean foliar N and P contents (21.8 ± 1.5 g kg-1 and 2.0 ± 0.2 g kg-1 at Strumpshaw, versus 16.3 ± 1.5 g kg-1 and 1.1 ± 0.1 g kg-1 at Sutton). Foliar NPK ratios showed Strumpshaw to be N limited, whereas Sutton was both N and P limited, depending on microsite. Surface peat N and P contents were also greater at Strumpshaw (28.3 ± 0.35 g kg-1 and 0.78 ± 0.02 g kg-1, respectively) than Sutton (18.32 ± 0.87 g kg-1 and 0.43 ± 0.1 g kg-1). These results indicate clear differences in nutrient status between the two sites despite their geographical proximity and other similarities. CH4 emissions were monitored monthly between 19th June 2012 and 2nd September 2013 using tall static chambers and glass funnel-traps, the latter for ebullition. Steady fluxes did not follow a clear seasonal pattern; however, emission was greatest in the summer months. Strumpshaw had a greater range in efflux (0.25 to 134

  14. Cloning and characterization of the Cerasus humilis sucrose phosphate synthase gene (ChSPS1)

    PubMed Central

    Du, Junjie; Mu, Xiaopeng; Wang, Pengfei

    2017-01-01

    Sucrose is crucial to the growth and development of plants, and sucrose phosphate synthase (SPS) plays a key role in sucrose synthesis. To understand the genetic and molecular mechanisms of sucrose synthesis in Cerasus humilis, ChSPS1, a homologue of SPS, was cloned using RT-PCR. Sequence analysis showed that the open reading frame (ORF) sequence of ChSPS1 is 3174 bp in length, encoding a predicted protein of 1057 amino acids. The predicted protein showed a high degree of sequence identity with SPS homologues from other species. Real-time RT-PCR analysis showed that ChSPS1 mRNA was detected in all tissues and the transcription level was the highest in mature fruit. There is a significant positive correlation between expression of ChSPS1 and sucrose content. Prokaryotic expression of ChSPS1 indicated that ChSPS1 protein was expressed in E. coli and it had the SPS activity. Overexpression of ChSPS1 in tobacco led to upregulation of enzyme activity and increased sucrose contents in transgenic plants. Real-time RT-PCR analysis showed that the expression of ChSPS1 in transgenic tobacco was significantly higher than in wild type plants. These results suggested that ChSPS1 plays an important role in sucrose synthesis in Cerasus humilis. PMID:29036229

  15. Joint CO2 and CH4 accountability for global warming.

    PubMed

    Smith, Kirk R; Desai, Manish A; Rogers, Jamesine V; Houghton, Richard A

    2013-07-30

    We propose a transparent climate debt index incorporating both methane (CH4) and carbon dioxide (CO2) emissions. We develop national historic emissions databases for both greenhouse gases to 2005, justifying 1950 as the starting point for global perspectives. We include CO2 emissions from fossil sources [CO2(f)], as well as, in a separate analysis, land use change and forestry. We calculate the CO2(f) and CH4 remaining in the atmosphere in 2005 from 205 countries using the Intergovernmental Panel on Climate Change's Fourth Assessment Report impulse response functions. We use these calculations to estimate the fraction of remaining global emissions due to each country, which is applied to total radiative forcing in 2005 to determine the combined climate debt from both greenhouse gases in units of milliwatts per square meter per country or microwatts per square meter per person, a metric we term international natural debt (IND). Australia becomes the most indebted large country per capita because of high CH4 emissions, overtaking the United States, which is highest for CO2(f). The differences between the INDs of developing and developed countries decline but remain large. We use IND to assess the relative reduction in IND from choosing between CO2(f) and CH4`control measures and to contrast the imposed versus experienced health impacts from climate change. Based on 2005 emissions, the same hypothetical impact on world 2050 IND could be achieved by decreasing CH4 emissions by 46% as stopping CO2 emissions entirely, but with substantial differences among countries, implying differential optimal strategies. Adding CH4 shifts the basic narrative about differential international accountability for climate change.

  16. FABP4-Cre mediated expression of constitutively active ChREBP protects against obesity

    USDA-ARS?s Scientific Manuscript database

    Carbohydrate response element binding protein (ChREBP) regulates cellular glucose and lipid homeostasis. Although ChREBP is highly expressed in many key metabolic tissues, the role of ChREBP in most of those tissues and consequent effects on whole-body glucose and lipid metabolism are not well under...

  17. CH/sub 3/xxx/sup 13/CO/sub 2/ pairs in irradiated single crystals of CH/sub 3//sup 13/CO/sub 2/Lix2D/sub 2/0. [Gamma rays

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Toriyama, K.; Iwasaki, M.

    1976-10-01

    The CH/sub 3/ radical trapped in irradiated single crystals of CH/sub 3//sup 13/CO/sub 2/Lix2D/sub 2/O has been found to interact with a /sup 13/CO/sub 2/ molecule, which is formed from the C--C bond breakage as a counterpart. The /sup 13/C superhyperfine coupling tensor was determined to be (-4.0, -3.3, -3.5) G. The /sup 13/CO/sub 2/ molecule is located in the direction of the unpaired electron orbital of CH/sub 3/ with the molecular axis perpendicular to it. The spectrum arising from the electron excess center CH/sub 3/ /sup 13/CO/sub 2//sup 2 -/ was also detected together with the CH/sub 3/ radical.more » Our results indicate that the CH/sub 3/xxx/sup 13/CO/sub 2/ pair is essentially a positive hole center formed from one electron loss followed by the C--C bond breakage. (AIP)« less

  18. Assessing diel variation of CH4 flux from rice paddies through temperature patterns

    NASA Astrophysics Data System (ADS)

    Centeno, Caesar Arloo R.; Alberto, Ma Carmelita R.; Wassmann, Reiner; Sander, Bjoern Ole

    2017-10-01

    The diel variation in methane (CH4) flux from irrigated rice was characterized during the dry and wet cropping seasons in 2013 and 2014 using the eddy covariance (EC) technique. The EC technique has the advantage of obtaining measurements of fluxes at an extremely high temporal resolution (10Hz), meaning it records 36,000 measurements per hour. The EC measurements can very well capture the temporal variations of the diel (both diurnal and nocturnal) fluxes of CH4 and the environmental factors (temperature, surface energy flux, and gross ecosystem photosynthesis) at 30-min intervals. The information generated by this technique is important to enhance our mechanistic understanding of the different factors affecting the landscape scale diel CH4 flux. Distinct diel patterns of CH4 flux were observed when the data were partitioned into different cropping periods (pre-planting, growth, and fallow). The temporal variations of the diel CH4 flux during the dry seasons were more pronounced than during the wet seasons because the latter had so much climatic disturbance from heavy monsoon rains and occasional typhoons. Pearson correlation analysis and Granger causality test were used to confirm if the environmental factors evaluated were not only correlated with but also Granger-causing the diel CH4 flux. Soil temperature at 2.5 cm depth (Ts 2.5 cm) can be used as simple proxy for predicting diel variations of CH4 fluxes in rice paddies using simple linear regression during both the dry and wet seasons. This simple site-specific temperature response function can be used for gap-filling CH4 flux data for improving the estimates of CH4 source strength from irrigated rice production.

  19. Full Genome Sequence of Giant Panda Rotavirus Strain CH-1

    PubMed Central

    Guo, Ling; Yang, Shaolin; Wang, Chengdong; Chen, Shijie; Yang, Xiaonong; Hou, Rong; Quan, Zifang; Hao, Zhongxiang

    2013-01-01

    We report here the complete genomic sequence of the giant panda rotavirus strain CH-1. This work is the first to document the complete genomic sequence (segments 1 to 11) of the CH-1 strain, which offers an effective platform for providing authentic research experiences to novice scientists. PMID:23469354

  20. Microsolvation effects on the reactivity of oxy-nucleophiles: the case of gas-phase SN2 reactions of YO-(CH3OH) n=1,2 towards CH3Cl.

    PubMed

    Yun-Yun, Liu; Fang-Zhou, Qiu; Jun, Zhu; Yi, Ren; Kai-Chung, Lau

    2017-06-01

    The modified G4(MP2) method was applied to explore microsolvation effects on the reactivity of four solvated normal oxy-nucleophiles YO - (CH 3 OH) n=1,2 (Y = CH 3 , C 2 H 5 , FC 2 H 4 , ClC 2 H 4 ), and five α-oxy-nucleophiles YO - (CH 3 OH) n=1,2 (Y = HO, CH 3 O, F, Cl, Br), in gas-phase S N 2 reactions towards the substrate CH 3 Cl. Based on a Brønsted-type plot, our calculations reveal that the overall activation barriers of five microsolvated α-oxy-nucleophiles are obviously smaller than the prediction from the correlation line constructed by four normal microsolvated ones to different degrees, and clearly demonstrate the existence of an α-effect in the presence of one or two methanol molecule(s). Moreover, it was found that the α-effect of the mono-methanol microsolvated α-nucleophile is stronger than that of the monohydrated α-nucleophile. However, the α-effect of YO - (CH 3 OH) 2 becomes weaker for Y = HO and CH 3 O, whereas it becomes stronger for Y = F, Cl, Br than that of YO - (H 2 O) 2 , which can be explained by analyses of the activation strain model in the two cases. It was also found that the rationale about the low ionization energy of α-nucleophile inducing the α-effect was not widely significant. Graphical abstract Variation of alpha-effect in the gas-phase S N 2 reaction with the microsolvation.

  1. Comparison of CH4 Emission from Rice Paddy Soils between Coastal Zone and Inland Regions

    NASA Astrophysics Data System (ADS)

    Sun, M.; Li, X.

    2016-12-01

    Numerous measurements of methane (CH4) emission fluxes have been carried out in rice paddy soil between coastal zone and inland regions. However, the differences of CH4 emission from rice paddy soils in these two locations were unavailable. A database of CH4 emission in paddy rice was compiled from previous published references and field observations with major parameters including water regimes, fertilizer application, CH4 fluxes, and environmental variables. Results showed that CH4 emission from inland paddy fields was significantly higher than that in the coastal zone (p < 0.05). Fertilizer application and water management played an important role in CH4 emission. The application of organic fertilizer and continuous flooding significantly promoted CH4 emission from paddy fields. CH4 fluxes showed significantly positive correlations with organic matter, total nitrogen, available potassium and annual temperature (R2 = 0.39, 0.53, 0.27 and 0.23, p < 0.05), and negative correlations with pH and available phosphorus (R2 = 0.29 and 0.37, p < 0.05). Significant differences occurred in available potassium between inland and coastal rice paddy (p < 0.05), which might account for the difference of CH4 emission between inland and coastal rice paddy. The contrasting of CH4 fluxes between inland and coastal wetlands could improve our understanding of the roles of rice paddies in the regional CH4 regulation. Our results also have implications for informing rice paddy management and climate change policy making the efforts being made by agricultural organizations and enterprises to restore coastal rice paddies for mitigating CH4 emissions.

  2. ChEMBL web services: streamlining access to drug discovery data and utilities.

    PubMed

    Davies, Mark; Nowotka, Michał; Papadatos, George; Dedman, Nathan; Gaulton, Anna; Atkinson, Francis; Bellis, Louisa; Overington, John P

    2015-07-01

    ChEMBL is now a well-established resource in the fields of drug discovery and medicinal chemistry research. The ChEMBL database curates and stores standardized bioactivity, molecule, target and drug data extracted from multiple sources, including the primary medicinal chemistry literature. Programmatic access to ChEMBL data has been improved by a recent update to the ChEMBL web services (version 2.0.x, https://www.ebi.ac.uk/chembl/api/data/docs), which exposes significantly more data from the underlying database and introduces new functionality. To complement the data-focused services, a utility service (version 1.0.x, https://www.ebi.ac.uk/chembl/api/utils/docs), which provides RESTful access to commonly used cheminformatics methods, has also been concurrently developed. The ChEMBL web services can be used together or independently to build applications and data processing workflows relevant to drug discovery and chemical biology. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  3. Spike-In Normalization of ChIP Data Using DNA-DIG-Antibody Complex.

    PubMed

    Eberle, Andrea B

    2018-01-01

    Chromatin immunoprecipitation (ChIP) is a widely used method to determine the occupancy of specific proteins within the genome, helping to unravel the function and activity of specific genomic regions. In ChIP experiments, normalization of the obtained data by a suitable internal reference is crucial. However, particularly when comparing differently treated samples, such a reference is difficult to identify. Here, a simple method to improve the accuracy and reliability of ChIP experiments by the help of an external reference is described. An artificial molecule, composed of a well-defined digoxigenin (DIG) labeled DNA fragment in complex with an anti-DIG antibody, is synthesized and added to each chromatin sample before immunoprecipitation. During the ChIP procedure, the DNA-DIG-antibody complex undergoes the same treatments as the chromatin and is therefore purified and quantified together with the chromatin of interest. This external reference compensates for variability during the ChIP routine and improves the similarity between replicates, thereby emphasizing the biological differences between samples.

  4. International management platform for children's interstitial lung disease (chILD-EU).

    PubMed

    Griese, Matthias; Seidl, Elias; Hengst, Meike; Reu, Simone; Rock, Hans; Anthony, Gisela; Kiper, Nural; Emiralioğlu, Nagehan; Snijders, Deborah; Goldbeck, Lutz; Leidl, Reiner; Ley-Zaporozhan, Julia; Krüger-Stollfuss, Ingrid; Kammer, Birgit; Wesselak, Traudl; Eismann, Claudia; Schams, Andrea; Neuner, Doerthe; MacLean, Morag; Nicholson, Andrew G; Lauren, McCann; Clement, Annick; Epaud, Ralph; de Blic, Jacques; Ashworth, Michael; Aurora, Paul; Calder, Alistair; Wetzke, Martin; Kappler, Matthias; Cunningham, Steve; Schwerk, Nicolaus; Bush, Andy

    2018-03-01

    Children's interstitial lung diseases (chILD) cover many rare entities, frequently not diagnosed or studied in detail. There is a great need for specialised advice and for internationally agreed subclassification of entities collected in a register.Our objective was to implement an international management platform with independent multidisciplinary review of cases at presentation for long-term follow-up and to test if this would allow for more accurate diagnosis. Also, quality and reproducibility of a diagnostic subclassification system were assessed using a collection of 25 complex chILD cases. A web-based chILD management platform with a registry and biobank was successfully designed and implemented. Over a 3-year period, 575 patients were included for observation spanning a wide spectrum of chILD. In 346 patients, multidisciplinary reviews were completed by teams at five international sites (Munich 51%, London 12%, Hannover 31%, Ankara 1% and Paris 5%). In 13%, the diagnosis reached by the referring team was not confirmed by peer review. Among these, the diagnosis initially given was wrong (27%), imprecise (50%) or significant information was added (23%).The ability of nine expert clinicians to subcategorise the final diagnosis into the chILD-EU register classification had an overall exact inter-rater agreement of 59% on first assessment and after training, 64%. Only 10% of the 'wrong' answers resulted in allocation to an incorrect category. Subcategorisation proved useful but training is needed for optimal implementation. We have shown that chILD-EU has generated a platform to help the clinical assessment of chILD. Results, NCT02852928. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

  5. FAST TRACK COMMUNICATION Multi-component generalizations of the CH equation: geometrical aspects, peakons and numerical examples

    NASA Astrophysics Data System (ADS)

    Holm, D. D.; Ivanov, R. I.

    2010-12-01

    The Lax pair formulation of the two-component Camassa-Holm equation (CH2) is generalized to produce an integrable multi-component family, CH(n, k), of equations with n components and 1 <= |k| <= n velocities. All of the members of the CH(n, k) family show fluid-dynamics properties with coherent solitons following particle characteristics. We determine their Lie-Poisson Hamiltonian structures and give numerical examples of their soliton solution behaviour. We concentrate on the CH(2, k) family with one or two velocities, including the CH(2, -1) equation in the Dym position of the CH2 hierarchy. A brief discussion of the CH(3, 1) system reveals the underlying graded Lie-algebraic structure of the Hamiltonian formulation for CH(n, k) when n >= 3. Fondly recalling our late friend Jerry Marsden.

  6. The vacuum-ultraviolet photoelectron spectra of CH2F2 and CH2Cl2 revisited

    NASA Astrophysics Data System (ADS)

    Tuckett, Richard; Harvey, Jonelle; Hemberger, Patrick; Bodi, Andras

    2015-09-01

    The threshold photoelectron spectrum (TPES) of difluoromethane and dichloromethane has been recorded at the Swiss Light Source with a resolution of 2 meV or 16 cm-1. Electronic and vibronic transitions are simulated and assigned with the help of Franck-Condon (FC) calculations based on coupled cluster electronic structure calculations for the equilibrium geometries and harmonic vibrational frequencies of the neutrals, and of the ground and excited electronic states of the cations. Notwithstanding a high-resolution pulsed-field ionisation study on CH2F2 (Forysinski et al., 2010) in which a number of transitions to the X∼+ state have been recorded with unprecedented accuracy, we report the first complete vibrationally resolved overview of the low-lying electronic states of CH2X2+, X = F or Cl. Hydrogen atom loss from CH2F2+ occurs at low energy, making the ground state rather anharmonic and interpretation of the X∼+ band challenging in the harmonic approximation. By Franck-Condon fits, the adiabatic ionisation energies to the A∼+ 2B2, C∼+ 2A2 and D∼+ 2B2 states have been determined as 14.3 ± 0.1, 15.57 ± 0.01 and 18.0 ± 0.1 eV, respectively. The first band in the CH2Cl2 TPES is complex for a different reason, as it is the result of two overlapping ionic states, X∼+ 2B2 and A∼+ 2B1, with derived ionisation energies of 11.0 ± 0.2 and 11.317 ± 0.006 eV, and dominated by an extended progression in the CCl2 bend (in X∼+) and a short progression in the CCl2 symmetric stretch (in A∼+), respectively. Furthermore, even though Koopmans' approximation holds for the vertical ionisations, the X∼+ state of CH2Cl2+ is stabilized by geometry relaxation and corresponds to ionisation from the (HOMO-1) orbital. That is, the first two vertical ionisation energies are in the same order as the negative of the orbital energies of the highest occupied orbitals, but the adiabatic ionisation energy corresponding to electron removal from the (HOMO-1) is lower than the

  7. Space-Based Remote Imaging Spectroscopy of the Aliso Canyon CH4 Superemitter

    NASA Technical Reports Server (NTRS)

    Thompson, D. R.; Thorpe, A. K.; Frankenberg, C.; Green, R. O.; Duren, R.; Guanter, L.; Hollstein, A.; Middleton, E.; Ong, L.; Ungar, S.

    2016-01-01

    The Aliso Canyon gas storage facility near Porter Ranch, California, produced a large accidental CH4 release from October 2015 to February 2016. The Hyperion imaging spectrometer on board the EO-1 satellite successfully detected this event, achieving the first orbital attribution of CH4 to a single anthropogenic superemitter. Hyperion measured shortwave infrared signatures of CH4 near 2.3 microns at 0.01 micron spectral resolution and 30 meter spatial resolution. It detected the plume on three overpasses, mapping its magnitude and morphology. These orbital observations were consistent with measurements by airborne instruments. We evaluate Hyperion instrument performance, draw implications for future orbital instruments, and extrapolate the potential for a global survey of CH4 superemitters.

  8. Effects of prolonged soil drought on CH4 oxidation in a temperate spruce forest

    NASA Astrophysics Data System (ADS)

    Borken, W.; Brumme, R.; Xu, Y.-J.

    2000-03-01

    Our objective was to determine potential impacts of changes in rainfall amount and distribution on soil CH4 oxidation in a temperate forest ecosystem. We constructed a roof below the canopy of a 65-year-old Norway spruce forest (Picea abies (L.) Karst.) and simulated two climate change scenarios: (1) an extensively prolonged summer drought of 172 days followed by a rewetting period of 19 days in 1993 and (2) a less intensive summer drought of 108 days followed by a rewetting period of 33 days in 1994. CH4 oxidation, soil matric potential, and soil temperature were measured hourly to daily over a 2-year period. The results showed that annual CH4 oxidation in the drought experiment increased by 102% for the climate change scenario 1 and by 41% for the climate change scenario 2, compared to those of the ambient plot (1.33 kg CH4 ha-1 in 1993 and 1.65 kg CH4 ha-1 in 1994). We tested the relationships between CH4 oxidation rates, water-filled pore space (WFPS), soil matric potential, gas diffusivity, and soil temperature. Temporal variability in the CH4 oxidation rates corresponded most closely to soil matric potential. Employing soil matric potential and soil temperature, we developed a nonlinear model for estimating CH4 oxidation rates. Modeled results were in strong agreement with the measured CH4 oxidation for the ambient (r2 = 0.80) and drought plots (r2 = 0.89) over two experimental years, suggesting that soil matric potential is a highly reliable parameter for modeling CH4 oxidation rate.

  9. Near-thermal reactions of Au(+)(1S,3D) with CH3X (X = F,Cl).

    PubMed

    Taylor, William S; Matthews, Cullen C; Hicks, Ashley J; Fancher, Kendall G; Chen, Li Chen

    2012-01-26

    Reactions of Au(+)((1)S) and Au(+)((3)D) with CH(3)F and CH(3)Cl have been carried out in a drift cell in He at a pressure of 3.5 Torr at both room temperature and reduced temperatures in order to explore the influence of the electronic state of the metal on reaction outcomes. State-specific product channels and overall two-body rate constants were identified using electronic state chromatography. These results indicate that Au(+)((1)S) reacts to yield an association product in addition to AuCH(2)(+) in parallel steps with both neutrals. Product distributions for association vs HX elimination were determined to be 79% association/21% HX elimination for X = F and 50% association/50% HX elimination when X = Cl. Reaction of Au(+)((3)D) with CH(3)F also results in HF elimination, which in this case is thought to produce (3)AuCH(2)(+). With CH(3)Cl, Au(+)((3)D) reacts to form AuCH(3)(+) and CH(3)Cl(+) in parallel steps. An additional product channel initiated by Au(+)((3)D) is also observed with both methyl halides, which yields CH(2)X(+) as a higher-order product. Kinetic measurements indicate that the reaction efficiency for both Au(+) states is significantly greater with CH(3)Cl than with CH(3)F. The observed two-body rate constant for depletion of Au(+)((1)S) by CH(3)F represents less than 5% of the limiting rate constant predicted by the average dipole orientation model (ADO) at room temperature and 226 K, whereas CH(3)Cl reacts with Au(+)((1)S) at the ADO limit at both room temperature and 218 K. Rate constants for depletion of Au(+)((3)D) by CH(3)F and CH(3)Cl were measured at 226 and 218 K respectively, and indicate that Au(+)((3)D) is consumed at approximately 2% of the ADO limit by CH(3)F and 69% of the ADO limit by CH(3)Cl. Product formation and overall efficiency for all four reactions are consistent with previous experimental results and available theoretical models.

  10. Cooperatively enhanced ionic hydrogen bonds in Cl-(CH3OH)(1-3)Ar clusters.

    PubMed

    Beck, Jordan P; Lisy, James M

    2010-09-23

    Infrared predissociation (IRPD) spectra of Cl−(CH3OH)1-3Ar and Cl-(CH3OD)1-3Ar were obtained in the OH and CH stretching regions. The use of methanol-d1 was necessary to distinguish between CH stretches and hydrogen-bonded OH features. The spectra of Cl-(CH3OH)2-3Ar show intense features at frequencies lower than the CH stretches, indicating structures with very strong hydrogen bonds. These strong hydrogen bonds arise from structures in which a Cl-···methanol ionic hydrogen bond is cooperatively enhanced by the presence of a second shell and, in the case of Cl-(CH3OH)3Ar, a third shell methanol. The strongest hydrogen bond is observed in the Cl-(CH3OH)3Ar spectrum at 2733 cm-1, shifted a remarkable -948 cm-1 from the neutral, gas-phase methanol value. Harmonic, ab initio frequency calculations are not adequate in describing these strong hydrogen bonds. Therefore, we describe a simple computational approach to better approximate the hydrogen bond frequencies. Overall, the results of this study indicate that high-energy isomers are very efficiently trapped using our experimental method of introducing Cl- into neutral, cold methanol-argon clusters.

  11. The dissociation of vibrationally excited CH3OSO radicals and their photolytic precursor, methoxysulfinyl chloride.

    PubMed

    Alligood, Bridget W; Womack, Caroline C; Straus, Daniel B; Blase, Frances R; Butler, Laurie J

    2011-05-21

    The dissociation dynamics of methoxysulfinyl radicals generated from the photodissociation of CH(3)OS(O)Cl at 248 nm is investigated using both a crossed laser-molecular beam scattering apparatus and a velocity map imaging apparatus. There is evidence of only a single photodissociation channel of the precursor: S-Cl fission to produce Cl atoms and CH(3)OSO radicals. Some of the vibrationally excited CH(3)OSO radicals undergo subsequent dissociation to CH(3) + SO(2). The velocities of the detected CH(3) and SO(2) products show that the dissociation occurs via a transition state having a substantial barrier beyond the endoergicity; appropriately, the distribution of velocities imparted to these momentum-matched products is fit by a broad recoil kinetic energy distribution extending out to 24 kcal/mol in translational energy. Using 200 eV electron bombardment detection, we also detect the CH(3)OSO radicals that have too little internal energy to dissociate. These radicals are observed both at the parent CH(3)OSO(+) ion as well as at the CH(3)(+) and SO(2)(+) daughter ions; they are distinguished by virtue of the velocity imparted in the original photolytic step. The detected velocities of the stable radicals are roughly consistent with the calculated barriers (both at the CCSD(T) and G3B3 levels of theory) for the dissociation of CH(3)OSO to CH(3) + SO(2) when we account for the partitioning of internal energy between rotation and vibration as the CH(3)OSOCl precursor dissociates. © 2011 American Institute of Physics.

  12. Child and adolescent service experience (ChASE): measuring service quality and therapeutic process.

    PubMed

    Day, Crispin; Michelson, Daniel; Hassan, Imren

    2011-11-01

    OBJECTIVES. Dissatisfaction with services has been associated with poorer child mental health outcomes, early treatment termination as well as disagreements over the nature of mental health difficulties, reasons for referral and therapy goals. The development of straightforward, reliable, and accurate methods of eliciting service users' views is essential within child and adolescent mental health care. This paper describes the development of the child and adolescent service experience (ChASE), a tool to measure children and young people's service experience DESIGN. The study comprises a non-experimental, cross-sectional design. METHODS. Participants were 132 mental health service users aged 8-18 years. Participants and their main carer completed the ChASE, Parent Satisfaction Questionnaire (PSQ) (Stallard, 1996) and Strengths and Difficulties (SDQ) Impact Supplement. Clinicians completed the SDQ Impact Supplement and provided clinical activity data. A sub-sample of participants completed the ChASE on a second occasion, 6 weeks after the completion of the first questionnaire. RESULTS. Scrutiny of ChASE data indicated high levels of completion. Principal axis factoring identified three factors within the ChASE: Relationship, Privacy, and Session Activity. The ChASE has good internal consistency and test-retest reliability. Significant correlations were found between the ChASE and carer satisfaction, service use, and youth clinical outcomes. CONCLUSIONS. The ChASE is a short, psychometrically robust tool for routine measurement of children, and young people's experience of mental health services, which users can complete easily. The results underline the importance of alliance factors to children and young people and their association with clinical improvement as well as the potential for the ChASE to be used a measure of children's therapeutic progress and alliance. ©2011 The British Psychological Society.

  13. Joint CO2 and CH4 accountability for global warming

    PubMed Central

    Smith, Kirk R.; Desai, Manish A.; Rogers, Jamesine V.; Houghton, Richard A.

    2013-01-01

    We propose a transparent climate debt index incorporating both methane (CH4) and carbon dioxide (CO2) emissions. We develop national historic emissions databases for both greenhouse gases to 2005, justifying 1950 as the starting point for global perspectives. We include CO2 emissions from fossil sources [CO2(f)], as well as, in a separate analysis, land use change and forestry. We calculate the CO2(f) and CH4 remaining in the atmosphere in 2005 from 205 countries using the Intergovernmental Panel on Climate Change’s Fourth Assessment Report impulse response functions. We use these calculations to estimate the fraction of remaining global emissions due to each country, which is applied to total radiative forcing in 2005 to determine the combined climate debt from both greenhouse gases in units of milliwatts per square meter per country or microwatts per square meter per person, a metric we term international natural debt (IND). Australia becomes the most indebted large country per capita because of high CH4 emissions, overtaking the United States, which is highest for CO2(f). The differences between the INDs of developing and developed countries decline but remain large. We use IND to assess the relative reduction in IND from choosing between CO2(f) and CH4`control measures and to contrast the imposed versus experienced health impacts from climate change. Based on 2005 emissions, the same hypothetical impact on world 2050 IND could be achieved by decreasing CH4 emissions by 46% as stopping CO2 emissions entirely, but with substantial differences among countries, implying differential optimal strategies. Adding CH4 shifts the basic narrative about differential international accountability for climate change. PMID:23847202

  14. Using carbon isotope fractionation for an improved quantification of CH4 oxidation efficiency in Arctic peatlands

    NASA Astrophysics Data System (ADS)

    Preuss, I.; Knoblauch, C.; Gebert, J.; Pfeiffer, E.-M.

    2012-04-01

    Much research effort is focused on identifying global CH4 sources and sinks to estimate their current and potential strength in response to land-use change and global warming. Aerobic CH4 oxidation is regarded as the key process reducing the strength of CH4 emissions in wetlands, but is hitherto difficult to quantify. Recent studies quantify the efficiency of CH4 oxidation based on CH4 stable isotope signatures. The approach utilizes the fact that a significant isotope fractionation occurs when CH4 is oxidized. Moreover, it also considers isotope fractionation by diffusion. For field applications the 'open-system equation' is applied to determine the CH4 oxidation efficiency: fox = (δE - δP)/ (αox - αtrans) where fox is the fraction of CH4 oxidized; δE is δ13C of emitted CH4; δP is δ13C of produced CH4; αox is the isotopic fractionation factor of oxidation; αtrans is the isotopic fractionation factor of transport. We quantified CH4 oxidation in polygonal tundra soils of Russia's Lena River Delta analyzing depth profiles of CH4 concentrations and stable isotope signatures. Therefore, both fractionation factors αox and αtrans were determined for three polygon centers with differing water table positions and a polygon rim. While most previous studies on landfill cover soils have assumed a gas transport dominated by advection (αtrans = 1), other CH4 transport mechanisms as diffusion have to be considered in peatlands and αtrans exceeds a value of 1. At our study we determined αtrans = 1.013 ± 0.003 for CH4 when diffusion is the predominant transport mechanism. Furthermore, results showed that αox differs widely between sites and horizons (αox = 1.013 ± 0.012) and has to be determined for each case. The impact of both fractionation factors on the quantification of CH4 oxidation was estimated by considering both the potential diffusion rate at different water contents and potential oxidation rates. Calculations for a water saturated tundra soil

  15. Transition-Metal-Catalyzed C-H Alkylation Using Alkenes.

    PubMed

    Dong, Zhe; Ren, Zhi; Thompson, Samuel J; Xu, Yan; Dong, Guangbin

    2017-07-12

    Alkylation reactions represent an important organic transformation to form C-C bonds. In addition to conventional approaches with alkyl halides or sulfonates as alkylating agents, the use of unactivated olefins for alkylations has become attractive from both cost and sustainability viewpoints. This Review summarizes transition-metal-catalyzed alkylations of various carbon-hydrogen bonds (addition of C-H bonds across olefins) using regular olefins or 1,3-dienes up to May 2016. According to the mode of activation, the Review is divided into two sections: alkylation via C-H activation and alkylation via olefin activation.

  16. Analysis of Protein-DNA Interaction by Chromatin Immunoprecipitation and DNA Tiling Microarray (ChIP-on-chip).

    PubMed

    Gao, Hui; Zhao, Chunyan

    2018-01-01

    Chromatin immunoprecipitation (ChIP) has become the most effective and widely used tool to study the interactions between specific proteins or modified forms of proteins and a genomic DNA region. Combined with genome-wide profiling technologies, such as microarray hybridization (ChIP-on-chip) or massively parallel sequencing (ChIP-seq), ChIP could provide a genome-wide mapping of in vivo protein-DNA interactions in various organisms. Here, we describe a protocol of ChIP-on-chip that uses tiling microarray to obtain a genome-wide profiling of ChIPed DNA.

  17. Infrared Spectroscopic Investigation on CH Bond Acidity in Cationic Alkanes

    NASA Astrophysics Data System (ADS)

    Matsuda, Yoshiyuki; Xie, Min; Fujii, Asuka

    2016-06-01

    We have demonstrated large enhancements of CH bond acidities in alcohol, ether, and amine cations through infrared predissociation spectroscopy based on the vacuum ultraviolet photoionization detection. In this study, we investigate for the cationic alkanes (pentane, hexane, and heptane) with different alkyl chain lengths. The σ electrons are ejected in the ionization of alkanes, while nonbonding electrons are ejected in ionization of alcohols, ethers, and amines. Nevertheless, the acidity enhancements of CH in these cationic alkanes have also been demonstrated by infrared spectroscopy. The correlations of their CH bond acidities with the alkyl chain lengths as well as the mechanisms of their acidity enhancements will be discussed by comparison of infrared spectra and theoretical calculations.

  18. Avian leukosis virus subgroup J induces its receptor--chNHE1 up-regulation.

    PubMed

    Feng, Weiguo; Meng, Wei; Cai, Liming; Cui, Xiyao; Pan, Zhifang; Wang, Guihua; Cheng, Ziqiang

    2016-04-02

    Avian leukosis virus subgroup J (ALV-J) is an oncogenic retrovirus which causes immunosuppression and neoplasia in meat-type and egg-type chickens. ALV-J infects host cells via specific interaction between the viral Env and the cell surface receptor -chicken sodium hydrogen exchanger type 1 (chNHE1). NHE1 involved in altering the cellular pH and playing a critical role in tumorigenesis. However, little is known about the other relationship between ALV-J and chNHE1. In ALV-J infected DF-1 cells, the mRNA level of chNHE1 was up-regulated with time-dependent manner tested by real time PCR, and accordingly, intracellular pH was increased tested by spectrofluorometer. In vivo, the mRNA level of chNHE1 was determined by real time PCR in ALV-J infected experimental chickens and field cases. The result showed that the mRNA level of chNHE1 was up-regulated after virus shedding, especially in continuous viremic shedders (CS group). However, no significant difference was found between non-shedding group (NS group) and control group. In field cases, mRNA level of chNHE1 was positively correlated with increasing ALV-J load in tumor bearing and immune tolerance chickens. Furthermore, immunohistochemistry results showed that the protein expression of chNHE1 was up-regulated in different organs of both experimental chickens and tumor bearing chickens compared with the control. Taken together, we conclude that ALV-J induces chNHE1 up-regulation in viremia and neoplasia chickens.

  19. Software for rapid time dependent ChIP-sequencing analysis (TDCA).

    PubMed

    Myschyshyn, Mike; Farren-Dai, Marco; Chuang, Tien-Jui; Vocadlo, David

    2017-11-25

    Chromatin immunoprecipitation followed by DNA sequencing (ChIP-seq) and associated methods are widely used to define the genome wide distribution of chromatin associated proteins, post-translational epigenetic marks, and modifications found on DNA bases. An area of emerging interest is to study time dependent changes in the distribution of such proteins and marks by using serial ChIP-seq experiments performed in a time resolved manner. Despite such time resolved studies becoming increasingly common, software to facilitate analysis of such data in a robust automated manner is limited. We have designed software called Time-Dependent ChIP-Sequencing Analyser (TDCA), which is the first program to automate analysis of time-dependent ChIP-seq data by fitting to sigmoidal curves. We provide users with guidance for experimental design of TDCA for modeling of time course (TC) ChIP-seq data using two simulated data sets. Furthermore, we demonstrate that this fitting strategy is widely applicable by showing that automated analysis of three previously published TC data sets accurately recapitulates key findings reported in these studies. Using each of these data sets, we highlight how biologically relevant findings can be readily obtained by exploiting TDCA to yield intuitive parameters that describe behavior at either a single locus or sets of loci. TDCA enables customizable analysis of user input aligned DNA sequencing data, coupled with graphical outputs in the form of publication-ready figures that describe behavior at either individual loci or sets of loci sharing common traits defined by the user. TDCA accepts sequencing data as standard binary alignment map (BAM) files and loci of interest in browser extensible data (BED) file format. TDCA accurately models the number of sequencing reads, or coverage, at loci from TC ChIP-seq studies or conceptually related TC sequencing experiments. TC experiments are reduced to intuitive parametric values that facilitate biologically

  20. Multiphoton Rydberg and valence dynamics of CH3Br probed by mass spectrometry and slice imaging.

    PubMed

    Hafliðason, Arnar; Glodic, Pavle; Koumarianou, Greta; Samartzis, Peter C; Kvaran, Ágúst

    2018-06-18

    The multiphoton dynamics of CH3Br were probed by Mass Resolved MultiPhoton Ionization (MR-MPI), Slice Imaging and Photoelectron Imaging in the two-photon excitation region of 66 000 to 80 000 cm-1. Slice images of the CH3+ and Br+ photoproducts of ten two-photon resonant transitions to np and nd Rydberg states of the parent molecule were recorded. CH3+ ions dominate the mass spectra. Kinetic energy release spectra (KERs) were derived from slice and photoelectron images and anisotropy parameters were extracted from the angular distributions of the ions to identify the processes and the dynamics involved. At all wavelengths we observe three-photon excitations, via the two-photon resonant transitions to molecular Rydberg states, forming metastable, superexcited (CH3Br#) states which dissociate to form CH3 Rydberg states (CH3**) along with Br/Br*. A correlation between the parent Rydberg states excited and CH3** formed is evident. For the three highest excitation energies used, the CH3Br# metastable states also generate high kinetic energy fragments of CH3(X) and Br/Br*. In addition for two out of these three wavelengths we also measure one-photon photolysis of CH3Br in the A band forming CH3(X) in various vibrational modes and bromine atoms in the ground (Br) and spin-orbit excited (Br*) states.

  1. CH4 emissions from European Major Population Centers: Results from aircraft-borne CH4 in-situ observations during EMeRGe-Europe campaign 2017

    NASA Astrophysics Data System (ADS)

    Roiger, A.; Klausner, T.; Schlager, H.; Ziereis, H.; Huntrieser, H.; Baumann, R.; Eirenschmalz, L.; Joeckel, P.; Mertens, M.; Fisher, R.; Bauguitte, S.; Young, S.; Andrés Hernández, M. D.

    2017-12-01

    Urban environments represent large and diffuse area sources of CH4 including emissions from pipeline leaks, industrial/sewage treatment plants, and landfills. However, there is little knowledge about the exact magnitude of these emissions and their contribution to total anthropogenic CH4. Especially in the context of an urbanizing world, a better understanding of the methane footprint of urban areas is crucial, both with respect to mitigation and projection of climate impacts. Aircraft-borne in-situ measurements are particularly useful to both quantify emissions from such area sources, as well as to study their impact on the regional distribution. However, airborne CH4 observations downstream of European cities are especially sparse.Here we report from aircraft-borne CH4 in-situ measurements as conducted during the HALO aircraft campaign EMeRGe (Effect of Megacities on the Transport and Transformation of Pollutants on the Regional to Global Scales) in July 2017, which was led by the University of Bremen, Germany. During seven research flights, emissions from a variety of European (Mega)-cities were probed at different altitudes from 3km down to 500m, including measurements in the outflows of London, Rome, Po Valley, Ruhr and Benelux. We will present and compare the CH4 distribution measured downstream of the various studied urban hot-spots. With the help of other trace gas measurements (including e.g. CO2, CO, O3, SO2), observed methane enhancements will be attributed to the different potential source types. Finally, by the combination of in-situ measurements and regional model simulations using the EMAC-MECO(n) model, the contribution of emissions from urban centers to the regional methane budget over Europe will be discussed.

  2. Photodissociation of the CH3Cl/+/ and N2O/+/ cations.

    NASA Technical Reports Server (NTRS)

    Dunbar, R. C.

    1971-01-01

    Use of the ion cyclotron resonance (icr) technique to observe the photodissociation of the cations CH3Cl(+) and N2O(+) in the gas phase. Ions were trapped in the icr cell for periods of the order of seconds, which permitted the photodissociation process to be observed with wavelength-selected light. A cyclotron resonance ejection technique was employed to show that CH3Cl(+) ions were being dissociated rather than the CH3ClH(+) ions which were also present. The photodissociation cross section for N2O(+) was found to be without strong wavelength dependence between 4000 and 6500 A. The cross section for CH3Cl(+) showed a large peak at 3150 A. Possible assignments of this peak are considered, and it is suggested that a photodissociation occurs through an ion excitation involving a change in occupation of the bonding or antibonding orbitals of the C-Cl bond.

  3. Anti-inflammatory activity of Arnica montana 6cH: preclinical study in animals.

    PubMed

    Macêdo, S B; Ferreira, L R; Perazzo, F F; Carvalho, J C

    2004-04-01

    The anti-inflammatory effect of Arnica montana 6cH was evaluated using acute and chronic inflammation models. In the acute, model, carrageenin-induced rat paw oedema, the group treated with Arnica montana 6cH showed 30% inhibition compared to control (P < 0.05). Treatment with Arnica 6cH, 30 min prior to carrageenin, did not produce any inhibition of the inflammatory process. In the chronic model, Nystatin-induced oedema, the group treated 3 days previously with Arnica montana 6cH had reduced inflammation 6 h after the inflammatory agent was applied (P < 0.05). When treatment was given 6 h after Nystatin treatment, there was no significant inhibitory effect. In a model based on histamine-induced increase of vascular permeability, pretreatment with Arnica montana 6cH blocked the action of histamine in increasing vascular permeability.

  4. Exploring mechanisms of a tropospheric archetype: CH{sub 3}O{sub 2} + NO

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Launder, Andrew M.; Agarwal, Jay; Schaefer, Henry F., E-mail: ccq@uga.edu

    Methylperoxy radical (CH{sub 3}O{sub 2}) and nitric oxide (NO) contribute to the propagation of photochemical smog in the troposphere via the production of methoxy radical (CH{sub 3}O) and nitrogen dioxide (NO{sub 2}). This reaction system also furnishes trace quantities of methyl nitrate (CH{sub 3}ONO{sub 2}), a sink for reactive NO{sub x} species. Here, the CH{sub 3}O{sub 2} + NO reaction is examined with highly reliable coupled-cluster methods. Specifically, equilibrium geometries for the reactants, products, intermediates, and transition states of the ground-state potential energy surface are characterized. Relative reaction enthalpies at 0 K (ΔH{sub 0K}) are reported; these values are comprisedmore » of electronic energies extrapolated to the complete basis set limit of CCSDT(Q) and zero-point vibrational energies computed at CCSD(T)/cc-pVTZ. A two-part mechanism involving CH{sub 3}O and NO{sub 2} production followed by radical recombination to CH{sub 3}ONO{sub 2} is determined to be the primary channel for formation of CH{sub 3}ONO{sub 2} under tropospheric conditions. Constrained optimizations of the reaction paths at CCSD(T)/cc-pVTZ suggest that the homolytic bond dissociations involved in this reaction path are barrierless.« less

  5. Binary properties of CH and carbon-enhanced metal-poor stars

    NASA Astrophysics Data System (ADS)

    Jorissen, A.; Van Eck, S.; Van Winckel, H.; Merle, T.; Boffin, H. M. J.; Andersen, J.; Nordström, B.; Udry, S.; Masseron, T.; Lenaerts, L.; Waelkens, C.

    2016-02-01

    The HERMES spectrograph installed on the 1.2-m Mercator telescope has been used to monitor the radial velocity of 13 low-metallicity carbon stars, among which seven carbon-enhanced metal-poor (CEMP) stars and six CH stars (including HIP 53522, a new member of the family, as revealed by a detailed abundance study). All stars but one show clear evidence for binarity. New orbits are obtained for eight systems. The sample covers an extended range in orbital periods, extending from 3.4 d (for the dwarf carbon star HE 0024-2523) to about 54 yr (for the CH star HD 26, the longest known among barium, CH, and extrinsic S stars). Three systems exhibit low-amplitude velocity variations with periods close to 1 yr superimposed on a long-term trend. In the absence of an accurate photometric monitoring of these systems, it is not clear yet whether these variations are the signature of a very low-mass companion or of regular envelope pulsations. The period - eccentricity (P - e) diagram for the 40 low-metallicity carbon stars with orbits now available shows no difference between CH and CEMP-s stars (the latter corresponding to those CEMP stars enriched in s-process elements, as are CH stars). We suggest that they must be considered as one and the same family and that their different names only stem from historical reasons. Indeed, these two families have as well very similar mass-function distributions, corresponding to companions with masses in the range 0.5-0.7 M⊙, indicative of white-dwarf companions, adopting 0.8-0.9 M⊙ for the primary component. This result confirms that CH and CEMP-s stars obey the same mass-transfer scenario as their higher-metallicity analogues, barium stars. The P - e diagrams of barium, CH, and CEMP-s stars are indeed very similar. They reveal two different groups of systems: one with short orbital periods (P< 1000 d) and mostly circular or almost circular orbits, and another with longer period and eccentric (e> 0.1) orbits. These two groups either

  6. LeChâtelier's Principle in the Sciences

    NASA Astrophysics Data System (ADS)

    Thomsen, Volker B. E.

    2000-02-01

    LeChâtelier's principle of chemical equilibrium is actually a very general statement about systems in equilibrium and their behavior when subjected to external force or stress. Although one almost never finds mention of his name or law in other sciences, analogous principles and concepts do exist. In this note we examine some of the similar forms taken by this chemical principle in the fields of physics, geology, biology, and economics. Lenz's law in physics is an example of electromagnetic equilibrium and the geological principle of isostatic uplift concerns mechanical equilibrium. Both are strictly consequences of conservation of energy. LeChâtelier's principle deals with thermodynamic equilibrium and involves both the first and second laws of thermodynamics. The concept of homeostasis in biology and the economic law of supply and demand are both equilibrium-like principles, but involve systems in the steady state. However, all these principles involve the stability of the system under consideration and the analogies presented may be useful in the teaching of LeChâtelier's principle.

  7. Flowing afterglow studies of the electron recombination of protonated cyanides (RCN)H+ and their proton-bound dimer ions (RCN)2H+ where R is H, CH3, and CH3CH2

    NASA Astrophysics Data System (ADS)

    McLain, J. L.; Molek, C. D.; , D. Osborne, Jr.; Adams, N. G.

    2009-05-01

    A study has been made of the electron-ion dissociative recombination of the protonated cyanides (RCNH+, R = H, CH3, C2H5) and their proton-bound dimers (RCN)2H+ at 300 K. This has been accomplished with the flowing afterglow technique using an electrostatic Langmuir probe to determine the electron density decay along the flow tube. For the protonated species, the recombination coefficients, [alpha]e(cm3 s-1), are (3.6 +/- 0.5) × 10-7, (3.4 +/- 0.5) × 10-7, (4.6 +/- 0.7) × 10-7 for R = H, CH3, C2H5, respectively. For the proton-bound dimers, the [alpha]e are substantially greater being (2.4 +/- 0.4) × 10-6, (2.8 +/- 0.4) × 10-6, (2.3 +/- 0.3) × 10-6 for R = H, CH3, C2H5, respectively. Fitting of the electron density decay data to a simple model has shown that the rate coefficients for the three-body association of RCNH+ with RCN are very large being (2.0 +/- 0.5) × 10-26 cm6 s-1. The significance of these data to the Titan ionosphere is discussed.

  8. Motif-based analysis of large nucleotide data sets using MEME-ChIP

    PubMed Central

    Ma, Wenxiu; Noble, William S; Bailey, Timothy L

    2014-01-01

    MEME-ChIP is a web-based tool for analyzing motifs in large DNA or RNA data sets. It can analyze peak regions identified by ChIP-seq, cross-linking sites identified by cLIP-seq and related assays, as well as sets of genomic regions selected using other criteria. MEME-ChIP performs de novo motif discovery, motif enrichment analysis, motif location analysis and motif clustering, providing a comprehensive picture of the DNA or RNA motifs that are enriched in the input sequences. MEME-ChIP performs two complementary types of de novo motif discovery: weight matrix–based discovery for high accuracy; and word-based discovery for high sensitivity. Motif enrichment analysis using DNA or RNA motifs from human, mouse, worm, fly and other model organisms provides even greater sensitivity. MEME-ChIP’s interactive HTML output groups and aligns significant motifs to ease interpretation. this protocol takes less than 3 h, and it provides motif discovery approaches that are distinct and complementary to other online methods. PMID:24853928

  9. Low Temperature Studies of the Removal Reactions of 1CH2 with Relevance to the Atmosphere of Titan

    NASA Astrophysics Data System (ADS)

    Douglas, Kevin; Slater, Eloise; Feng, Wuhu; Blitz, Mark; Plane, John; Heard, Dwayne; Seakins, Paul

    2017-04-01

    The photolysis of methane by UV photons is the primary source of hydrocarbon radicals in the atmosphere of Titan and the giant planets. Although there is still significant uncertainty in the branching ratios of products, the production of the first singlet excited state of methylene, 1CH2, is thought to be a significant channel. Reactions of 1CH2 with methane (R1a) and hydrogen (R2a) are a significant source of methyl radicals, the recombination of which is the primary route to ethane on Titan (R3). The reaction of 1CH2 with acetylene is also a source of propargyl, C3H3, the recombination of which is the primary route to benzene on Titan. However, in addition to these reactions of 1CH2 leading to chemical products, there is also competition between inelastic electronic relaxation to form ground triplet state methylene, 3CH2 (R1b and R2b). Triplet methylene is much less reactive, and cannot undergo the complex insertion elimination reactions of singlet methylene. The main reaction of 3CH2 occurs with other radical species such as H (R4). 1CH2 + CH4 → CH3 + H2 (R1a) 1CH2 + CH4 → 3CH2 + CH4 (R1b) 1CH2 + H2 → CH3 + H (R2a) 1CH2 + H2 → 3CH2 + H2 (R2a) CH3 + CH3 (+M) → C2H6 (R3) 3CH2 + H → CH + H2 (R4) Using pulsed laser photolysis laser-induced fluorescence, we have studied the reaction kinetics for the removal of 1CH2 with N2, H2, CH4, C2H6, C2H4, C2H6, and O2 as a function of temperature. Low temperatures between 43 and 135 K were obtained using a pulsed Laval nozzle apparatus, while data at 160 K was obtained using a low flow reaction cell with cryogenic cooling. In addition to measuring total removal rates, the fraction of 1CH2 removed via electronic relaxation versus chemical reaction to products has also been investigated for H2 and CH4 at 160 and 73 K. Results show that that removal of 1CH2 by electronic relaxation increases with decreasing temperature. These experimental results indicate that the majority of 1CH2 formed in Titan's atmosphere will be

  10. Investigation of Wyoming Bentonite Hydration in Dry to Water-Saturated Supercritical CH4 and CH4/CO2 Mixtures: Implications for CO2-Enhanced Gas Production

    NASA Astrophysics Data System (ADS)

    Loring, J.; Thompson, C.; Ilton, E. S.; McGrail, B. P.; Schaef, T.

    2014-12-01

    Injection of CO2 into low permeability shale formations leads to additional gas recovery and reduces the flux of CO2 into the atmosphere, thus combining a strong economic incentive with a permanent storage option for CO2. Reduced formation transmissivity due to clay swelling is a concern in CO2 -enhanced gas production. Clay minerals partly determine the physical (i.e. permeability, brittleness) and certain chemical properties (i.e. wetting ability, gas adsorption) of shales, and montmorillonites are of particular interest because they swell by the uptake of species in their interlayer. In this study, the hydration and expansion of a Na-saturated montmorillonite (Na-SWy-2) in high-pressure (90 bar) and moderate temperature (50 °C) methane and mixtures of methane and carbon dioxide were investigated usingCH4 IR spectroscopic titrations andCH4 XRD. The goals were to (1) determine if the hydration/expansion behavior of the clay in supercritical methane is different than in supercritical CO2, (2) determine if methane intercalates the clay, and (3) probe the effects of increasing CO2 concentrations. IR spectra were collected as Na-SWy-2 was titrated with water under several fluid exposures: pure methane, 25, 50, and 75 mole% CO2 in methane, and pure CO2. ComplementaryCH4 XRD experiments were conducted in the same fluids at discrete dissolved water concentrations to measure the d001 values of the clay and thus its volume change on hydration and CH4 and/or CO2 intercalation. In pure methane, no direct evidence of CH4 intercalation was detected in CH bending or stretching regions of the IR spectra. Similarly, in situ XRD indicated the montmorillonite structure was stable in the presence of CH4 and no measurable changes to the basal spacing were observed. However, under low water conditions where the montmorillonite structure was partially expanded (~sub 1W), the IR data indicated a rapid intercalation of CO2 into the interlayer, even with fluid mixtures containing the

  11. Ultrastructural localization of ChAT-like immunoreactivity in the human vestibular periphery.

    PubMed

    Kong, W J; Hussl, B; Thumfart, W F; Schrott-Fischer, A

    1998-05-01

    Acetylcholine (ACh) has long been considered a neurotransmitter candidate in the efferent vestibular system of mammals. Recently, choline acetyltransferase (ChAT), the synthesizing enzyme for ACh, was immunocytochemically localized in all five end-organs of the rat vestibule (Kong et al. (1994) Hear. Res. 75, 192-200). However, there is little information in the literature concerning the cholinergic innervation in the vestibular periphery of man. In the present study the ultrastructural localization of the ChAT-like immunoreactivity in the human vestibular periphery was investigated in order to reveal the cholinergic innervation in the human vestibular end-organs. A modified method of pre-embedding immunoelectron microscopy was applied. It was found that the ChAT-like immunoreactivity was located in the bouton-type vesiculated nerve terminals in the vestibular neurosensory epithelia of man. These ChAT-like immunostained nerve terminals make synaptic contacts either with afferent chalices surrounding type I vestibular sensory hair cells, or with type II vestibular sensory hair cells. These results show that the ChAT-like immunoreactivity in the human vestibular periphery is confined to the efferent vestibular system. The ChAT-containing efferents innervate both type I hair cells and type II hair cells, making postsynaptic and presynaptic contacts, respectively. This study presents evidence that ACh is a neurotransmitter candidate in the efferent vestibular system of man.

  12. C-H Hot Bands in the Near-IR Emission Spectra of Leonids

    NASA Technical Reports Server (NTRS)

    Freund, F. T.; Scoville, J.; Holm, R.; Seelemann, R.; Freund, M. M.

    2002-01-01

    The reported infrared (IR) emission spectra from 1999 Leonid fireballs show a 3.4 micron C-H emission band and unidentified bands at longer wavelengths. Upon atmospheric entry, the Leonid meteorites were flash-heated to temperatures around 2400K, which would destroy any organics on the surface of the meteorite grains. We propose that the nu(sub )CH emission band in the Leonid emission spectra arises from matrix-embedded C(sub n)-H-O entities that are protected from instant pyrolysis. Our model is based on IR absorption nu(sub )CH bands, which we observed in laboratory-grown MgO and natural olivine single crystals, where they arise from C(sub n)-H-O units imbedded in the mineral matrix, indicative of aliphatic -CH2- and -CH3 organics. Instead of being pyrolyzed, the C(sub n)-H-O entities in the Leonid trails become vibrationally excited to higher levels n = 1, 2, 3 etc. During de-excitation they emit at 3.4 microns, due to the (0 => 1) transition, and at longer wavelengths, due to hot bands. As a first step toward verifying this hypothesis we measured the C-H vibrational manifold of hexane (C6H14). The calculated positions of the (2 => l ) , (3 => 2), and possibly (4 => 3) hot bands agree with the Leonid emission bands at 3.5, 3.8 and 4.l microns.

  13. Validation of a Brief Structured Interview: The Children's Interview for Psychiatric Syndromes (ChIPS).

    PubMed

    Young, Matthew E; Bell, Ziv E; Fristad, Mary A

    2016-12-01

    Evidence-based assessment is important in the treatment of childhood psychopathology. While researchers and clinicians frequently use structured diagnostic interviews to ensure reliability, the most commonly used instrument, the Schedule for Affective Disorders and Schizophrenia for School Aged Children (K-SADS) is too long for most clinical applications. The Children's Interview for Psychiatric Syndromes (ChIPS/P-ChIPS) is a highly-structured brief diagnostic interview. The present study compared K-SADS and ChIPS/P-ChIPS diagnoses in an outpatient clinical sample of 50 parent-child pairs aged 7-14. Agreement between most diagnoses was moderate to high between the instruments and with consensus clinical diagnoses. ChIPS was significantly briefer to administer than the K-SADS. Interviewer experience level and participant demographics did not appear to affect agreement. Results provide further evidence for the validity of the ChIPS and support its use in clinical and research settings.

  14. Infrared absorption of CH3OSO detected with time-resolved Fourier-transform spectroscopy.

    PubMed

    Chen, Jin-Dah; Lee, Yuan-Pern

    2011-03-07

    A step-scan Fourier-transform spectrometer coupled with a multipass absorption cell was employed to detect temporally resolved infrared absorption spectra of CH(3)OSO produced upon irradiation of a flowing gaseous mixture of CH(3)OS(O)Cl in N(2) or CO(2) at 248 nm. Two intense transient features with origins near 1152 and 994 cm(-1) are assigned to syn-CH(3)OSO; the former is attributed to overlapping bands at 1154 ± 3 and 1151 ± 3 cm(-1), assigned to the S=O stretching mixed with CH(3) rocking (ν(8)) and the S=O stretching mixed with CH(3) wagging (ν(9)) modes, respectively, and the latter to the C-O stretching (ν(10)) mode at 994 ± 6 cm(-1). Two weak bands at 2991 ± 6 and 2956 ± 3 cm(-1) are assigned as the CH(3) antisymmetric stretching (ν(2)) and symmetric stretching (ν(3)) modes, respectively. Observed vibrational transition wavenumbers agree satisfactorily with those predicted with quantum-chemical calculations at level B3P86∕aug-cc-pVTZ. Based on rotational parameters predicted at that level, the simulated rotational contours of these bands agree satisfactorily with experimental results. The simulation indicates that the S=O stretching mode of anti-CH(3)OSO near 1164 cm(-1) likely makes a small contribution to the observed band near 1152 cm(-1). A simple kinetic model of self-reaction is employed to account for the decay of CH(3)OSO and yields a second-order rate coefficient k=(4 ± 2)×10(-10) cm(3)molecule(-1)s(-1). © 2011 American Institute of Physics.

  15. Aviation NOx-induced CH4 effect: Fixed mixing ratio boundary conditions versus flux boundary conditions

    NASA Astrophysics Data System (ADS)

    Khodayari, Arezoo; Olsen, Seth C.; Wuebbles, Donald J.; Phoenix, Daniel B.

    2015-07-01

    Atmospheric chemistry-climate models are often used to calculate the effect of aviation NOx emissions on atmospheric ozone (O3) and methane (CH4). Due to the long (∼10 yr) atmospheric lifetime of methane, model simulations must be run for long time periods, typically for more than 40 simulation years, to reach steady-state if using CH4 emission fluxes. Because of the computational expense of such long runs, studies have traditionally used specified CH4 mixing ratio lower boundary conditions (BCs) and then applied a simple parameterization based on the change in CH4 lifetime between the control and NOx-perturbed simulations to estimate the change in CH4 concentration induced by NOx emissions. In this parameterization a feedback factor (typically a value of 1.4) is used to account for the feedback of CH4 concentrations on its lifetime. Modeling studies comparing simulations using CH4 surface fluxes and fixed mixing ratio BCs are used to examine the validity of this parameterization. The latest version of the Community Earth System Model (CESM), with the CAM5 atmospheric model, was used for this study. Aviation NOx emissions for 2006 were obtained from the AEDT (Aviation Environmental Design Tool) global commercial aircraft emissions. Results show a 31.4 ppb change in CH4 concentration when estimated using the parameterization and a 1.4 feedback factor, and a 28.9 ppb change when the concentration was directly calculated in the CH4 flux simulations. The model calculated value for CH4 feedback on its own lifetime agrees well with the 1.4 feedback factor. Systematic comparisons between the separate runs indicated that the parameterization technique overestimates the CH4 concentration by 8.6%. Therefore, it is concluded that the estimation technique is good to within ∼10% and decreases the computational requirements in our simulations by nearly a factor of 8.

  16. MOBE-ChIP: Probing Cell Type-Specific Binding Through Large-Scale Chromatin Immunoprecipitation.

    PubMed

    Wang, Shenqi; Lau, On Sun

    2018-01-01

    In multicellular organisms, the initiation and maintenance of specific cell types often require the activity of cell type-specific transcriptional regulators. Understanding their roles in gene regulation is crucial but probing their DNA targets in vivo, especially in a genome-wide manner, remains a technical challenge with their limited expression. To improve the sensitivity of chromatin immunoprecipitation (ChIP) for detecting the cell type-specific signals, we have developed the Maximized Objects for Better Enrichment (MOBE)-ChIP, where ChIP is performed at a substantially larger experimental scale and under low background conditions. Here, we describe the procedure in the study of transcription factors in the model plant Arabidopsis. However, with some modifications, the technique should also be implemented in other systems. Besides cell type-specific studies, MOBE-ChIP can also be used as a general strategy to improve ChIP signals.

  17. Synergistic Manganese(I) C-H Activation Catalysis in Continuous Flow: Chemoselective Hydroarylation.

    PubMed

    Wang, Hui; Pesciaioli, Fabio; Oliveira, João C A; Warratz, Svenja; Ackermann, Lutz

    2017-11-20

    Chemoselective hydroarylations were accomplished by a novel synergistic Brønsted acid/manganese(I)-catalyzed C-H activation manifold. Thus, alkynes bearing O-leaving groups could, for the first time, be employed for C-H alkenylations without concurrent β-O elimination, thereby setting the stage for versatile late-stage diversifications. Also described is the first manganese-catalyzed C-H activation in continuous flow, thus enabling efficient hydroarylations within only 20 minutes. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Charge-transfer-directed radical substitution enables para-selective C-H functionalization

    NASA Astrophysics Data System (ADS)

    Boursalian, Gregory B.; Ham, Won Seok; Mazzotti, Anthony R.; Ritter, Tobias

    2016-08-01

    Efficient C-H functionalization requires selectivity for specific C-H bonds. Progress has been made for directed aromatic substitution reactions to achieve ortho and meta selectivity, but a general strategy for para-selective C-H functionalization has remained elusive. Herein we introduce a previously unappreciated concept that enables nearly complete para selectivity. We propose that radicals with high electron affinity elicit arene-to-radical charge transfer in the transition state of radical addition, which is the factor primarily responsible for high positional selectivity. We demonstrate with a simple theoretical tool that the selectivity is predictable and show the utility of the concept through a direct synthesis of aryl piperazines. Our results contradict the notion, widely held by organic chemists, that radical aromatic substitution reactions are inherently unselective. The concept of radical substitution directed by charge transfer could serve as the basis for the development of new, highly selective C-H functionalization reactions.

  19. Inference of hierarchical regulatory network of estrogen-dependent breast cancer through ChIP-based data

    PubMed Central

    2010-01-01

    Background Global profiling of in vivo protein-DNA interactions using ChIP-based technologies has evolved rapidly in recent years. Although many genome-wide studies have identified thousands of ERα binding sites and have revealed the associated transcription factor (TF) partners, such as AP1, FOXA1 and CEBP, little is known about ERα associated hierarchical transcriptional regulatory networks. Results In this study, we applied computational approaches to analyze three public available ChIP-based datasets: ChIP-seq, ChIP-PET and ChIP-chip, and to investigate the hierarchical regulatory network for ERα and ERα partner TFs regulation in estrogen-dependent breast cancer MCF7 cells. 16 common TFs and two common new TF partners (RORA and PITX2) were found among ChIP-seq, ChIP-chip and ChIP-PET datasets. The regulatory networks were constructed by scanning the ChIP-peak region with TF specific position weight matrix (PWM). A permutation test was performed to test the reliability of each connection of the network. We then used DREM software to perform gene ontology function analysis on the common genes. We found that FOS, PITX2, RORA and FOXA1 were involved in the up-regulated genes. We also conducted the ERα and Pol-II ChIP-seq experiments in tamoxifen resistance MCF7 cells (denoted as MCF7-T in this study) and compared the difference between MCF7 and MCF7-T cells. The result showed very little overlap between these two cells in terms of targeted genes (21.2% of common genes) and targeted TFs (25% of common TFs). The significant dissimilarity may indicate totally different transcriptional regulatory mechanisms between these two cancer cells. Conclusions Our study uncovers new estrogen-mediated regulatory networks by mining three ChIP-based data in MCF7 cells and ChIP-seq data in MCF7-T cells. We compared the different ChIP-based technologies as well as different breast cancer cells. Our computational analytical approach may guide biologists to further study the

  20. Multiplexed ChIP-Seq Using Direct Nucleosome Barcoding: A Tool for High-Throughput Chromatin Analysis.

    PubMed

    Chabbert, Christophe D; Adjalley, Sophie H; Steinmetz, Lars M; Pelechano, Vicent

    2018-01-01

    Chromatin immunoprecipitation followed by sequencing (ChIP-Seq) or microarray hybridization (ChIP-on-chip) are standard methods for the study of transcription factor binding sites and histone chemical modifications. However, these approaches only allow profiling of a single factor or protein modification at a time.In this chapter, we present Bar-ChIP, a higher throughput version of ChIP-Seq that relies on the direct ligation of molecular barcodes to chromatin fragments. Bar-ChIP enables the concurrent profiling of multiple DNA-protein interactions and is therefore amenable to experimental scale-up, without the need for any robotic instrumentation.

  1. Vibrational overtone spectra of metallocenes: effect of the coordinating metal on the CH bond lengths

    NASA Astrophysics Data System (ADS)

    Billinghurst, Brant E.; Gough, Kathleen M.

    2003-03-01

    The first through third overtone spectra of ferrocene, ruthenocene, nickelocene, cobaltocene, dicyclopentadienyl magnesium and sodium cyclopentadienyl are examined with particular attention to the CH stretching of the cyclopentadienyl. Using semi-empirical correlations between CH bond length and CH stretching frequencies in each overtone region, we have determined that the type of metal atom within a metallocene complex has little effect on the CH bond length in the cyclopentadienyl. The only exception is cobaltocene where there is evidence that the Jahn-Teller effect results in several different CH bond lengths. Evidence that bis(cyclopentadienyl) magnesium is not ionic has been observed.

  2. Temperature-Dependent Kinetics Studies of the Reactions Br((sup 2)P3/2) + H2S yields SH + HBr and Br((sup 2)P3/2) + CH3SH yields CH3S + HBr. Heats of Formation of SH and CH3S Radicals

    NASA Technical Reports Server (NTRS)

    Nicovich, J. M.; Kreutter, K. D.; vanDijk, C. A.; Wine, P. H.

    1997-01-01

    Time resolved resonance fluorescence detection of Br(sup 2)P3/2) atom disappearance or appearance following 266-nm laser flash photolysis of CF2Br2/H2S/H2/N2, CF2Br2/CH3SH/H2/N2, Cl2CO/H2S/HBr/N2, and CH3SSCH3/HBr/H2/N2 mixtures has been employed to study the kinetics of the reactions Br((sup 2)P3/2) + H2S = SH + HBr (1,-1) and Br((sup2)P3/2) + CH3SH = CH3S + HBr (2, -2) as a function of temperature over the range 273-431K. Arrhenius expressions in units of 10(exp -12) cu cm/molecule/s which describe the results are k1 = (14.2 +/- 3.4) exp[(-2752 +/- 90)/T],(k-1) = (4.40 +/- 0.92) exp[(-971 +/- 73)/T],k(2) = (9.24 +/- 1.15) exp[(-386 +/- 41)/T], and k(-2) = (1.46 +/-0.21) exp[(-399 +/-41)/T; errors are 2 sigma and represent precision only. By examining Br((sup 2)P3/2) equilibrium kinetics following 355nm laser flash photolysis of Br2/CH3SH/H2/N2 mixtures, a 298 K rate coefficient of (1.7 +/- 0.5) x 10(exp -10) cu cm/molecule/s has been obtained for the reaction CH3S + Br2 yields CH3SBr + Br. To our knowledge, these are the first kinetic data reported for each of the reactions studied. Measured rate coefficients, along with known rate coefficients for similar radical + H2S, CH3SH, HBr,Br2 reactions are considered in terms of possible correlations of reactivity with reaction thermochemistry and with IP - EA, the difference between the ionization potential of the electron donor and the electron affinity of the electron acceptor. Both thermochemical and charge-transfer effects appear to be important in controlling observed reactivities. Second and third law analyses of the equilibrium data for reactions 1 and 2 have been employed to obtain the following enthalpies of reaction in units of kcal/mol: for reaction 1, Delta-H(298) = 3.64 +/- 0.43 and Delta-H(0) = 3.26 +/-0.45; for reaction 2, Delta-H(298) = -0.14 +/- 0.28 and Delta-H(0) = -0.65 +/- 0.36. Combining the above enthalpies of reaction with the well-known heats of formation of Br, HBr, H2S, and CH3SH gives the

  3. Silicon nitride and silicon etching by CH{sub 3}F/O{sub 2} and CH{sub 3}F/CO{sub 2} plasma beams

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Kaler, Sanbir S.; Lou, Qiaowei; Donnelly, Vincent M., E-mail: vmdonnelly@uh.edu

    2016-07-15

    Silicon nitride (SiN, where Si:N ≠ 1:1) films low pressure-chemical vapor deposited on Si substrates, Si films on Ge on Si substrates, and p-Si samples were exposed to plasma beams emanating from CH{sub 3}F/O{sub 2} or CH{sub 3}F/CO{sub 2} inductively coupled plasmas. Conditions within the plasma beam source were maintained at power of 300 W (1.9 W/cm{sup 3}), pressure of 10 mTorr, and total gas flow rate of 10 sccm. X-ray photoelectron spectroscopy was used to determine the thicknesses of Si/Ge in addition to hydrofluorocarbon polymer films formed at low %O{sub 2} or %CO{sub 2} addition on p-Si and SiN. Polymer film thickness decreasedmore » sharply as a function of increasing %O{sub 2} or %CO{sub 2} addition and dropped to monolayer thickness above the transition point (∼48% O{sub 2} or ∼75% CO{sub 2}) at which the polymer etchants (O and F) number densities in the plasma increased abruptly. The C(1s) spectra for the polymer films deposited on p-Si substrates appeared similar to those on SiN. Spectroscopic ellipsometry was used to measure the thickness of SiN films etched using the CH{sub 3}F/O{sub 2} and CH{sub 3}F/CO{sub 2} plasma beams. SiN etching rates peaked near 50% O{sub 2} addition and 73% CO{sub 2} addition. Faster etching rates were measured in CH{sub 3}F/CO{sub 2} than CH{sub 3}F/O{sub 2} plasmas above 70% O{sub 2} or CO{sub 2} addition. The etching of Si stopped after a loss of ∼3 nm, regardless of beam exposure time and %O{sub 2} or %CO{sub 2} addition, apparently due to plasma assisted oxidation of Si. An additional GeO{sub x}F{sub y} peak was observed at 32.5 eV in the Ge(3d) region, suggesting deep penetration of F into Si, under the conditions investigated.« less

  4. Study on the electronic structure of Al12N12 and Al12P12 fullerene-like nano-clusters upon adsorption of CH3F and CH3Cl

    NASA Astrophysics Data System (ADS)

    Shokuhi Rad, A.; Zareyee, D.; Pouralijan Foukolaei, V.; Kamyab Moghadas, B.; Peyravi, M.

    2016-11-01

    We study the interaction of two mono-halomethanes (CH3F and CH3Cl) on Al12N12 and Al12P12 fullerene-like nano-clusters based on density functional theory (DFT). We search on fully optimised adsorbed systems by theoretical investigation considering binding energies, total density of states, natural bond orbital (NBO) charges, and molecular electrostatic potential. We found that the direction of electron transfer is from halomethane to nano-cluster for all systems, indicating p-type semiconductor property of the mentioned nano-clusters. The interaction energy of halomethanes on nano-clusters is evaluated with dispersion corrected (wB97XD) and non-corrected (B3LYP) methods in order to estimate the dispersion effects. The binding energies are found in order of Al12N12-CH3F > Al12N12-CH3Cl > Al12P12-CH3F > Al12P12-CH3Cl with the values of -102.7, -83.7, -64.2, and -48.9 kJ mol-1 based on wB97XD, respectively. We found significant changes in the location of HOMO as well as LUMO of nano-clusters upon adsorption of the above-mentioned molecules. As a result, we suggest the suitability of Al12N12 nano-cluster as a strong adsorbent for practical applications.

  5. cChIP-seq: a robust small-scale method for investigation of histone modifications.

    PubMed

    Valensisi, Cristina; Liao, Jo Ling; Andrus, Colin; Battle, Stephanie L; Hawkins, R David

    2015-12-21

    ChIP-seq is highly utilized for mapping histone modifications that are informative about gene regulation and genome annotations. For example, applying ChIP-seq to histone modifications such as H3K4me1 has facilitated generating epigenomic maps of putative enhancers. This powerful technology, however, is limited in its application by the large number of cells required. ChIP-seq involves extensive manipulation of sample material and multiple reactions with limited quality control at each step, therefore, scaling down the number of cells required has proven challenging. Recently, several methods have been proposed to overcome this limit but most of these methods require extensive optimization to tailor the protocol to the specific antibody used or number of cells being profiled. Here we describe a robust, yet facile method, which we named carrier ChIP-seq (cChIP-seq), for use on limited cell amounts. cChIP-seq employs a DNA-free histone carrier in order to maintain the working ChIP reaction scale, removing the need to tailor reactions to specific amounts of cells or histone modifications to be assayed. We have applied our method to three different histone modifications, H3K4me3, H3K4me1 and H3K27me3 in the K562 cell line, and H3K4me1 in H1 hESCs. We successfully obtained epigenomic maps for these histone modifications starting with as few as 10,000 cells. We compared cChIP-seq data to data generated as part of the ENCODE project. ENCODE data are the reference standard in the field and have been generated starting from tens of million of cells. Our results show that cChIP-seq successfully recapitulates bulk data. Furthermore, we showed that the differences observed between small-scale ChIP-seq data and ENCODE data are largely to be due to lab-to-lab variability rather than operating on a reduced scale. Data generated using cChIP-seq are equivalent to reference epigenomic maps from three orders of magnitude more cells. Our method offers a robust and straightforward

  6. Infrared observations and laboratory simulations of interstellar CH_4_ and SO_2_.

    NASA Astrophysics Data System (ADS)

    Boogert, A. C. A.; Schutte, W. A.; Helmich, F. P.; Tielens, A. G. G. M.; Wooden, D. H.

    1997-02-01

    Interstellar CH_4_ may consume a fair amount of the carbon budget in dense molecular clouds, but probably less than CO, CH_3_OH, and CO_2_. However, it can only be observed at wavelength regions in the infrared that are heavily affected by the earth atmosphere. With new space and airborne missions (e.g. ISO, SOFIA) in mind we have studied the near infrared absorption spectra of solid and gaseous CH_4_. We obtained laboratory spectra of the ν_4_ deformation mode (1302cm^-1^, 7.68μm) of solid CH_4_ in astrophysically relevant mixtures. We found that the peak position and width of this absorption band vary strongly as a function of molecular environment, compared to temperature and particle shape effects. Hence, observations of this feature will provide a powerful probe of the molecular composition of interstellar ices. Also the gas phase CH_4_ ro-vibrational spectrum of the same band has been calculated. Using observed physical conditions around the protostar W 33A, we show that unresolved gaseous CH_4_ lines are detectable (at the 2-5% level) at a resolution R>1000, when the column density N>=10^16^ cm^-2^. An astrophysically relevant molecule with a very strong transition in the same wavelength regime, is SO_2_. We studied the ν _3_ asymmetric stretching mode (1319 cm^-1^, 7.58 μm) of solid SO_2_ in several mixtures, revealing that the peak position, width and detailed profile of this band are very sensitive to the molecular environment. Besides probing the composition of ice mantles, observations of solid SO_2_ will provide important information on the sulfur budget locked up in grain mantles, which is currently poorly known. We compare the laboratory and calculated spectra of CH_4_ and SO_2_ with previously published ground based spectra and new airborne observations of young stellar objects in the 7-8μm region. W 33A, NGC 7538 : IRS1 and IRS9 show a feature near 7.68μm that is consistent with absorption by solid CH_4_ or the Q-branch of gaseous CH_4_. The

  7. Photoelectric characteristics of CH3NH3PbI3/p-Si heterojunction

    NASA Astrophysics Data System (ADS)

    Yamei, Wu; Ruixia, Yang; Hanmin, Tian; Shuai, Chen

    2016-05-01

    Organic-inorganic hybrid perovskite CH3NH3PbI3 film is prepared on p-type silicon substrate using the one-step solution method to form a CH3NH3PbI3/p-Si heterojunction. The film morphology and structure are characterized by atomic force microscopy (AFM) and scanning electron microscopy (SEM). The photoelectric properties of the CH3NH3PbI3/p-Si heterojunction are studied by testing the current-voltage (I-V) with and without illumination and capacitance-voltage (C-V) characteristics. It turns out from the I-V curve without illumination that the CH3NH3PbI3/p-Si heterojunction has a rectifier feature with the rectification ratio over 70 at the bias of ±5 V. Also, there appears a photoelectric conversion phenomenon on this heterojunction with a short circuit current (Isc) of 0.16 μA and an open circuit voltage (Voc) of about 10 mV The high frequency C-V characteristic of the Ag/CH3NH3PbI3/p-Si heterojunction turns out to be similar to that of the metal-insulator-semiconductor (MIS) structure, and a parallel translation of the C-V curve along the forward voltage axis is found. This parallel translation means the existence of defects at the CH3NH3PbI3/p-Si interface and positive fixed charges in the CH3NH3PbI3 layer. The defects at the interface of the CH3NH3PbI3/p-Si heterojunction result in the dramatic decline of the Voc. Besides, the C-V test of CH3NH3PbI3 film shows a non-linear dielectric property and the dielectric value is about 4.64 as calculated. Project supported by the Hebei Province Natural Science Foundation of China (No. F2014202184) and the Tianjin Natural Science Foundation of China (No. 15JCZDJC37800).

  8. Improved quantification of microbial CH4 oxidation efficiency in arctic wetland soils using carbon isotope fractionation

    NASA Astrophysics Data System (ADS)

    Preuss, I.; Knoblauch, C.; Gebert, J.; Pfeiffer, E.-M.

    2013-04-01

    Permafrost-affected tundra soils are significant sources of the climate-relevant trace gas methane (CH4). The observed accelerated warming of the arctic will cause deeper permafrost thawing, followed by increased carbon mineralization and CH4 formation in water-saturated tundra soils, thus creating a positive feedback to climate change. Aerobic CH4 oxidation is regarded as the key process reducing CH4 emissions from wetlands, but quantification of turnover rates has remained difficult so far. The application of carbon stable isotope fractionation enables the in situ quantification of CH4 oxidation efficiency in arctic wetland soils. The aim of the current study is to quantify CH4 oxidation efficiency in permafrost-affected tundra soils in Russia's Lena River delta based on stable isotope signatures of CH4. Therefore, depth profiles of CH4 concentrations and δ13CH4 signatures were measured and the fractionation factors for the processes of oxidation (αox) and diffusion (αdiff) were determined. Most previous studies employing stable isotope fractionation for the quantification of CH4 oxidation in soils of other habitats (such as landfill cover soils) have assumed a gas transport dominated by advection (αtrans = 1). In tundra soils, however, diffusion is the main gas transport mechanism and diffusive stable isotope fractionation should be considered alongside oxidative fractionation. For the first time, the stable isotope fractionation of CH4 diffusion through water-saturated soils was determined with an αdiff = 1.001 ± 0.000 (n = 3). CH4 stable isotope fractionation during diffusion through air-filled pores of the investigated polygonal tundra soils was αdiff = 1.013 ± 0.003 (n = 18). Furthermore, it was found that αox differs widely between sites and horizons (mean αox = 1.017 ± 0.009) and needs to be determined on a case by case basis. The impact of both fractionation factors on the quantification of CH4 oxidation was analyzed by considering both the

  9. Improved quantification of microbial CH4 oxidation efficiency in Arctic wetland soils using carbon isotope fractionation

    NASA Astrophysics Data System (ADS)

    Preuss, I.; Knoblauch, C.; Gebert, J.; Pfeiffer, E.-M.

    2012-12-01

    Permafrost-affected tundra soils are significant sources of the climate-relevant trace gas methane (CH4). The observed accelerated warming of the Arctic will cause a deeper permafrost thawing followed by increased carbon mineralization and CH4 formation in water saturated tundra soils which might cause a positive feedback to climate change. Aerobic CH4 oxidation is regarded as the key process reducing CH4 emissions from wetlands, but quantification of turnover rates has remained difficult so far. The application of carbon stable isotope fractionation enables the in situ quantification of CH4 oxidation efficiency in arctic wetland soils. The aim of the current study is to quantify CH4 oxidation efficiency in permafrost-affected tundra soils in Russia's Lena River Delta based on stable isotope signatures of CH4. Therefore, depth profiles of CH4 concentrations and δ13CH4-signatures were measured and the fractionation factors for the processes of oxidation (αox) and diffusion (αdiff) were determined. Most previous studies employing stable isotope fractionation for the quantification of CH4 oxidation in soils of other habitats (e.g. landfill cover soils) have assumed a gas transport dominated by advection (αtrans = 1). In tundra soils, however, diffusion is the main gas transport mechanism, aside from ebullition. Hence, diffusive stable isotope fractionation has to be considered. For the first time, the stable isotope fractionation of CH4 diffusion through water-saturated soils was determined with an αdiff = 1.001 ± 0.000 (n = 3). CH4 stable isotope fractionation during diffusion through air-filled pores of the investigated polygonal tundra soils was αdiff = 1.013 ± 0.003 (n = 18). Furthermore, it was found that αox differs widely between sites and horizons (mean αox, = 1.017 ± 0.009) and needs to be determined individually. The impact of both fractionation factors on the quantification of CH4 oxidation was analyzed by considering both the potential diffusion

  10. CH Cygni. I. Observational Evidence for a Disk-Jet Connection

    NASA Astrophysics Data System (ADS)

    Sokoloski, J. L.; Kenyon, S. J.

    2003-02-01

    We investigate the role of accretion in the production of jets in the symbiotic star CH Cygni. Assuming that the rapid stochastic optical variations in CH Cygni come from the accretion disk, as in cataclysmic variables, we use changes in this flickering to diagnose the state of the disk in 1997. At that time, CH Cygni dropped to a very low optical state, and Karovska et al. report that a radio jet was produced. For approximately 1 yr after the jet production, the amplitude of the fastest (timescale of minutes) variations was significantly reduced, although smooth, hour-timescale variations were still present. This light-curve evolution indicates that the inner disk may have been disrupted, or emission from this region suppressed, in association with the mass ejection event. We describe optical spectra that support this interpretation of the flickering changes. The simultaneous state change, jet ejection, and disk disruption suggest a comparison between CH Cygni and some black hole candidate X-ray binaries that show changes in the inner-disk radius in conjunction with discrete ejection events on a wide range of timescales (e.g., the microquasar GRS 1915+105 and XTE J1550-564).

  11. Global Analysis of Transcription Factor-Binding Sites in Yeast Using ChIP-Seq

    PubMed Central

    Lefrançois, Philippe; Gallagher, Jennifer E. G.; Snyder, Michael

    2016-01-01

    Transcription factors influence gene expression through their ability to bind DNA at specific regulatory elements. Specific DNA-protein interactions can be isolated through the chromatin immunoprecipitation (ChIP) procedure, in which DNA fragments bound by the protein of interest are recovered. ChIP is followed by high-throughput DNA sequencing (Seq) to determine the genomic provenance of ChIP DNA fragments and their relative abundance in the sample. This chapter describes a ChIP-Seq strategy adapted for budding yeast to enable the genome-wide characterization of binding sites of transcription factors (TFs) and other DNA-binding proteins in an efficient and cost-effective way. Yeast strains with epitope-tagged TFs are most commonly used for ChIP-Seq, along with their matching untagged control strains. The initial step of ChIP involves the cross-linking of DNA and proteins. Next, yeast cells are lysed and sonicated to shear chromatin into smaller fragments. An antibody against an epitope-tagged TF is used to pull down chromatin complexes containing DNA and the TF of interest. DNA is then purified and proteins degraded. Specific barcoded adapters for multiplex DNA sequencing are ligated to ChIP DNA. Short DNA sequence reads (28–36 base pairs) are parsed according to the barcode and aligned against the yeast reference genome, thus generating a nucleotide-resolution map of transcription factor-binding sites and their occupancy. PMID:25213249

  12. Mechanistic Comparison Between Pd-Catalyzed Ligand Directed C-H Chlorination and C-H Acetoxylation

    PubMed Central

    Stowers, Kara J.; Sanford, Melanie S.

    2009-01-01

    This communication describes detailed investigations of the mechanism of the Pd-catalyzed C-H chlorination and acetoxylation of 2-ortho-tolylpyridine. Under the conditions examined, both reactions proceed via rate limiting cyclopalladation. However, substrate and catalyst order as well as Hammett data indicate that the intimate mechanism of cyclopalladation differs significantly between PdCl2-catalyzed chlorination and Pd(OAc)2-catalyzed acetoxylation. PMID:19754074

  13. Global methane emission estimates for 2000-2012 from CarbonTracker Europe-CH4 v1.0

    NASA Astrophysics Data System (ADS)

    Tsuruta, Aki; Aalto, Tuula; Backman, Leif; Hakkarainen, Janne; van der Laan-Luijkx, Ingrid T.; Krol, Maarten C.; Spahni, Renato; Houweling, Sander; Laine, Marko; Dlugokencky, Ed; Gomez-Pelaez, Angel J.; van der Schoot, Marcel; Langenfelds, Ray; Ellul, Raymond; Arduini, Jgor; Apadula, Francesco; Gerbig, Christoph; Feist, Dietrich G.; Kivi, Rigel; Yoshida, Yukio; Peters, Wouter

    2017-03-01

    We present a global distribution of surface methane (CH4) emission estimates for 2000-2012 derived using the CarbonTracker Europe-CH4 (CTE-CH4) data assimilation system. In CTE-CH4, anthropogenic and biospheric CH4 emissions are simultaneously estimated based on constraints of global atmospheric in situ CH4 observations. The system was configured to either estimate only anthropogenic or biospheric sources per region, or to estimate both categories simultaneously. The latter increased the number of optimizable parameters from 62 to 78. In addition, the differences between two numerical schemes available to perform turbulent vertical mixing in the atmospheric transport model TM5 were examined. Together, the system configurations encompass important axes of uncertainty in inversions and allow us to examine the robustness of the flux estimates. The posterior emission estimates are further evaluated by comparing simulated atmospheric CH4 to surface in situ observations, vertical profiles of CH4 made by aircraft, remotely sensed dry-air total column-averaged mole fraction (XCH4) from the Total Carbon Column Observing Network (TCCON), and XCH4 from the Greenhouse gases Observing Satellite (GOSAT). The evaluation with non-assimilated observations shows that posterior XCH4 is better matched with the retrievals when the vertical mixing scheme with faster interhemispheric exchange is used. Estimated posterior mean total global emissions during 2000-2012 are 516 ± 51 Tg CH4 yr-1, with an increase of 18 Tg CH4 yr-1 from 2000-2006 to 2007-2012. The increase is mainly driven by an increase in emissions from South American temperate, Asian temperate and Asian tropical TransCom regions. In addition, the increase is hardly sensitive to different model configurations ( < 2 Tg CH4 yr-1 difference), and much smaller than suggested by EDGAR v4.2 FT2010 inventory (33 Tg CH4 yr-1), which was used for prior anthropogenic emission estimates. The result is in good agreement with other

  14. Ionization yields, total absorption, and dissociative photoionization cross sections of CH4 from 110-950 A

    NASA Technical Reports Server (NTRS)

    Samson, James A. R.; Haddad, G. N.; Masuoka, T.; Pareek, P. N.; Kilcoyne, D. A. L.

    1989-01-01

    Absolute absorption and photoionization cross sections of methane have been measured with an accuracy of about 2 or 3 percent over most of the wavelength range from 950 to 110 A. Also, dissociative photoionization cross sections were measured for the production of CH4(+), CH3(+), CH2(+), CH(+), and C(+) from their respective thresholds to 159 A, and for H(+) and H2(+) measurements were made down to 240 A. Fragmentation was observed at all excited ionic states of CH4.

  15. C+/H2 gas in star-forming clouds and galaxies

    NASA Astrophysics Data System (ADS)

    Nordon, Raanan; Sternberg, Amiel

    2016-11-01

    We present analytic theory for the total column density of singly ionized carbon (C+) in the optically thick photon dominated regions (PDRs) of far-UV irradiated (star-forming) molecular clouds. We derive a simple formula for the C+ column as a function of the cloud (hydrogen) density, the far-UV field intensity, and metallicity, encompassing the wide range of galaxy conditions. When assuming the typical relation between UV and density in the cold neutral medium, the C+ column becomes a function of the metallicity alone. We verify our analysis with detailed numerical PDR models. For optically thick gas, most of the C+ column is mixed with hydrogen that is primarily molecular (H2), and this `C+/H2' gas layer accounts for almost all of the `CO-dark' molecular gas in PDRs. The C+/H2 column density is limited by dust shielding and is inversely proportional to the metallicity down to ˜0.1 solar. At lower metallicities, H2 line blocking dominates and the C+/H2 column saturates. Applying our theory to CO surveys in low-redshift spirals, we estimate the fraction of C+/H2 gas out of the total molecular gas to be typically ˜0.4. At redshifts 1 < z < 3 in massive disc galaxies the C+/H2 gas represents a very small fraction of the total molecular gas (≲ 0.16). This small fraction at high redshifts is due to the high gas surface densities when compared to local galaxies.

  16. Sustained delivery of thermostabilized chABC enhances axonal sprouting and functional recovery after spinal cord injury.

    PubMed

    Lee, Hyunjung; McKeon, Robert J; Bellamkonda, Ravi V

    2010-02-23

    Chondroitin sulfate proteoglycans (CSPGs) are a major class of axon growth inhibitors that are up-regulated after spinal cord injury (SCI) and contribute to regenerative failure. Chondroitinase ABC (chABC) digests glycosaminoglycan chains on CSPGs and can thereby overcome CSPG-mediated inhibition. But chABC loses its enzymatic activity rapidly at 37 degrees C, necessitating the use of repeated injections or local infusions for a period of days to weeks. These infusion systems are invasive, infection-prone, and clinically problematic. To overcome this limitation, we have thermostabilized chABC and developed a system for its sustained local delivery in vivo, obviating the need for chronically implanted catheters and pumps. Thermostabilized chABC remained active at 37 degrees C in vitro for up to 4 weeks. CSPG levels remained low in vivo up to 6 weeks post-SCI when thermostabilized chABC was delivered by a hydrogel-microtube scaffold system. Axonal growth and functional recovery following the sustained local release of thermostabilized chABC versus a single treatment of unstabilized chABC demonstrated significant differences in CSPG digestion. Animals treated with thermostabilized chABC in combination with sustained neurotrophin-3 delivery showed significant improvement in locomotor function and enhanced growth of cholera toxin B subunit-positive sensory axons and sprouting of serotonergic fibers. Therefore, improving chABC thermostability facilitates minimally invasive, sustained, local delivery of chABC that is potentially effective in overcoming CSPG-mediated regenerative failure. Combination therapy with thermostabilized chABC with neurotrophic factors enhances axonal regrowth, sprouting, and functional recovery after SCI.

  17. Engineered antibody CH2 domains binding to nucleolin: Isolation, characterization and improvement of aggregation.

    PubMed

    Li, Dezhi; Gong, Rui; Zheng, Jun; Chen, Xihai; Dimitrov, Dimiter S; Zhao, Qi

    2017-04-01

    Smaller recombinant antibody fragments are now emerging as alternatives of conventional antibodies. Especially, immunoglobulin (Ig) constant CH2 domain and engineered CH2 with improved stability are promising as scaffolds for selection of specific binders to various antigens. We constructed a yeast display library based on an engineered human IgG1 CH2 scaffold with diversified loop regions. A group of CH2 binders were isolated from this yeast display library by panning against nucleolin, which is a tumor-associated antigen involved in cell proliferation, tumor cell growth and angiogenesis. Out of 20 mutants, we selected 3 clones exhibiting relatively high affinities to nucleolin on yeasts. However, recombinant CH2 mutants aggregated when they were expressed. To find the mechanism of the aggregation, we employed computational prediction approaches through structural homology models of CH2 binders. The analysis of potential aggregation prone regions (APRs) and solvent accessible surface areas (ASAs) indicated two hydrophobic residues, Val 264 and Leu 309 , in the β-sheet, in which replacement of both charged residues led to significant decrease of the protein aggregation. The newly identified CH2 binders could be improved to use as candidate therapeutics or research reagents in the future. Copyright © 2017 Elsevier Inc. All rights reserved.

  18. Quantum Dynamics Study of the Isotopic Effect on Capture Reactions: HD, D2 + CH3

    NASA Technical Reports Server (NTRS)

    Wang, Dunyou; Kwak, Dochan (Technical Monitor)

    2002-01-01

    Time-dependent wave-packet-propagation calculations are reported for the isotopic reactions, HD + CH3 and D2 + CH3, in six degrees of freedom and for zero total angular momentum. Initial state selected reaction probabilities for different initial rotational-vibrational states are presented in this study. This study shows that excitations of the HD(D2) enhances the reactivities; whereas the excitations of the CH3 umbrella mode have the opposite effects. This is consistent with the reaction of H2 + CH3. The comparison of these three isotopic reactions also shows the isotopic effects in the initial-state-selected reaction probabilities. The cumulative reaction probabilities (CRP) are obtained by summing over initial-state-selected reaction probabilities. The energy-shift approximation to account for the contribution of degrees of freedom missing in the six dimensionality calculation is employed to obtain approximate full-dimensional CRPs. The rate constant comparison shows H2 + CH3 reaction has the biggest reactivity, then HD + CH3, and D2 + CH3 has the smallest.

  19. Synergistic effects of plasma-catalyst interactions for CH4 activation.

    PubMed

    Kim, Jongsik; Go, David B; Hicks, Jason C

    2017-05-24

    The elucidation of catalyst surface-plasma interactions is a challenging endeavor and therefore requires thorough and rigorous assessment of the reaction dynamics on the catalyst in the plasma environment. The first step in quantifying and defining catalyst-plasma interactions is a detailed kinetic study that can be used to verify appropriate reaction conditions for comparison and to discover any unexpected behavior of plasma-assisted reactions that might prevent direct comparison. In this paper, we provide a kinetic evaluation of CH 4 activation in a dielectric barrier discharge plasma in order to quantify plasma-catalyst interactions via kinetic parameters. The dry reforming of CH 4 with CO 2 was studied as a model reaction using Ni supported on γ-Al 2 O 3 at temperatures of 790-890 K under atmospheric pressure, where the partial pressures of CH 4 (or CO 2 ) were varied over a range of ≤25.3 kPa. Reaction performance was monitored by varying gas hourly space velocity, plasma power, bulk gas temperature, and reactant concentration. After correcting for gas-phase plasma reactions, a linear relationship was observed in the log of the measured rate constant with respect to reciprocal power (1/power). Although thermal catalysis displays typical Arrhenius behavior for this reaction, plasma-assisted catalysis occurs from a complex mixture of sources and shows non-Arrhenius behavior. However, an energy barrier was obtained from the relationship between the reaction rate constant and input power to exhibit ≤∼20 kJ mol -1 (compared to ∼70 kJ mol -1 for thermal catalysis). Of additional importance, the energy barriers measured during plasma-assisted catalysis were relatively consistent with respect to variations in total flow rates, types of diluent, or bulk reaction temperature. These experimental results suggest that plasma-generated vibrationally-excited CH 4 favorably interacts with Ni sites at elevated temperatures, which helps reduce the energy barrier

  20. Rotational spectrum of CH3CN⋯ClF and evidence for the +I effect of a CH3 group on the ‘chlorine’ bond N⋯ClF

    NASA Astrophysics Data System (ADS)

    Page, M. D.; Waclawik, E. R.; Holloway, J. H.; Legon, A. C.

    1999-10-01

    The ground-state rotational spectra of the isotopomers CH 3C 14N⋯ 35ClF, CH 3C 14N⋯ 37ClF, CD 3C 14N⋯ 35ClF and CH 3C 15N⋯ 35ClF of a symmetric-rotor complex formed by methyl cyanide and chlorine monofluoride have been observed and analysed to give the spectroscopic constants B0, DJ, DJK, χaa( 14N), χaa(Cl) and Mbb. Interpretations of these quantities on the basis of simple models enabled the geometry and strength of binding of the complex to be determined. It is found that the atoms C-CN⋯ClF lie on the C 3 axis of this complex of C 3v symmetry and that the distance r(N⋯Cl)=2.561(2) Å. The quadratic force constants associated with the intermolecular stretching mode and with the bending motion of the CH 3CN subunit pivoted at its mass centre were determined from the centrifugal distortion constants DJ and 2 DJ+ DJK. Their values were k σ=13.9(3) N m -1 and k α=3.0(1)×10 -20 J rad -2, respectively. A comparison of r(N⋯Cl) values and of k σ values establishes that the +I effect of the CH 3 group when it replaces H in HCN leads to a similar shortening of r(N⋯Cl) and to a similar increase in k σ in the two series RCN⋯ClF and RCN⋯HCl (R=H or CH 3).

  1. Local- and regional-scale measurements of CH4, δ13CH4, and C2H6 in the Uintah Basin using a mobile stable isotope analyzer

    NASA Astrophysics Data System (ADS)

    Rella, C. W.; Hoffnagle, J.; He, Y.; Tajima, S.

    2015-10-01

    In this paper, we present an innovative CH4, δ13CH4, and C2H6 instrument based on cavity ring-down spectroscopy (CRDS). The design and performance of the analyzer is presented in detail. The instrument is capable of precision of less than 1 ‰ on δ13CH4 with 1 in. of averaging and about 0.1 ‰ in an hour. Using this instrument, we present a comprehensive approach to atmospheric methane emissions attribution. Field measurements were performed in the Uintah Basin (Utah, USA) in the winter of 2013, using a mobile lab equipped with the CRDS analyzer, a high-accuracy GPS, a sonic anemometer, and an onboard gas storage and playback system. With a small population and almost no other sources of methane and ethane other than oil and gas extraction activities, the Uintah Basin represents an ideal location to investigate and validate new measurement methods of atmospheric methane and ethane. We present the results of measurements of the individual fugitive emissions from 23 natural gas wells and six oil wells in the region. The δ13CH4 and C2H6 signatures that we observe are consistent with the signatures of the gases found in the wells. Furthermore, regional measurements of the atmospheric CH4, δ13CH4, and C2H6 signatures throughout the basin have been made, using continuous sampling into a 450 m long tube and laboratory reanalysis with the CRDS instrument. These measurements suggest that 85 ± 7 % of the total emissions in the basin are from natural gas production.

  2. A flash photolysis resonance fluorescence investigation of the reaction OH + CH3CCl3 yields H2O + CH2CCl3. [in troposphere

    NASA Technical Reports Server (NTRS)

    Kurylo, M. J.; Anderson, P. C.; Klais, O.

    1979-01-01

    The absolute rate constant for the reaction OH + CH3CCl3 yields H2O + CH2CCl3 was determined by the flash photolysis resonance fluorescence method from 253 to 363K. The use of the Arrhenius equation with atmospheric observational data on methyl chloroform nearly doubles the predicted tropospheric OH reaction sink strength for the removal of atmospheric gases whose lifetimes are controlled by OH. The increased use of methyl chloroform instead of the restricted trichloroethylene focused attention to its role in stratospheric ozone depletion, producing modeling analyses to determine the amount of released methyl chloroform which reaches the stratosphere. Since the primary atmospheric loss of CH3CCl3 is considered by reaction with OH radicals, these data are used to compute an average tropospheric OH concentration and the strength of the 'global tropospheric OH reaction sink'.

  3. Microbial CH4 and N2O Consumption in Acidic Wetlands

    PubMed Central

    Kolb, Steffen; Horn, Marcus A.

    2012-01-01

    Acidic wetlands are global sources of the atmospheric greenhouse gases methane (CH4), and nitrous oxide (N2O). Consumption of both atmospheric gases has been observed in various acidic wetlands, but information on the microbial mechanisms underlying these phenomena is scarce. A substantial amount of CH4 is consumed in sub soil by aerobic methanotrophs at anoxic–oxic interfaces (e.g., tissues of Sphagnum mosses, rhizosphere of vascular plant roots). Methylocystis-related species are likely candidates that are involved in the consumption of atmospheric CH4 in acidic wetlands. Oxygen availability regulates the activity of methanotrophs of acidic wetlands. Other parameters impacting on the methanotroph-mediated CH4 consumption have not been systematically evaluated. N2O is produced and consumed by microbial denitrification, thus rendering acidic wetlands as temporary sources or sinks for N2O. Denitrifier communities in such ecosystems are diverse, and largely uncultured and/or new, and environmental factors that control their consumption activity are unresolved. Analyses of the composition of N2O reductase genes in acidic wetlands suggest that acid-tolerant Proteobacteria have the potential to mediate N2O consumption in such soils. Thus, the fragmented current state of knowledge raises open questions concerning methanotrophs and denitrifiers that consume atmospheric CH4 and N2O in acidic wetlands. PMID:22403579

  4. ChAMP: updated methylation analysis pipeline for Illumina BeadChips.

    PubMed

    Tian, Yuan; Morris, Tiffany J; Webster, Amy P; Yang, Zhen; Beck, Stephan; Feber, Andrew; Teschendorff, Andrew E

    2017-12-15

    The Illumina Infinium HumanMethylationEPIC BeadChip is the new platform for high-throughput DNA methylation analysis, effectively doubling the coverage compared to the older 450 K array. Here we present a significantly updated and improved version of the Bioconductor package ChAMP, which can be used to analyze EPIC and 450k data. Many enhanced functionalities have been added, including correction for cell-type heterogeneity, network analysis and a series of interactive graphical user interfaces. ChAMP is a BioC package available from https://bioconductor.org/packages/release/bioc/html/ChAMP.html. a.teschendorff@ucl.ac.uk or s.beck@ucl.ac.uk or a.feber@ucl.ac.uk. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

  5. Substrate-Mediated C-C and C-H Coupling after Dehalogenation.

    PubMed

    Kong, Huihui; Yang, Sha; Gao, Hongying; Timmer, Alexander; Hill, Jonathan P; Díaz Arado, Oscar; Mönig, Harry; Huang, Xinyan; Tang, Qin; Ji, Qingmin; Liu, Wei; Fuchs, Harald

    2017-03-15

    Intermolecular C-C coupling after cleavage of C-X (mostly, X = Br or I) bonds has been extensively studied for facilitating the synthesis of polymeric nanostructures. However, the accidental appearance of C-H coupling at the terminal carbon atoms would limit the successive extension of covalent polymers. To our knowledge, the selective C-H coupling after dehalogenation has not so far been reported, which may illuminate another interesting field of chemical synthesis on surfaces besides in situ fabrication of polymers, i.e., synthesis of novel organic molecules. By combining STM imaging, XPS analysis, and DFT calculations, we have achieved predominant C-C coupling on Au(111) and more interestingly selective C-H coupling on Ag(111), which in turn leads to selective synthesis of polymeric chains or new organic molecules.

  6. Eight-dimensional quantum reaction rate calculations for the H+CH{sub 4} and H{sub 2}+CH{sub 3} reactions on recent potential energy surfaces

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Zhou, Yong; Zhang, Dong H., E-mail: zhangdh@dicp.ac.cn

    2014-11-21

    Eight-dimensional (8D) transition-state wave packet simulations have been performed on two latest potential energy surfaces (PES), the Zhou-Fu-Wang-Collins-Zhang (ZFWCZ) PES [Y. Zhou, B. Fu, C. Wang, M. A. Collins, and D. H. Zhang, J. Chem. Phys. 134, 064323 (2011)] and the Xu-Chen-Zhang (XCZ)-neural networks (NN) PES [X. Xu, J. Chen, and D. H. Zhang, Chin. J. Chem. Phys. 27, 373 (2014)]. Reaction rate constants for both the H+CH{sub 4} reaction and the H{sub 2}+CH{sub 3} reaction are calculated. Simulations of the H+CH{sub 4} reaction based on the XCZ-NN PES show that the ZFWCZ PES predicts rate constants with reasonable highmore » accuracy for low temperatures while leads to slightly lower results for high temperatures, in line with the distribution of interpolation error associated with the ZFWCZ PES. The 8D H+CH{sub 4} rate constants derived on the ZFWCZ PES compare well with full-dimensional 12D results based on the equivalent m-ZFWCZ PES, with a maximum relative difference of no more than 20%. Additionally, very good agreement is shown by comparing the 8D XCZ-NN rate constants with the 12D results obtained on the ZFWCZ-WM PES, after considering the difference in static barrier height between these two PESs. The reaction rate constants calculated for the H{sub 2}+CH{sub 3} reaction are found to be in good consistency with experimental observations.« less

  7. Factors influencing CO2 and CH4 emissions from coastal wetlands in the Liaohe Delta, Northeast China

    NASA Astrophysics Data System (ADS)

    Olsson, L.; Ye, S.; Yu, X.; Wei, M.; Krauss, K. W.; Brix, H.

    2015-08-01

    Many factors are known to influence greenhouse gas emissions from coastal wetlands, but it is still unclear which factors are most important under field conditions when they are all acting simultaneously. The objective of this study was to assess the effects of water table, salinity, soil temperature and vegetation on CH4 emissions and ecosystem respiration (Reco) from five coastal wetlands in the Liaohe Delta, Northeast China: two Phragmites australis (common reed) wetlands, two Suaeda salsa (sea blite) marshes and a rice (Oryza sativa) paddy. Throughout the growing season, the Suaeda wetlands were net CH4 sinks whereas the Phragmites wetlands and the rice paddy were net CH4 sources emitting 1.2-6.1 g CH4 m-2 yr-1. The Phragmites wetlands emitted the most CH4 per unit area and the most CH4 relative to CO2. The main controlling factors for the CH4 emissions were water table, temperature, soil organic carbon and salinity. The CH4 emission was accelerated at high and constant (or managed) water tables and decreased at water tables below the soil surface. High temperatures enhanced CH4 emissions, and emission rates were consistently low (< 1 mg CH4 m-2 h-1) at soil temperatures < 18 °C. At salinity levels > 18 ppt, the CH4 emission rates were always low (< 1 mg CH4 m-2 h-1) probably because methanogens were out-competed by sulphate-reducing bacteria. Saline Phragmites wetlands can, however, emit significant amounts of CH4 as CH4 produced in deep soil layers are transported through the air-space tissue of the plants to the atmosphere. The CH4 emission from coastal wetlands can be reduced by creating fluctuating water tables, including water tables below the soil surface, as well as by occasional flooding by high-salinity water. The effects of water management schemes on the biological communities in the wetlands must, however, be carefully studied prior to the management in order to avoid undesirable effects on the wetland communities.

  8. Factors influencing CO2 and CH4 emissions from coastal wetlands in the Liaohe Delta, Northeast China

    NASA Astrophysics Data System (ADS)

    Olsson, L.; Ye, S.; Yu, X.; Wei, M.; Krauss, K. W.; Brix, H.

    2015-02-01

    Many factors are known to influence greenhouse gas emissions from coastal wetlands, but it is still unclear which factors are most important under field conditions when they are all acting simultaneously. The objective of this study was to assess the effects of water table, salinity, soil temperature and vegetation on CH4 emissions and ecosystem respiration (Reco) from five coastal wetlands in the Liaohe Delta, northeast China: two Phragmites australis (common reed) wetlands, two Suaeda salsa (sea blite) marshes and a rice (Oryza sativa) paddy. Throughout the growing season, the Suaeda wetlands were net CH4 sinks whereas the Phragmites wetlands and the rice paddy were net CH4 sources emitting 1.2-6.1 g CH4 m-2 y-1. The Phragmites wetlands emitted the most CH4 per unit area and the most CH4 relative to CO2. The main controlling factors for the CH4 emissions were water table, temperature and salinity. The CH4 emission was accelerated at high and constant (or managed) water tables and decreased at water tables below the soil surface. High temperatures enhanced CH4 emissions, and emission rates were consistently low (< 1 mg CH4 m-2 h) at soil temperatures <18 °C. At salinity levels > 18 ppt, the CH4 emission rates were always low (< 1 mg CH4 m-2 h-1) probably because methanogens were outcompeted by sulphate reducing bacteria. Saline Phragmites wetlands can, however, emit significant amounts of CH4 as CH4 produced in deep soil layers are transported through the air-space tissue of the plants to the atmosphere. The CH4 emission from coastal wetlands can be reduced by creating fluctuating water tables, including water tables below the soil surface, as well as by occasional flooding by high-salinity water. The effects of water management schemes on the biological communities in the wetlands must, however, be carefully studied prior to the management in order to avoid undesirable effects on the wetland communities.

  9. Infrared absorption of 2-hydroxyethyl (HOCH2CH2) in solid Ar

    NASA Astrophysics Data System (ADS)

    Kuo, Yu-Ping; Wann, Gwo-Huei; Lee, Yuan-Pern

    1993-09-01

    An argon matrix containing C2H4 and H2O2 was irradiated at 12 K with the 248 nm emission of a KrF excimer laser; IR spectra were recorded after various periods of photolysis. In addition to lines ascribed to ethylene oxide, acetaldehyde, and vinyl alcohol, absorptions at 2991.0, 2842.7, 1355.4, 1172.5, and 1040.1 cm-1 have been assigned to HOCH2CH2; weaker lines at 3625.8, 2922.4, and 873.9 cm-1 may also be due to HOCH2CH2. Corresponding lines at 2970.6, 2829.3, 1346.5, 1171.3, and 1020.5 (and probably 3625.8, 2915.1, and 860.7) cm-1 were observed for HO13CH2 13CH2. The results are consistent with ab initio calculations.

  10. Journey of the ALK-inhibitor CH5424802 to phase II clinical trial.

    PubMed

    Latif, Muhammad; Saeed, Aamer; Kim, Seong Hwan

    2013-09-01

    The anaplastic lymphoma kinase (ALK) receptor tyrosine kinase represents a potential therapeutic target. Specially, a variety of alterations in the ALK gene including mutations, overexpression, amplification, translocations and structural rearrangements, are involved in human cancer tumorigenesis. The second-generation ALK inhibitor CH5424802 (development code: AF802; Chugai Pharmaceutical, a subsidiary of Roche) achieves tumor regression with excellent tolerance and shows promising efficacy in patients with ALK-positive non-small cell lung cancer. CH5424802 shows good kinase selectivity, has a promising pharmacokinetics profile, and has strong antiproliferative activity in several ALK-driven tumor models. CH5424802 has also shown anti-tumor activity in mouse xenograft studies. Here, we summarize recent advances and the evidence that CH5424802 acts as an ALK inhibitor. We also discuss its potential for further development as an anticancer drug in clinical trials.

  11. Disproportionation and thermochemical sulfate reduction reactions in S-H20-Ch4 and S-D2O-CH4 systems from 200 to 340 °C at elevated pressures

    USGS Publications Warehouse

    Yuan, Shunda; Chou, I-Ming; Burruss, Robert A.

    2013-01-01

    Elemental sulfur, as a transient intermediate compound, by-product, or catalyst, plays significant roles in thermochemical sulfate reduction (TSR) reactions. However, the mechanisms of the reactions in S-H2O-hydrocarbons systems are not clear. To improve our understanding of reaction mechanisms, we conducted a series of experiments between 200 and 340 °C for S-H2O-CH4, S-D2O-CH4, and S-CH4-1m ZnBr2 systems in fused silica capillary capsules (FSCC). After a heating period ranging from 24 to 2160 hours (hrs), the quenched samples were analyzed by Raman spectroscopy. Combined with the in situ Raman spectra collected at high temperatures and pressures in the S-H2O and S-H2O-CH4 systems, our results showed that (1) the disproportionation of sulfur in the S-H2O-CH4 system occurred at temperatures above 200 °C and produced H2S, SO42-, and possibly trace amount of HSO4-; (2) sulfate (and bisulfate), in the presence of sulfur, can be reduced by methane between 250 and 340 °C to produce CO2 and H2S, and these TSR temperatures are much closer to those of the natural system (2O-CH4 system may take place simultaneously, with TSR being favored at higher temperatures; and (4) in the system S-D2O-CH4, both TSR and the competitive disproportionation reactions occurred simultaneously at temperatures above 300 °C, but these reactions were very slow at lower temperatures. Our observation of methane reaction at 250 °C in a laboratory time scale suggests that, in a geologic time scale, methane may be destroyed by TSR reactions at temperatures > 200 °C that can be reached by deep drilling for hydrocarbon resources.

  12. Expression, purification and characterization of GAPDH-ChSase ABC I from Proteus vulgaris in Escherichia coli.

    PubMed

    Li, Ye; Chen, Zhenya; Zhou, Zhao; Yuan, Qipeng

    2016-12-01

    Chondroitinases (ChSases) are a family of polysaccharide lyases that can depolymerize high molecular weight chondroitin sulfate (CS) and dermatan sulfate (DS). In this study, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), which is stably expressed in different cells like normal cells and cancer cells and the expression is relatively insensitive to experimental conditions, was expressed as a fusion protein with ChSase ABC I. Results showed that the expression level and enzyme activity of GAPDH-ChSase ABC I were about 2.2 and 3.0 times higher than those of ChSase ABC I. By optimization of fermentation conditions, higher productivity of ChSase ABC I was achieved as 880 ± 61 IU/g wet cell weight compared with the reported ones. The optimal temperature and pH of GAPDH-ChSase ABC I were 40 °C and 7.5, respectively. GAPDH-ChSase ABC I had a kcat/Km of 131 ± 4.1 L/μmol s and the catalytic efficiency was decreased as compared to ChSase ABC I. The relative activity of GAPDH-ChSase ABC I remained 89% after being incubated at 30 °C for 180 min and the thermostability of ChSase ABC I was enhanced by GAPDH when it was incubated at 30, 35, 40 and 45 °C. Copyright © 2016 Elsevier Inc. All rights reserved.

  13. Altered Baseline and Nicotine-Mediated Behavioral and Cholinergic Profiles in ChAT-Cre Mouse Lines.

    PubMed

    Chen, Edison; Lallai, Valeria; Sherafat, Yasmine; Grimes, Nickolas P; Pushkin, Anna N; Fowler, J P; Fowler, Christie D

    2018-02-28

    The recent development of transgenic rodent lines expressing cre recombinase in a cell-specific manner, along with advances in engineered viral vectors, has permitted in-depth investigations into circuit function. However, emerging evidence has begun to suggest that genetic modifications may introduce unexpected caveats. In the current studies, we sought to extensively characterize male and female mice from both the ChAT (BAC) -Cre mouse line, created with the bacterial artificial chromosome (BAC) method, and ChAT (IRES) -Cre mouse line, generated with the internal ribosome entry site (IRES) method. ChAT (BAC) -Cre transgenic and wild-type mice did not differ in general locomotor behavior, anxiety measures, drug-induced cataplexy, nicotine-mediated hypolocomotion, or operant food training. However, ChAT (BAC) -Cre transgenic mice did exhibit significant deficits in intravenous nicotine self-administration, which paralleled an increase in vesicular acetylcholine transporter and choline acetyltransferase (ChAT) hippocampal expression. For the ChAT (IRES) -Cre line, transgenic mice exhibited deficits in baseline locomotor, nicotine-mediated hypolocomotion, and operant food training compared with wild-type and hemizygous littermates. No differences among ChAT (IRES) -Cre wild-type, hemizygous, and transgenic littermates were found in anxiety measures, drug-induced cataplexy, and nicotine self-administration. Given that increased cre expression was present in the ChAT (IRES) -Cre transgenic mice, as well as a decrease in ChAT expression in the hippocampus, altered neuronal function may underlie behavioral phenotypes. In contrast, ChAT (IRES) -Cre hemizygous mice were more similar to wild-type mice in both protein expression and the majority of behavioral assessments. As such, interpretation of data derived from ChAT-Cre rodents must consider potential limitations dependent on the line and/or genotype used in research investigations. SIGNIFICANCE STATEMENT Altered

  14. A pan-Arctic synthesis of CH4 and CO2 production from anoxic soil incubations

    USGS Publications Warehouse

    Treat, C.C.; Natali, Susan M.; Ernakovich, Jessica; Iverson, Colleen M.; Lupasco, Massimo; McGuire, A. David; Norby, Richard J.; Roy Chowdhury, Taniya; Richter, Andreas; Šantrůčková, Hana; Schädel, C.; Schuur, Edward A.G.; Sloan, Victoria L.; Turetsky, Merritt R.; Waldrop, Mark P.

    2015-01-01

    Permafrost thaw can alter the soil environment through changes in soil moisture, frequently resulting in soil saturation, a shift to anaerobic decomposition, and changes in the plant community. These changes, along with thawing of previously frozen organic material, can alter the form and magnitude of greenhouse gas production from permafrost ecosystems. We synthesized existing methane (CH4) and carbon dioxide (CO2) production measurements from anaerobic incubations of boreal and tundra soils from the geographic permafrost region to evaluate large-scale controls of anaerobic CO2 and CH4 production and compare the relative importance of landscape-level factors (e.g., vegetation type and landscape position), soil properties (e.g., pH, depth, and soil type), and soil environmental conditions (e.g., temperature and relative water table position). We found fivefold higher maximum CH4 production per gram soil carbon from organic soils than mineral soils. Maximum CH4 production from soils in the active layer (ground that thaws and refreezes annually) was nearly four times that of permafrost per gram soil carbon, and CH4 production per gram soil carbon was two times greater from sites without permafrost than sites with permafrost. Maximum CH4 and median anaerobic CO2 production decreased with depth, while CO2:CH4 production increased with depth. Maximum CH4 production was highest in soils with herbaceous vegetation and soils that were either consistently or periodically inundated. This synthesis identifies the need to consider biome, landscape position, and vascular/moss vegetation types when modeling CH4 production in permafrost ecosystems and suggests the need for longer-term anaerobic incubations to fully capture CH4 dynamics. Our results demonstrate that as climate warms in arctic and boreal regions, rates of anaerobic CO2 and CH4 production will increase, not only as a result of increased temperature, but also from shifts in vegetation and increased

  15. Multiple bonds between transition metals and main-group elements. 73. Synthetic routes to rhenium(V) alkyl and rhenium(VII) alkylidyne complexes. X-ray crystal structures of (. eta. sup 5 -C sub 5 Me sub 5 )Re( double bond O)(CH sub 3 )(CH sub 2 C(CH sub 3 ) sub 3 ) and (. eta. sup 5 -C sub 5 Me sub 5 )(Br) sub 3 Re triple bond CC(CH sub 3 ) sub 3

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Herrmann, W.A.; Felixberger, J.K.; Anwander, R.

    1990-05-01

    Dialkyloxo({eta}{sup 5}pentamethylcyclopentadienyl)rhenium(V) complexes ({eta}{sup 5}-C{sub 5}Me{sub 5})Re({double bond}O)(CH{sub 3})R{prime}(R{prime} = C{sub 2}H{sub 5}, CH{sub 2}Si(CH{sub 3}){sub 3}, CH{sub 2}C(CH{sub 3}){sub 3}), 1c-e, have become accessible through alkylation of ({eta}{sup 5}-C{sub 5}Me{sub 5})Re({double bond}O)(Cl)(CH{sub 3}) (7) with R{prime}MgCl. 1c-e are the first rhenium complexes containing different alkyl ligands. The neopentyl derivative 1e (R{prime} = CH{sub 2}C(CH{sub 3}){sub 3}) crystallizes in the orthorhombic space group Pbca with a = 960.7 (2), b = 2.844.5 (4), c = 1,260.7 (2) pm, and Z = 8. The X-ray crystal structure was refined to R{sub W} = 3.9%. The chiral molecule shows a distorted tetrahedralmore » geometry around the rhenium center. The tribromide 3b has been structurally characterized. Brown crystals of 3b belong to space group P2{sub 1}/c with unit cell dimensions a = 1,311.5 (2), b = 723.0 (1), c = 1,901.6 (2) pm, {beta} = 92.68 (1){degree}, and Z = 4. The structure exhibits a four-legged piano stool geometry with no trans influence of the neopentylidyne ligand to the bromine atom.« less

  16. Q-nexus: a comprehensive and efficient analysis pipeline designed for ChIP-nexus.

    PubMed

    Hansen, Peter; Hecht, Jochen; Ibn-Salem, Jonas; Menkuec, Benjamin S; Roskosch, Sebastian; Truss, Matthias; Robinson, Peter N

    2016-11-04

    ChIP-nexus, an extension of the ChIP-exo protocol, can be used to map the borders of protein-bound DNA sequences at nucleotide resolution, requires less input DNA and enables selective PCR duplicate removal using random barcodes. However, the use of random barcodes requires additional preprocessing of the mapping data, which complicates the computational analysis. To date, only a very limited number of software packages are available for the analysis of ChIP-exo data, which have not yet been systematically tested and compared on ChIP-nexus data. Here, we present a comprehensive software package for ChIP-nexus data that exploits the random barcodes for selective removal of PCR duplicates and for quality control. Furthermore, we developed bespoke methods to estimate the width of the protected region resulting from protein-DNA binding and to infer binding positions from ChIP-nexus data. Finally, we applied our peak calling method as well as the two other methods MACE and MACS2 to the available ChIP-nexus data. The Q-nexus software is efficient and easy to use. Novel statistics about duplication rates in consideration of random barcodes are calculated. Our method for the estimation of the width of the protected region yields unbiased signatures that are highly reproducible for biological replicates and at the same time very specific for the respective factors analyzed. As judged by the irreproducible discovery rate (IDR), our peak calling algorithm shows a substantially better reproducibility. An implementation of Q-nexus is available at http://charite.github.io/Q/ .

  17. Experimental ion mobility measurements in Xe-CH4

    NASA Astrophysics Data System (ADS)

    Perdigoto, J. M. C.; Cortez, A. F. V.; Veenhof, R.; Neves, P. N. B.; Santos, F. P.; Borges, F. I. G. M.; Conde, C. A. N.

    2017-09-01

    Data on ion mobility is important to improve the performance of large volume gaseous detectors. In the present work, the method, experimental setup and results for the ion mobility measurements in Xe-CH4 mixtures are presented. The results for this mixture show the presence of two distinct groups of ions. The nature of the ions depend on the mixture ratio since they are originated by both Xe and CH4. The results here presented were obtained for low reduced electric fields, E/N, 10-25 Td (2.4-6.1 kV ṡ cm-1 ṡ bar-1), at low pressure (8 Torr) (10.6 mbar), and at room temperature.

  18. Infrared identification of the Criegee intermediates syn- and anti-CH3CHOO, and their distinct conformation-dependent reactivity

    PubMed Central

    Lin, Hui-Yu; Huang, Yu-Hsuan; Wang, Xiaohong; Bowman, Joel M.; Nishimura, Yoshifumi; Witek, Henryk A.; Lee, Yuan-Pern

    2015-01-01

    The Criegee intermediates are carbonyl oxides that play critical roles in ozonolysis of alkenes in the atmosphere. So far, the mid-infrared spectrum of only the simplest Criegee intermediate CH2OO has been reported. Methyl substitution of CH2OO produces two conformers of CH3CHOO and consequently complicates the infrared spectrum. Here we report the transient infrared spectrum of syn- and anti-CH3CHOO, produced from CH3CHI + O2 in a flow reactor, using a step-scan Fourier-transform spectrometer. Guided and supported by high-level full-dimensional quantum calculations, rotational contours of the four observed bands are simulated successfully and provide definitive identification of both conformers. Furthermore, anti-CH3CHOO shows a reactivity greater than syn-CH3CHOO towards NO/NO2; at the later period of reaction, the spectrum can be simulated with only syn-CH3CHOO. Without NO/NO2, anti-CH3CHOO also decays much faster than syn-CH3CHOO. The direct infrared detection of syn- and anti-CH3CHOO should prove useful for field measurements and laboratory investigations of the Criegee mechanism. PMID:25959902

  19. Dissociative photoionization mechanism of methanol isotopologues (CH3OH, CD3OH, CH3OD and CD3OD) by iPEPICO: energetics, statistical and non-statistical kinetics and isotope effects.

    PubMed

    Borkar, Sampada; Sztáray, Bálint; Bodi, Andras

    2011-07-28

    The dissociative photoionization of energy selected methanol isotopologue (CH(3)OH, CD(3)OH, CH(3)OD and CD(3)OD) cations was investigated using imaging Photoelectron Photoion Coincidence (iPEPICO) spectroscopy. The first dissociation is an H/D-atom loss from the carbon, also confirmed by partial deuteration. Somewhat above 12 eV, a parallel H(2)-loss channel weakly asserts itself. At photon energies above 15 eV, in a consecutive hydrogen molecule loss to the first H-atom loss, the formation of CHO(+)/CDO(+) dominates as opposed to COH(+)/COD(+) formation. We see little evidence for H-atom scrambling in these processes. In the photon energy range corresponding to the B[combining tilde] and C[combining tilde] ion states, a hydroxyl radical loss appears yielding CH(3)(+)/CD(3)(+). Based on the branching ratios, statistical considerations and ab initio calculations, this process is confirmed to take place on the first electronically excited Ã(2)A' ion state. Uncharacteristically, internal conversion is outcompeted by unimolecular dissociation due to the apparently weak Renner-Teller-like coupling between the X[combining tilde] and the à ion states. The experimental 0 K appearance energies of the ions CH(2)OH(+), CD(2)OH(+), CH(2)OD(+) and CD(2)OD(+) are measured to be 11.646 ± 0.003 eV, 11.739 ± 0.003 eV, 11.642 ± 0.003 eV and 11.737 ± 0.003 eV, respectively. The E(0)(CH(2)OH(+)) = 11.6454 ± 0.0017 eV was obtained based on the independently measured isotopologue results and calculated zero point effects. The 0 K heat of formation of CH(2)OH(+), protonated formaldehyde, was determined to be 717.7 ± 0.7 kJ mol(-1). This yields a 0 K heat of formation of CH(2)OH of -11.1 ± 0.9 kJ mol(-1) and an experimental 298 K proton affinity of formaldehyde of 711.6 ± 0.8 kJ mol(-1). The reverse barrier to homonuclear H(2)-loss from CH(3)OH(+) is determined to be 36 kJ mol(-1), whereas for heteronuclear H(2)-loss from CH(2)OH(+) it is found to be 210 kJ mol(-1). This

  20. Noncentrosymmetric rare-earth copper gallium chalcogenides RE3CuGaCh7 (RE=La-Nd; Ch=S, Se): An unexpected combination

    NASA Astrophysics Data System (ADS)

    Iyer, Abishek K.; Rudyk, Brent W.; Lin, Xinsong; Singh, Harpreet; Sharma, Arzoo Z.; Wiebe, Christopher R.; Mar, Arthur

    2015-09-01

    The quaternary rare-earth chalcogenides RE3CuGaS7 and RE3CuGaSe7 (RE=La-Nd) have been prepared by reactions of the elements at 1050 °C and 900 °C, respectively. They crystallize in the noncentrosymmetric La3CuSiS7-type structure (hexagonal, space group P63, Z=2) in which the a-parameter is largely controlled by the RE component (a=10.0-10.3 Å for the sulfides and 10.3-10.6 Å for the selenides) whereas the c-parameter is essentially fixed by the choice of Ga and chalcogen atoms within tetrahedral units (c=6.1 Å for the sulfides and 6.4 Å for the selenides). They extend the series RE3MGaCh7, previously known for divalent metal atoms (M=Mn-Ni), differing in that the Cu atoms in RE3CuGaCh7 occupy trigonal planar sites instead of octahedral sites. Among quaternary chalcogenides RE3MM‧Ch7, the combination of monovalent (M=Cu) and trivalent (M‧=Ga) metals is unusual because it appears to violate the condition of charge balance satisfied by most La3CuSiS7-type compounds. The possibility of divalent Cu atoms was ruled out by bond valence sum analysis, magnetic measurements, and X-ray photoelectron spectroscopy. The electron deficiency in RE3CuGaCh7 is accommodated through S-based holes at the top of the valence band, as shown by band structure calculations on La3CuGaS7. An optical band gap of about 2.0 eV was found for La3CuGaSe7.

  1. Trầm Cảm Ở Thành Viên Gia Đình Của Nam Tiêm Chích Ma Túy Nhiễm HIV Tại Hà Nội Năm 2016

    PubMed Central

    Thúy, Đào Thị Diệu; Hoàng, Trần Minh; Thúy, Đinh Thanh; Mai, Phạm Phương; Giang, Lê Minh

    2018-01-01

    Đa số người tiêm chích ma túy ở Việt Nam đang sống cùng gia đình và điều này tạo ra gánh nặng không nhỏ trong việc chăm sóc. Mục tiêu nghiên cứu là mô tả đặc điểm trầm cảm ở thành viên gia đình của nam tiêm chích ma túy nhiễm HIV và một số yếu tố liên quan. Số liệu nghiên cứu cắt ngang thu thập từ 138 người là thành viên gia đình của nam tiêm chích ma túy nhiễm HIV tại Hà Nội. Kết quả nghiên cứu cho thấy có xấp xỉ 20% mẫu nghiên cứu có dấu hiệu trầm cảm ở mức độ từ nhẹ đến rất nặng. Gánh nặng chăm sóc và mối quan hệ gia đình có liên quan với trầm cảm ở thành viên gia đình. Nghiên cứu cho thấy nhu cầu can thiệp để cải thiện mối quan hệ gia đình, giảm bớt gánh nặng chăm sóc nhằm nâng cao sức khỏe tinh thần ở thành viên gia đình người tiêm chích ma túy nhiễm HIV. PMID:29367942

  2. The atmospheric degradation of methyl isocyanate (CH3NCO), a toxic substance

    NASA Astrophysics Data System (ADS)

    Papanastasiou, D. K.; Bernard, F.; Burkholder, J. B.

    2016-12-01

    Alkyl isocyanates (R-NCO), as well as isocyanic acid (HNCO), are toxic substances that are emitted into the atmosphere during incomplete combustion of biomass and also formed as products in the atmospheric photooxidation of nitrogen-containing organic species. For example, methyl isocyanate (MIC, CH3NCO) is formed in the atmospheric photochemical transformation of methylisothiocyanate (CH3NCS), a widely used soil fumigant, as well as in the atmospheric photooxidation of amides, such as N-methylformamide. MIC is of particular interest to society because of the possible exposure to this toxic trace compound (recommended exposure limit is 0.02 ppm) in the aftermath of fumigation. Although, there are limited observations of atmospheric MIC (mostly nearby agricultural/fumigation activities) the possibility of emission from combustion processes, such as wildfires, warrants future study. The atmospheric lifetime and fate (gas phase and heterogeneous chemistry) of CH3NCO are presently not well characterized with only a single study of the OH + CH3NCO reaction rate coefficient available in the literature. Additional results from fundamental laboratory studies regarding the major atmospheric degradation pathways of MIC are needed for input to air quality, health, and environmental impact studies. In this study, the reaction of CH3NCO with OH radicals was investigated using pulsed laser photolysis coupled with laser induced fluorescence detection of the OH radical. The rate coefficients, k(OH+CH3NCO), were determined over a range of temperature (295-375 K) and pressure (40-100 Torr, He). The present results are in significant disagreement with the recently published relative rate study. A relative rate kinetic method was also used in this study for comparison and the problems associated with these measurements will be discussed. The atmospheric lifetime of MIC with respect to its gas-phase reaction with OH radicals is estimated to be 85 days, which implies the possibility for

  3. ChR2 transgenic animals in peripheral sensory system: Sensing light as various sensations.

    PubMed

    Ji, Zhi-Gang; Wang, Hongxia

    2016-04-01

    Since the introduction of Channelrhodopsin-2 (ChR2) to neuroscience, optogenetics technology was developed, making it possible to activate specific neurons or circuits with spatial and temporal precision. Various ChR2 transgenic animal models have been generated and are playing important roles in revealing the mechanisms of neural activities, mapping neural circuits, controlling the behaviors of animals as well as exploring new strategy for treating the neurological diseases in both central and peripheral nervous system. An animal including humans senses environments through Aristotle's five senses (sight, hearing, smell, taste and touch). Usually, each sense is associated with a kind of sensory organ (eyes, ears, nose, tongue and skin). Is it possible that one could hear light, smell light, taste light and touch light? When ChR2 is targeted to different peripheral sensory neurons by viral vectors or generating ChR2 transgenic animals, the animals can sense the light as various sensations such as hearing, touch, pain, smell and taste. In this review, we focus on ChR2 transgenic animals in the peripheral nervous system. Firstly the working principle of ChR2 as an optogenetic actuator is simply described. Then the current transgenic animal lines where ChR2 was expressed in peripheral sensory neurons are presented and the findings obtained by these animal models are reviewed. Copyright © 2016 Elsevier Inc. All rights reserved.

  4. Comment on Chem. Phys. Lett. 371 (2003) 568: Barrier height for dissociation of acetaldehyde, CH 3CHO → CH 3 + HCO, in the triplet state T 1

    NASA Astrophysics Data System (ADS)

    Robert Huber, J.

    2003-08-01

    Based on recently reported experimental results from various groups, the barrier height (or transition state energy) for the T 1 dissociation of acetaldehyde, CH 3CHO → CH 3 + HCO, is determined to lie between 12.3 and 12.9 kcal mol -1. This result is compared with predictions from recent ab initio calculations.

  5. SAPO-34 Membranes for N-2/CH4 separation: Preparation, characterization, separation performance and economic evaluation

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Li, SG; Zong, ZW; Zhou, SJ

    2015-08-01

    SAPO-34 membranes were synthesized by several routes towards N-2/CH4 separation. Membrane synthesis parameters including water content in the gel, crystallization time, support pore size, and aluminum source were investigated. High performance N-2-selective membranes were obtained on 100-nm-pore alumina tubes by using Al(i-C3H7O)(3) as aluminum source with a crystallization time of 6 h. These membranes separated N-2 from CH, with N-2 permeance as high as 500 GPU with separation selectivity of 8 at 24 degrees C. for a 50/50 N-2/CH4 mixture. Nitrogen and CH, adsorption isotherms were measured on SAPO-34 crystals. The N-2 and CH, heats of adsorption were 11 andmore » 15 kJ/mol, respectively, which lead to a preferential adsorption of CE-H-4 over N-2 in the N-2/CH4 mixture. Despite this, the SAPO-34 membranes were selective for N-2 over CH4 in the mixture because N-2 diffuses much faster than CH4 and differences in diffusivity played a more critical role than the competitive adsorption. Preliminary economic evaluation indicates that the required N-2/CH4 selectivity would be 15 in order to maintain a CH4 loss below 10%. For small nitrogen-contaminated gas wells, our current SAPO-34 membranes have potential to compete with the benchmark technology cryogenic distillation for N-2 rejection. (C) 2015 Elsevier B.V. All rights reserved,« less

  6. Activation of CH4 by Th(+) as studied by guided ion beam mass spectrometry and quantum chemistry.

    PubMed

    Cox, Richard M; Armentrout, P B; de Jong, Wibe A

    2015-04-06

    The reaction of atomic thorium cations with CH4 (CD4) and the collision-induced dissociation (CID) of ThCH4(+) with Xe are studied using guided ion beam tandem mass spectrometry. In the methane reactions at low energies, ThCH2(+) (ThCD2(+)) is the only product; however, the energy dependence of the cross-section is inconsistent with a barrierless exothermic reaction as previously assumed on the basis of ion cyclotron resonance mass spectrometry results. The dominant product at higher energies is ThH(+) (ThD(+)), with ThCH3(+) (ThCD3(+)) having a similar threshold energy. The latter product subsequently decomposes at still higher energies to ThCH(+) (ThCD(+)). CID of ThCH4(+) yields atomic Th(+) as the exclusive product. The cross-sections of all product ions are modeled to provide 0 K bond dissociation energies (in eV) of D0(Th(+)-H) ≥ 2.25 ± 0.18, D0(Th(+)-CH) = 6.19 ± 0.16, D0(Th(+)-CH2) ≥ 4.54 ± 0.09, D0(Th(+)-CH3) = 2.60 ± 0.30, and D0(Th(+)-CH4) = 0.47 ± 0.05. Quantum chemical calculations at several levels of theory are used to explore the potential energy surfaces for activation of methane by Th(+), and the effects of spin-orbit coupling are carefully considered. When spin-orbit coupling is explicitly considered, a barrier for C-H bond activation that is consistent with the threshold measured for ThCH2(+) formation (0.17 ± 0.02 eV) is found at all levels of theory, whereas this barrier is observed only at the BHLYP and CCSD(T) levels otherwise. The observation that the CID of the ThCH4(+) complex produces Th(+) as the only product with a threshold of 0.47 eV indicates that this species has a Th(+)(CH4) structure, which is also consistent with a barrier for C-H bond activation. This barrier is thought to exist as a result of the mixed ((4)F,(2)D) electronic character of the Th(+) J = (3)/2 ground level combined with extensive spin-orbit effects.

  7. Factors influencing CO2 and CH4 emissions from coastal wetlands in the Liaohe Delta, northeast China

    USGS Publications Warehouse

    Olsson, Linda; Ye, Siyuan; Yu, Xueyang; Wei, Mengjie; Krauss, Ken W.; Brix, Hans

    2015-01-01

    Many factors are known to influence greenhouse gas emissions from coastal wetlands, but it is still unclear which factors are most important under field conditions when they are all acting simultaneously. The objective of this study was to assess the effects of water table, salinity, soil temperature and vegetation on CH4 emissions and ecosystem respiration (Reco) from five coastal wetlands in the Liaohe Delta, northeast China: two Phragmites australis (common reed) wetlands, two Suaeda salsa (sea blite) marshes and a rice (Oryza sativa) paddy. Throughout the growing season, the Suaeda wetlands were net CH4 sinks whereas the Phragmites wetlands and the rice paddy were net CH4sources emitting 1.2–6.1 g CH4 m−2 y−1. The Phragmites wetlands emitted the most CH4 per unit area and the most CH4 relative to CO2. The main controlling factors for the CH4 emissions were water table, temperature and salinity. The CH4 emission was accelerated at high and constant (or managed) water tables and decreased at water tables below the soil surface. High temperatures enhanced CH4 emissions, and emission rates were consistently low (< 1 mg CH4 m−2 h) at soil temperatures <18 °C. At salinity levels > 18 ppt, the CH4 emission rates were always low (< 1 mg CH4 m−2 h−1) probably because methanogens were outcompeted by sulphate reducing bacteria. Saline Phragmites wetlands can, however, emit significant amounts of CH4 as CH4 produced in deep soil layers are transported through the air-space tissue of the plants to the atmosphere. The CH4 emission from coastal wetlands can be reduced by creating fluctuating water tables, including water tables below the soil surface, as well as by occasional flooding by high-salinity water. The effects of water management schemes on the biological communities in the wetlands must, however, be carefully studied prior to the management in order to avoid undesirable effects on the wetland communities.

  8. Insights into the structure of mixed CO 2/CH 4 in gas hydrates

    DOE PAGES

    Everett, S. Michelle; Rawn, Claudia J.; Chakoumakos, Bryan C.; ...

    2015-05-12

    The exchange of carbon dioxide for methane in natural gas hydrates is an attractive approach to harvesting CH 4 for energy production while simultaneously sequestering CO 2. In addition to the energy and environmental implications, the solid solution of clathrate hydrate (CH 4) 1-x(CO 2) x·5.75H 2O provides a model system to study how the distinct bonding and shapes of CH 4 and CO 2 influence the structure and properties of the compound. In this paper, high-resolution neutron diffraction was used to examine mixed CO 2/CH 4 gas hydrates. CO 2-rich hydrates had smaller lattice parameters, which were attributed tomore » the higher affinity of the CO 2 molecule interacting with H 2O molecules that form the surrounding cages, and resulted in a reduction in the unit-cell volume. Experimental nuclear scattering densities illustrate how the cage occupants and energy landscape change with composition. Finally, these results provide important insights on the impact and mechanisms for the structure of mixed CH 4/CO 2 gas hydrate.« less

  9. Detection of CH+, SH+, and their 13C- and 34S-isotopologues toward PKS 1830-211

    NASA Astrophysics Data System (ADS)

    Muller, S.; Müller, H. S. P.; Black, J. H.; Gérin, M.; Combes, F.; Curran, S.; Falgarone, E.; Guélin, M.; Henkel, C.; Martín, S.; Menten, K. M.; Roueff, E.; Aalto, S.; Beelen, A.; Wiklind, T.; Zwaan, M. A.

    2017-10-01

    The z = 0.89 molecular absorber toward PKS 1830-211 provides us with the opportunity to probe the chemical and physical properties of the interstellar medium in the disk of a galaxy at a look-back time of half the present age of the Universe. Recent ALMA observations of hydrides have unveiled the multi-phase composition of this source's interstellar medium along two absorbing sightlines. Here, we report ALMA observations of CH+ and SH+, and of their 13C- and 34S-isotopologues, as potential tracers of energetic processes in the interstellar medium. CH+ and 13CH+ are detected toward both images of PKS 1830-211, CH+ showing the deepest and broadest absorption among all species observed so far. The [CH+]/[13CH+] abundance ratio is 100 in the south-west line of sight. This value is larger than any previous [12CX]/[13CX] ratios determined from other species toward this source and suggests either that the latter might be affected by fractionation or that CH+ might be tracing a different gas component. Toward the north-east image, we find an even larger value of [CH+]/[13CH+], 146 ± 43, although with a large uncertainty. This sightline intercepts the absorber at a larger galactocentric radius than the southwestern one, where material might be less processed in stellar nucleosynthesis. In contrast to CH+ and its 13C isotopologue, SH+ and 34SH+ are only detected on the south-west sightline. These are the first detections of extragalactic SH+ and interstellar 34SH+. The spectroscopic parameters of SH+ are reevaluated and improved rest frequencies of 34SH+ are obtained. The [CH+]/[SH+] column density ratios show a large difference between the two lines of sight: 25 and >600 toward the SW and NE image, respectively. We are not able to shed light on the formation process of CH+ and SH+ with these data, but the differences between the two sightlines toward PKS 1830-211 suggest that their absorptions arise from gas with a molecular fraction of ≳10%, with SH+ tracing

  10. Calcium-aluminum-rich inclusions recycled during formation of porphyritic chondrules from CH carbonaceous chondrites

    NASA Astrophysics Data System (ADS)

    Krot, Alexander N.; Nagashima, Kazuhide; van Kooten, Elishevah M. M.; Bizzarro, Martin

    2017-03-01

    We report on the mineralogy, petrography, and O-isotope compositions of ∼60 Ca, Al-rich inclusions (CAIs) incompletely melted during formation of porphyritic chondrules from the CH metal-rich carbonaceous chondrites and Isheyevo (CH/CB). These include (i) relict polymineralic CAIs in porphyritic chondrules, (ii) CAIs surrounded by chondrule-like igneous rims, (iii) igneous pyroxene-rich and Type C-like CAIs, and (iv) plagioclase-rich chondrules with clusters of relict spinel grains. 26Al-26Mg systematics were measured in 10 relict CAIs and 11 CAI-bearing plagioclase-rich chondrules. Based on the mineralogy, the CH CAIs incompletely melted during chondrule formation can be divided into grossite-rich (n = 13), hibonite-rich (n = 11), spinel ± melilite-rich (n = 33; these include plagioclase-rich chondrules with clusters of relict spinel grains) types. Mineralogical observations indicate that these CAIs were mixed with different proportions of ferromagnesian silicates and experienced incomplete melting and gas-melt interaction during chondrule formation. These processes resulted in partial or complete destruction of the CAI Wark-Lovering rims, replacement of melilite by Na-bearing plagioclase, and dissolution and overgrowth of nearly end-member spinel by chromium- and iron-bearing spinel. Only two relict CAIs and two CAI-bearing chondrules show resolvable excess of radiogenic 26Mg; the inferred initial 26Al/27Al ratios are (1.7 ± 1.3) × 10-6, (3.7 ± 3.1) × 10-7, (1.9 ± 0.9) × 10-6 and (4.9 ± 2.6) × 10-6. There is a large range of Δ17O among the CH CAIs incompletely melted during chondrule formation, from ∼-37‰ to ∼-5‰; the unmelted minerals in individual CAIs, however, are isotopically uniform and systematically 16O-enriched relative to the host chondrules and chondrule-like igneous rims, which have Δ17O ranging from ∼-7‰ to ∼+4‰. Most of the CH CAIs incompletely melted during chondrule formation are mineralogically and isotopically

  11. CH 3NO 2 decomposition/isomerization mechanism and product branching ratios: An ab initio chemical kinetic study

    NASA Astrophysics Data System (ADS)

    Zhu, R. S.; Lin, M. C.

    2009-08-01

    The low-lying energy pathways for the decomposition/isomerization of nitromethane (NM) have been investigated using different molecular orbital methods. Our results show that in addition to the commonly known CH 3 + NO 2 products formed by direct C-N bond breaking and the trans-CH 3ONO formed by nitro-nitrite isomerization, NM can also isomerize to cis-CH 3ONO via a very loose transition state (TS) lying 59.2 kcal/mol above CH 3NO 2 or 0.6 kcal/mol below the CH 3 + NO 2 asymptote predicted at the UCCSD(T)/CBS level of theory. Kinetic results indicate that in the energy range of 59 ± 1 kcal/mol, production of CH 3O + NO is dominant, whereas above the C-N bond breaking threshold, the formation of CH 3 + NO 2 sharply increases and becomes dominant. The k( E) values predicted at different energies clearly indicate that CH 3O + NO could be detected in an infrared multi-photon dissociation study, whereas in UV dissociation experiments with energies high above the C-N bond breaking threshold the CH 3 + NO 2 products are generated predominantly.

  12. A new metal-organic framework for separation of C2H2/CH4 and CO2/CH4 at room temperature

    NASA Astrophysics Data System (ADS)

    Duan, Xing; Zhou, You; Lv, Ran; Yu, Ben; Chen, Haodong; Ji, Zhenguo; Cui, Yuanjing; Yang, Yu; Qian, Guodong

    2018-04-01

    A 3D microporous metal-organic framework with open Cu2+ sites and suitable pore space, [Cu2(L)(H2O)2]·(H2O)4(DMF)8 (ZJU-15, H4L = 5,5‧-(9H-carbazole-2,7-diyl)diisophthalic acid; DMF = N,N-dimethylformamide; ZJU = Zhejiang University), has been constructed and characterized. The activated ZJU-15a has three different types of cages and exhibits BET surface area of 1660 m2 g-1, and can separate gas mixture of C2H2/CH4 and CO2/CH4 at room temperature.

  13. Quantitative Measurements of CH* Concentration in Normal Gravity and Microgravity Coflow Laminar Diffusion Flames

    NASA Technical Reports Server (NTRS)

    Giassi, D.; Cao, S.; Stocker, D. P.; Takahashi, F.; Bennett, B. A.; Smooke, M. D.; Long, M. B.

    2015-01-01

    With the conclusion of the SLICE campaign aboard the ISS in 2012, a large amount of data was made available for the analysis of the effect of microgravity on laminar coflow diffusion flames. Previous work focused on the study of sooty flames in microgravity as well as the ability of numerical models to predict its formation in a simplified buoyancy-free environment. The current work shifts the investigation to soot-free flames, putting an emphasis on the chemiluminescence emission from electronically excited CH (CH*). This radical species is of significant interest in combustion studies: it has been shown that the CH* spatial distribution is indicative of the flame front position and, given the relatively simple diagnostic involved with its measurement, several works have been done trying to understand the ability of CH* chemiluminescence to predict the total and local flame heat release rate. In this work, a subset of the SLICE nitrogen-diluted methane flames has been considered, and the effect of fuel and coflow velocity on CH* concentration is discussed and compared with both normal gravity results and numerical simulations. Experimentally, the spectral characterization of the DSLR color camera used to acquire the flame images allowed the signal collected by the blue channel to be considered representative of the CH* emission centered around 431 nm. Due to the axisymmetric flame structure, an Abel deconvolution of the line-of-sight chemiluminescence was used to obtain the radial intensity profile and, thanks to an absolute light intensity calibration, a quantification of the CH* concentration was possible. Results show that, in microgravity, the maximum flame CH* concentration increases with the coflow velocity, but it is weakly dependent on the fuel velocity; normal gravity flames, if not lifted, tend to follow the same trend, albeit with different peak concentrations. Comparisons with numerical simulations display reasonably good agreement between measured and

  14. High-pressure LOX/CH4 injector program

    NASA Technical Reports Server (NTRS)

    Wheeler, D. B.; Kirby, F. M.

    1979-01-01

    Two injector types, either coaxial or impinging elements, for high pressure LOX/CH4 operation with an existing 40K chamber are examined. A comparison is presented. The detailed fabrication drawings and supporting analysis are presented.

  15. Constraining the Molecular Complexity in the Interstellar Medium—The Formation of Ethyl Methyl Ether (CH3OCH2CH3) in Star-forming Regions

    NASA Astrophysics Data System (ADS)

    Bergantini, Alexandre; Frigge, Robert; Kaiser, Ralf I.

    2018-05-01

    We report the first confirmed synthesis of ethyl methyl ether (EME, CH3CH2OCH3) within astrophysical model ices containing water (H2O) and methane (CH4) exposed to ionizing radiation at ultra-low temperatures of 5 K. EME (also known as methoxyethane), was recently observed toward Orion KL and currently is the largest confirmed oxygen-bearing molecule found in the interstellar medium. Exploiting isomer-selective photoionization (PI) of the subliming molecules in the temperature-programmed desorption phase at 10.49, 9.92, and 9.70 eV, coupled with reflectron time-of-flight mass spectrometry and isotopic substitution experiments (H2 18O–CH4), the detection of fragment ions of EME at m/z = 45 (C2H5O+) and m/z = 59 (C3H7O+), and probing the proton transfer in subliming ethanol–EME complexes via m/z = 61 (C3H9O+), the present study reveals that EME can be formed from suprathermal reactions initiated by cosmic rays and secondary electrons generated within astrophysical ices. The detection of EME in our experiments represents a significant advance in the understanding of formation pathways of complex organic molecules present in hot cores and helps to constrain astrochemical models on the formation of such species within molecular clouds.

  16. Biogeochemical controls on microbial CH4 and CO2 production in Arctic polygon tundra

    NASA Astrophysics Data System (ADS)

    Zheng, J.

    2016-12-01

    Accurately simulating methane (CH4) and carbon dioxide (CO2) emissions from high latitude soils is critically important for reducing uncertainties in soil carbon-climate feedback predictions. The signature polygonal ground of Arctic tundra generates high level of heterogeneity in soil thermal regime, hydrology and oxygen availability, which limits the application of current land surface models with simple moisture response functions. We synthesized CH4 and CO2 production measurements from soil microcosm experiments across a wet-to dry permafrost degradation gradient from low-centered (LCP) to flat-centered (FCP), and high-centered polygons (HCP) to evaluate the relative importance of biogeochemical processes and their response to warming. More degraded polygon (HCP) showed much less carbon loss as CO2 or CH4, while the total CO2 production from FCP is comparable to that from LCP. Maximum CH4 production from the active layer of LCP was nearly 10 times that of permafrost and FCP. Multivariate analyses identifies gravimetric water content and organic carbon content as key predictors for CH4 production, and iron reduction as a key regulator of pH. The synthesized data are used to validate the geochemical model PHREEQC with extended anaerobic organic substrate turnover, fermentation, iron reduction, and methanogenesis reactions. Sensitivity analyses demonstrate that better representations of anaerobic processes and their pH dependency could significantly improve estimates of CH4 and CO2 production. The synthesized data suggest local decreases in CH4 production along the polygon degradation gradient, which is consistent with previous surface flux measurements. Methane oxidation occurring through the soil column of degraded polygons contributes to their low CH4 emissions as well.

  17. Measuring the Distribution and Excitation of Cometary CH3OH Using ALMA

    NASA Astrophysics Data System (ADS)

    Cordiner, M. A.; Charnley, S. B.; Mumma, M. J.; Bockelée-Morvan, D.; Biver, N.; Villanueva, G.; Paganini, L.; Milam, S. N.; Remijan, A. J.; Lis, D. C.; Crovisier, J.; Boissier, J.; Kuan, Y.-J.; Coulson, I. M.

    2016-10-01

    The Atacama Large Millimeter/submillimeter Array (ALMA) was used to obtain measurements of spatially and spectrally resolved CH3OH emission from comet C/2012 K1 (PanSTARRS) on 28-29 June 2014. Detection of 12-14 emission lines of CH3OH on each day permitted the derivation of spatially-resolved rotational temperature profiles (averaged along the line of sight), for the innermost 5000 km of the coma. On each day, the CH3OH distribution was centrally peaked and approximately consistent with spherically symmetric, uniform outflow. The azimuthally-averaged CH3OH rotational temperature (T rot) as a function of sky-projected nucleocentric distance (ρ), fell by about 40 K between ρ= 0 and 2500 km on 28 June, whereas on 29 June, T rot fell by about 50 K between ρ =0 km and 1500 km. A remarkable (~50 K) rise in T rot at ρ = 1500-2500 km on 29 June was not present on 28 June. The observed variations in CH3OH rotational temperature are interpreted primarily as a result of variations in the coma kinetic temperature due to adiabatic cooling, and heating through Solar irradiation, but collisional and radiative non-LTE excitation processes also play a role.

  18. Theoretical study of methyl hypofluorite (CH sub 3 OF) and related compounds

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Curtiss, L.A.; Pople, J.A.

    1991-12-01

    The Gaussian-2 (G2) theoretical procedure, based on {ital ab} {ital initio} molecular orbital theory, is used to calculate the energies of CH{sub 3}OF, CH{sub 3}OF{sup +}, and related compounds. In this study we have found methyl hypofluorite to have a trans {ital C}{sub {ital s}} structure and to be stable with respect to loss of fluorine by 45.9 kcal/mol. The energies of fragmentation processes of methyl hypofluorite calculated from G2 theory are in agreement with those measured by Ruscic, Appelman, and Berkowitz (J. Chem. Phys. {bold 95}, XXX (1991)) and support their interpretation of the photoionization data. The theoretical enthalpymore » of formation {Delta}{ital H}{sup 0}{sub {ital f}0}(CH{sub 3}OF) of {minus}21.0 kcal/mol is in agreement with the experimental value ({ge}{minus}23.0{plus minus}0.7 kcal/mol) derived from the photoionization data. The ordering of the O--F bond strengths in the series of molecules OF, HOF, and CH{sub 3}OF is OF{gt}HOF{gt}CH{sub 3}OF and the C--O bond strength is 6--8 kcal/mol weaker in methyl hypofluorite than in methanol.« less

  19. Year-round measurements of CH4 exchange in a forested drained peatland using automated chambers

    NASA Astrophysics Data System (ADS)

    Korkiakoski, Mika; Koskinen, Markku; Penttilä, Timo; Arffman, Pentti; Ojanen, Paavo; Minkkinen, Kari; Laurila, Tuomas; Lohila, Annalea

    2016-04-01

    Pristine peatlands are usually carbon accumulating ecosystems and sources of methane (CH4). Draining peatlands for forestry increases the thickness of the oxic layer, thus enhancing CH4 oxidation which leads to decreased CH4 emissions. Closed chambers are commonly used in estimating the greenhouse gas exchange between the soil and the atmosphere. However, the closed chamber technique alters the gas concentration gradient making the concentration development against time non-linear. Selecting the correct fitting method is important as it can be the largest source of uncertainty in flux calculation. We measured CH4 exchange rates and their diurnal and seasonal variations in a nutrient-rich drained peatland located in southern Finland. The original fen was drained for forestry in 1970s and now the tree stand is a mixture of Scots pine, Norway spruce and Downy birch. Our system consisted of six transparent polycarbonate chambers and stainless steel frames, positioned on different types of field and moss layer. During winter, the frame was raised above the snowpack with extension collars and the height of the snowpack inside the chamber was measured regularly. The chambers were closed hourly and the sample gas was sucked into a cavity ring-down spectrometer and analysed for CH4, CO2 and H2O concentration with 5 second time resolution. The concentration change in time in the beginning of a closure was determined with linear and exponential fits. The results show that linear regression systematically underestimated the CH4 flux when compared to exponential regression by 20-50 %. On the other hand, the exponential regression seemed not to work reliably with small fluxes (< 3.5 μg CH4 m-2 h-1): using exponential regression in such cases typically resulted in anomalously large fluxes and high deviation. Due to these facts, we recommend first calculating the flux with the linear regression and, if the flux is high enough, calculate the flux again using the exponential

  20. Role of plant-mediated gas transport in CH4 emissions from Phragmites-dominated peatlands

    NASA Astrophysics Data System (ADS)

    van den Berg, Merit; Ingwersen, Joachim; van den Elzen, Eva; Lamers, Leon P. M.; Streck, Thilo

    2016-04-01

    A large part of the methane (CH4) produced in peatlands is directly oxidized and the extent of its oxidation depends on the gas transport pathway. In wetland ecosystems, CH4 can be transported from the soil to the atmosphere via diffusion, ebullition and via aerenchyma of roots and stems of vascular plants. Compared to other wetland plants, the very common species Phragmites australis (Common reed) appears to have a high ability to transport gases between the soil and atmosphere. The gas exchange within Phragmites plants takes place via convective flow through the culm, which is believed to be achieved by a humidity-induced pressure gradient and is more than 5-times as efficient as diffusion. By this mechanism, CH4 surpasses the upper (oxic) soil layers and therefore oxidation of CH4 may well be reduced. On the other hand, transport of oxygen in Phragmites plants tends to enhance O2concentration in the rhizosphere, which will foster CH4oxidation in deeper soil layers. It is therefore unknown whether humidity-induced convection leads to higher or lower overall CH4 emission in Phragmites, which is essential to understand their role in the emissions from these very common peatland types. To investigate whether this internal gas transport mechanism of reed promotes or reduces CH4 fluxes to the atmosphere, we conducted manipulative field experiments in a large Phragmites peatland in South-West Germany in October 2014 and July 2015. Using large chambers, we compared CH4 fluxes from intact plots, plots with cut reed, and plots with cut + sealed reed to exclude gas transport through the plants. Additionally, pore water samples from the plots were analyzed for possible changes in soil chemistry due to the change of oxygen transport into the soil by the treatments. Based on our results, we will explain the potential role of rhizosphere oxygenation and convective flow on CH4 emissions from Phragmites-dominated peatlands in relation to other environmental condition.

  1. CH4 Hydrate Formation between Silica and Graphite Surfaces: Insights from Microsecond Molecular Dynamics Simulations.

    PubMed

    He, Zhongjin; Linga, Praveen; Jiang, Jianwen

    2017-10-31

    Microsecond simulations have been performed to investigate CH 4 hydrate formation from gas/water two-phase systems between silica and graphite surfaces, respectively. The hydrophilic silica and hydrophobic graphite surfaces exhibit substantially different effects on CH 4 hydrate formation. The graphite surface adsorbs CH 4 molecules to form a nanobubble with a flat or negative curvature, resulting in a low aqueous CH 4 concentration, and hydrate nucleation does not occur during 2.5 μs simulation. Moreover, an ordered interfacial water bilayer forms between the nanobubble and graphite surface thus preventing their direct contact. In contrast, the hydroxylated-silica surface prefers to be hydrated by water, with a cylindrical nanobubble formed in the solution, leading to a high aqueous CH 4 concentration and hydrate nucleation in the bulk region; during hydrate growth, the nanobubble is gradually covered by hydrate solid and separated from the water phase, hence slowing growth. The silanol groups on the silica surface can form strong hydrogen bonds with water, and hydrate cages need to match the arrangements of silanols to form more hydrogen bonds. At the end of the simulation, the hydrate solid is separated from the silica surface by liquid water, with only several cages forming hydrogen bonds with the silica surface, mainly due to the low CH 4 aqueous concentrations near the surface. To further explore hydrate formation between graphite surfaces, CH 4 /water homogeneous solution systems are also simulated. CH 4 molecules in the solution are adsorbed onto graphite and hydrate nucleation occurs in the bulk region. During hydrate growth, the adsorbed CH 4 molecules are gradually converted into hydrate solid. It is found that the hydrate-like ordering of interfacial water induced by graphite promotes the contact between hydrate solid and graphite. We reveal that the ability of silanol groups on silica to form strong hydrogen bonds to stabilize incipient hydrate solid

  2. Gas-phase kinetics during diamond growth: CH4 as-growth species

    NASA Astrophysics Data System (ADS)

    Harris, Stephen J.

    1989-04-01

    We have used a one-dimensional kinetic analysis to model the gas-phase chemistry that occurred during the diamond growth experiments of Chauhan, Angus, and Gardner [J. Appl. Phys. 47, 4746 (1976)]. In those experiments the weight of diamond seed crystals heated by lamps in a CH4/H2 environment was monitored by a microbalance. No filament or electric discharge was present. Our analysis shows that diamond growth occurred in this system by direct reaction of CH4 on the diamond surface. C2H2 and CH3, which have been proposed as diamond growth species, played no significant role there, although our results do not address their possible contributions in other systems such as filament- or plasma-assisted diamond growth.

  3. DIVERSITY in binding, regulation, and evolution revealed from high-throughput ChIP.

    PubMed

    Mitra, Sneha; Biswas, Anushua; Narlikar, Leelavati

    2018-04-01

    Genome-wide in vivo protein-DNA interactions are routinely mapped using high-throughput chromatin immunoprecipitation (ChIP). ChIP-reported regions are typically investigated for enriched sequence-motifs, which are likely to model the DNA-binding specificity of the profiled protein and/or of co-occurring proteins. However, simple enrichment analyses can miss insights into the binding-activity of the protein. Note that ChIP reports regions making direct contact with the protein as well as those binding through intermediaries. For example, consider a ChIP experiment targeting protein X, which binds DNA at its cognate sites, but simultaneously interacts with four other proteins. Each of these proteins also binds to its own specific cognate sites along distant parts of the genome, a scenario consistent with the current view of transcriptional hubs and chromatin loops. Since ChIP will pull down all X-associated regions, the final reported data will be a union of five distinct sets of regions, each containing binding sites of one of the five proteins, respectively. Characterizing all five different motifs and the corresponding sets is important to interpret the ChIP experiment and ultimately, the role of X in regulation. We present diversity which attempts exactly this: it partitions the data so that each partition can be characterized with its own de novo motif. Diversity uses a Bayesian approach to identify the optimal number of motifs and the associated partitions, which together explain the entire dataset. This is in contrast to standard motif finders, which report motifs individually enriched in the data, but do not necessarily explain all reported regions. We show that the different motifs and associated regions identified by diversity give insights into the various complexes that may be forming along the chromatin, something that has so far not been attempted from ChIP data. Webserver at http://diversity.ncl.res.in/; standalone (Mac OS X/Linux) from https

  4. Oxidative esterification via photocatalytic C-H activation

    EPA Science Inventory

    Direct oxidative esterification of alcohol via photocatalytic C-H activation has been developed using VO@g-C3N4 catalyst; an expeditious esterification of alcohols occurs under neutral conditions using visible light as the source of energy.

  5. Mapping of transcription factor binding regions in mammalian cells by ChIP: Comparison of array- and sequencing-based technologies

    PubMed Central

    Euskirchen, Ghia M.; Rozowsky, Joel S.; Wei, Chia-Lin; Lee, Wah Heng; Zhang, Zhengdong D.; Hartman, Stephen; Emanuelsson, Olof; Stolc, Viktor; Weissman, Sherman; Gerstein, Mark B.; Ruan, Yijun; Snyder, Michael

    2007-01-01

    Recent progress in mapping transcription factor (TF) binding regions can largely be credited to chromatin immunoprecipitation (ChIP) technologies. We compared strategies for mapping TF binding regions in mammalian cells using two different ChIP schemes: ChIP with DNA microarray analysis (ChIP-chip) and ChIP with DNA sequencing (ChIP-PET). We first investigated parameters central to obtaining robust ChIP-chip data sets by analyzing STAT1 targets in the ENCODE regions of the human genome, and then compared ChIP-chip to ChIP-PET. We devised methods for scoring and comparing results among various tiling arrays and examined parameters such as DNA microarray format, oligonucleotide length, hybridization conditions, and the use of competitor Cot-1 DNA. The best performance was achieved with high-density oligonucleotide arrays, oligonucleotides ≥50 bases (b), the presence of competitor Cot-1 DNA and hybridizations conducted in microfluidics stations. When target identification was evaluated as a function of array number, 80%–86% of targets were identified with three or more arrays. Comparison of ChIP-chip with ChIP-PET revealed strong agreement for the highest ranked targets with less overlap for the low ranked targets. With advantages and disadvantages unique to each approach, we found that ChIP-chip and ChIP-PET are frequently complementary in their relative abilities to detect STAT1 targets for the lower ranked targets; each method detected validated targets that were missed by the other method. The most comprehensive list of STAT1 binding regions is obtained by merging results from ChIP-chip and ChIP-sequencing. Overall, this study provides information for robust identification, scoring, and validation of TF targets using ChIP-based technologies. PMID:17568005

  6. On the growth of CH3NH3PbI3-xClx single crystal and characterization

    NASA Astrophysics Data System (ADS)

    Su, J.; Wang, W. F.; Lei, Y.; Zhang, L.; Xu, L. H.; Wang, D.; Lu, D.; Bai, Y.

    2018-05-01

    In this paper, CH3NH3PbI3-xClx crystal was grown by solution cooling method with CH3NH3I and PbCl2 as raw materials. Lead compounds and CH3NH3PbI3-xClx crystal with size about 6 mm × 4 mm × 2 mm were obtained. The chemical reactions with different CH3NH3I/PbCl2 ratios were analyzed. XPS shows the content of chlorine in CH3NH3PbI3-xClx is about 0.91%. PXRD, FT-IR, Raman and absorbance spectra were used to study the structure and optical properties of CH3NH3PbI3-xClx by comparing with CH3NH3PbI3 crystal. The CH3NH3PbI3-xClx crystal grown is of tetragonal structure with the lattice constants a = b = 8.8165 Å, c = 12.7920 Å and the bandgap value of 1.57 eV.

  7. The Band of CH_3CH_2D from 770-880 wn

    NASA Astrophysics Data System (ADS)

    Daly, Adam M.; Drouin, Brian; Pearson, John; Groner, Peter; Sung, Keeyoon; Brown, Linda; Mantz, Arlan; Smith, Mary Ann H.

    2015-06-01

    To extend the ethane database we recorded a 0.0028 wn resolution spectrum of CH_3CH_2D from 650 to 1500 wn using a Bruker IFS-125HR at the Jet Propulsion Laboratory. The 98% deuterium-enriched sample was contained in the 0.2038 m absorption cell; one scan was taken with the sample cryogenically cooled to 130 K and another at room temperature. From the cold data, we retrieved line positions and intensities of 8704 individual absorption features from 770 - 880 wn using a least squares curve fitting algorithm. From this set of measurements, we assigned 5041 transitions to the νb{17} fundamental at 805.3427686(234) wn; this band is a c-type vibration, with A and E components arising from internal rotation. The positions were modeled using a 22 term torsional Hamiltonian using SPFIT producing the A and E energy splitting of 5.409(25)x10-3 wn (162.2(8) MHz) with a standard deviation of 7x10-4 wn (21 MHz). The calculated line intensities at 130 K agree very well with retrieved intensities. To predict line intensities at different temperatures, the partition function value was determined at eight temperatures between 9.8 and 300 K by summing individual energy levels up to J = 99 and Ka = 99 for the six states up through νb{17} at 805 wn. The resulting prediction of singly-deuterated ethane absorption at 12.5 μm enables its detection in planetary atmospheres, including those of Titan and exoplanets.

  8. Rare-earth transition-metal gallium chalcogenides RE3MGaCh7 (M=Fe, Co, Ni; Ch=S, Se)

    NASA Astrophysics Data System (ADS)

    Rudyk, Brent W.; Stoyko, Stanislav S.; Oliynyk, Anton O.; Mar, Arthur

    2014-02-01

    Six series of quaternary rare-earth transition-metal chalcogenides RE3MGaCh7 (M=Fe, Co, Ni; Ch=S, Se), comprising 33 compounds in total, have been prepared by reactions of the elements at 1050 °C (for the sulphides) or 900 °C (for the selenides). They adopt noncentrosymmetric hexagonal structures (ordered Ce3Al1.67S7-type, space group P63, Z=2) with cell parameters in the ranges of a=9.5-10.2 Å and c=6.0-6.1 Å for the sulphides and a=10.0-10.5 Å and c=6.3-6.4 Å for the selenides as refined from powder X-ray diffraction data. Single-crystal structures were determined for five members of the sulphide series RE3FeGaS7 (RE=La, Pr, Tb) and RE3CoGaS7 (RE=La, Tb). The highly anisotropic crystal structures consist of one-dimensional chains of M-centred face-sharing octahedra and stacks of Ga-centred tetrahedra all pointing in the same direction. Magnetic measurements on the sulphides reveal paramagnetic behaviour in some cases and long-range antiferromagnetic behaviour with low Néel temperatures (15 K or lower) in others. Ga L-edge XANES spectra support the presence of highly cationic Ga tetrahedral centres with a tendency towards more covalent Ga-Ch character on proceeding from the sulphides to the selenides. Band structure calculations on La3FeGaS7 indicate that the electronic structure is dominated by Fe 3d-based states near the Fermi level.

  9. Hydrogen Migration and Vinylidene Pathway for Formation of Methane in the 193 nm Photodissociation of Propene: CH3CH=CH2 and CD3CD=CD2

    NASA Technical Reports Server (NTRS)

    Zhao, Yi-Lei; Laufer, Allan H.; Halpern, Joshua B.; Fahr, Askar

    2007-01-01

    Photodissociation channels and the final product yields from the 193 nm photolysis of propene-h6 (CH2=CHCH3) and propene-d6 (CD2=CDCD3) have been investigated, employing gas chromatography, mass spectroscopy, and flame ionization (GC/MS/FID) detection methods. The yields of methane as well as butadiene relative to ethane show considerable variations when propene-h6 or propene-d6 are photolyzed. This suggests significant variances in the relative importance of primary photolytic processes and/or secondary radical reactions, occurring subsequent to the photolysis. Theoretical calculations suggest the potential occurrence of an intramolecular dissociation through a mechanism involving vinylidene formation, accompanied by an ethylenic H-migration through the pi-orbitals. This process affects the final yields of methane-h4 versus methane-d4 with respect to other products. The product yields from previous studies of the 193 nm photolysis of methyl vinyl ketone-h6 and -d6 (CH2=CHCOCH3, CD2=CDCOCD3), alternative precursors for generating methyl and vinyl radicals, are compared with the current results for propene.

  10. Transannular E···E' Interactions in Neutral, Radical Cationic, and Dicationic Forms of cyclo-[E(CH2CH2CH2)2E'] (E, E' = S, Se, Te, and O) with Structural Feature: Dynamic and Static Behavior of E···E' Elucidated by QTAIM Dual Functional Analysis.

    PubMed

    Hayashi, Satoko; Matsuiwa, Kohei; Nishizawa, Nozomu; Nakanishi, Waro

    2015-12-18

    The nature of the transannular E-∗-E' interactions in neutral, radical cationic, and dicationic forms of cyclo-E(CH2CH2CH2)2E' (1) (E, E' = S, Se, Te, and O) (1, 1(•+), and 1(2+), respectively) is elucidated by applying QTAIM dual functional analysis (QTAIM-DFA). Hb(rc) are plotted versus Hb(rc) - Vb(rc)/2 for the data of E-∗-E' at BCPs in QTAIM-DFA, where ∗ emphasizes the existence of BCP. Plots for the fully optimized structures are analyzed by the polar coordinate (R, θ) representation. Those containing the perturbed structures are by (θp, κp): θp corresponds to the tangent line of the plot, and κp is the curvature. While (R, θ) describes the static nature, (θp, κp) represents the dynamic nature of interactions. The nature is well-specified by (R, θ) and (θp, κp). E-∗-E' becomes stronger in the order of 1 < 1(•+) < 1(2+), except for O-∗-O. While E-∗-E' (E, E' = S, Se, and Te) in 1(2+) are characterized as weak covalent bonds, except for S-∗-Te (MC nature through CT) and Se-∗-Te (TBP nature through CT), O-∗-E' seems more complex. The behavior of E-∗-E' in 1(2+) is very close to that of cyclo-E(CH2CH2CH2)E' (E, E' = S, Se, Te, and O), except for O-∗-O.

  11. CH4 dissociation in the early stage of graphene growth on Fe-Cu(100) surface: Theoretical insights

    NASA Astrophysics Data System (ADS)

    Tian, Baoyang; Liu, Tianhui; Yang, YanYan; Li, Kai; Wu, Zhijian; Wang, Ying

    2018-01-01

    The mechanism of CH4 dissociation and carbon nucleation process on the Fe doped Cu(100) surface were investigated systematically by using the density functional theory (DFT) calculations and microkinetic model. The activity of the Cu(100) surface was improved by the doped Fe atom and the atomic Fe on the Fe-Cu(100) surface was the reaction center due to the synergistic effect. In the dissociation process of CH4, CH3 → CH2 + H was regarded as the rate-determining step. The results obtained from the microkinetic model showed that the coverage of CHx(x = 1-3) was gradually decreased with the temperature increasing and CH3 was always the major intermediate at the broad range of the temperature (from 1035 to 1080 °C) and the ratio of H2/CH4 (from 0 to 5). It is also found that the reaction rates were increased with the temperature increasing. However, the reaction rates were reduced (or increased) at the range of H2/CH4 = 0-0.2 (or H2/CH4 > 0.2). It is noted that controlling the H2 partial pressure was an effective method to regulate the major intermediates and reaction rates of CH4 dissociation and further influence the growing process of graphene.

  12. Pt/Cu single-atom alloys as coke-resistant catalysts for efficient C-H activation

    NASA Astrophysics Data System (ADS)

    Marcinkowski, Matthew D.; Darby, Matthew T.; Liu, Jilei; Wimble, Joshua M.; Lucci, Felicia R.; Lee, Sungsik; Michaelides, Angelos; Flytzani-Stephanopoulos, Maria; Stamatakis, Michail; Sykes, E. Charles H.

    2018-03-01

    The recent availability of shale gas has led to a renewed interest in C-H bond activation as the first step towards the synthesis of fuels and fine chemicals. Heterogeneous catalysts based on Ni and Pt can perform this chemistry, but deactivate easily due to coke formation. Cu-based catalysts are not practical due to high C-H activation barriers, but their weaker binding to adsorbates offers resilience to coking. Using Pt/Cu single-atom alloys (SAAs), we examine C-H activation in a number of systems including methyl groups, methane and butane using a combination of simulations, surface science and catalysis studies. We find that Pt/Cu SAAs activate C-H bonds more efficiently than Cu, are stable for days under realistic operating conditions, and avoid the problem of coking typically encountered with Pt. Pt/Cu SAAs therefore offer a new approach to coke-resistant C-H activation chemistry, with the added economic benefit that the precious metal is diluted at the atomic limit.

  13. Carbon dioxide utilization via carbonate-promoted C-H carboxylation.

    PubMed

    Banerjee, Aanindeeta; Dick, Graham R; Yoshino, Tatsuhiko; Kanan, Matthew W

    2016-03-10

    Using carbon dioxide (CO2) as a feedstock for commodity synthesis is an attractive means of reducing greenhouse gas emissions and a possible stepping-stone towards renewable synthetic fuels. A major impediment to synthesizing compounds from CO2 is the difficulty of forming carbon-carbon (C-C) bonds efficiently: although CO2 reacts readily with carbon-centred nucleophiles, generating these intermediates requires high-energy reagents (such as highly reducing metals or strong organic bases), carbon-heteroatom bonds or relatively acidic carbon-hydrogen (C-H) bonds. These requirements negate the environmental benefit of using CO2 as a substrate and limit the chemistry to low-volume targets. Here we show that intermediate-temperature (200 to 350 degrees Celsius) molten salts containing caesium or potassium cations enable carbonate ions (CO3(2-)) to deprotonate very weakly acidic C-H bonds (pKa > 40), generating carbon-centred nucleophiles that react with CO2 to form carboxylates. To illustrate a potential application, we use C-H carboxylation followed by protonation to convert 2-furoic acid into furan-2,5-dicarboxylic acid (FDCA)--a highly desirable bio-based feedstock with numerous applications, including the synthesis of polyethylene furandicarboxylate (PEF), which is a potential large-scale substitute for petroleum-derived polyethylene terephthalate (PET). Since 2-furoic acid can readily be made from lignocellulose, CO3(2-)-promoted C-H carboxylation thus reveals a way to transform inedible biomass and CO2 into a valuable feedstock chemical. Our results provide a new strategy for using CO2 in the synthesis of multi-carbon compounds.

  14. Carbon dioxide utilization via carbonate-promoted C-H carboxylation

    NASA Astrophysics Data System (ADS)

    Banerjee, Aanindeeta; Dick, Graham R.; Yoshino, Tatsuhiko; Kanan, Matthew W.

    2016-03-01

    Using carbon dioxide (CO2) as a feedstock for commodity synthesis is an attractive means of reducing greenhouse gas emissions and a possible stepping-stone towards renewable synthetic fuels. A major impediment to synthesizing compounds from CO2 is the difficulty of forming carbon-carbon (C-C) bonds efficiently: although CO2 reacts readily with carbon-centred nucleophiles, generating these intermediates requires high-energy reagents (such as highly reducing metals or strong organic bases), carbon-heteroatom bonds or relatively acidic carbon-hydrogen (C-H) bonds. These requirements negate the environmental benefit of using CO2 as a substrate and limit the chemistry to low-volume targets. Here we show that intermediate-temperature (200 to 350 degrees Celsius) molten salts containing caesium or potassium cations enable carbonate ions (CO32-) to deprotonate very weakly acidic C-H bonds (pKa > 40), generating carbon-centred nucleophiles that react with CO2 to form carboxylates. To illustrate a potential application, we use C-H carboxylation followed by protonation to convert 2-furoic acid into furan-2,5-dicarboxylic acid (FDCA)—a highly desirable bio-based feedstock with numerous applications, including the synthesis of polyethylene furandicarboxylate (PEF), which is a potential large-scale substitute for petroleum-derived polyethylene terephthalate (PET). Since 2-furoic acid can readily be made from lignocellulose, CO32--promoted C-H carboxylation thus reveals a way to transform inedible biomass and CO2 into a valuable feedstock chemical. Our results provide a new strategy for using CO2 in the synthesis of multi-carbon compounds.

  15. Mechanism of the reaction, CH4+O(1D2)→CH3+OH, studied by ultrafast and state-resolved photolysis/probe spectroscopy of the CH4ṡO3 van der Waals complex

    NASA Astrophysics Data System (ADS)

    Miller, C. Cameron; van Zee, Roger D.; Stephenson, John C.

    2001-01-01

    The mechanism of the reaction CH4+O(1D2)→CH3+OH was investigated by ultrafast, time-resolved and state-resolved experiments. In the ultrafast experiments, short ultraviolet pulses photolyzed ozone in the CH4ṡO3 van der Waals complex to produce O(1D2). The ensuing reaction with CH4 was monitored by measuring the appearance rate of OH(v=0,1;J,Ω,Λ) by laser-induced fluorescence, through the OH A←X transition, using short probe pulses. These spectrally broad pulses, centered between 307 and 316 nm, probe many different OH rovibrational states simultaneously. At each probe wavelength, both a fast and a slow rise time were evident in the fluorescence signal, and the ratio of the fast-to-slow signal varied with probe wavelength. The distribution of OH(v,J,Ω,Λ) states, Pobs(v,J,Ω,Λ), was determined by laser-induced fluorescence using a high-resolution, tunable dye laser. The Pobs(v,J,Ω,Λ) data and the time-resolved data were analyzed under the assumption that different formation times represent different reaction mechanisms and that each mechanism produces a characteristic rovibrational distribution. The state-resolved and the time-resolved data can be fit independently using a two-mechanism model: Pobs(v,J,Ω,Λ) can be decomposed into two components, and the appearance of OH can be fit by two exponential rise times. However, these independent analyses are not mutually consistent. The time-resolved and state-resolved data can be consistently fit using a three-mechanism model. The OH appearance signals, at all probe wavelengths, were fit with times τfast≈0.2 ps, τinter≈0.5 ps and τslow≈5.4 ps. The slowest of these three is the rate for dissociation of a vibrationally excited methanol intermediate (CH3OH*) predicted by statistical theory after complete intramolecular energy redistribution following insertion of O(1D2) into CH4. The Pobs(v,J,Ω,Λ) was decomposed into three components, each with a linear surprisal, under the assumption that the

  16. Comparison of atmospheric CH4 concentration observed by GOSAT and in-situ measurements in Thailand and India

    NASA Astrophysics Data System (ADS)

    Hayashida, S.; Ono, A.; Ishikawa, S.; Terao, Y.; Takeuchi, W.

    2012-12-01

    The concentration of atmospheric methane (CH4) has more than doubled since pre-industrial levels and the observed long-term changes in the CH4 concentration have been attributed to anthropogenic activity. However, despite the importance of atmospheric CH4 in global warming, the strength of individual sources of CH4 remains highly uncertain [e.g.,Dlugokencky et al., 2011]. To characterize and quantify the emissions of CH4 especially in Monsoon Asia and Siberia, which are the most important regions as CH4 source, we started a new project, "Characterization and Quantification of global methane emissions by utilizing GOSAT and in-situ measurements " by support of the Environment Research and Technology Development Fund (ERTDF) from June 2012 under the umbrella of Ministry of Environment Japan. The projects includes (1) satellite data applications, (2) in-situ measurements in Siberia, over Western Pacific and in Monsoon Asia, (3) development of the inverse model to derive CH4 emissions by top-down approach, and (4) flux measurements in Siberia and Asia to improve the bottom-up inventories. As an initiatory approach in the project, we started air sampling in Thailand and India where there are only a few CH4 data of direct sampling with high precision. We took eight air samples at Kohn Kaen and Pimai in Thailand on June 9 and 10, 2012. The high CH4 concentration near rice paddy field contrasted to the lower CH4 concentration near Cassava field. We are planning to take more samples in India in mid-August. The satellite CH4 data including GOSAT and SCIAMACHY are also compared with the Land Surface Water Coverage (LSWC) and the Normalized Difference Vegetation Index (NDVI). The analysis revealed the seasonal variation in of xCH4 is closely related to the variation of the LSWC, coupled with NDVI. However, the satellite measurements are all column-averaged mixing ratio (xCH4), and therefore do not necessarily reflect high CH4 concentration near the surface over the emission

  17. Picking ChIP-seq peak detectors for analyzing chromatin modification experiments

    PubMed Central

    Micsinai, Mariann; Parisi, Fabio; Strino, Francesco; Asp, Patrik; Dynlacht, Brian D.; Kluger, Yuval

    2012-01-01

    Numerous algorithms have been developed to analyze ChIP-Seq data. However, the complexity of analyzing diverse patterns of ChIP-Seq signals, especially for epigenetic marks, still calls for the development of new algorithms and objective comparisons of existing methods. We developed Qeseq, an algorithm to detect regions of increased ChIP read density relative to background. Qeseq employs critical novel elements, such as iterative recalibration and neighbor joining of reads to identify enriched regions of any length. To objectively assess its performance relative to other 14 ChIP-Seq peak finders, we designed a novel protocol based on Validation Discriminant Analysis (VDA) to optimally select validation sites and generated two validation datasets, which are the most comprehensive to date for algorithmic benchmarking of key epigenetic marks. In addition, we systematically explored a total of 315 diverse parameter configurations from these algorithms and found that typically optimal parameters in one dataset do not generalize to other datasets. Nevertheless, default parameters show the most stable performance, suggesting that they should be used. This study also provides a reproducible and generalizable methodology for unbiased comparative analysis of high-throughput sequencing tools that can facilitate future algorithmic development. PMID:22307239

  18. Picking ChIP-seq peak detectors for analyzing chromatin modification experiments.

    PubMed

    Micsinai, Mariann; Parisi, Fabio; Strino, Francesco; Asp, Patrik; Dynlacht, Brian D; Kluger, Yuval

    2012-05-01

    Numerous algorithms have been developed to analyze ChIP-Seq data. However, the complexity of analyzing diverse patterns of ChIP-Seq signals, especially for epigenetic marks, still calls for the development of new algorithms and objective comparisons of existing methods. We developed Qeseq, an algorithm to detect regions of increased ChIP read density relative to background. Qeseq employs critical novel elements, such as iterative recalibration and neighbor joining of reads to identify enriched regions of any length. To objectively assess its performance relative to other 14 ChIP-Seq peak finders, we designed a novel protocol based on Validation Discriminant Analysis (VDA) to optimally select validation sites and generated two validation datasets, which are the most comprehensive to date for algorithmic benchmarking of key epigenetic marks. In addition, we systematically explored a total of 315 diverse parameter configurations from these algorithms and found that typically optimal parameters in one dataset do not generalize to other datasets. Nevertheless, default parameters show the most stable performance, suggesting that they should be used. This study also provides a reproducible and generalizable methodology for unbiased comparative analysis of high-throughput sequencing tools that can facilitate future algorithmic development.

  19. Preparation of Low-Input and Ligation-Free ChIP-seq Libraries Using Template-Switching Technology.

    PubMed

    Bolduc, Nathalie; Lehman, Alisa P; Farmer, Andrew

    2016-10-10

    Chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing (ChIP-seq) has become the gold standard for mapping of transcription factors and histone modifications throughout the genome. However, for ChIP experiments involving few cells or targeting low-abundance transcription factors, the small amount of DNA recovered makes ligation of adapters very challenging. In this unit, we describe a ChIP-seq workflow that can be applied to small cell numbers, including a robust single-tube and ligation-free method for preparation of sequencing libraries from sub-nanogram amounts of ChIP DNA. An example ChIP protocol is first presented, resulting in selective enrichment of DNA-binding proteins and cross-linked DNA fragments immobilized on beads via an antibody bridge. This is followed by a protocol for fast and easy cross-linking reversal and DNA recovery. Finally, we describe a fast, ligation-free library preparation protocol, featuring DNA SMART technology, resulting in samples ready for Illumina sequencing. © 2016 by John Wiley & Sons, Inc. Copyright © 2016 John Wiley & Sons, Inc.

  20. Validation of a Brief Structured Interview: The Children’s Interview for Psychiatric Syndromes (ChIPS)

    PubMed Central

    Young, Matthew E.; Bell, Ziv E.; Fristad, Mary A.

    2016-01-01

    Evidence-based assessment is important in the treatment of childhood psychopathology (Jensen-Doss, 2011). While researchers and clinicians frequently use structured diagnostic interviews to ensure reliability, the most commonly used instrument, the Schedule for Affective Disorders and Schizophrenia for School Aged Children (K-SADS; Kaufman et al., 1997), is too long for most clinical applications. The Children’s Interview for Psychiatric Syndromes, (ChIPS/P-ChIPS; Weller, Weller, Rooney, & Fristad, 1999a; 1999b) is a highly-structured brief diagnostic interview. The present study compared K-SADS and ChIPS/P-ChIPS diagnoses in an outpatient clinical sample of 50 parent-child pairs aged 7–14. Agreement between most diagnoses was moderate to high between instruments and with consensus clinical diagnoses. ChIPS was significantly briefer to administer than the K-SADS. Interviewer experience level and participant demographics did not appear to affect agreement. Results provide further evidence for the validity of the ChIPS and support its use in clinical and research settings. PMID:27761777

  1. Normalization, bias correction, and peak calling for ChIP-seq

    PubMed Central

    Diaz, Aaron; Park, Kiyoub; Lim, Daniel A.; Song, Jun S.

    2012-01-01

    Next-generation sequencing is rapidly transforming our ability to profile the transcriptional, genetic, and epigenetic states of a cell. In particular, sequencing DNA from the immunoprecipitation of protein-DNA complexes (ChIP-seq) and methylated DNA (MeDIP-seq) can reveal the locations of protein binding sites and epigenetic modifications. These approaches contain numerous biases which may significantly influence the interpretation of the resulting data. Rigorous computational methods for detecting and removing such biases are still lacking. Also, multi-sample normalization still remains an important open problem. This theoretical paper systematically characterizes the biases and properties of ChIP-seq data by comparing 62 separate publicly available datasets, using rigorous statistical models and signal processing techniques. Statistical methods for separating ChIP-seq signal from background noise, as well as correcting enrichment test statistics for sequence-dependent and sonication biases, are presented. Our method effectively separates reads into signal and background components prior to normalization, improving the signal-to-noise ratio. Moreover, most peak callers currently use a generic null model which suffers from low specificity at the sensitivity level requisite for detecting subtle, but true, ChIP enrichment. The proposed method of determining a cell type-specific null model, which accounts for cell type-specific biases, is shown to be capable of achieving a lower false discovery rate at a given significance threshold than current methods. PMID:22499706

  2. A Spiking Strategy for ChIP-chip Data Normalization in S. cerevisiae.

    PubMed

    Jeronimo, Célia; Robert, François

    2017-01-01

    Chromatin immunoprecipitation coupled to DNA microarrays (ChIP-chip) is widely used in the chromatin field, notably to map the position of histone variants or histone modifications along the genome. Often, the position and the occupancy of these epigenetic marks are to be compared between different experiments. It is now increasingly recognized that such cross-sample comparison is better done using externally added exogenous controls for normalization but no such method has been described for ChIP-chip. Here we describe a spiking normalization strategy that makes use of phiX174 phage DNA as a spiked control for normalization of ChIP-chip signals across different experiments.

  3. Highly Permeable AlPO-18 Membranes for N 2 /CH 4 Separation

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Zong, Zhaowang; Elsaidi, Sameh K.; Thallapally, Praveen K.

    Herein we demonstrate that AlPO-18 membranes can separate N2/CH4 gas mixtures at unprecedented N2 permeances. The best membranes separated N2/CH4 mixtures with N2 permeances as high as 3076 GPU and separation selectivities as high as 4.6. Gas mixture separation data, N2 and CH4 adsorption isotherms, ideal adsorbed solution theory (IAST), and breakthrough experiments were collected to understand the separation mechanisms. Competitive adsorption and differences in diffusivities were identified as the prevailing separation mechanisms. Differences in diffusivity played a more dominant role than the competitive adsorption, and led to nitrogen selective membranes.

  4. Version 1.3 AIM SOFIE measured methane (CH4): Validation and seasonal climatology

    NASA Astrophysics Data System (ADS)

    Rong, P. P.; Russell, J. M.; Marshall, B. T.; Siskind, D. E.; Hervig, M. E.; Gordley, L. L.; Bernath, P. F.; Walker, K. A.

    2016-11-01

    The V1.3 methane (CH4) measured by the Aeronomy of Ice in the Mesosphere (AIM) Solar Occultation for Ice Experiment (SOFIE) instrument is validated in the vertical range of 25-70 km. The random error for SOFIE CH4 is 0.1-1% up to 50 km and degrades to 9% at ˜ 70 km. The systematic error remains at 4% throughout the stratosphere and lower mesosphere. Comparisons with CH4 data taken by the SCISAT Atmospheric Chemistry Experiment-Fourier Transform Spectrometer (ACE-FTS) and the Envisat Michelson Interferometer for Passive Atmospheric Sounding (MIPAS) show an agreement within 15% in the altitude range 30-60 km. Below 25 km SOFIE CH4 is systematically higher (≥20%), while above 65 km it is lower by a similar percentage. The sign change from the positive to negative bias occurs between 55 km and 60 km (or 40 km and 45 km) in the Northern (or Southern) Hemisphere. Methane, H2O, and 2CH4 + H2O yearly differences from their values in 2009 are examined using SOFIE and MIPAS CH4 and the Aura Microwave Limb Sounder (MLS) measured H2O. It is concluded that 2CH4 + H2O is conserved with altitude up to an upper limit between 35 km and 50 km depending on the season. In summer this altitude is higher. In the Northern Hemisphere the difference relative to 2009 is the largest in late spring and the established difference prevails throughout summer and fall, suggesting that summer and fall are dynamically quiet. In both hemispheres during winter there are disturbances (with a period of 1 month) that travel downward throughout the stratosphere with a speed similar to the winter descent.

  5. Enhanced Oxidation Capacity from Photolytic HOx/NOx Recycling: Implications for CH4 Growth

    NASA Astrophysics Data System (ADS)

    Madronich, S.

    2017-12-01

    Oxidation by OH radicals converts many emitted compounds (CO, CH4, VOCs as well as NOx, SO2, HCFCs, and others) to more soluble forms that can be removed rapidly from the atmosphere, e.g., by deposition. In a chemically stable atmosphere (without runaway concentration growth) the rate of OH production must generally exceed the emission rates of the reduced compounds, but secondary chemistry complicates OH budgets. If emission rates (e.g., E for CH4) increase, OH concentrations can either decrease or increase depending on NOx conditions, causing a non-linear dependence of CH4 concentrations on its emissions, [CH4] Ef where f, the methane feedback factor, is currently estimated in global 3d models to be 1.3-1.4. This feature is robust among models, and can be reproduced in simpler box models with the canonical Ox-HOx-NOx chemistry, in which global OH is increased by NOx emissions and decreased by CO, CH4, and VOC emissions. Scenarios with lower NOx emissions but higher CH4 emissions point to substantially lower global oxidation capacity in the future. Several newly hypothesized processes have attracted attention in recent years, including the photolytic recycling of OH from biogenic VOCs, and the photolysis of particulate nitrates to regenerate NOx. The latter process could be particularly significant in regions far from NOx emissions, where low NOx levels are more efficient at generating O3 and OH. To the extent that these processes do occur, they may provide some buffering of global OH against CH4 variations (f nearer 1), and more generally against anthropogenic perturbations. However, critical measurements from both lab and field are needed to assess the importance of these proposed processes.

  6. A novel statistical method for quantitative comparison of multiple ChIP-seq datasets.

    PubMed

    Chen, Li; Wang, Chi; Qin, Zhaohui S; Wu, Hao

    2015-06-15

    ChIP-seq is a powerful technology to measure the protein binding or histone modification strength in the whole genome scale. Although there are a number of methods available for single ChIP-seq data analysis (e.g. 'peak detection'), rigorous statistical method for quantitative comparison of multiple ChIP-seq datasets with the considerations of data from control experiment, signal to noise ratios, biological variations and multiple-factor experimental designs is under-developed. In this work, we develop a statistical method to perform quantitative comparison of multiple ChIP-seq datasets and detect genomic regions showing differential protein binding or histone modification. We first detect peaks from all datasets and then union them to form a single set of candidate regions. The read counts from IP experiment at the candidate regions are assumed to follow Poisson distribution. The underlying Poisson rates are modeled as an experiment-specific function of artifacts and biological signals. We then obtain the estimated biological signals and compare them through the hypothesis testing procedure in a linear model framework. Simulations and real data analyses demonstrate that the proposed method provides more accurate and robust results compared with existing ones. An R software package ChIPComp is freely available at http://web1.sph.emory.edu/users/hwu30/software/ChIPComp.html. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  7. [Spatiotemporal variations of natural wetland CH4 emissions over China under future climate change].

    PubMed

    Liu, Jian-gong; Zhu, Qiu-an; Shen, Yan; Yang, Yan-zheng; Luo, Yun-peng; Peng, Chang-hui

    2015-11-01

    Based on a new process-based model, TRIPLEX-GHG, this paper analyzed the spatio-temporal variations of natural wetland CH4 emissions over China under different future climate change scenarios. When natural wetland distributions were fixed, the amount of CH4 emissions from natural wetland ecosystem over China would increase by 32.0%, 55.3% and 90.8% by the end of 21st century under three representative concentration pathways (RCPs) scenarios, RCP2. 6, RCP4.5 and RCP8.5, respectively, compared with the current level. Southern China would have higher CH4 emissions compared to that from central and northern China. Besides, there would be relatively low emission fluxes in western China while relatively high emission fluxes in eastern China. Spatially, the areas with relatively high CH4 emission fluxes would be concentrated in the middle-lower reaches of the Yangtze River, the Northeast and the coasts of the Pearl River. In the future, most natural wetlands would emit more CH4 for RCP4.5 and RCP8.5 than that of 2005. However, under RCP2.6 scenario, the increasing trend would be curbed and CH4 emissions (especially from the Qinghai-Tibet Plateau) begin to decrease in the late 21st century.

  8. C-H and H-H Activation in Transition Metal Complexes and on Surfaces.

    DTIC Science & Technology

    1983-01-01

    IEEIIIIIEEEEI EEEIIEIIIIIII EEIIIEIIIEIII IIIEEEIIEIIII La.𔃻 m41. 12.2 1.4o 12.0 1.25 111.4 11. MICROCOP RE SOO TESTCHAR NATIONA BUREA OfSANAD 16m ~4 OFFICE...ML4 plane, bringing a C-H bond in proximity to the metal. The compounds will minimize M. . C-H re- -27 - pulsion by bringing the H atom into an axial...h) C-H activation has been shown also with organolanthanides and organo- actinide compounds : Watson, P.L. J.Chem.Soc. Chem.Commun. 1983, 176-177

  9. Photovoltaic properties of Cu-doped CH3NH3PbI3 with perovskite structure

    NASA Astrophysics Data System (ADS)

    Shirahata, Yasuhiro; Oku, Takeo

    2017-01-01

    Photovoltaic properties of copper (Cu)-doped perovskite (CH3NH3PbCuxI3+x) photovoltaic devices with different Cu content were investigated. The CH3NH3PbCuxI3+x films were polycrystalline with a tetragonal system, and their lattice constants and crystallite size varied with Cu doping. Compared to conversion efficiencies of non-doped CH3NH3PbI3 photovoltaic device, those of CH3NH3PbCuxI3+x photovoltaic devises increased. The improvement of photovoltaic properties was attributed to partial substitution of Cu at the Pb sites.

  10. Geophysical Evolution of Ch Asteroids and Testable Hypotheses for Future Missions

    NASA Astrophysics Data System (ADS)

    Castillo, J. C.

    2017-12-01

    The main population of asteroids related to meteorites in the collections remains to be explored in situ. Ch asteroids are the only midsized asteroids that display a signature of hydration (besides Pallas) and the spectral connection between Ch asteroids and CM chondrites suggests that the former represent potential parent bodies for the latter. This class of asteroids is particularly interesting because it hosts many objects 100-200 km in size, which are believed to belong to a primordial population of planetesimals. This presentation will explore multiple evolution pathways for Ch-asteroids leading to possible hypotheses on the geological, petrological, and geophysical properties that a disrupted parent body would present to a future mission. This work is being carried out at the Jet Propulsion Laboratory, California Institute of Technology, under contract to NASA.

  11. Investigating CH4 production in an oxic plant-soil system -a new approach combining isotopic labelling (13C) and inhibitors

    NASA Astrophysics Data System (ADS)

    Lenhart, Katharina; Keppler, Frank

    2017-04-01

    Typically, aerated soil are net sinks of atmospheric methane (CH4), being highest in native ecosystems (pristine forests > managed forests > grasslands > crop fields). However, this does not exclude a simultaneous endogenic CH4 production in the plant-soil system, which cannot be detected simply via CH4 flux measurements. Methanogenic archaea producing CH4 under anoxic conditions were thought to be the only biotic source of CH4 in the soil. However, until recently a non-archaeal pathway of CH4 formation is known where CH4 is produced under oxic conditions in plants (Keppler et al. 2006) and fungi (Lenhart et al. 2012). Additionally, abiotic formation of CH4 from soil organic matter was reported (Jugold et al. 2012) and may be ubiquitous in terrestrial ecosystems. The major goal of this project was to determine soil endogenic CH4 sources and to estimate their contribution to the endogenic CH4 production. Especially the effect of plants and fungi on soil CH4 production was investigated. Therefore, a series of experiments was carried out on field fresh soil collected in a grassland and a forest ecosystem under controlled laboratory conditions. By combining selective inhibitors and 13C labelling, CH4 production rates of several CH4 sources were quantified. The major difficulty was to detect the comparatively small flux of CH4 production against the background of the high CH4 consumption rates due to methanotrophic bacteria. Therefore, we supplemented bare soil and soil with vegetation with selective inhibitors and 13C labelled substrates in a closed chamber system. In a first step, CH4 production was determined by the inhibition of CH4 oxidizing bacteria with Difluoromethane (DFM, 2ml l-1). In the following, a 13C labelled substrate (either CO2, Acetate, or Methionine -S-CH3 labelled) was added in combination with a specific inhibitor -either for archaeal methanogenesis (Bromoethanesulfonate), bacteria (Streptomycin), or fungi (Captan, Cycloheximide). Gas samples were

  12. The Arctic CH4 sink and its implications for the permafrost carbon feedbacks to the global climate system

    NASA Astrophysics Data System (ADS)

    Juncher Jørgensen, Christian; Christiansen, Jesper; Mariager, Tue; Hugelius, Gustaf

    2016-04-01

    Using atmospheric methane (CH4), certain soil microbes are able to sustain their metabolism, and in turn remove this powerful greenhouse gas from the atmosphere. While the process of CH4 oxidation is a common feature in most natural and unmanaged ecosystems in temperate and boreal ecosystems, the interactions between soil physical properties and abiotic process drivers, net landscape exchange and spatial patterns across Arctic drylands remains highly uncertain. Recent works show consistent CH4 comsumption in upland dry tundra soils in Arctic and High Arctic environments (Christiansen et al., 2014, Biogeochemistry 122; Jørgensen et al., 2015, Nature Geoscience 8; Lau et al., 2015, The ISME Journal 9). In these dominantly dry or barren soil ecosystems, CH4 consumption has been observed to significantly exceed the amounts of CH4 emitted from adjacent wetlands. These observations point to a potentially important but largely overlooked component of the global soil-climate system interaction and a counterperspective to the conceptual understanding of the Arctic being a only a source of CH4. However, due to our limited knowledge of spatiotemporal occurrence of CH4 consumption across a wider range of the Arctic landscape we are left with substantial uncertainites and an overall unconstrained range estimate of this terrestrial CH4 sink and its potential effects on permafrost carbon feedback to the atmospheric CH4 concentration. To address this important knowledge gap and identify the most relevant spatial scaling parameters, we studied in situ CH4 net exchange across a large landscape transect on West Greenland. The transect representated soils formed from the dominant geological parent materials of dry upland tundra soils found in the ice-free land areas of Western Greenland, i.e. 1) granitic/gneissic parent material, 2) basaltic parent material and 3) sedimentary deposits. Results show that the dynamic variations in soil physical properties and soil hydrology exerts an

  13. Time-resolved photoelectron imaging of iodide-nitromethane (I-·CH3NO2) photodissociation dynamics.

    PubMed

    Kunin, Alice; Li, Wei-Li; Neumark, Daniel M

    2016-12-07

    Femtosecond time-resolved photoelectron spectroscopy is used to probe the decay channels of iodide-nitromethane (I - ·CH 3 NO 2 ) binary clusters photoexcited at 3.56 eV, near the vertical detachment energy (VDE) of the cluster. The production of I - is observed, and its photoelectron signal exhibits a mono-exponential rise time of 21 ± 1 ps. Previous work has shown that excitation near the VDE of the I - ·CH 3 NO 2 complex transfers an electron from iodide to form a dipole-bound state of CH 3 NO 2 - that rapidly converts to a valence bound (VB) anion. The long appearance time for the I - fragment suggests that the VB anion decays by back transfer of the excess electron to iodide, reforming the I - ·CH 3 NO 2 anion and resulting in evaporation of iodide. Comparison of the measured lifetime to that predicted by RRKM theory suggests that the dissociation rate is limited by intramolecular vibrational energy redistribution in the re-formed anion between the high frequency CH 3 NO 2 vibrational modes and the much lower frequency intermolecular I - ·CH 3 NO 2 stretch and bends, the predominant modes involved in cluster dissociation to form I - . Evidence for a weak channel identified as HI + CH 2 NO 2 - is also observed.

  14. Fall season atypically warm weather event leads to substantial CH4 loss in Arctic ecosystems?

    NASA Astrophysics Data System (ADS)

    Zona, Donatella; Moreaux, Virginie; Liljedahl, Anna; Losacco, Salvatore; Murphy, Patrick; Oechel, Walter

    2014-05-01

    In the last century (during 1875-2008) high-latitudes are warming at a rate of 1.360C century-1, almost 2 times faster than the Northern Hemisphere trend (Bekryaev et al., 2010). This warming has been more intense outside of the summer season, with anomalies of 1.09, 1.59, 1.730C in the fall, winter, and spring season respectively (Bekryaev et al., 2010). This substantial temperature anomalies have the potential to increase the emission of greenhouse gas (CO2 and CH4) fluxes from arctic tundra ecosystems. In particular, CH4 emissions, which are primarily controlled by temperature (in addition to water table), can steeply increase with warming. Despite the potential relevance of CH4 emissions, very few measurements have been performed outside of the growing season across the entire Arctic, due to logistic constrains. Importantly, no flux measurements achieved a temporal and spatial data coverage sufficient to estimate with confidence an annual CH4 emissions from tundra ecosystem in Alaska, and its sensitivity to warming. Fall 2013 was unusually warm in central and northern Alaska. Following a relatively warm summer with dramatically above-average rainfall, the October mean monthly temperatures was the 4th and top warmest in Barrow (1949-2013) and Ivotuk (1998-2013), respectively. As we just upgraded several eddy covariance towers to measure CO2 and CH4 fluxes year-round, the atypical weather conditions of fall 2013 represented a unique chance for testing the sensitivity of CH4 loss to these atypically warm temperatures. All our sites across a latitudinal gradient (from the northern site, Barrow, to the southern site, Ivotuk), presented substantial CH4 loss in the fall. Importantly, in two of these sites (Barrow, Ivotuk) where the fall weather was substantially warmer than the long term trend, fall CH4 emission represented between 44-63% of the June-November cumulative emission. Surprisingly, in the southernmost site (Ivotuk), when the temperature anomaly was the

  15. CH4 concentrations and fluxes in a subtropical metropolitan river network: Watershed urbanization impacts and environmental controls.

    PubMed

    Wang, Xiaofeng; He, Yixin; Chen, Huai; Yuan, Xingzhong; Peng, Changhui; Yue, Junsheng; Zhang, Qiaoyong; Zhou, Lilei

    2018-05-01

    Urbanization and greenhouse gas emissions are of great global concern, especially in developing countries such as China. However, little is known about the relationship between the two. In this study, we examined the influences of the urbanization of Chongqing Municipality, which covers an area of 5494km 2 , in China, on the CH 4 emissions of in its metropolitan river network. The results from 84 sampling locations showed an overall mean CH 4 concentration of 0.69±1.37μmol·L -1 and a CH 4 flux from the river network of 1.40±2.53mmolCH 4 m -2 d -1 . The CH 4 concentrations and fluxes presented a clear seasonal pattern, with the highest value in the spring and the lowest in the summer. Such seasonal variations were probably co-regulated by the dilution effect, temperature and supply of fresh organic matter by algal blooms. Another important result was that the CH 4 concentrations and fluxes increased with the degree of urbanization or the proportion of urban land use, being approximately 3-13 times higher in urban and suburban areas than in rural ones. The total nitrogen, dissolved oxygen (O%) and possible sewage discharge, which could affect the in situ CH 4 production and exogenous CH 4 input respectively, were important factors that influenced the spatial patterns of CH 4 in human-dominated river networks, while the nitrogen (N) and phosphorus (P) could be good predictors of the CH 4 emissions in urban watersheds. Hydrologic drivers, including bottom sediment type, flow velocity and river width, were strongly correlated with the CH 4 concentrations and could also affect the spatial variance and predict the CH 4 hotspots in such metropolitan river networks. With increasing urbanization, we should pay more attention to the increasing greenhouse gas emissions associated with urbanization. Copyright © 2017 Elsevier B.V. All rights reserved.

  16. Field-scale simulation of methane emissions from coastal wetlands in China using an improved version of CH4MODwetland.

    PubMed

    Li, Tingting; Xie, Baohua; Wang, Guocheng; Zhang, Wen; Zhang, Qing; Vesala, Timo; Raivonen, Maarit

    2016-07-15

    Coastal wetlands are important CH4 sources to the atmosphere. Coastal wetlands account for ~10% of the total area of natural wetlands in China, but the size of this potential CH4 source remains highly uncertain. We introduced the influence of salinity on CH4 production and CH4 diffusion into a biogeophysical model named CH4MODwetland so that it can be used in coastal wetlands. The improved model can generally simulate seasonal CH4 variations from tidal marshes dominated by Phragmites and Scirpus. However, the model underestimated winter CH4 fluxes from tidal marshes in the Yellow River Delta and YanCheng Estuary. It also failed to capture the accurate timing of the CH4 peaks in YanCheng Estuary and ChongMing Island in 2012. The improved model could generally simulate the difference between the annual mean CH4 fluxes from mangrove sites in GuangZhou and HaiKou city under different salinity and water table depth conditions, although fluxes were systematically underestimated in the mangrove site of HaiKou city. Using the improved model, the seasonal CH4 emissions simulated across all of the coastal wetlands ranged from 0.1 to 44.90gm(-2), with an average value of 7.89gm(-2), which is in good agreement with the observed values. The improved model significantly decreased the RMSE and RMD from 424% to 14% and 314% to -2%, respectively, and improved the EF from -18.30 to 0.99. Model sensitivity analysis showed that CH4 emissions were most sensitive to Pox in the tidal marshes and salinity in the mangroves. The results show that previous studies may have overestimated CH4 emissions on a regional or global scale by neglecting the influence of salinity. In general, the CH4MODwetland model can simulate seasonal CH4 emissions from different types of coastal wetlands under various conditions. Further improvements of CH4MODwetland should include the specific characteristics of CH4 processes in mangroves to decrease the uncertainty in estimating regional or global CH4 emissions

  17. High-temperature shock tube and modeling studies on the reactions of methanol with D-atoms and CH3-radicals.

    PubMed

    Peukert, S L; Michael, J V

    2013-10-10

    The shock tube technique has been used to study the hydrogen abstraction reactions D + CH3OH → CH2O + H + HD (A) and CH3 + CH3OH → CH2O + H + CH4 (B). For reaction A, the experiments span a T-range of 1016 K ≤ T ≤ 1325 K, at pressures 0.25 bar ≤ P ≤ 0.46 bar. The experiments on reaction B, CH3 + CH3OH, cover a T-range of 1138 K ≤ T ≤ 1270 K, at pressures around 0.40 bar. Reflected shock tube experiments, monitoring the depletion of D-atoms by applying D-atom atomic resonance absorption spectrometry (ARAS), were performed on reaction A using gas mixtures of C2D5I and CH3OH in Kr bath gas. C2D5I was used as precursor for D-atoms. For reaction B, reflected shock tube experiments monitoring H-atom formation with H-ARAS, were carried out using gas mixtures of diacetyl ((CH3CO)2) and CH3OH in Kr bath gas. (CH3CO)2 was used as the source of CH3-radicals. Detailed reaction models were assembled to fit the D-atom and H-atom time profiles in order to obtain experimental rate constants for reactions A and B. Total rate constants from the present experiments on D + CH3OH and CH3 + CH3OH can be represented by the Arrhenius equations kA(T) = 1.51 × 10(-10) exp(-3843 K/T) cm(3) molecules(-1) s(-1) (1016 K ≤ T ≤ 1325 K) and kB(T) = 9.62 × 10(-12) exp(-7477 K/T) cm(3) molecules(-1) s(-1) (1138 K ≤ T ≤ 1270 K). The experimentally obtained rate constants were compared with available rate data from the literature. The results from quantum chemical studies on reaction A were found to be in good agreement with the present results. The present work represents the first direct experimental study on these bimolecular reactions at combustion temperatures and is important to the high-temperature oxidation of CH3OH.

  18. Vibrational autoionization of state-selective jet-cooled methanethiol (CH 3SH) investigated with infrared + vacuum-ultraviolet photoionization

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Xie, Min; Shen, Zhitao; Pratt, S. T.

    Vibrational autoionization of Rydberg states provides key information about nonadiabatic processes above an ionization threshold. In this work, we employed time-of-flight mass detection of CH 3SH + to record vibrational-state selective photo-ionization efficiency (PIE) spectra of jet-cooled methanethiol (CH 3SH) on exciting CH 3SH to a specific vibrationally excited state with an infrared (IR) laser, followed by excitation with a tunable laser in the vacuum-ultraviolet (VUV) region for ionization. Autoionizing Rydberg states assigned to the ns, np, nd and nf series are identified. When IR light at 2601 (ν 3, SH stretching mode) and 2948 cm -1 (ν 2, CHmore » 3 symmetric stretching mode) was employed, the Rydberg series converged to the respective vibrationally excited (ν 3 and ν 2) states of CH 3SH +. When IR light at 3014 cm -1 (overlapped ν 1/ν 9, CH 3 antisymmetric stretching and CH 2 antisymmetric stretching modes) was employed, Rydberg series converging to two vibrationally excited states (ν 1 and ν 9) of CH 3SH + were observed. When IR light at 2867 cm -1 (2ν 10, overtone of CH 3 deformation mode) and 2892 cm -1 (2ν 4, overtone of CH 2 scissoring mode) was employed, both Δν = -1 and Δν = -2 ionization transitions were observed; there is evidence for direct ionization from the initial state into the CH 3SH + (ν 4 + = 1) continuum. In all observed IR-VUV-PIE spectra, the ns and nd series show intensity greater than the other Rydberg series, which is consistent with the fact that the highest-occupied molecular orbital of CH 3SH is a p-like lone pair orbital on the S atom. Finally, the quantum yields for autoionization of various vibrational excited states are discussed. Values of ν 1 = 3035, ν 2 = 2884, ν 3 = 2514, and ν 9 = 2936 cm -1 for CH 3SH + derived from the converged limits agree satisfactorily with values observed for Ar-tagged CH 3SH + at 3026, 2879, 2502, and 2933 cm -1.« less

  19. Dual stable isotopes of CH 4 from Yellowstone hot-springs suggest hydrothermal processes involving magmatic CO 2

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Moran, James J.; Whitmore, Laura M.; Jay, Zackary J.

    Volcanism and post-magmatism contribute significant annual methane (CH 4) fluxes to the atmosphere (on par with other natural sources such as forest fire and wild animal emissions) and have been implicated in past climate-change events. The Yellowstone hot spot is one of the largest volcanic systems on Earth and is known to emit CH 4 (as well as carbon dioxide (CO 2) and other gases), but the ultimate sources of this CH 4 flux have not been elucidated. In this paper, we use dual stable isotope analysis (δ 2H and δ 13C) of CH 4 sampled from ten high-temperature geothermalmore » pools in Yellowstone National Park along with other isotopic and gas analyses to evaluate potential sources of methane. The average δ 13C and δ 2H values of CH 4 emitted from hot springs ( 26.7 (± 2.4) and - 236.9 (± 12.0) ‰, respectively) are inconsistent with microbial methanogenesis but do not allow distinction between thermogenic and abiotic sources. Correlation between δ 13C CH4 and δ 13C of dissolved inorganic C (DIC) is consistent with DIC as the parent C source for the observed CH 4, or with equilibration of CH 4 and DIC. Methane formation temperatures estimated by isotopic geothermometry based on δ 13C CH4 and δ 13C CO2 ranged from ~ 250–350 °C, which is just below previous temperature estimates for the hydrothermal reservoir. Further, the δ 2H H2O of the thermal springs and the measured δ 2H CH4 values are consistent with equilibration between the source water and the CH 4 at the formation temperatures. Though the ultimate origin of the CH 4 could be attributed to either abiotic of themorgenic processes with subsequent isotopic equilibration, the C 1/C 2+ composition of the gases is more consistent with abiotic origins for most of the samples. Finally, our data support the hypothesis that subsurface rock-water interactions are responsible for at least a significant fraction of the CH 4 flux from the Yellowstone National Park volcanic system.« less

  20. Dual stable isotopes of CH 4 from Yellowstone hot-springs suggest hydrothermal processes involving magmatic CO 2

    DOE PAGES

    Moran, James J.; Whitmore, Laura M.; Jay, Zackary J.; ...

    2017-05-16

    Volcanism and post-magmatism contribute significant annual methane (CH 4) fluxes to the atmosphere (on par with other natural sources such as forest fire and wild animal emissions) and have been implicated in past climate-change events. The Yellowstone hot spot is one of the largest volcanic systems on Earth and is known to emit CH 4 (as well as carbon dioxide (CO 2) and other gases), but the ultimate sources of this CH 4 flux have not been elucidated. In this paper, we use dual stable isotope analysis (δ 2H and δ 13C) of CH 4 sampled from ten high-temperature geothermalmore » pools in Yellowstone National Park along with other isotopic and gas analyses to evaluate potential sources of methane. The average δ 13C and δ 2H values of CH 4 emitted from hot springs ( 26.7 (± 2.4) and - 236.9 (± 12.0) ‰, respectively) are inconsistent with microbial methanogenesis but do not allow distinction between thermogenic and abiotic sources. Correlation between δ 13C CH4 and δ 13C of dissolved inorganic C (DIC) is consistent with DIC as the parent C source for the observed CH 4, or with equilibration of CH 4 and DIC. Methane formation temperatures estimated by isotopic geothermometry based on δ 13C CH4 and δ 13C CO2 ranged from ~ 250–350 °C, which is just below previous temperature estimates for the hydrothermal reservoir. Further, the δ 2H H2O of the thermal springs and the measured δ 2H CH4 values are consistent with equilibration between the source water and the CH 4 at the formation temperatures. Though the ultimate origin of the CH 4 could be attributed to either abiotic of themorgenic processes with subsequent isotopic equilibration, the C 1/C 2+ composition of the gases is more consistent with abiotic origins for most of the samples. Finally, our data support the hypothesis that subsurface rock-water interactions are responsible for at least a significant fraction of the CH 4 flux from the Yellowstone National Park volcanic system.« less

  1. Vibrational autoionization of state-selective jet-cooled methanethiol (CH 3SH) investigated with infrared + vacuum-ultraviolet photoionization

    DOE PAGES

    Xie, Min; Shen, Zhitao; Pratt, S. T.; ...

    2017-10-24

    Vibrational autoionization of Rydberg states provides key information about nonadiabatic processes above an ionization threshold. In this work, we employed time-of-flight mass detection of CH 3SH + to record vibrational-state selective photo-ionization efficiency (PIE) spectra of jet-cooled methanethiol (CH 3SH) on exciting CH 3SH to a specific vibrationally excited state with an infrared (IR) laser, followed by excitation with a tunable laser in the vacuum-ultraviolet (VUV) region for ionization. Autoionizing Rydberg states assigned to the ns, np, nd and nf series are identified. When IR light at 2601 (ν 3, SH stretching mode) and 2948 cm -1 (ν 2, CHmore » 3 symmetric stretching mode) was employed, the Rydberg series converged to the respective vibrationally excited (ν 3 and ν 2) states of CH 3SH +. When IR light at 3014 cm -1 (overlapped ν 1/ν 9, CH 3 antisymmetric stretching and CH 2 antisymmetric stretching modes) was employed, Rydberg series converging to two vibrationally excited states (ν 1 and ν 9) of CH 3SH + were observed. When IR light at 2867 cm -1 (2ν 10, overtone of CH 3 deformation mode) and 2892 cm -1 (2ν 4, overtone of CH 2 scissoring mode) was employed, both Δν = -1 and Δν = -2 ionization transitions were observed; there is evidence for direct ionization from the initial state into the CH 3SH + (ν 4 + = 1) continuum. In all observed IR-VUV-PIE spectra, the ns and nd series show intensity greater than the other Rydberg series, which is consistent with the fact that the highest-occupied molecular orbital of CH 3SH is a p-like lone pair orbital on the S atom. Finally, the quantum yields for autoionization of various vibrational excited states are discussed. Values of ν 1 = 3035, ν 2 = 2884, ν 3 = 2514, and ν 9 = 2936 cm -1 for CH 3SH + derived from the converged limits agree satisfactorily with values observed for Ar-tagged CH 3SH + at 3026, 2879, 2502, and 2933 cm -1.« less

  2. The relationships between termite mound CH4/CO2 emissions and internal concentration ratios are species specific

    NASA Astrophysics Data System (ADS)

    Jamali, H.; Livesley, S. J.; Hutley, L. B.; Fest, B.; Arndt, S. K.

    2013-04-01

    We investigated the relative importance of CH4 and CO2 fluxes from soil and termite mounds at four different sites in the tropical savannas of northern Australia near Darwin and assessed different methods to indirectly predict CH4 fluxes based on CO2 fluxes and internal gas concentrations. The annual flux from termite mounds and surrounding soil was dominated by CO2 with large variations among sites. On a carbon dioxide equivalent (CO2-e) basis, annual CH4 flux estimates from termite mounds were 5- to 46-fold smaller than the concurrent annual CO2 flux estimates. Differences between annual soil CO2 and soil CH4 (CO2-e) fluxes were even greater, soil CO2 fluxes being almost three orders of magnitude greater than soil CH4 (CO2-e) fluxes at site. The contribution of CH4 and CO2 emissions from termite mounds to the total CH4 and CO2 emissions from termite mounds and soil in CO2-e was less than 1%. There were significant relationships between mound CH4 flux and mound CO2 flux, enabling the prediction of CH4 flux from measured CO2 flux; however, these relationships were clearly termite species specific. We also observed significant relationships between mound flux and gas concentration inside mound, for both CH4 and CO2, and for all termite species, thereby enabling the prediction of flux from measured mound internal gas concentration. However, these relationships were also termite species specific. Using the relationship between mound internal gas concentration and flux from one species to predict mound fluxes from other termite species (as has been done in the past) would result in errors of more than 5-fold for mound CH4 flux and 3-fold for mound CO2 flux. This study highlights that CO2 fluxes from termite mounds are generally more than one order of magnitude greater than CH4 fluxes. There are species-specific relationships between CH4 and CO2 fluxes from a mound, and between the inside mound concentration of a gas and the mound flux emission of the same gas, but

  3. Spatio-temporal variability of lake CH4 fluxes and its influence on annual estimates

    NASA Astrophysics Data System (ADS)

    Natchimuthu, S.; Sundgren, I.; Gålfalk, M.; Klemedtsson, L.; Crill, P. M.; Danielsson, Å.; Bastviken, D.

    2014-12-01

    Lakes are major sources of methane (CH4) to the atmosphere and it has been shown that lakes contribute significantly to the global CH4 budget. However, the data behind these global estimates are snapshots in time and space only and they typically lack information on spatial and temporal variability of fluxes which can potentially lead to biased estimates. Recent studies have shown that diffusive flux, gas exchange velocity (k), ebullition and concentration of CH4 in the surface water can vary significantly in space within lakes. CH4 fluxes can also change at a broad range of temporal scales in response to seasons, temperature, lake mixing events, short term weather events like pressure variations, shifting winds and diel cycles. We sampled CH4 fluxes and surface water concentrations from three lakes of differing characteristics in southwest Sweden over two annual cycles, approximately every 14 days from April to October 2012 and from April to November 2013. CH4 fluxes were measured using floating chambers distributed in the lakes based on depth categories and dissolved CH4 concentrations were determined by a headspace equilibration method. We observed significant differences in CH4 concentration, diffusion, ebullition and total fluxes between and within the lakes. The fluxes increased exponentially with temperature in all three lakes and water temperature, for example, explained 53-78% of variations in total fluxes in the lakes. Based on our data which relied on improved spatial and temporal information, we demonstrate that measurements which do not take into account of the spatial variability in the lakes could substantially bias the whole lake estimates. For instance, in one of the lakes, measurements from the central parts of the lake represented only 58% of our estimates from all chambers on an average. In addition, we consider how intensive sampling in one season of the year may affect the annual estimates due to the complex interaction of temperature, air

  4. Bioorthogonal Diversification of Peptides through Selective Ruthenium(II)-Catalyzed C-H Activation.

    PubMed

    Schischko, Alexandra; Ren, Hongjun; Kaplaneris, Nikolaos; Ackermann, Lutz

    2017-02-01

    Methods for the chemoselective modification of amino acids and peptides are powerful techniques in biomolecular chemistry. Among other applications, they enable the total synthesis of artificial peptides. In recent years, significant momentum has been gained by exploiting palladium-catalyzed cross-coupling for peptide modification. Despite major advances, the prefunctionalization elements on the coupling partners translate into undesired byproduct formation and lengthy synthetic operations. In sharp contrast, we herein illustrate the unprecedented use of versatile ruthenium(II)carboxylate catalysis for the step-economical late-stage diversification of α- and β-amino acids, as well as peptides, through chemo-selective C-H arylation under racemization-free reaction conditions. The ligand-accelerated C-H activation strategy proved water-tolerant and set the stage for direct fluorescence labelling as well as various modes of peptide ligation with excellent levels of positional selectivity in a bioorthogonal fashion. The synthetic utility of our approach is further demonstrated by twofold C-H arylations for the complexity-increasing assembly of artificial peptides within a multicatalytic C-H activation manifold. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. A simple and rapid radiochemical choline acetyltransferase (ChAT) assay screening test.

    PubMed

    Shiba, Kazuhiro; Ogawa, Kazuma; Kinuya, Seigo; Yajima, Kazuyoshi; Mori, Hirofumi

    2006-10-15

    A simple radiochemical choline acetyltransferase (ChAT) assay screening test was developed by measuring for [(3)H]acetylcholine ([(3)H]ACh) formed from 0.2 mM [(3)H]acetyl-coenzyme A ([(3)H]acetyl-CoA) and 1 mM choline by 0.2 mg of rat brain homogenates containing ChAT into 96-well microplates. A simple and rapid procedure for isolating [(3)H]ACh from the incubation mixture into 96-well microplates was achieved by using a sodium tetraphenylboron (Kalibor) solution (in ethyl acetate, 0.75%, w/v) and a hydrophobic liquid scintillator mixture (1:5, v/v, 0.2 mL) as an extraction solvent. The benefits of this radiochemical method using 96-well microplates are as follows: (1) this method is reliable and reproducible; (2) many samples can be examined at the same time by this method; (3) this method is economical and effective in reducing radioactive waste. The development of a new simple radiochemical ChAT assay screening test is the first stage of development of radiolabeled ChAT mapping agent.

  6. Intercomparison of six ambient [CH2O] measurement techniques

    NASA Astrophysics Data System (ADS)

    Gilpin, Tim; Apel, Eric; Fried, Alan; Wert, Bryan; Calvert, Jack; Genfa, Zhang; Dasgupta, Purnendu; Harder, Jerry W.; Heikes, Brian; Hopkins, Brian; Westberg, Hal; Kleindienst, Tad; Lee, Yin-Nan; Zhou, Xianliang; Lonneman, William; Sewell, Scott

    1997-09-01

    From May 29 to June 3, 1995 a blind intercomparison of six ambient formaldehyde measurement techniques took place at a field site near the National Center for Atmospheric Research in Boulder, Colorado. The continuous measurement methods intercompared were tunable diode laser absorption spectroscopy, (TDLAS); coil/2,4-dinitrophenylhydrazine, (CDNPH); 1,3-cyclohexanedione-diffusion scrubber (CHDDS); and the coil enzyme method (CENZ). In addition, two different cartridge methods were compared: silica gel-2,4-dinitrophenylhydrazine (DPNH) systems and a C-18-DNPH system. The intercomparison was conducted with spiked zero air (part 1) and ambient air (part 2). The CH2O standards for part 1 were calibrated by several independent methods and delivered to participants via a common glass manifold with potential trace gas interférants common to ambient air (O3, SO2, NO2, isoprene, H2O). The TDLAS system was used to confirm the absolute accuracy of the standards and served as a mission reference for part 1. The ambient phase lasted 44 hours with all participants sampling from a common glass tower. Differences between the ambient [CH2O] observed by the TDLAS and the other continuous methods were significant in some cases. For matched ambient measurement times the average ratios (±1σ) [CH2O]measured/[CH2O]TDLAS were: 0.89±0.12 (CDNPH); 1.30±0.02 (CHDDS); 0.63±0.03 (CENZ). The methods showed similar variations but different absolute values and the divergences appeared to result largely from calibration differences (no gas phase standards were used by groups other than NCAR). When the regressions of the participant [CH2O] values versus the TDLAS values, (measured in part 1), were used to normalize all of the results to the common gas phase standards of the NCAR group, the average ratios (±1σ), [CH2O]corrected/[CH2O]TDLAS for the first measurement period were much closer to unity: 1.04±0.14 (CDNPH), 1.00±0.11 (CHDDS), and 0.82±0.08 (CENZ). With the continuous methods

  7. Transition metal-catalyzed C-H activation reactions: diastereoselectivity and enantioselectivity.

    PubMed

    Giri, Ramesh; Shi, Bing-Feng; Engle, Keary M; Maugel, Nathan; Yu, Jin-Quan

    2009-11-01

    This critical review discusses historical and contemporary research in the field of transition metal-catalyzed carbon-hydrogen (C-H) bond activation through the lens of stereoselectivity. Research concerning both diastereoselectivity and enantioselectivity in C-H activation processes is examined, and the application of concepts in this area for the development of novel carbon-carbon and carbon-heteroatom bond-forming reactions is described. Throughout this review, an emphasis is placed on reactions that are (or may soon become) relevant in the realm of organic synthesis (221 references).

  8. The CH-53K: Are We Purchasing the Right Amount?

    DTIC Science & Technology

    2009-01-01

    QUOTATION FROM, ABSTRACTION FROM, OR REPRODUCTION OF ALL OR ANY PART OF THIS DOCUMENT IS PERMITTED PROVIDED PROPER ACKNOWLEDGEMENT IS MADE. 2 Table of...In August 1962, the Marine Corps was in search for a new heavy lift helicopter and placed its initial order for the CH-53A Sea Stallion (Figure A). At...November 2003, the last Super Stallion helicopter arrived at HMH-461, nearly 23 years after the fIrst CH-53E made it to the fleet.4 The aging fleet of

  9. Non-equilibrium simulation of CH4 production through the depressurization method from gas hydrate reservoirs

    NASA Astrophysics Data System (ADS)

    Qorbani, Khadijeh; Kvamme, Bjørn

    2016-04-01

    Natural gas hydrates (NGHs) in nature are formed from various hydrate formers (i.e. aqueous, gas, and adsorbed phases). As a result, due to Gibbs phase rule and the combined first and second laws of thermodynamics CH4-hydrate cannot reach thermodynamic equilibrium in real reservoir conditions. CH4 is the dominant component in NGH reservoirs. It is formed as a result of biogenic degradation of biological material in the upper few hundred meters of subsurface. It has been estimated that the amount of fuel-gas reserve in NGHs exceed the total amount of fossil fuel explored until today. Thus, these reservoirs have the potential to satisfy the energy requirements of the future. However, released CH4 from dissociated NGHs could find its way to the atmosphere and it is a far more aggressive greenhouse gas than CO2, even though its life-time is shorter. Lack of reliable field data makes it difficult to predict the production potential, as well as safety of CH4 production from NGHs. Computer simulations can be used as a tool to investigate CH4 production through different scenarios. Most hydrate simulators within academia and industry treat hydrate phase transitions as an equilibrium process and those which employ the kinetic approach utilize simple laboratory data in their models. Furthermore, it is typical to utilize a limited thermodynamic description where only temperature and pressure projections are considered. Another widely used simplification is to assume only a single route for the hydrate phase transitions. The non-equilibrium nature of hydrate indicates a need for proper kinetic models to describe hydrate dissociation and reformation in the reservoir with respect to thermodynamics variables, CH4 mole-fraction, pressure and temperature. The RetrasoCodeBright (RCB) hydrate simulator has previously been extended to model CH4-hydrate dissociation towards CH4 gas and water. CH4-hydrate is added to the RCB data-base as a pseudo mineral. Phase transitions are treated

  10. Intramolecular vibrational redistribution of CH 2I 2 dissolved in supercritical Xe

    NASA Astrophysics Data System (ADS)

    Sekiguchi, K.; Shimojima, A.; Kajimoto, O.

    2003-03-01

    Intramolecular vibrational energy redistribution (IVR) of CH 2I 2 in supercritical Xe has been studied. The first overtone of the C-H stretching mode was excited with a near infrared laser pulse and the transient UV absorption near 390 nm was monitored. Signals showed a rise and decay profile, which gave the IVR and VET (intermolecular vibrational energy transfer) rates, respectively. Solvent density dependence of each rate was obtained by tuning the pressure at a constant temperature. The IVR rate in supercritical Xe increased with increasing solvent density and asymptotically reached a limiting value. This result suggests that the IVR process of CH 2I 2 in condensed phase is a solvent-assisted process.

  11. Long-lived nuclear spin states in rapidly rotating CH2D groups

    NASA Astrophysics Data System (ADS)

    Elliott, Stuart J.; Brown, Lynda J.; Dumez, Jean-Nicolas; Levitt, Malcolm H.

    2016-11-01

    Although monodeuterated methyl groups support proton long-lived states, hindering of the methyl rotation limits the singlet relaxation time. We demonstrate an experimental case in which the rapid rotation of the CH2D group extends the singlet lifetime but does not quench the chemical shift difference between the CH2D protons, induced by the chiral environment. Proton singlet order is accessed using Spin-Lock Induced Crossing (SLIC) experiments, showing that the singlet relaxation time TS is over 2 min, exceeding the longitudinal relaxation time T1 by a factor of more than 10. This result shows that proton singlet states may be accessible and long-lived in rapidly rotating CH2D groups.

  12. The MCH2+ Systems: Do ScCH2+ and TiCH2+ Have C(sub s) or C(sub 2v) Symmetry and A Comparison of the B3LYP Method to Other Approaches

    NASA Technical Reports Server (NTRS)

    Ricca, Alessandra; Bauschlicher, Charles W., Jr.; Langhoff, Stephen R. (Technical Monitor)

    1995-01-01

    ScCH2(+) and TiCH2(+) are found to have C(sub s) symmetry, while the remaining systems have the expected C(sub 2v) symmetry. The C(sub s) symmetry structure is favored for ScCH2(+) and TiCH2(+) because it allows donation from one of the CH bonds into an empty 3d orbital. This distortion stabilizes the systems by less than 2 kcal/mol at the B3LYP, CASSCF, and CCSD(T) levels of theory. The SCF and B3LYP approaches find the C2(sub v) structure to be a saddle point, while the CASSCF approach finds the C(sub 2v) structure to be a stationary point. For V-Cu there are no empty 3d orbitals of the correct symmetry, and therefore the distortion to C(sub s), is unfavorable. The B3LYP binding energies are in good agreement with experiment and our previous best estimates.

  13. The Distribution and Excitation of CH3CN in a Solar Nebula Analog

    NASA Astrophysics Data System (ADS)

    Loomis, Ryan A.; Cleeves, L. Ilsedore; Öberg, Karin I.; Aikawa, Yuri; Bergner, Jennifer; Furuya, Kenji; Guzman, V. V.; Walsh, Catherine

    2018-06-01

    Cometary studies suggest that the organic composition of the early Solar Nebula was rich in complex nitrile species such CH3CN. Recent ALMA detections in protoplanetary disks suggest that these species may be common during planet and comet formation, but connecting gas-phase measurements to cometary abundances first requires constraints on formation chemistry and distributions of these species. We present here the detection of seven spatially resolved transitions of CH3CN in the protoplanetary disk around the T-Tauri star TW Hya. Using a rotational diagram analysis, we find a disk-averaged column density of {N}T={1.45}-0.15+0.19× {10}12 cm‑2 and a rotational temperature of {T}rot}={32.7}-3.4+3.9 K. A radially resolved rotational diagram shows the rotational temperature to be constant across the disk, suggesting that the CH3CN emission originates from a layer at z/r ∼ 0.3. Through comparison of the observations with predictions from a disk chemistry model, we find that grain-surface reactions likely dominate CH3CN formation and that in situ disk chemistry is sufficient to explain the observed CH3CN column density profile without invoking inheritance from the protostellar phase. However, the same model fails to reproduce a solar system cometary abundance of CH3CN relative to H2O in the midplane, suggesting that either vigorous vertical mixing or some degree of inheritance from interstellar ices occurred in the Solar Nebula.

  14. Rhodium-Catalyzed C-C Bond Formation via Heteroatom-Directed C-H Bond Activation

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Colby, Denise; Bergman, Robert; Ellman, Jonathan

    2010-05-13

    Once considered the 'holy grail' of organometallic chemistry, synthetically useful reactions employing C-H bond activation have increasingly been developed and applied to natural product and drug synthesis over the past decade. The ubiquity and relative low cost of hydrocarbons makes C-H bond functionalization an attractive alternative to classical C-C bond forming reactions such as cross-coupling, which require organohalides and organometallic reagents. In addition to providing an atom economical alternative to standard cross - coupling strategies, C-H bond functionalization also reduces the production of toxic by-products, thereby contributing to the growing field of reactions with decreased environmental impact. In the areamore » of C-C bond forming reactions that proceed via a C-H activation mechanism, rhodium catalysts stand out for their functional group tolerance and wide range of synthetic utility. Over the course of the last decade, many Rh-catalyzed methods for heteroatom-directed C-H bond functionalization have been reported and will be the focus of this review. Material appearing in the literature prior to 2001 has been reviewed previously and will only be introduced as background when necessary. The synthesis of complex molecules from relatively simple precursors has long been a goal for many organic chemists. The ability to selectively functionalize a molecule with minimal pre-activation can streamline syntheses and expand the opportunities to explore the utility of complex molecules in areas ranging from the pharmaceutical industry to materials science. Indeed, the issue of selectivity is paramount in the development of all C-H bond functionalization methods. Several groups have developed elegant approaches towards achieving selectivity in molecules that possess many sterically and electronically similar C-H bonds. Many of these approaches are discussed in detail in the accompanying articles in this special issue of Chemical Reviews. One approach

  15. Chemical Complexity in Local Diffuse and Translucent Clouds: Ubiquitous Linear C3H and CH3CN, a Detection of HC3N and an Upper Limit on the Abundance of CH2CN

    NASA Astrophysics Data System (ADS)

    Liszt, Harvey; Gerin, Maryvonne; Beasley, Anthony; Pety, Jerome

    2018-04-01

    We present Jansky Very Large Array observations of 20–37 GHz absorption lines from nearby Galactic diffuse molecular gas seen against four cosmologically distant compact radio continuum sources. The main new observational results are that l-C3H and CH3CN are ubiqitous in the local diffuse molecular interstellar medium at {\\text{}}{A}{{V}} ≲ 1, while HC3N was seen only toward B0415 at {\\text{}}{A}{{V}} > 4 mag. The linear/cyclic ratio is much larger in C3H than in C3H2 and the ratio CH3CN/HCN is enhanced compared to TMC-1, although not as much as toward the Horsehead Nebula. More consequentially, this work completes a long-term program assessing the abundances of small hydrocarbons (CH, C2H, linear and cyclic C3H and C3 {{{H}}}2, and C4H and C4H‑) and the CN-bearing species (CN, HCN, HNC, HC3N, HC5N, and CH3CN): their systematics in diffuse molecular gas are presented in detail here. We also observed but did not strongly constrain the abundances of a few oxygen-bearing species, most prominently HNCO. We set limits on the column density of CH2CN, such that the anion CH2CN‑ is only viable as a carrier of diffuse interstellar bands if the N(CH2CN)/N(CH2CN‑) abundance ratio is much smaller in this species than in any others for which the anion has been observed. We argue that complex organic molecules (COMS) are not present in clouds meeting a reasonable definition of diffuse molecular gas, i.e., {\\text{}}{A}{{V}} ≲ 1 mag. Based on observations obtained with the NRAO Jansky Very Large Array (VLA).

  16. Reducing CH4 emission from rice paddy fields by altering water management

    NASA Astrophysics Data System (ADS)

    Sudo, S.; Itoh, M.

    2010-12-01

    Percentage of atmospheric methane emitted form rice paddy is estimated at 60Tg/yr (20 - 100Tg/yr) which is near 10% of total global methane emission of 535Tg/yr (410 - 660Tg) (IPCC(1995), and which is near 30% of anthropogenic CH4 emission. Thus, mitigation of CH4 emission is urgently required. CH4 in paddy soil is emanated by the activities of anaerobic bacteria which is called methane producer through reduction of CO2 or decomposition of acetic acid, and it is transported to atmosphere through soil or paddy water surface. It is effective to control methane emission from rice paddy that period is extended on intermittent drainage, composted rice straw is incorporated as fertilizer instead of flesh one, or other. However, empirical approach of these kinds of experiments had not been sufficient because such a kind of experiment required significant times and efforts. In this study, we conducted demonstrative experiments to verify the effects of water management method differences in order to reduce CH4 emission from rice paddy at 9 experimental sites in 8 prefectures. In this, we used new gas analyzer which can measure CH4, CO2 and N2O at once developed by National Institute for Agro-Environmental Sciences (NIAES), Japan. In this report, we show the results in two years of this study. 'Nakaboshi' (mid-season-drainage) is one of cultivation methods in rice paddy that surface water in paddy field is once drained for about 10 days and the field is maintained like upland field to give adequate stress to rice plant for better harvest qualities and yields. Our targeted evaluation was dependencies of Nakaboshi periods lengths and Nakaboshi periods to CH4 emission reduction amounts for total cultivation periods within harvest yield maintained. The longer length of Nakaboshi period was extended, the lesser CH4 emitted even after when Nakaboshi period lasted, as a whole. In some cases, for example in Kagoshima, exceptional phenomena of that significant high emission were

  17. Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology

    PubMed Central

    2013-01-01

    Background The Gene Ontology (GO) facilitates the description of the action of gene products in a biological context. Many GO terms refer to chemical entities that participate in biological processes. To facilitate accurate and consistent systems-wide biological representation, it is necessary to integrate the chemical view of these entities with the biological view of GO functions and processes. We describe a collaborative effort between the GO and the Chemical Entities of Biological Interest (ChEBI) ontology developers to ensure that the representation of chemicals in the GO is both internally consistent and in alignment with the chemical expertise captured in ChEBI. Results We have examined and integrated the ChEBI structural hierarchy into the GO resource through computationally-assisted manual curation of both GO and ChEBI. Our work has resulted in the creation of computable definitions of GO terms that contain fully defined semantic relationships to corresponding chemical terms in ChEBI. Conclusions The set of logical definitions using both the GO and ChEBI has already been used to automate aspects of GO development and has the potential to allow the integration of data across the domains of biology and chemistry. These logical definitions are available as an extended version of the ontology from http://purl.obolibrary.org/obo/go/extensions/go-plus.owl. PMID:23895341

  18. Synthesis, structure and reactivity of rare-earth metallacarborane alkyls [η(1):η(5)-O(CH2)2C2B9H9]Ln(σ:η(1)-CH2C6H4-o-NMe2)(THF)2.

    PubMed

    Yang, Jingying; Xie, Zuowei

    2015-04-14

    Rare-earth metallacarborane alkyls can be stabilized by the incorporation of a functional sidearm into both π and σ ligands. Reaction of [Me3NH][7,8-O(CH2)2-7,8-C2B9H10] with one equiv. of Ln(CH2C6H4-o-NMe2)3 gave metallacarborane alkyls [η(1):η(5)-O(CH2)2C2B9H9]Ln(σ:η(1)-CH2C6H4-o-NMe2)(THF)2 (Ln = Y (), Gd (), Er ()) via alkane elimination. They represent the first examples of rare-earth metallacarborane alkyls. Treatment of with RN[double bond, length as m-dash]C[double bond, length as m-dash]NR (R = Cy, (i)Pr) or 2-benzoylpyridine afforded the corresponding mono-insertion products [η(1):η(5)-O(CH2)2C2B9H9]Y[η(2)-(RN)2C(CH2C6H4-o-NMe2)](DME) (R = Cy (), (i)Pr ()) or [η(1):η(5)-O(CH2)2C2B9H9]Y[C5H4NC(Ph)(CH2C6H4-o-NMe2)O](THF)2 (), respectively. Complex also reacted with ArNCO or ArNC (Ar = 2,6-diisopropylphenyl, 2,6-dimethylphenyl) to give di-insertion products [η(1):η(5)-O(CH2)2C2B9H9]Y[OC([double bond, length as m-dash]NC6H3Me2)N(C6H3Me2)C(CH2C6H4-o-NMe2)O](THF)2 () or [η(1):η(5)-O(CH2)2C2B9H9]Y[C([double bond, length as m-dash]NC6H3(i)Pr2)C([double bond, length as m-dash]NC6H3(i)Pr2)(CH2C6H4-o-NMe2)](DME) (). These results showed that the reactivity pattern of the Ln-C σ bond in rare-earth metallacarborane alkyls was dependent on the nature of the unsaturated organic molecules. New complexes were characterized by various spectroscopic techniques and elemental analysis. Some were further confirmed by single-crystal X-ray analysis.

  19. Combining multiple ChIP-seq peak detection systems using combinatorial fusion.

    PubMed

    Schweikert, Christina; Brown, Stuart; Tang, Zuojian; Smith, Phillip R; Hsu, D Frank

    2012-01-01

    Due to the recent rapid development in ChIP-seq technologies, which uses high-throughput next-generation DNA sequencing to identify the targets of Chromatin Immunoprecipitation, there is an increasing amount of sequencing data being generated that provides us with greater opportunity to analyze genome-wide protein-DNA interactions. In particular, we are interested in evaluating and enhancing computational and statistical techniques for locating protein binding sites. Many peak detection systems have been developed; in this study, we utilize the following six: CisGenome, MACS, PeakSeq, QuEST, SISSRs, and TRLocator. We define two methods to merge and rescore the regions of two peak detection systems and analyze the performance based on average precision and coverage of transcription start sites. The results indicate that ChIP-seq peak detection can be improved by fusion using score or rank combination. Our method of combination and fusion analysis would provide a means for generic assessment of available technologies and systems and assist researchers in choosing an appropriate system (or fusion method) for analyzing ChIP-seq data. This analysis offers an alternate approach for increasing true positive rates, while decreasing false positive rates and hence improving the ChIP-seq peak identification process.

  20. Kinetic conversion of CO to CH4 in the Solar System

    NASA Technical Reports Server (NTRS)

    Yung, Y. L.; Allen, M.; Pinto, J. P.

    1991-01-01

    Some of the most interesting chemistry in the Solar System involves changes in the oxidation state of the simple carbon species. The chemical pathways for the conversion of CH4 to CO and CO2 are for the most part known. The reverse process, the reduction of CO to CH4, is, however, poorly understood. This is surprising in view of the importance of the reduction process in the chemistry of the Solar System. Recently we investigated the chemical kinetics of a hitherto unsuspected reaction. It is argued that the formation of the methoxy radical (CH3O) from H+H2CO may play an essential role in the reduction of CO to CH4. The rate coefficient for this reaction has been estimated using the approximate theory of J. Troe and transition state theory. We will discuss the implications of this reaction for the chemistry of CO on Jupiter, in the solar nebula, for interpreting the laboratory experiments of A. Bar-Nun and A. Shaviv and A. Bar-Nun and S. Chang, and for organic synthesis in the prebiotic terrestrial atmosphere. The possible relation of CO reduction in the solar nebula and polyoxymethylene observed in comet Halley will be discussed.

  1. Time resolved infrared studies of C-H bond activation by organometallics

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Asplund, M.C.

    This work describes how step-scan Fourier Transform Infrared spectroscopy and visible and near infrared ultrafast lasers have been applied to the study of the photochemical activation of C-H bonds in organometallic systems, which allow for the selective breaking of C-H bonds in alkanes. The author has established the photochemical mechanism of C-H activation by Tp{sup *}Rh(CO){sub 2}(Tp{sup *} = HB-Pz{sup *}{sub 3}, Pz = 3,5-dimethylpyrazolyl) in alkane solution. The initially formed monocarbonyl forms a weak solvent complex, which undergoes a change in Tp{sup *} ligand connectivity. The final C-H bond breaking step occurs at different time scales depending on themore » structure of the alkane. In linear solvents, the time scale is <50 ns and cyclic alkanes is {approximately}200 ps. The reactivity of the Tp{sup *}Rh(CO){sub 2} system has also been studied in aromatic solvents. Here the reaction proceeds through two different pathways, with very different time scales. The first proceeds in a manner analogous to alkanes and takes <50 ns. The second proceeds through a Rh-C-C complex, and takes place on a time scale of 1.8 {micro}s.« less

  2. Simulations of laser-driven ion acceleration from a thin CH target

    NASA Astrophysics Data System (ADS)

    Park, Jaehong; Bulanov, Stepan; Ji, Qing; Steinke, Sven; Treffert, Franziska; Vay, Jean-Luc; Schenkel, Thomas; Esarey, Eric; Leemans, Wim; Vincenti, Henri

    2017-10-01

    2D and 3D computer simulations of laser driven ion acceleration from a thin CH foil using code WARP were performed. As the foil thickness varies from a few nm to μm, the simulations confirm that the acceleration mechanism transitions from the RPA (radiation pressure acceleration) to the TNSA (target normal sheath acceleration). In the TNSA regime, with the CH target thickness of 1 μ m and a pre-plasma ahead of the target, the simulations show the production of the collimated proton beam with the maximum energy of about 10 MeV. This agrees with the experimental results obtained at the BELLA laser facility (I 5 × 18 W / cm2 , λ = 800 nm). Furthermore, the maximum proton energy dependence on different setups of the initialization, i.e., different angles of the laser incidence from the target normal axis, different gradient scales and distributions of the pre-plasma, was explored. This work was supported by LDRD funding from LBNL, provided by the U.S. DOE under Contract No. DE-AC02-05CH11231, and used resources of the NERSC, a DOE office of Science User Facility supported by the U.S. DOE under Contract No. DE-AC02-05CH11231.

  3. Microstructure and thermal history of metal particles in CH chondrites

    NASA Astrophysics Data System (ADS)

    Goldstein, J. I.; Jones, R. H.; Kotula, P. G.; Michael, J. R.

    2007-06-01

    We have studied metal microstructures in four CH chondrites, Patuxent Range (PAT) 91546, Allan Hills (ALH) 85085, Acfer 214, and Northwest Africa (NWA) 739, to examine details of the thermal histories of individual particles. Four types of metal particles are common in all of these chondrites. Zoned and unzoned particles probably formed as condensates from a gas of chondritic composition in a monotonic cooling regime, as has been shown previously. We have demonstrated that these particles were cooled rapidly to temperatures below 500 K after they formed, and that condensation effectively closed around 700 K. Zoned and unzoned particles with exsolution precipitates, predominantly high-Ni taenite, have considerably more complex thermal histories. Precipitates grew in reheating episodes, but the details of the heating events vary among individual grains. Reheating temperatures are typically in the range 800-1000 K. Reheating could have been the result of impact events on the CH parent body. Some particles with precipitates may have been incorporated into chondrules, with further brief heating episodes taking place during chondrule formation. In addition to the four dominant types of metal particles, rare Ni-rich metal particles and Si-rich metal particles indicate that the metal assemblage in CH chondrites was a mixture of material that formed at different redox conditions. Metal in CH chondrites consists of a mechanical mixture of particles that underwent a variety of thermal histories prior to being assembled into the existing brecciated meteorites.

  4. BOREAS TGB-1 CH4 Concentration and Flux Data from NSA Tower Sites

    NASA Technical Reports Server (NTRS)

    Hall, Forrest G. (Editor); Conrad, Sara K. (Editor); Crill, Patrick; Varner, Ruth K.

    2000-01-01

    The BOREAS TGB-1 team made numerous measurements of trace gas concentrations and fluxes at various NSA sites. This data set contains half-hourly averages of ambient methane (CH4) measurements and calculated fluxes for the NSA-Fen in 1996 and the NSA-BP and NSA-OJP tower sites in 1994. The purpose of this study was to determine the CH4 flux from the study area by measuring ambient CH 4 concentrations. This flux can then be compared to the chamber flux measurements taken at the same sites. The data are provided in tabular ASCII files.

  5. Methyl isocyanate (CH3NCO): an important missing organic in current astrochemical networks

    NASA Astrophysics Data System (ADS)

    Majumdar, L.; Loison, J.-C.; Ruaud, M.; Gratier, P.; Wakelam, V.; Coutens, A.

    2018-01-01

    Methyl isocyanate (CH3NCO) is one of the important complex organic molecules detected on the comet 67P/Churyumov-Gerasimenko by Rosetta's Philae lander. It was also detected in hot cores around high-mass protostars along with a recent detection in the solar-type protostar IRAS 16293-2422. We propose here a gas-grain chemical model to form CH3NCO after reviewing various formation pathways with quantum chemical computations. We have used NAUTILUS three-phase gas-grain chemical model to compare observed abundances in the IRAS 16293-2422. Our chemical model clearly indicates the ice phase origin of CH3NCO.

  6. Extraterrestrial amino acids identified in metal-rich CH and CB carbonaceous chondrites from Antarctica

    NASA Astrophysics Data System (ADS)

    Burton, Aaron S.; Elsila, Jamie E.; Hein, Jason E.; Glavin, Daniel P.; Dworkin, Jason P.

    2013-03-01

    Carbonaceous chondrites contain numerous indigenous organic compounds and could have been an important source of prebiotic compounds required for the origin of life on Earth or elsewhere. Extraterrestrial amino acids have been reported in five of the eight groups of carbonaceous chondrites and are most abundant in CI, CM, and CR chondrites but are also present in the more thermally altered CV and CO chondrites. We report the abundance, distribution, and enantiomeric and isotopic compositions of simple primary amino acids in six metal-rich CH and CB carbonaceous chondrites that have not previously been investigated for amino acids: Allan Hills (ALH) 85085 (CH3), Pecora Escarpment (PCA) 91467 (CH3), Patuxent Range (PAT) 91546 (CH3), MacAlpine Hills (MAC) 02675 (CBb), Miller Range (MIL) 05082 (CB), and Miller Range (MIL) 07411 (CB). Amino acid abundances and carbon isotopic values were obtained by using both liquid chromatography time-of-flight mass spectrometry and fluorescence, and gas chromatography isotope ratio mass spectrometry. The δ13C/12C ratios of multiple amino acids fall outside of the terrestrial range and support their extraterrestrial origin. Extracts of CH chondrites were found to be particularly rich in amino acids (13-16 parts per million, ppm) while CB chondrite extracts had much lower abundances (0.2-2 ppm). The amino acid distributions of the CH and CB chondrites were distinct from the distributions observed in type 2 and 3 CM and CR chondrites and contained elevated levels of β-, γ-, and δ-amino acids compared to the corresponding α-amino acids, providing evidence that multiple amino acid formation mechanisms were important in CH and CB chondrites.

  7. Extraterrestrial Amino Acids Identified in Metal-Rich CH and CB Carbonaceous Chondrites from Antarctica

    NASA Technical Reports Server (NTRS)

    Burton, Aaron S.; Elsila, Jamie E.; Hein, Jason E.; Glavin, Daniel P.; Dworkin, Jason P.

    2013-01-01

    Carbonaceous chondrites contain numerous indigenous organic compounds and could have been an important source of prebiotic compounds required for the origin of life on Earth or elsewhere. Extraterrestrial amino acids have been reported in five of the eight groups of carbonaceous chondrites and are most abundant in CI, CM, and CR chondritesbut are also present in the more thermally altered CV and CO chondrites. We report the abundance, distribution, and enantiomeric and isotopic compositions of simple primary amino acids in six metal-rich CH and CB carbonaceous chondrites that have not previously been investigated for amino acids: Allan Hills (ALH) 85085 (CH3), Pecora Escarpment(PCA) 91467 (CH3), Patuxent Range (PAT) 91546 (CH3), MacAlpine Hills (MAC) 02675(CBb), Miller Range (MIL) 05082 (CB), and Miller Range (MIL) 07411 (CB). Amino acid abundances and carbon isotopic values were obtained by using both liquid chromatography time-of-flight mass spectrometry and fluorescence, and gas chromatography isotope ratiomass spectrometry. The (delta D, delta C-13, delta N-15) ratios of multiple amino acids fall outside of the terrestrial range and support their extraterrestrial origin. Extracts of CH chondrites were found to be particularly rich in amino acids (1316 parts per million, ppm) while CB chondrite extracts had much lower abundances (0.22 ppm). The amino acid distributions of the CH and CB chondrites were distinct from the distributions observed in type 2 and 3 CM and CR chondrites and contained elevated levels of beta-, gamma-, and delta-amino acids compared to the corresponding alpha-amino acids, providing evidence that multiple amino acid formation mechanisms were important in CH and CB chondrites.

  8. Spectroscopy of the low-frequency vibrational modes of CH3+ isotopologues

    NASA Astrophysics Data System (ADS)

    Asvany, Oskar; Thorwirth, Sven; Redlich, Britta; Schlemmer, Stephan

    2018-05-01

    The low-frequency stretching and bending vibrations of the isotopologues CH2D+,CD2H+ and CD3+ have been recorded at low temperature and low resolution. For this, a cryogenic 22-pole trapping machine coupled to an IR beamline of the FELIX free electron laser facility has been used. To record the overview spectra, the laser induced reactions CDm Hn+ + H2 → hν CDm-1 Hn+1+ +HD have been applied for these species. As this scheme is not applicable to CH3+, the latter has been tagged with He and subsequently dissociated by the IR beam. For the resulting CH3+ -He spectrum, broad features are observed below 1000 cm-1 possibly related to vibrational motions involving the He atom. The extracted vibrational band positions for all species are compared to results from high-level quantum-chemical calculations.

  9. SureChEMBL: a large-scale, chemically annotated patent document database

    PubMed Central

    Papadatos, George; Davies, Mark; Dedman, Nathan; Chambers, Jon; Gaulton, Anna; Siddle, James; Koks, Richard; Irvine, Sean A.; Pettersson, Joe; Goncharoff, Nicko; Hersey, Anne; Overington, John P.

    2016-01-01

    SureChEMBL is a publicly available large-scale resource containing compounds extracted from the full text, images and attachments of patent documents. The data are extracted from the patent literature according to an automated text and image-mining pipeline on a daily basis. SureChEMBL provides access to a previously unavailable, open and timely set of annotated compound-patent associations, complemented with sophisticated combined structure and keyword-based search capabilities against the compound repository and patent document corpus; given the wealth of knowledge hidden in patent documents, analysis of SureChEMBL data has immediate applications in drug discovery, medicinal chemistry and other commercial areas of chemical science. Currently, the database contains 17 million compounds extracted from 14 million patent documents. Access is available through a dedicated web-based interface and data downloads at: https://www.surechembl.org/. PMID:26582922

  10. Large-scale patterns in summer diffusive CH4 fluxes across boreal lakes, and contribution to diffusive C emissions.

    PubMed

    Rasilo, Terhi; Prairie, Yves T; Del Giorgio, Paul A

    2015-03-01

    Lakes are a major component of boreal landscapes, and whereas lake CO2 emissions are recognized as a major component of regional C budgets, there is still much uncertainty associated to lake CH4 fluxes. Here, we present a large-scale study of the magnitude and regulation of boreal lake summer diffusive CH4 fluxes, and their contribution to total lake carbon (C) emissions, based on in situ measurements of concentration and fluxes of CH4 and CO2 in 224 lakes across a wide range of lake type and environmental gradients in Québec. The diffusive CH4 flux was highly variable (mean 11.6 ± 26.4 SD mg m(-2)  d(-1) ), and it was positively correlated with temperature and lake nutrient status, and negatively correlated with lake area and colored dissolved organic matter (CDOM). The relationship between CH4 and CO2 concentrations fluxes was weak, suggesting major differences in their respective sources and/or regulation. For example, increasing water temperature leads to higher CH4 flux but does not significantly affect CO2 flux, whereas increasing CDOM concentration leads to higher CO2 flux but lower CH4 flux. CH4 contributed to 8 ± 23% to the total lake C emissions (CH4  + CO2 ), but 18 ± 25% to the total flux in terms of atmospheric warming potential, expressed as CO2 -equivalents. The incorporation of ebullition and plant-mediated CH4 fluxes would further increase the importance of lake CH4 . The average Q10 of CH4 flux was 3.7, once other covarying factors were accounted for, but this apparent Q10 varied with lake morphometry and was higher for shallow lakes. We conclude that global climate change and the resulting shifts in temperature will strongly influence lake CH4 fluxes across the boreal biome, but these climate effects may be altered by regional patterns in lake morphometry, nutrient status, and browning. © 2014 John Wiley & Sons Ltd.

  11. Infrared and reflectron time-of-flight mass spectroscopic study on the synthesis of glycolaldehyde in methanol (CH3OH) and methanol-carbon monoxide (CH3OH-CO) ices exposed to ionization radiation.

    PubMed

    Maity, Surajit; Kaiser, Ralf I; Jones, Brant M

    2014-01-01

    We present conclusive evidence on the formation of glycolaldehyde (HOCH2CHO) synthesized within astrophysically relevant ices of methanol (CH3OH) and methanol-carbon monoxide (CH3OH-CO) upon exposure to ionizing radiation at 5.5 K. The radiation induced chemical processes of the ices were monitored on line and in situ via infrared spectroscopy which was complimented by temperature programmed desorption studies post irradiation, utilizing highly sensitive reflectron time-of-flight mass spectrometry coupled with single photon fragment free photoionization (ReTOF-PI) at 10.49 eV. Specifically, glycolaldehyde was observed via the v14 band and further enhanced with the associated frequency shifts of the carbonyl stretching mode observed in irradiated isotopologue ice mixtures. Furthermore, experiments conducted with mixed isotopic ices of methanol-carbon monoxide (13CH3OH-CO, CH3(18)OH-CO, CD3OD-13CO and CH3OH-C18O) provide solid evidence of at least three competing reaction pathways involved in the formation of glycolaldehyde via non-equilibrium chemistry, which were identified as follows: (i) radical-radical recombination of HCO and CH2OH formed via decomposition of methanol--the "two methanol pathway"; (ii) via the reaction of one methanol unit (CH2OH from the decomposition of CH3OH) with one carbon monoxide unit (HCO from the hydrogenation of CO)--the "one methanol, one carbon monoxide pathway"; and (iii) formation via hydrogenation of carbon monoxide resulting in radicals of HCO and CH2OH--the "two carbon monoxide pathway". In addition, temperature programmed desorption studies revealed an increase in the amount of glycolaldehyde formed, suggesting further thermal chemistry of trapped radicals within the ice matrix. Sublimation of glycolaldehyde during the warm up was also monitored via ReTOF-PI and validated via the mutual agreement of the associated isotopic frequency shifts within the infrared band positions and the identical sublimation profiles obtained from

  12. Ion imaging study of dissociative charge transfer in the N{sub 2}{sup +}+ CH{sub 4} system

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Pei Linsen; Farrar, James M.

    The velocity map ion imaging method is applied to the dissociative charge transfer reactions of N{sub 2}{sup +} with CH{sub 4} studied in crossed beams. The velocity space images are collected at four collision energies between 0.5 and 1.5 eV, providing both product kinetic energy and angular distributions for the reaction products CH{sub 3}{sup +} and CH{sub 2}{sup +}. The general shapes of the images are consistent with long range electron transfer from CH{sub 4} to N{sub 2}{sup +} preceding dissociation, and product kinetic energy distributions are consistent with energy resonance in the initial electron transfer step. The branching ratiomore » for CH{sub 3}{sup +}:CH{sub 2}{sup +} is 85:15 over the full collision energy range, consistent with literature reports.« less

  13. The rate of charge tunneling is insensitive to polar terminal groups in self-assembled monolayers in Ag(TS)S(CH2)(n)M(CH2)(m)T//Ga2O3/EGaIn junctions.

    PubMed

    Yoon, Hyo Jae; Bowers, Carleen M; Baghbanzadeh, Mostafa; Whitesides, George M

    2014-01-08

    This paper describes a physical-organic study of the effect of uncharged, polar, functional groups on the rate of charge transport by tunneling across self-assembled monolayer (SAM)-based large-area junctions of the form Ag(TS)S(CH2)(n)M(CH2)(m)T//Ga2O3/EGaIn. Here Ag(TS) is a template-stripped silver substrate, -M- and -T are "middle" and "terminal" functional groups, and EGaIn is eutectic gallium-indium alloy. Twelve uncharged polar groups (-T = CN, CO2CH3, CF3, OCH3, N(CH3)2, CON(CH3)2, SCH3, SO2CH3, Br, P(O)(OEt)2, NHCOCH3, OSi(OCH3)3), having permanent dipole moments in the range 0.5 < μ < 4.5, were incorporated into the SAM. A comparison of the electrical characteristics of these junctions with those of junctions formed from n-alkanethiolates led to the conclusion that the rates of charge tunneling are insensitive to the replacement of terminal alkyl groups with the terminal polar groups in this set. The current densities measured in this work suggest that the tunneling decay parameter and injection current for SAMs terminated in nonpolar n-alkyl groups, and polar groups selected from common polar organic groups, are statistically indistinguishable.

  14. Atmospheric CH4 oxidation by Arctic permafrost and mineral cryosols as a function of water saturation and temperature.

    PubMed

    Stackhouse, B; Lau, M C Y; Vishnivetskaya, T; Burton, N; Wang, R; Southworth, A; Whyte, L; Onstott, T C

    2017-01-01

    The response of methanotrophic bacteria capable of oxidizing atmospheric CH 4 to climate warming is poorly understood, especially for those present in Arctic mineral cryosols. The atmospheric CH 4 oxidation rates were measured in microcosms incubated at 4 °C and 10 °C along a 1-m depth profile and over a range of water saturation conditions for mineral cryosols containing type I and type II methanotrophs from Axel Heiberg Island (AHI), Nunavut, Canada. The cryosols exhibited net consumption of ~2 ppmv CH 4 under all conditions, including during anaerobic incubations. Methane oxidation rates increased with temperature and decreased with increasing water saturation and depth, exhibiting the highest rates at 10 °C and 33% saturation at 5 cm depth (260 ± 60 pmol CH 4 gdw -1 d -1 ). Extrapolation of the CH 4 oxidation rates to the field yields net CH 4 uptake fluxes ranging from 11 to 73 μmol CH 4  m -2 d -1 , which are comparable to field measurements. Stable isotope mass balance indicates ~50% of the oxidized CH 4 is incorporated into the biomass regardless of temperature or saturation. Future atmospheric CH 4 uptake rates at AHI with increasing temperatures will be determined by the interplay of increasing CH 4 oxidation rates vs. water saturation and the depth to the water table during summer thaw. © 2016 John Wiley & Sons Ltd.

  15. Background CH4 and N2O fluxes in low-input short rotation coppice

    NASA Astrophysics Data System (ADS)

    Görres, Carolyn-Monika; Zenone, Terenzio; Ceulemans, Reinhart

    2016-04-01

    Extensively managed short rotation coppice systems are characterized by low fluxes of CH4 and N2O. However due to the large global warming potential of these trace gases (GWP100: CH4: 34, N2O: 298), such background fluxes can still significantly contribute to offsetting the CO2 uptake of short rotation coppice systems. Recent technological advances in fast-response CH4 and N2O analysers have improved our capability to capture these background fluxes, but their quantification still remains a challenge. As an example, we present here CH4 and N2O fluxes from a short-rotation bioenergy plantation in Belgium. Poplars have been planted in a double-row system on a loamy sand in 2010 and coppiced in the beginning of 2012 and 2014 (two-year rotation system). In 2013 (June - November) and 2014 (April - August), the plantation's CH4 and N2O fluxes were measured in parallel with an eddy covariance tower (EC) and an automated chamber system (AC). The EC had a detection limit of 13.68 and 0.76 μmol m-2 h-1 for CH4 and N2O, respectively. The median detection limit of the AC was 0.38 and 0.08 μmol m-2 h-1 for CH4 and N2O, respectively. The EC picked up a few high CH4 emission events with daily averages >100 μmol m-2 h-1, but a large proportion of the measured fluxes were within the EC's detection limit. The same was true for the EC-derived N2O fluxes where the daily average flux was often close to the detection limit. Sporadically, some negative (uptake) fluxes of N2O were observed. On the basis of the EC data, no clear link was found between CH4 and N2O fluxes and environmental variables. The problem with fluxes within the EC detection limit is that a significant amount of the values can show the opposite sign, thus "mirroring" the true flux. Subsequently, environmental controls of background trace gas fluxes might be disguised in the analysis. As a next step, it will be tested if potential environmental drivers of background CH4 and N2O fluxes at the plantation can be

  16. Probing the global potential energy minimum of (CH2O)2: THz absorption spectrum of (CH2O)2 in solid neon and para-hydrogen

    NASA Astrophysics Data System (ADS)

    Andersen, J.; Voute, A.; Mihrin, D.; Heimdal, J.; Berg, R. W.; Torsson, M.; Wugt Larsen, R.

    2017-06-01

    The true global potential energy minimum configuration of the formaldehyde dimer (CH2O)2, including the presence of a single or a double weak intermolecular CH⋯O hydrogen bond motif, has been a long-standing subject among both experimentalists and theoreticians as two different energy minima conformations of Cs and C2h symmetry have almost identical energies. The present work demonstrates how the class of large-amplitude hydrogen bond vibrational motion probed in the THz region provides excellent direct spectroscopic observables for these weak intermolecular CH⋯O hydrogen bond motifs. The combination of concentration dependency measurements, observed isotopic spectral shifts associated with H/D substitutions and dedicated annealing procedures, enables the unambiguous assignment of three large-amplitude infrared active hydrogen bond vibrational modes for the non-planar Cs configuration of (CH2O)2 embedded in cryogenic neon and enriched para-hydrogen matrices. A (semi)-empirical value for the change of vibrational zero-point energy of 5.5 ± 0.3 kJ mol-1 is proposed for the dimerization process. These THz spectroscopic observations are complemented by CCSD(T)-F12/aug-cc-pV5Z (electronic energies) and MP2/aug-cc-pVQZ (force fields) electronic structure calculations yielding a (semi)-empirical value of 13.7 ± 0.3 kJ mol-1 for the dissociation energy D0 of this global potential energy minimum.

  17. Effect of CH3COOH on Hydrometallurgical Purification of Metallurgical-Grade Silicon Using HCl-HF Leaching

    NASA Astrophysics Data System (ADS)

    Tian, Chunjin; Lu, Haifei; Wei, Kuixian; Ma, Wenhui; Xie, Keqiang; Wu, Jijun; Lei, Yun; Yang, Bin; Morita, Kazuki

    2018-04-01

    The present study investigated the effects of adding CH3COOH to HCl and HF used to purify metallurgical-grade Si (MG-Si). After 6 h of leaching MG-Si with an acid mixture consisting of 4 mol L-1 HCl, 3 mol L-1 HF, and 3 mol L-1 CH3COOH at 348 K, the total impurity removal efficiency was 88.5%, exceeding the 81.5% removal efficiency obtained without addition of CH3COOH. The microstructural evolution of Si after etching with the two lixiviants indicated better dissolution of metal impurities in MG-Si when using the HCl-HF-CH3COOH mixture. Furthermore, the leaching kinetics of Fe using the HCl-HF and HCl-HF-CH3COOH mixtures were observed to depend on the interfacial chemical reactions.

  18. Strong CH/O interactions between polycyclic aromatic hydrocarbons and water: Influence of aromatic system size.

    PubMed

    Veljković, Dušan Ž

    2018-03-01

    Energies of CH/O interactions between water molecule and polycyclic aromatic hydrocarbons with a different number of aromatic rings were calculated using ab initio calculations at MP2/cc-PVTZ level. Results show that an additional aromatic ring in structure of polycyclic aromatic hydrocarbons significantly strengthens CH/O interactions. Calculated interaction energies in optimized structures of the most stable tetracene/water complex is -2.27 kcal/mol, anthracene/water is -2.13 kcal/mol and naphthalene/water is -1.97 kcal/mol. These interactions are stronger than CH/O contacts in benzene/water complex (-1.44 kcal/mol) while CH/O contacts in tetracene/water complex are even stronger than CH/O contacts in pyridine/water complexes (-2.21 kcal/mol). Electrostatic potential maps for different polycyclic aromatic hydrocarbons were calculated and used to explain trends in the energies of interactions. Copyright © 2017 Elsevier Inc. All rights reserved.

  19. Enhanced reactivity in dioxirane C-H oxidations via strain release: a computational and experimental study.

    PubMed

    Zou, Lufeng; Paton, Robert S; Eschenmoser, Albert; Newhouse, Timothy R; Baran, Phil S; Houk, K N

    2013-04-19

    The site selectivities and stereoselectivities of C-H oxidations of substituted cyclohexanes and trans-decalins by dimethyldioxirane (DMDO) were investigated computationally with quantum mechanical density functional theory (DFT). The multiconfiguration CASPT2 method was employed on model systems to establish the preferred mechanism and transition state geometry. The reaction pathway involving a rebound step is established to account for the retention of stereochemistry. The oxidation of sclareolide with dioxirane reagents is reported, including the oxidation by the in situ generated tBu-TFDO, a new dioxirane that better discriminates between C-H bonds on the basis of steric effects. The release of 1,3-diaxial strain in the transition state contributes to the site selectivity and enhanced equatorial C-H bond reactivity for tertiary C-H bonds, a result of the lowering of distortion energy. In addition to this strain release factor, steric and inductive effects contribute to the rates of C-H oxidation by dioxiranes.

  20. Nitrate loading and CH4 and N2O Flux from headwater streams

    NASA Astrophysics Data System (ADS)

    Sousa, C. H. R. D.; Hilker, T.; Hall, F. G.; Moura, Y. M.; McAdam, E.

    2014-12-01

    Freshwater ecosystems transport and process significant amounts of terrestrial carbon and can be considerable sources of CO2, CH4, and N2O. A great deal of uncertainty, however, remains in both global estimates and our understanding of drivers of freshwater greenhouse gas emissions. Furthermore, small headwater streams have received insufficient attention to date and may contribute disproportionately to global GHG flux. Our objective was to quantify GHG flux and assess the impact of changes in DOC and NO3 concentrations in surface and subsurface water on flux rates in three streams in the Lamprey River watershed in New Hampshire, USA, that contrast in surface water DOC:NO3. We measured DOC, NO3 and dissolved gas concentrations in surface waters of each stream monthly from May 2011 to April 2012. Empirical measurements of reaeration coefficients were used to convert dissolved gas concentrations to fluxes. We found higher GHG concentrations and fluxes in the two streams with high DOC concentrations, particularly gases produced by anaerobic metabolism (CH4, N2O from methanogenesis and denitrification, respectively). The stream with high DOC and high NO3 showed high N2O and low CH4 flux, while the high DOC, low NO3 stream showed high CH4 and low N2O flux. Our results are consistent with a model in which C inputs drive total GHG production, while NO3 input regulates the relative importance of CH4 and N2O by suppressing methanogenesis and stimulating denitrification. The magnitude of GHG fluxes suggests that streams in this region are likely to be small sources of CO2, but potentially important sources of CH4 and N2O. Since CH4 and N2O are many times more powerful than CO2 at trapping heat in the atmosphere, freshwater emissions of these gases have the potential to offset a significant proportion of the climate benefits of the terrestrial carbon sink, a possibility that has not been sufficiently incorporated into climate models.