Formation of novel rare-gas-containing molecules by molecular photodissociation in clusters.

PubMed

Cohen, A; Niv, M Y; Gerber, R B

2001-01-01

Recent work by Räsänen and coworkers showed that photolysis of hydrides in rare-gas matrices results in part in formation of novel, rare-gas-containing molecules. Thus, photolysis of HCl in Xe and of H2O in Xe result respectively in formation of HXeCl and HXeOH in the Xe matrices. Ab initio calculations show that the compounds HRgY so formed are stable in isolation, and that by the strength and nature of the bonding these are molecules, very different from the corresponding weakly bound clusters Rg...HY. This paper presents a study of the formation mechanism of HRgY following the photolysis of HY in clusters Rgn(HY). Calculations are described for HXeCl, as a representative example. Potential energy surfaces that govern the formation of HXeCl in the photolysis of HCl in xenon clusters are obtained, and the dynamics on these surfaces is analyzed, partly with insight from trajectories of molecular dynamics simulations. The potential surfaces are obtained by a new variant of the DIM (diatomics in molecules) and DIIS (diatomics in ionic systems) models. Non-adiabatic couplings are also obtained. The main results are: (1) Properties of HXeCl predicted by the DIM-DIIS model are in reasonable accord with results of ab initio calculations. (2) The potential along the isomerization path HXeCl-->Xe...HCl predicted by DIM is in semiquantitative accord with the ab initio results. (3) Surface-hopping molecular dynamics simulations of the process in clusters, with "on the fly" calculations of the DIM-DIIS potentials and non-adiabatic couplings are computationally feasible. (4) Formation of HXeCl, following photolysis of HCl in Xe54(HCl), requires cage-exit of the H atom as a precondition. The H atom and the Cl can then attack the same Xe atom on opposite sides, leading to charge transfer and production of the ionic HXeCl. (5) Non-adiabatic processes play an important role, both in the reagent configurations, and at the charge-transfer stage. The results open the way to predictions of the formation of new HRgY species.

Cooperative effects in the structuring of fluoride water clusters: Ab initio hybrid quantum mechanical/molecular mechanical model incorporating polarizable fluctuating charge solvent

NASA Astrophysics Data System (ADS)

Bryce, Richard A.; Vincent, Mark A.; Malcolm, Nathaniel O. J.; Hillier, Ian H.; Burton, Neil A.

1998-08-01

A new hybrid quantum mechanical/molecular mechanical model of solvation is developed and used to describe the structure and dynamics of small fluoride/water clusters, using an ab initio wave function to model the ion and a fluctuating charge potential to model the waters. Appropriate parameters for the water-water and fluoride-water interactions are derived, with the fluoride anion being described by density functional theory and a large Gaussian basis. The role of solvent polarization in determining the structure and energetics of F(H2O)4- clusters is investigated, predicting a slightly greater stability of the interior compared to the surface structure, in agreement with ab initio studies. An extended Lagrangian treatment of the polarizable water, in which the water atomic charges fluctuate dynamically, is used to study the dynamics of F(H2O)4- cluster. A simulation using a fixed solvent charge distribution indicates principally interior, solvated states for the cluster. However, a preponderance of trisolvated configurations is observed using the polarizable model at 300 K, which involves only three direct fluoride-water hydrogen bonds. Ab initio calculations confirm this trisolvated species as a thermally accessible state at room temperature, in addition to the tetrasolvated interior and surface structures. Extension of this polarizable water model to fluoride clusters with five and six waters gave less satisfactory agreement with experimental energies and with ab initio geometries. However, our results do suggest that a quantitative model of solvent polarization is fundamental for an accurate understanding of the properties of anionic water clusters.

An ab initio-based Er–He interatomic potential in hcp Er

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

Yang, Li; ye, Yeting; Fan, K. M.

2014-09-01

We have developed an empirical erbium-helium (Er-He) potential by fitting to the results calculated from ab initio method. Based on the electronic hybridization between Er and He atoms, an s-band model, along with a repulsive pair potential, has been derived to describe the Er-He interaction. The atomic configurations and the formation energies of single He defects, small He interstitial clusters (Hen) and He-vacancy (HenV ) clusters obtained by ab initio calculations are used as the fitting database. The binding energies and relative stabilities of the HnVm clusters are studied by the present potential and compared with the ab initio calculations.more » The Er-He potential is also applied to study the migration of He in hcp-Er at different temperatures, and He clustering is found to occur at 600 K in hcp Er crystal, which may be due to the anisotropic migration behavior of He interstitials.« less

Theoretical gas to liquid shift of (15)N isotropic nuclear magnetic shielding in nitromethane using ab initio molecular dynamics and GIAO/GIPAW calculations.

PubMed

Gerber, Iann C; Jolibois, Franck

2015-05-14

Chemical shift requires the knowledge of both the sample and a reference magnetic shielding. In few cases as nitrogen (15N), the standard experimental reference corresponds to its liquid phase. Theoretical estimate of NMR magnetic shielding parameters of compounds in their liquid phase is then mandatory but usually replaced by an easily-get gas phase value, forbidding direct comparisons with experiments. We propose here to combine ab initio molecular dynamic simulations with the calculations of magnetic shielding using GIAO approach on extracted cluster's structures from MD. Using several computational strategies, we manage to accurately calculate 15N magnetic shielding of nitromethane in its liquid phase. Theoretical comparison between liquid and gas phase allows us to extrapolate an experimental value for the 15N magnetic shielding of nitromethane in gas phase between -121.8 and -120.8 ppm.

Ab initio theoretical calculations of the electronic excitation energies of small water clusters.

PubMed

Tachikawa, Hiroto; Yabushita, Akihiro; Kawasaki, Masahiro

2011-12-14

A direct ab initio molecular dynamics method has been applied to a water monomer and water clusters (H(2)O)(n) (n = 1-3) to elucidate the effects of zero-point energy (ZPE) vibration on the absorption spectra of water clusters. Static ab initio calculations without ZPE showed that the first electronic transitions of (H(2)O)(n), (1)B(1)←(1)A(1), are blue-shifted as a function of cluster size (n): 7.38 eV (n = 1), 7.58 eV (n = 2) and 8.01 eV (n = 3). The inclusion of the ZPE vibration strongly affects the excitation energies of a water dimer, and a long red-tail appears in the range of 6.42-6.90 eV due to the structural flexibility of a water dimer. The ultraviolet photodissociation of water clusters and water ice surfaces is relevant to these results.

Materials Screening for the Discovery of New Half-Heuslers: Machine Learning versus ab Initio Methods.

PubMed

Legrain, Fleur; Carrete, Jesús; van Roekeghem, Ambroise; Madsen, Georg K H; Mingo, Natalio

2018-01-18

Machine learning (ML) is increasingly becoming a helpful tool in the search for novel functional compounds. Here we use classification via random forests to predict the stability of half-Heusler (HH) compounds, using only experimentally reported compounds as a training set. Cross-validation yields an excellent agreement between the fraction of compounds classified as stable and the actual fraction of truly stable compounds in the ICSD. The ML model is then employed to screen 71 178 different 1:1:1 compositions, yielding 481 likely stable candidates. The predicted stability of HH compounds from three previous high-throughput ab initio studies is critically analyzed from the perspective of the alternative ML approach. The incomplete consistency among the three separate ab initio studies and between them and the ML predictions suggests that additional factors beyond those considered by ab initio phase stability calculations might be determinant to the stability of the compounds. Such factors can include configurational entropies and quasiharmonic contributions.

Structure determination and total synthesis of a novel antibacterial substance, AB0022A, produced by a cellular slime mold.

PubMed

Sawada, T; Aono, M; Asakawa, S; Ito, A; Awano, K

2000-09-01

A novel antibacterial substance, AB0022A, was isolated from the cellular slime mold Dictyostelium purpureum K1001. It inhibited the growth of Gram-positive bacteria, and its MICs ranged from 0.39 to 50 microg/ml. Because AB0022A was a highly substituted aromatic compound, we could not determine its structure based on only its physico-chemical and spectral data. We therefore used a dehalogenated derivative from AB0022A and deduced that its structure was 1,9-dihydroxy-3,7-dimethoxy-2-hexanoyl-4,6,8-trichlorodibenzofuran . To confirm this structure, we synthesized the compound having the deduced structure. The synthetic compound was identical to naturally occurring AB0022A.

The structure and unconventional dihydrogen bonding of a pressure-stabilized hydrogen-rich (NH 3BH 3)(H 2) x(x = 1.5) compound

DOE PAGES

Lin, Yu; Welchman, Evan; Thonhauser, Timo; ...

2017-03-15

Combining X-ray diffraction, Raman spectroscopy, and ab initio simulations we characterize an extremely hydrogen-rich phase with the chemical formula (NH 3BH 3)(H 2) x (x = 1.5). This phase was formed by compressing ammonia borane (AB, NH 3BH 3) in an environment with an excess of molecular hydrogen (H 2). This compound can store a total of 26.8 wt% hydrogen, both as molecular hydrogen and chemically bonded hydrogen in AB, making it one of the most hydrogen-rich solids currently known. The new compound possesses a layered AB structure where additional H 2 molecules reside in channels created through the weavingmore » of AB layers. The unconventional dihydrogen bonding network of the new compound is significantly modified from its parent AB phase and contains H•••H contacts between adjacent AB molecules and between AB and H 2 molecules. H–H can be either a proton donor or a proton acceptor that forms new types of dihydrogen bonding with the host AB molecules, which are depicted as H–H•••H–B or H–H•••H–N, respectively. Furthermore, this study not only demonstrates the strategy and the promise of using pressure for new material synthesis, but also unleashes the power of combining experiments and ab initio calculations for elucidating novel structures and unusual bonding configurations in dense low-Z materials.« less

The structure and unconventional dihydrogen bonding of a pressure-stabilized hydrogen-rich (NH 3BH 3)(H 2) x(x = 1.5) compound

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

Lin, Yu; Welchman, Evan; Thonhauser, Timo

Combining X-ray diffraction, Raman spectroscopy, and ab initio simulations we characterize an extremely hydrogen-rich phase with the chemical formula (NH 3BH 3)(H 2) x (x = 1.5). This phase was formed by compressing ammonia borane (AB, NH 3BH 3) in an environment with an excess of molecular hydrogen (H 2). This compound can store a total of 26.8 wt% hydrogen, both as molecular hydrogen and chemically bonded hydrogen in AB, making it one of the most hydrogen-rich solids currently known. The new compound possesses a layered AB structure where additional H 2 molecules reside in channels created through the weavingmore » of AB layers. The unconventional dihydrogen bonding network of the new compound is significantly modified from its parent AB phase and contains H•••H contacts between adjacent AB molecules and between AB and H 2 molecules. H–H can be either a proton donor or a proton acceptor that forms new types of dihydrogen bonding with the host AB molecules, which are depicted as H–H•••H–B or H–H•••H–N, respectively. Furthermore, this study not only demonstrates the strategy and the promise of using pressure for new material synthesis, but also unleashes the power of combining experiments and ab initio calculations for elucidating novel structures and unusual bonding configurations in dense low-Z materials.« less

Ionic Vapor Composition in Critical and Supercritical States of Strongly Interacting Ionic Compounds.

PubMed

Chaban, Vitaly V; Prezhdo, Oleg V

2016-05-12

The critical point, CP (T, P), of the phase diagram quantifies the minimum amount of kinetic energy needed to prevent a substance from existing in a condensed phase. Therefore, the CP is closely related to the properties of the fluid far below the critical temperature. Approaches designed to predict thermophysical properties of a system necessarily aim to provide reliable estimates of the CP. Vice versa, CP estimation is impossible without knowledge of the vapor phase behavior. We report ab initio Born-Oppenheimer molecular dynamics (BOMD) simulations of sodium and potassium chlorides, NaCl and KCl, at and above their expected CPs. We advance the present knowledge regarding the existence of ionic species in the vapor phase by establishing significant percentages of atomic clusters: 29-30% in NaCl and 34-38% in KCl. A neutral pair of counterions is the most abundant cluster in the ionic vapors (ca. 35% of all vaporized ions exist in this form). Unexpectedly, an appreciable fraction of clusters is charged. The ionic vapor composition is determined by the vapor density, rather than the nature of the alkali ion. The previously suggested CPs of NaCl and KCl appear overestimated, based on the present simulations. The reported results offer essential insights into the ionic fluid properties and assist in development of thermodynamic theories. The ab initio BOMD method has been applied to investigate the vapor phase composition of an ionic fluid for the first time.

Ab-initio study of B{sub 2}-type technetium AB (A=Tc, B=Nb and Ta) intermetallic compounds

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

Acharya, Nikita, E-mail: acharyaniks30@gmail.com; Fatima, Bushra; Sanyal, Sankar P.

2016-05-06

The structural, electronic and elastic properties of AB type (A = Tc, B = Nb and Ta) technetium intermetallic compounds are studied using full potential linearized plane wave (FP-LAPW) method within generalized gradient approximation (GGA). The calculated lattice parameters agree well with the experimental results. The elastic constants obey the stability criteria for cubic system. Ductility for these compounds has been analyzed using the Pugh’s rule and Cauchy’s pressure and found that all the compounds are ductile in nature. Bonding nature is discussed in terms of Fermi surface and band structures.

A large microRNA cluster on chromosome 19 is a transcriptional hallmark of WHO type A and AB thymomas.

PubMed

Radovich, Milan; Solzak, Jeffrey P; Hancock, Bradley A; Conces, Madison L; Atale, Rutuja; Porter, Ryan F; Zhu, Jin; Glasscock, Jarret; Kesler, Kenneth A; Badve, Sunil S; Schneider, Bryan P; Loehrer, Patrick J

2016-02-16

Thymomas are one of the most rarely diagnosed malignancies. To better understand its biology and to identify therapeutic targets, we performed next-generation RNA sequencing. The RNA was sequenced from 13 thymic malignancies and 3 normal thymus glands. Validation of microRNA expression was performed on a separate set of 35 thymic malignancies. For cell-based studies, a thymoma cell line was used. Hierarchical clustering revealed 100% concordance between gene expression clusters and WHO subtype. A substantial differentiator was a large microRNA cluster on chr19q13.42 that was significantly overexpressed in all A and AB tumours and whose expression was virtually absent in the other thymomas and normal tissues. Overexpression of this microRNA cluster activates the PI3K/AKT/mTOR pathway. Treatment of a thymoma AB cell line with a panel of PI3K/AKT/mTOR inhibitors resulted in marked reduction of cell viability. A large microRNA cluster on chr19q13.42 is a transcriptional hallmark of type A and AB thymomas. Furthermore, this cluster activates the PI3K pathway, suggesting the possible exploration of PI3K inhibitors in patients with these subtypes of tumour. This work has led to the initiation of a phase II clinical trial of PI3K inhibition in relapsed or refractory thymomas (http://clinicaltrials.gov/ct2/show/NCT02220855).

A large microRNA cluster on chromosome 19 is a transcriptional hallmark of WHO type A and AB thymomas

PubMed Central

Radovich, Milan; Solzak, Jeffrey P; Hancock, Bradley A; Conces, Madison L; Atale, Rutuja; Porter, Ryan F; Zhu, Jin; Glasscock, Jarret; Kesler, Kenneth A; Badve, Sunil S; Schneider, Bryan P; Loehrer, Patrick J

2016-01-01

Background: Thymomas are one of the most rarely diagnosed malignancies. To better understand its biology and to identify therapeutic targets, we performed next-generation RNA sequencing. Methods: The RNA was sequenced from 13 thymic malignancies and 3 normal thymus glands. Validation of microRNA expression was performed on a separate set of 35 thymic malignancies. For cell-based studies, a thymoma cell line was used. Results: Hierarchical clustering revealed 100% concordance between gene expression clusters and WHO subtype. A substantial differentiator was a large microRNA cluster on chr19q13.42 that was significantly overexpressed in all A and AB tumours and whose expression was virtually absent in the other thymomas and normal tissues. Overexpression of this microRNA cluster activates the PI3K/AKT/mTOR pathway. Treatment of a thymoma AB cell line with a panel of PI3K/AKT/mTOR inhibitors resulted in marked reduction of cell viability. Conclusions: A large microRNA cluster on chr19q13.42 is a transcriptional hallmark of type A and AB thymomas. Furthermore, this cluster activates the PI3K pathway, suggesting the possible exploration of PI3K inhibitors in patients with these subtypes of tumour. This work has led to the initiation of a phase II clinical trial of PI3K inhibition in relapsed or refractory thymomas (http://clinicaltrials.gov/ct2/show/NCT02220855). PMID:26766736

Nonconventional screening of the Coulomb interaction in FexOy clusters: An ab initio study

NASA Astrophysics Data System (ADS)

Peters, L.; Şaşıoǧlu, E.; Rossen, S.; Friedrich, C.; Blügel, S.; Katsnelson, M. I.

2017-04-01

From microscopic point-dipole model calculations of the screening of the Coulomb interaction in nonpolar systems by polarizable atoms, it is known that screening strongly depends on dimensionality. For example, in one-dimensional systems, the short-range interaction is screened, while the long-range interaction is antiscreened. This antiscreening is also observed in some zero-dimensional structures, i.e., molecular systems. By means of ab initio calculations in conjunction with the random-phase approximation (RPA) within the FLAPW method, we study screening of the Coulomb interaction in FexOy clusters. For completeness, these results are compared with their bulk counterpart magnetite. It appears that the on-site Coulomb interaction is very well screened both in the clusters and bulk. On the other hand, for the intersite Coulomb interaction, the important observation is made that it is almost constant throughout the clusters, while for the bulk it is almost completely screened. More precisely and interestingly, in the clusters antiscreening is observed by means of ab initio calculations.

AB-CHMINACA, AB-PINACA, and FUBIMINA: Affinity and Potency of Novel Synthetic Cannabinoids in Producing Δ9-Tetrahydrocannabinol–Like Effects in Mice

PubMed Central

Marusich, Julie A.; Lefever, Timothy W.; Antonazzo, Kateland R.; Wallgren, Michael T.; Cortes, Ricardo A.; Patel, Purvi R.; Grabenauer, Megan; Moore, Katherine N.

2015-01-01

Diversion of synthetic cannabinoids for abuse began in the early 2000s. Despite legislation banning compounds currently on the drug market, illicit manufacturers continue to release new compounds for recreational use. This study examined new synthetic cannabinoids, AB-CHMINACA (N-[1-amino-3-methyl-oxobutan-2-yl]-1-[cyclohexylmethyl]-1H-indazole-3-carboxamide), AB-PINACA [N-(1-amino-3-methyl-1-oxobutan-2-yl)-1-pentyl-1H-indazole-3-carboxamide], and FUBIMINA [(1-(5-fluoropentyl)-1H-benzo[d]imadazol-2-yl)(naphthalen-1-yl)methanone], with the hypothesis that these compounds, like those before them, would be highly susceptible to abuse. Cannabinoids were examined in vitro for binding and activation of CB1 receptors, and in vivo for pharmacological effects in mice and in Δ9-tetrahydrocannabinol (Δ9-THC) discrimination. AB-CHMINACA, AB-PINACA, and FUBIMINA bound to and activated CB1 and CB2 receptors, and produced locomotor suppression, antinociception, hypothermia, and catalepsy. Furthermore, these compounds, along with JWH-018 [1-pentyl-3-(1-naphthoyl)indole], CP47,497 [rel-5-(1,1-dimethylheptyl)-2-[(1R,3S)-3-hydroxycyclohexyl]-phenol], and WIN55,212-2 ([(3R)-2,3-dihydro-5-methyl-3-(4-morpholinylmethyl)pyrrolo[1,2,3-de]-1,4-benzoxazin-6-yl]-1-naphthalenyl-methanone, monomethanesulfonate), substituted for Δ9-THC in Δ9-THC discrimination. Rank order of potency correlated with CB1 receptor-binding affinity, and all three compounds were full agonists in [35S]GTPγS binding, as compared with the partial agonist Δ9-THC. Indeed, AB-CHMINACA and AB-PINACA exhibited higher efficacy than most known full agonists of the CB1 receptor. Preliminary analysis of urinary metabolites of the compounds revealed the expected hydroxylation. AB-PINACA and AB-CHMINACA are of potential interest as research tools due to their unique chemical structures and high CB1 receptor efficacies. Further studies on these chemicals are likely to include research on understanding cannabinoid receptors and other components of the endocannabinoid system that underlie the abuse of synthetic cannabinoids. PMID:26105953

Hierarchical Cluster Formation in Concentrated Monoclonal Antibody Formulations

NASA Astrophysics Data System (ADS)

Godfrin, P. Douglas; Zarzar, Jonathan; Zarraga, Isidro Dan; Porcar, Lionel; Falus, Peter; Wagner, Norman; Liu, Yun

Reversible cluster formation has been identified as an underlying cause of large solution viscosities observed in some concentrated monoclonal antibody (mAb) formulations. As high solution viscosity prevents the use of subcutaneous injection as a delivery method for some mAbs, a fundamental understanding of the interactions responsible for high viscosities in concentrated mAb solutions is of significant relevance to mAb applications in human health care as well as of intellectual interest. Here, we present a detailed investigation of a well-studied IgG1 based mAb to relate the short time dynamics and microstructure to significant viscosity changes over a range of pharmaceutically relevant physiochemical conditions. Using a combination of experimental techniques, it is found that upon adding Na2SO4, these antibodies dimerize in solution. Proteins form strongly bounded reversible dimers at dilute concentrations that, when concentrated, interact with each other to form loosely bounded, large, transient clusters. The combined effect of forming strongly bounded dimers and a large transient network is a significant increase in the solution viscosity. Strongly bounded, reversible dimers may exist in many IgG1 based mAb systems such that these results contribute to a more comprehensive understanding of the physical mechanisms producing high viscosities in concentrated protein solutions.

Simple and ultra-fast recognition and quantitation of compounded monoclonal antibodies: Application to flow injection analysis combined to UV spectroscopy and matching method.

PubMed

Jaccoulet, E; Schweitzer-Chaput, A; Toussaint, B; Prognon, P; Caudron, E

2018-09-01

Compounding of monoclonal antibody (mAbs) constantly increases in hospital. Quality control (QC) of the compounded mAbs based on quantification and identification is required to prevent potential errors and fast method is needed to manage outpatient chemotherapy administration. A simple and ultra-fast (less than 30 s) method using flow injection analysis associated to least square matching method issued from the analyzer software was performed and evaluated for the routine hospital QC of three compounded mAbs: bevacizumab, infliximab and rituximab. The method was evaluated through qualitative and quantitative parameters. Preliminary analysis of the UV absorption and second derivative spectra of the mAbs allowed us to adapt analytical conditions according to the therapeutic range of the mAbs. In terms of quantitative QC, linearity, accuracy and precision were assessed as specified in ICH guidelines. Very satisfactory recovery was achieved and the RSD (%) of the intermediate precision were less than 1.1%. Qualitative analytical parameters were also evaluated in terms of specificity, sensitivity and global precision through a matrix of confusion. Results showed to be concentration and mAbs dependant and excellent (100%) specificity and sensitivity were reached within specific concentration range. Finally, routine application on "real life" samples (n = 209) from different batch of the three mAbs complied with the specifications of the quality control i.e. excellent identification (100%) and ± 15% of targeting concentration belonging to the calibration range. The successful use of the combination of second derivative spectroscopy and partial least square matching method demonstrated the interest of FIA for the ultra-fast QC of mAbs after compounding using matching method. Copyright © 2018 Elsevier B.V. All rights reserved.

Character Decomposition and Transposition Processes in Chinese Compound Words Modulates Attentional Blink.

PubMed

Cao, Hongwen; Gao, Min; Yan, Hongmei

2016-01-01

The attentional blink (AB) is the phenomenon in which the identification of the second of two targets (T2) is attenuated if it is presented less than 500 ms after the first target (T1). Although the AB is eliminated in canonical word conditions, it remains unclear whether the character order in compound words affects the magnitude of the AB. Morpheme decomposition and transposition of Chinese two-character compound words can provide an effective means to examine AB priming and to assess combinations of the component representations inherent to visual word identification. In the present study, we examined the processing of consecutive targets in a rapid serial visual presentation (RSVP) paradigm using Chinese two-character compound words in which the two characters were transposed to form meaningful words or meaningless combinations (reversible, transposed, or canonical words). We found that when two Chinese characters that form a compound word, regardless of their order, are presented in an RSVP sequence, the likelihood of an AB for the second character is greatly reduced or eliminated compared to when the two characters constitute separate words rather than a compound word. Moreover, the order of the report for the two characters is more likely to be reversed when the normal order of the two characters in a compound word is reversed, especially when the interval between the presentation of the two characters is extremely short. These findings are more consistent with the cognitive strategy hypothesis than the resource-limited hypothesis during character decomposition and transposition of Chinese two-character compound words. These results suggest that compound characters are perceived as a unit, rather than two separate words. The data further suggest that readers could easily understand the text with character transpositions in compound words during Chinese reading.

Atomic Theory and Multiple Combining Proportions: The Search for Whole Number Ratios.

PubMed

Usselman, Melvyn C; Brown, Todd A

2015-04-01

John Dalton's atomic theory, with its postulate of compound formation through atom-to-atom combination, brought a new perspective to weight relationships in chemical reactions. A presumed one-to-one combination of atoms A and B to form a simple compound AB allowed Dalton to construct his first table of relative atomic weights from literature analyses of appropriate binary compounds. For such simple binary compounds, the atomic theory had little advantages over affinity theory as an explanation of fixed proportions by weight. For ternary compounds of the form AB2, however, atomic theory made quantitative predictions that were not deducible from affinity theory. Atomic theory required that the weight of B in the compound AB2 be exactly twice that in the compound AB. Dalton, Thomas Thomson and William Hyde Wollaston all published within a few years of each other experimental data that claimed to give the predicted results with the required accuracy. There are nonetheless several experimental barriers to obtaining the desired integral multiple proportions. In this paper I will discuss replication experiments which demonstrate that only Wollaston's results are experimentally reliable. It is likely that such replicability explains why Wollaston's experiments were so influential.

Complete Genomic Structure of the Cultivated Rice Endophyte Azospirillum sp. B510

PubMed Central

Kaneko, Takakazu; Minamisawa, Kiwamu; Isawa, Tsuyoshi; Nakatsukasa, Hiroki; Mitsui, Hisayuki; Kawaharada, Yasuyuki; Nakamura, Yasukazu; Watanabe, Akiko; Kawashima, Kumiko; Ono, Akiko; Shimizu, Yoshimi; Takahashi, Chika; Minami, Chiharu; Fujishiro, Tsunakazu; Kohara, Mitsuyo; Katoh, Midori; Nakazaki, Naomi; Nakayama, Shinobu; Yamada, Manabu; Tabata, Satoshi; Sato, Shusei

2010-01-01

We determined the nucleotide sequence of the entire genome of a diazotrophic endophyte, Azospirillum sp. B510. Strain B510 is an endophytic bacterium isolated from stems of rice plants (Oryza sativa cv. Nipponbare). The genome of B510 consisted of a single chromosome (3 311 395 bp) and six plasmids, designated as pAB510a (1 455 109 bp), pAB510b (723 779 bp), pAB510c (681 723 bp), pAB510d (628 837 bp), pAB510e (537 299 bp), and pAB510f (261 596 bp). The chromosome bears 2893 potential protein-encoding genes, two sets of rRNA gene clusters (rrns), and 45 tRNA genes representing 37 tRNA species. The genomes of the six plasmids contained a total of 3416 protein-encoding genes, seven sets of rrns, and 34 tRNAs representing 19 tRNA species. Eight genes for plasmid-specific tRNA species are located on either pAB510a or pAB510d. Two out of eight genomic islands are inserted in the plasmids, pAB510b and pAB510e, and one of the islands is inserted into trnfM-CAU in the rrn located on pAB510e. Genes other than the nif gene cluster that are involved in N2 fixation and are homologues of Bradyrhizobium japonicum USDA110 include fixABCX, fixNOQP, fixHIS, fixG, and fixLJK. Three putative plant hormone-related genes encoding tryptophan 2-monooxytenase (iaaM) and indole-3-acetaldehyde hydrolase (iaaH), which are involved in IAA biosynthesis, and ACC deaminase (acdS), which reduces ethylene levels, were identified. Multiple gene-clusters for tripartite ATP-independent periplasmic-transport systems and a diverse set of malic enzymes were identified, suggesting that B510 utilizes C4-dicarboxylate during its symbiotic relationship with the host plant. PMID:20047946

Composition design for Laves phase-related body-centered cubic-V solid solution alloys with large hydrogen storage capacities.

PubMed

Wang, H B; Wang, Q; Dong, C; Yuan, L; Xu, F; Sun, L X

2008-03-19

This paper analyzes the characteristics of alloy compositions with large hydrogen storage capacities in Laves phase-related body-centered cubic (bcc) solid solution alloy systems using the cluster line approach. Since a dense-packed icosahedral cluster A(6)B(7) characterizes the local structure of AB(2) Laves phases, in an A-B-C ternary system, such as Ti-Cr (Mn, Fe)-V, where A-B forms AB(2) Laves phases while A-C and B-C tend to form solid solutions, a cluster line A(6)B(7)-C is constructed by linking A(6)B(7) to C. The alloy compositions with large hydrogen storage capacities are generally located near this line and are approximately expressed with the cluster-plus-glue-atom model. The cluster line alloys (Ti(6)Cr(7))(100-x)V(x) (x = 2.5-70 at.%) exhibit different structures and hence different hydrogen storage capacities with increasing V content. The alloys (Ti(6)Cr(7))(95)V(5) and Ti(30)Cr(40)V(30) with bcc solid solution structure satisfy the cluster-plus-glue-atom model.

Black soybean promotes the formation of active components with antihepatoma activity in the fermentation product of Agaricus blazei.

PubMed

Su, Zheng-Yuan; Hwang, Lucy Sun; Kuo, Yueh-Hsiung; Shu, Chin-Hang; Sheen, Lee-Yan

2008-10-22

The antihepatoma activity and related active components in the fermentation products of Agaricus blazei (AB) cultured in the medium containing soybean (S) or black soybean (BS) were investigated. AB(BS)-pE and AB(S)-pE were the ethanolic extracts from the fermentation products of AB(BS) and AB(S), respectively. According to the IC 50 values, AB(BS)-pE (161.1 and 24.0 microg/mL for Hep 3B and Hep G2 cells, respectively) exhibited stronger cytotoxicities against hepatoma cells than AB(S)-pE (>200 and 99.9 microg/mL for Hep 3B and Hep G2 cells, respectively). AB(BS)-pE was separated by silica gel column chromatography and eluted with n-hexane/ethyl acetate/methanol gradient solvent system into 21 fractions. Fraction 3 [AB(BS)-pE-F3], eluted with n-hexane/ethyl acetate (97:3 and 19:1, v/v), was the most active fraction having inhibitory activity on the proliferation of Hep 3B and Hep G2 cells (IC 50 of 3.6 and 1.9 microg/mL, respectively). Three major compounds, compounds 1- 3, were further isolated from the AB(BS)-pE-F3 fraction by reversed-phase semipreparative high-performance liquid chromatography. Compounds 2 and 3 gave better antihepatoma activity than that of compound 1. The IC 50 values of compounds 2 and 3 were 2.8 and 4.5 microg/mL for Hep 3B cells and 1.4 and 2.0 microg/mL for Hep G2 cells, respectively. The structures of compounds 2 and 3 were identified by UV, IR, electron impact mass spectrometry, and (1)H and (13)C NMR to be blazeispirols A and C, respectively. Blazeispirols A and C existed in the mycelia but not in the broth and were more in AB(BS)-pE (49.9 +/- 8.9 and 14.2 +/- 2.4 mg/g, respectively) than AB(S)-pE (15.9 +/- 1.7 and 3.9 +/- 0.6 mg/g, respectively). Additionally, the result shows that the production of blazeispirols A and C was increased after cultivation in the medium containing black soybean on day 6 and reached the maximum on day 12, and the contents of blazeispirols A and C were negatively correlated with Hep 3B and Hep G2 cell viabilities ( r = -0.84 to -0.93, P < 0.01). It suggests that blazeispirols A and C could be used as biomarkers to produce the fermentation product of A. blazei with antihepatoma activity.

Insights into water-mediated ion clustering in aqueous CaSO4 solutions: pre-nucleation cluster characteristics studied by ab initio calculations and molecular dynamics simulations.

PubMed

Li, Hui-Ji; Yan, Dan; Cai, Hou-Qin; Yi, Hai-Bo; Min, Xiao-Bo; Xia, Fei-Fei

2017-05-10

The molecular structure of growth units building crystals is a fundamental issue in the crystallization processes from aqueous solutions. In this work, a systematic investigation of pre-nucleation clusters and their hydration characteristics in aqueous CaSO 4 solutions was performed using ab initio calculations and molecular dynamics (MD) simulations. The results of ab initio calculations and MD simulations indicate that the dominant species in aqueous CaSO 4 solutions are monodentate ion-associated structures. Compared with charged ion clusters, neutral clusters are more likely to be present in an aqueous CaSO 4 solution. Neutral (CaSO 4 ) m clusters are probably the growth units involved in the pre-nucleation or crystallization processes. Meanwhile, hydration behavior around ion associated species in aqueous CaSO 4 solutions plays an important role in related phase/polymorphism selections. Upon ion clustering, the residence of some water molecules around Ca 2+ in ion-associated species is weakened while that of some bridging waters is enhanced due to dual interaction by Ca 2+ and SO 4 2- . Some phase/polymorphism selections can be achieved in aqueous CaSO 4 solutions by controlling the hydration around pre-nucleation clusters. Moreover, the association trend between calcium and sulfate is found to be relatively strong, which hints at the low solubility of calcium sulfate in water.

Three-cluster dynamics within an ab initio framework

DOE PAGES

Quaglioni, Sofia; Romero-Redondo, Carolina; Navratil, Petr

2013-09-26

In this study, we introduce a fully antisymmetrized treatment of three-cluster dynamics within the ab initio framework of the no-core shell model/resonating-group method. Energy-independent nonlocal interactions among the three nuclear fragments are obtained from realistic nucleon-nucleon interactions and consistent ab initio many-body wave functions of the clusters. The three-cluster Schrödinger equation is solved with bound-state boundary conditions by means of the hyperspherical-harmonic method on a Lagrange mesh. We discuss the formalism in detail and give algebraic expressions for systems of two single nucleons plus a nucleus. Using a soft similarity-renormalization-group evolved chiral nucleon-nucleon potential, we apply the method to amore » 4He+n+n description of 6He and compare the results to experiment and to a six-body diagonalization of the Hamiltonian performed within the harmonic-oscillator expansions of the no-core shell model. Differences between the two calculations provide a measure of core ( 4He) polarization effects.« less

Ab initio and empirical energy landscapes of (MgF2)n clusters (n = 3, 4).

PubMed

Neelamraju, S; Schön, J C; Doll, K; Jansen, M

2012-01-21

We explore the energy landscape of (MgF(2))(3) on both the empirical and ab initio level using the threshold algorithm. In order to determine the energy landscape and the dynamics of the trimer we investigate not only the stable isomers but also the barriers separating these isomers. Furthermore, we study the probability flows in order to estimate the stability of all the isomers found. We find that there is reasonable qualitative agreement between the ab initio and empirical potential, and important features such as sub-basins and energetic barriers follow similar trends. However, we observe that the energies are systematically different for the less compact clusters, when comparing empirical and ab initio energies. Since the underlying motivation of this work is to identify the possible clusters present in the gas phase during a low-temperature atom beam deposition synthesis of MgF(2), we employ the same procedure to additionally investigate the energy landscape of the tetramer. For this case, however, we use only the empirical potential.

Quantum wavepacket ab initio molecular dynamics: an approach for computing dynamically averaged vibrational spectra including critical nuclear quantum effects.

PubMed

Sumner, Isaiah; Iyengar, Srinivasan S

2007-10-18

We have introduced a computational methodology to study vibrational spectroscopy in clusters inclusive of critical nuclear quantum effects. This approach is based on the recently developed quantum wavepacket ab initio molecular dynamics method that combines quantum wavepacket dynamics with ab initio molecular dynamics. The computational efficiency of the dynamical procedure is drastically improved (by several orders of magnitude) through the utilization of wavelet-based techniques combined with the previously introduced time-dependent deterministic sampling procedure measure to achieve stable, picosecond length, quantum-classical dynamics of electrons and nuclei in clusters. The dynamical information is employed to construct a novel cumulative flux/velocity correlation function, where the wavepacket flux from the quantized particle is combined with classical nuclear velocities to obtain the vibrational density of states. The approach is demonstrated by computing the vibrational density of states of [Cl-H-Cl]-, inclusive of critical quantum nuclear effects, and our results are in good agreement with experiment. A general hierarchical procedure is also provided, based on electronic structure harmonic frequencies, classical ab initio molecular dynamics, computation of nuclear quantum-mechanical eigenstates, and employing quantum wavepacket ab initio dynamics to understand vibrational spectroscopy in hydrogen-bonded clusters that display large degrees of anharmonicities.

Single-Cell Genome and Group-Specific dsrAB Sequencing Implicate Marine Members of the Class Dehalococcoidia (Phylum Chloroflexi) in Sulfur Cycling

PubMed Central

Cooper, Myriel; Schreiber, Lars; Lloyd, Karen G.; Baker, Brett J.; Petersen, Dorthe G.; Jørgensen, Bo Barker; Stepanauskas, Ramunas; Reinhardt, Richard; Schramm, Andreas; Loy, Alexander; Adrian, Lorenz

2016-01-01

ABSTRACT The marine subsurface sediment biosphere is widely inhabited by bacteria affiliated with the class Dehalococcoidia (DEH), phylum Chloroflexi, and yet little is known regarding their metabolisms. In this report, genomic content from a single DEH cell (DEH-C11) with a 16S rRNA gene that was affiliated with a diverse cluster of 16S rRNA gene sequences prevalent in marine sediments was obtained from sediments of Aarhus Bay, Denmark. The distinctive gene content of this cell suggests metabolic characteristics that differ from those of known DEH and Chloroflexi. The presence of genes encoding dissimilatory sulfite reductase (Dsr) suggests that DEH could respire oxidized sulfur compounds, although Chloroflexi have never been implicated in this mode of sulfur cycling. Using long-range PCR assays targeting DEH dsr loci, dsrAB genes were amplified and sequenced from various marine sediments. Many of the amplified dsrAB sequences were affiliated with the DEH Dsr clade, which we propose equates to a family-level clade. This provides supporting evidence for the potential for sulfite reduction by diverse DEH species. DEH-C11 also harbored genes encoding reductases for arsenate, dimethyl sulfoxide, and halogenated organics. The reductive dehalogenase homolog (RdhA) forms a monophyletic clade along with RdhA sequences from various DEH-derived contigs retrieved from available metagenomes. Multiple facts indicate that this RdhA may not be a terminal reductase. The presence of other genes indicated that nutrients and energy may be derived from the oxidation of substituted homocyclic and heterocyclic aromatic compounds. Together, these results suggest that marine DEH play a previously unrecognized role in sulfur cycling and reveal the potential for expanded catabolic and respiratory functions among subsurface DEH. PMID:27143384

Biological activity and molecular docking studies of curcumin-related α,β-unsaturated carbonyl-based synthetic compounds as anticancer agents and mushroom tyrosinase inhibitors.

PubMed

Bukhari, Syed Nasir Abbas; Jantan, Ibrahim; Unsal Tan, Oya; Sher, Muhammad; Naeem-Ul-Hassan, M; Qin, Hua-Li

2014-06-18

Hyperpigmentation in human skin and enzymatic browning in fruits, which are caused by tyrosinase enzyme, are not desirable. Investigations in the discovery of tyrosinase enzyme inhibitors and search for improved cytotoxic agents continue to be an important line in drug discovery and development. In present work, a new series of 30 compounds bearing α,β-unsaturated carbonyl moiety was designed and synthesized following curcumin as model. All compounds were evaluated for their effects on human cancer cell lines and mushroom tyrosinase enzyme. Moreover, the structure-activity relationships of these compounds are also explained. Molecular modeling studies of these new compounds were carried out to explore interactions with tyrosinase enzyme. Synthetic curcumin-like compounds (2a-b) were identified as potent anticancer agents with 81-82% cytotoxicity. Five of these newly synthesized compounds (1a, 8a-b, 10a-b) emerged to be the potent inhibitors of mushroom tyrosinase, providing further insight into designing compounds useful in fields of food, health, and agriculture.

Ab Initio Molecular Dynamics Studies of Pb m Sb n ( m + n ≤ 9) Alloy Clusters

NASA Astrophysics Data System (ADS)

Song, Bingyi; Xu, Baoqiang; Yang, Bin; Jiang, Wenlong; Chen, Xiumin; Xu, Na; Liu, Dachun; Dai, Yongnian

2017-10-01

Structure, stability, and dynamics of Pb m Sb n ( m + n ≤ 9) clusters were investigated using ab initio molecular dynamics. Size dependence of binding energies, the second-order energy difference of clusters, dissociation energy, HOMO-LUMO gaps, Mayer bond order, and the diffusion coefficient of Pb m Sb n clusters were discussed. Results suggest that Pb3Sb2, Pb4Sb2, and Pb5Sb4 ( n = 2 or 4) clusters have higher stability than other clusters, which is consistent with previous findings. In case of Pb-Sb alloy, the dynamics results show that Pb4Sb2 (Pb-22.71 wt pct Sb) can exist in gas phase at 1073 K (800 °C), which reasonably explains the azeotropic phenomenon, and the calculated values are in agreement with the experimental results (Pb-22 wt pct Sb).

JBIR-23 and -24, novel anticancer agents from Streptomyces sp. AK-AB27.

PubMed

Motohashi, Keiichiro; Hwang, Ji-Hwan; Sekido, Yoshitaka; Takagi, Motoki; Shin-ya, Kazuo

2009-01-15

The screening for active compounds against malignant pleural mesothelioma (MPM) cells produced by Streptomyces sp. AK-AB27 resulted in the isolation of two compounds with a dodecahydrodibenzo[b,d]furan skeleton named JBIR-23 (1) and -24 (2). Their structures were established on the basis of extensive NMR and MS analyses. Compounds 1 and 2 exhibited cytotoxic effects against several MPM cell lines.

Molecular evolution of the HoxA cluster in the three major gnathostome lineages

PubMed Central

Chiu, Chi-hua; Amemiya, Chris; Dewar, Ken; Kim, Chang-Bae; Ruddle, Frank H.; Wagner, Günter P.

2002-01-01

The duplication of Hox clusters and their maintenance in a lineage has a prominent but little understood role in chordate evolution. Here we examined how Hox cluster duplication may influence changes in cluster architecture and patterns of noncoding sequence evolution. We sequenced the entire duplicated HoxAa and HoxAb clusters of zebrafish (Danio rerio) and extended the 5′ (posterior) part of the HoxM (HoxA-like) cluster of horn shark (Heterodontus francisci) containing the hoxa11 and hoxa13 orthologs as well as intergenic and flanking noncoding sequences. The duplicated HoxA clusters in zebrafish each house considerably fewer genes and are dramatically shorter than the single HoxA clusters of human and horn shark. We compared the intergenic sequences of the HoxA clusters of human, horn shark, zebrafish (Aa, Ab), and striped bass and found extensive conservation of noncoding sequence motifs, i.e., phylogenetic footprints, between the human and horn shark, representing two of the three gnathostome lineages. These are putative cis-regulatory elements that may play a role in the regulation of the ancestral HoxA cluster. In contrast, homologous regions of the duplicated HoxAa and HoxAb clusters of zebrafish and the HoxA cluster of striped bass revealed a striking loss of conservation of these putative cis-regulatory sequences in the 3′ (anterior) segment of the cluster, where zebrafish only retains single representatives of group 1, 3, 4, and 5 (HoxAa) and group 2 (HoxAb) genes and in the 5′ part of the clusters, where zebrafish retains two copies of the group 13, 11, and 9 genes, i.e., AbdB-like genes. In analyzing patterns of cis-sequence evolution in the 5′ part of the clusters, we explicitly looked for evidence of complementary loss of conserved noncoding sequences, as predicted by the duplication-degeneration-complementation model in which genetic redundancy after gene duplication is resolved because of the fixation of complementary degenerative mutations. Our data did not yield evidence supporting this prediction. We conclude that changes in the pattern of cis-sequence conservation after Hox cluster duplication are more consistent with being the outcome of adaptive modification rather than passive mechanisms that erode redundancy created by the duplication event. These results support the view that genome duplications may provide a mechanism whereby master control genes undergo radical modifications conducive to major alterations in body plan. Such genomic revolutions may contribute significantly to the evolutionary process. PMID:11943847

Anisotropy of atomic bonds formed by p-type dopants in bulk GaN crystals

NASA Astrophysics Data System (ADS)

Lawniczak-Jablonska, K.; Suski, T.; Gorczyca, I.; Christensen, N. E.; Libera, J.; Kachniarz, J.; Lagarde, P.; Cortes, R.; Grzegory, I.

The anisotropy of atomic bonds formed by acceptor dopants with nitrogen in bulk wurtzite GaN crystals was studied by means of linearly polarized synchrotron radiation used in measurements of X-ray-absorption spectra for the K-edgeof Mg and Zn dopants. These spectra correspond to i) a single acceptor N bond along the c-axis and ii) three bonds realized with N atoms occupying the ab-plane perpendicular to the c-axis. The Zn dopant formed resonant spectra similar to that characteristic for Ga cations. In the case of the Mg dopant, similarity to Ga cations was observed for triple bonds in the ab-plane, only. Practically no resonant structure for spectra detected along the c-axis was observed. The absorption spectra were compared with ab initio calculations using the full-potential linear muffin-tin-orbital method. These calculations were also used for determination of the bond length for Mg-N and Zn-N in wurtzite GaN crystals and show that introducing dopants causes an increase of the lengths of the bonds formed by both dopants. Extended X-ray-absorption fine-structure measurements performed for bulk GaN:Zn confirmed the prediction of the theory in the case of the Zn-N bond. Finally, it is suggested that the anisotropy in the length of the Mg-N bonds, related to their larger strength in the case of bonds in the ab-plane, can explain preferential formation of a superlattice consisting of Mg-rich layers arranged in ab-planes of several bulk GaN:Mg crystals observed by transmission electron microscopy. Within the sensitivity of the method used, no parasitic metallic clusters or oxide compounds formed by the considered acceptors in GaN crystals were found.

Arsenic speciation in edible mushrooms.

PubMed

Nearing, Michelle M; Koch, Iris; Reimer, Kenneth J

2014-12-16

The fruiting bodies, or mushrooms, of terrestrial fungi have been found to contain a high proportion of the nontoxic arsenic compound arsenobetaine (AB), but data gaps include a limited phylogenetic diversity of the fungi for which arsenic speciation is available, a focus on mushrooms with higher total arsenic concentrations, and the unknown formation and role of AB in mushrooms. To address these, the mushrooms of 46 different fungus species (73 samples) over a diverse range of phylogenetic groups were collected from Canadian grocery stores and background and arsenic-contaminated areas. Total arsenic was determined using ICP-MS, and arsenic speciation was determined using HPLC-ICP-MS and complementary X-ray absorption spectroscopy (XAS). The major arsenic compounds in mushrooms were found to be similar among phylogenetic groups, and AB was found to be the major compound in the Lycoperdaceae and Agaricaceae families but generally absent in log-growing mushrooms, suggesting the microbial community may influence arsenic speciation in mushrooms. The high proportion of AB in mushrooms with puffball or gilled morphologies may suggest that AB acts as an osmolyte in certain mushrooms to help maintain fruiting body structure. The presence of an As(III)-sulfur compound, for the first time in mushrooms, was identified in the XAS analysis. Except for Agaricus sp. (with predominantly AB), inorganic arsenic predominated in most of the store-bought mushrooms (albeit with low total arsenic concentrations). Should inorganic arsenic predominate in these mushrooms from contaminated areas, the risk to consumers under these circumstances should be considered.

Movement and fate of detergents in groundwater: a field study

USGS Publications Warehouse

Thurman, E.M.; Barber, L.B.; LeBlanc, D.

1986-01-01

The major cations, anions, and detergents in a plume of contaminated groundwater at Otis Air Base on Cape Cod (Mass., U.S.A.) have moved approximately 3.5 km down gradient from the disposal beds. We hypothesize that the detergents form two distinct plumes, which consist of alkyl benzene sulfonates (ABS) detergents and linear alkyl sulfonates (LAS) and sodium dodecyl sulfate (NaLS) detergents. The ABS detergents were deposited from approximately 1940 through 1965, when ABS detergents were banned. From 1965 to the present, LAS and NaLS detergents were in the sewage. The ABS detergents appear to be transported in the aquifer at the same rate as the specific conductance (major cations and anions) and boron, which are currently used as conservative tracers of the plume of contaminated groundwater. There appears to be little or no biological degradation of the ABS detergents in the aquifer, based on their concentration in the plume. On the other hand, the LAS and NaLS detergents have degraded rapidly and have been detected only 0.6 km down gradient. The roleof the detergents in the transport of other organic compounds in the plume is nuclear. There is a separation of the ABS detergent plume and the volatile organic compound plume; however, the time of entry of the detergents and the volatile organic compounds is unknown. Therefore, it is not possible to conclude on the interaction of these two classes of compounds. ?? 1986.

Analysis of cytokine release assay data using machine learning approaches.

PubMed

Xiong, Feiyu; Janko, Marco; Walker, Mindi; Makropoulos, Dorie; Weinstock, Daniel; Kam, Moshe; Hrebien, Leonid

2014-10-01

The possible onset of Cytokine Release Syndrome (CRS) is an important consideration in the development of monoclonal antibody (mAb) therapeutics. In this study, several machine learning approaches are used to analyze CRS data. The analyzed data come from a human blood in vitro assay which was used to assess the potential of mAb-based therapeutics to produce cytokine release similar to that induced by Anti-CD28 superagonistic (Anti-CD28 SA) mAbs. The data contain 7 mAbs and two negative controls, a total of 423 samples coming from 44 donors. Three (3) machine learning approaches were applied in combination to observations obtained from that assay, namely (i) Hierarchical Cluster Analysis (HCA); (ii) Principal Component Analysis (PCA) followed by K-means clustering; and (iii) Decision Tree Classification (DTC). All three approaches were able to identify the treatment that caused the most severe cytokine response. HCA was able to provide information about the expected number of clusters in the data. PCA coupled with K-means clustering allowed classification of treatments sample by sample, and visualizing clusters of treatments. DTC models showed the relative importance of various cytokines such as IFN-γ, TNF-α and IL-10 to CRS. The use of these approaches in tandem provides better selection of parameters for one method based on outcomes from another, and an overall improved analysis of the data through complementary approaches. Moreover, the DTC analysis showed in addition that IL-17 may be correlated with CRS reactions, although this correlation has not yet been corroborated in the literature. Copyright © 2014 Elsevier B.V. All rights reserved.

Ab Initio Study of KCl and AgCl Clusters.

NASA Astrophysics Data System (ADS)

McKeough, James; Hira, Ajit; Cathey, Tommy; Valdez, Alexandra

This paper presents a theoretical study of molecular clusters that examines the chemical and physical properties of small KnCln and AgnCln clusters (n = 2 - 24). Due to combinations of attractive and repulsive long-range forces, such clusters exhibit structural and dynamical behavior different from that of homogeneous clusters. The potentially important role of these molecular species in biochemical and medicinal processes is widely known. This work applies the hybrid ab initio methods to derive the different alkali-halide (MnHn) geometries. Of particular interest is the competition between hexagonal ring geometries and rock salt structures. Electronic energies, rotational constants, dipole moments, and vibrational frequencies for these geometries are calculated. Magic numbers for cluster stability are identified and are related to the property of cluster compactness. Mapping of the singlet, triplet, and quintet, potential energy surfaces is performed. Calculations were performed to examine the interactions of these clusters with some atoms and molecules of biological interest, including O, O2, and Fe. Potential design of new medicinal drugs is explored. We will also investigate model and material dependence of the results. AMP program of the National Science Foundation.

Past Experience Influences the Processing of Stimulus Compounds in Human Pavlovian Conditioning

ERIC Educational Resources Information Center

Melchers, Klaus G.; Lachnit, Harold; Shanks, David R.

2004-01-01

In two human skin conductance conditioning experiments we investigated whether processing of stimulus compounds can be influenced by past experience. Participants were either pre-trained with a discrimination problem that could be solved elementally (A+, B-, AB+, C- in Experiment 1 and A+, AB+, C-, CB- in Experiment 2) or one that required a…

Discovery of Intermetallic Compounds from Traditional to Machine-Learning Approaches.

PubMed

Oliynyk, Anton O; Mar, Arthur

2018-01-16

Intermetallic compounds are bestowed by diverse compositions, complex structures, and useful properties for many materials applications. How metallic elements react to form these compounds and what structures they adopt remain challenging questions that defy predictability. Traditional approaches offer some rational strategies to prepare specific classes of intermetallics, such as targeting members within a modular homologous series, manipulating building blocks to assemble new structures, and filling interstitial sites to create stuffed variants. Because these strategies rely on precedent, they cannot foresee surprising results, by definition. Exploratory synthesis, whether through systematic phase diagram investigations or serendipity, is still essential for expanding our knowledge base. Eventually, the relationships may become too complex for the pattern recognition skills to be reliably or practically performed by humans. Complementing these traditional approaches, new machine-learning approaches may be a viable alternative for materials discovery, not only among intermetallics but also more generally to other chemical compounds. In this Account, we survey our own efforts to discover new intermetallic compounds, encompassing gallides, germanides, phosphides, arsenides, and others. We apply various machine-learning methods (such as support vector machine and random forest algorithms) to confront two significant questions in solid state chemistry. First, what crystal structures are adopted by a compound given an arbitrary composition? Initial efforts have focused on binary equiatomic phases AB, ternary equiatomic phases ABC, and full Heusler phases AB 2 C. Our analysis emphasizes the use of real experimental data and places special value on confirming predictions through experiment. Chemical descriptors are carefully chosen through a rigorous procedure called cluster resolution feature selection. Predictions for crystal structures are quantified by evaluating probabilities. Major results include the discovery of RhCd, the first new binary AB compound to be found in over 15 years, with a CsCl-type structure; the connection between "ambiguous" prediction probabilities and the phenomenon of polymorphism, as illustrated in the case of TiFeP (with TiNiSi- and ZrNiAl-type structures); and the preparation of new predicted Heusler phases MRu 2 Ga and RuM 2 Ga (M = first-row transition metal) that are not obvious candidates. Second, how can the search for materials with desired properties be accelerated? One particular application of strong current interest is thermoelectric materials, which present a particular challenge because their optimum performance depends on achieving a balance of many interrelated physical properties. Making use of a recommendation engine developed by Citrine Informatics, we have identified new candidates for thermoelectric materials, including previously unknown compounds (e.g., TiRu 2 Ga with Heusler structure; Mn(Ru 0.4 Ge 0.6 ) with CsCl-type structure) and previously reported compounds but counterintuitive candidates (e.g., Gd 12 Co 5 Bi). An important lesson in these investigations is that the machine-learning models are only as good as the experimental data used to develop them. Thus, experimental work will continue to be necessary to improve the predictions made by machine learning.

Validation of an automated method for compounding monoclonal antibody patient doses

PubMed Central

Peters, Bas J.M.; Capelle, Martinus A.H.; Arvinte, Tudor; van de Garde, Ewoudt M.W.

2013-01-01

Automation robots have recently come to the market as an alternative for manual compounding of drugs for intravenous administration. Our aim was to assess whether robotic compounding can be performed with monoclonal antibodies (mAbs) without influencing the aggregation state of the proteins. Three frequently used mAbs were studied: infliximab (Remicade®, Janssen Biotech) and trastuzumab (Herceptin®, Roche) in lyophilised form, and bevacizumab (Avastin®, Roche) as a liquid formulation stored at 2°C to 8°C. The effects of different procedures to prepare the patient doses on antibody aggregation were evaluated. Remicade® and Herceptin® were reconstituted both manually and by a robotic arm (i.v.STATION®, Health Robotics). Additionally, the influence of vigorous shaking during reconstitution was investigated. The effects of rapid aspiration and dispensing on antibody aggregation were investigated for all three mAbs. Aggregation state was assessed by UV-Vis absorbance, 90° light scatter, fluorescence spectroscopy, Nile red fluorescence microscopy, and field flow fractionation without cross and focus flow. Robotic reconstituted samples showed similar findings compared with manual reconstitution if performed exactly according to the summary of product characteristics (SPC). Vials that were vigorously shaken showed a significant increase in aggregates. Similarly, rapid aspiration/dispense cycles resulted in a strong increase in the number and sizes of aggregates for all three mAbs; this result was observed after just one rapid aspiration/dispense cycle. Our study showed that robotic compounding of mAbs is feasible if the robot is exactly programmed according to the SPC, indicating that robotic compounding can be used to achieve reproducible high-quality compounding for delicate formulations. PMID:23255057

The individual and cumulative effect of brominated flame retardant and polyvinylchloride (PVC) on thermal degradation of acrylonitrile-butadiene-styrene (ABS) copolymer.

PubMed

Brebu, Mihai; Bhaskar, Thallada; Murai, Kazuya; Muto, Akinori; Sakata, Yusaku; Uddin, Md Azhar

2004-08-01

Acrylonitrile-butadiene-styrene (ABS) copolymers without and with a polybrominated epoxy type flame retardant were thermally degraded at 450 degrees C alone (10 g) and mixed with polyvinylchloride (PVC) (8 g/2 g). Gaseous and liquid products of degradation were analysed by various gas chromatographic methods (GC with TCD, FID, AED, MSD) in order to determine the individual and cumulative effect of bromine and chlorine on the quality and quantity of degradation compounds. It was found that nitrogen, chlorine, bromine and oxygen are present as organic compounds in liquid products, their quantity depends on the pyrolysed polymer or polymer mixture. Bromophenol and dibromophenols were the main brominated compounds that come from the flame retardant. 1-Chloroethylbenzene was the main chlorine compound observed in liquid products. It was also determined that interactions appear at high temperatures during decomposition between the flame retardant, PVC and the ABS copolymer.

Analysis of monoclonal antibodies reactive with molecules upregulated or expressed only on activated lymphocytes.

PubMed

Davis, W C; Naessens, J; Brown, W C; Ellis, J A; Hamilton, M J; Cantor, G H; Barbosa, J I; Ferens, W; Bohach, G A

1996-08-01

Monoclonal antibodies potentially specific for antigens expressed or upregulated on activated leukocytes were selected for further analysis from the panel submitted to the third international workshop on ruminant leukocyte antigens. The kinetics of expression of these activation antigens on resting peripheral mononuclear cells (PBMC) and PBMC stimulated with concanavalin A or staphylococcal superantigen SECI for 4, 24 or 96 h were compared, as well as their appearance on various subsets of cells. For some of them, a molecular mass could be determined after immunoprecipitation from radio-labeled, lectin-stimulated cells. Based on the results from the clustering, kinetic studies and biochemical data, evidence was gathered for assigning two additional mAbs to cluster BoCD25 (IL-2 receptor) and two mAbs to cluster BoCD71 (transferrin receptor). Four mAbs recognized an early activation antigen predominantly expressed on gamma delta T cells in short-term cultures. A number of other activation antigens were further characterized.

Ab initio study of the structural properties of acetonitrile-water mixtures

NASA Astrophysics Data System (ADS)

Chen, Jinfan; Sit, Patrick H.-L.

2015-08-01

Structural properties of acetonitrile and acetonitrile-water mixtures are studied using Density Functional Theory (DFT) and ab initio molecular dynamics simulations. Stable molecular clusters consisted of several water and acetonitrile molecules are identified to provide microscopic understanding of the interaction among water and acetonitrile molecules. Ab initio molecular dynamics simulations are performed to study the liquid structure at the finite temperature. Three mixing compositions in which the mole fraction of acetonitrile equals 0.109, 0.5 and 0.891 are studied. These compositions correspond to three distinct structural regimes. At the 0.109 and 0.891 mole fraction of acetonitrile, the majority species are mostly connected among themselves and the minority species are either isolated or forming small clusters without disrupting the network of the majority species. At the 0.5 mole fraction of acetonitrile, large water and acetonitrile clusters persist throughout the simulation, exhibiting the microheterogeneous behavior in acetonitrile-water mixtures in the mid-range mixing ratio.

Fourfold Clusters of Rovibrational Energies in H2Te Studied With an Ab Initio Potential Energy Function

NASA Technical Reports Server (NTRS)

Jensen, Per; Li, Yan; Hirsch, Gerhard; Buenker, Robert J.; Lee, Timothy J.; Arnold, James O. (Technical Monitor)

1994-01-01

We report an ab initio investigation of the cluster effect (i.e., the formation of nearly degenerate, four member groups of rotation-vibration energy levels at higher J and K(sub a). values) in the H2Te molecule. The potential energy function has been calculated ab initio at a total of 334 molecular geometries by means of the CCSD(T) method where the (1s-4f) core electrons of Te were described by an effective core potential. The values of the potential energy function obtained cover the region up to around 10,000/cm above the equilibrium energy. On the basis of the ab initio potential, the rotation-vibration energy spectra of H2Te-130 and its deuterated isotopomers have been calculated with the MORBID (Morse Oscillator Rigid Bender Internal Dynamics) Hamiltonian and computer program. In particular, we have calculated the rotational energy manifolds for J less than or = 40 in the vibrational ground state, the upsilon(sub 2) state, the "first triad" (the upsilon(sub l)/upsilon(sub 3)/2upsilon(sub 2) interacting vibrational states), and the "second triad" (the upsilon(sub 1) + upsilon(sub 2/upsilon(sub 2) + upsilon(sub 3)/3upsilon(sub 2) states) of H2Te-130. We find that the cluster formation in H2Te is very similar to those of of H2Se and H2S, which we have studied previously. However, contrary to semiclassical predictions, we do not determine any significant displacement of the clusters towards lower J values relative to H2Se. Hence the experimental observation of the cluster states in H2Te will be at least as difficult as in H2Se.

Ab initio calculations of optical properties of silver clusters: cross-over from molecular to nanoscale behavior

NASA Astrophysics Data System (ADS)

Titantah, John T.; Karttunen, Mikko

2016-05-01

Electronic and optical properties of silver clusters were calculated using two different ab initio approaches: (1) based on all-electron full-potential linearized-augmented plane-wave method and (2) local basis function pseudopotential approach. Agreement is found between the two methods for small and intermediate sized clusters for which the former method is limited due to its all-electron formulation. The latter, due to non-periodic boundary conditions, is the more natural approach to simulate small clusters. The effect of cluster size is then explored using the local basis function approach. We find that as the cluster size increases, the electronic structure undergoes a transition from molecular behavior to nanoparticle behavior at a cluster size of 140 atoms (diameter ~1.7 nm). Above this cluster size the step-like electronic structure, evident as several features in the imaginary part of the polarizability of all clusters smaller than Ag147, gives way to a dominant plasmon peak localized at wavelengths 350 nm ≤ λ ≤ 600 nm. It is, thus, at this length-scale that the conduction electrons' collective oscillations that are responsible for plasmonic resonances begin to dominate the opto-electronic properties of silver nanoclusters.

Speciation of Mg in biogenic calcium carbonates

NASA Astrophysics Data System (ADS)

Farges, F.; Meibom, A.; Flank, A.-M.; Lagarde, P.; Janousch, M.; Stolarski, J.

2009-11-01

A selection of marine biominerals, mostly aragonitic coral skeletons were probed at the Mg K-edge by XANES spectroscopy coupled to μXRF methods and compared to an extensive set of relevant model compounds (silicates, carbonates, oxides and organic). Extensive methodologies are required to better describe the speciation of Mg in those minerals. A combination of ab-initio XANES calculations for defective clusters around Mg in aragonite together with wavelets analyzes of the XANES region are required to robustly interpret the spectra. When using those methodologies, the speciation of Mg ranges from a magnesite-type environment in some scleractinian corals to an organic-type environment. In all environments, the Mg-domains probed appear to be less than 1 nm in size.

Electronic structure of the alkyne-bridged dicobalt hexacarbonyl complex Co(2) micro-C(2)H(2) (CO)(6): evidence for singlet diradical character and implications for metal-metal bonding.

PubMed

Platts, James A; Evans, Gareth J S; Coogan, Michael P; Overgaard, Jacob

2007-08-06

A series of ab initio calculations are presented on the alkyne-bridged dicobalt hexacarbonyl cluster Co2 micro-C2H2 (CO)6, indicating that this compound has substantial multireference character, which we interpret as evidence of singlet diradical behavior. As a result, standard theoretical methods such as restricted Hartree-Fock (RHF) or Kohn-Sham (RKS) density functional theory cannot properly describe this compound. We have therefore used complete active space (CAS) methods to explore the bonding in and spectroscopic properties of Co2 micro-C2H2 (CO)6. CAS methods identify significant population of a Co-Co antibonding orbital, along with Co-pi* back-bonding, and a relatively large singlet-triplet energy splitting. Analysis of the electron density and related quantities, such as energy densities and atomic overlaps, indicates a small but significant amount of covalent bonding between cobalt centers.

Ab initio molecular dynamics simulation of binary Cu64Zr36 bulk metallic glass: Validation of the cluster-plus-glue-atom model

NASA Astrophysics Data System (ADS)

Tian, Hua; Zhang, Chong; Wang, Lu; Zhao, JiJun; Dong, Chuang; Wen, Bin; Wang, Qing

2011-06-01

We have performed ab initio molecular dynamics simulation of Cu64Zr36 alloy at descending temperatures (from 2000 K to 400 K) and discussed the evolution of short-range order with temperature. The pair-correlation functions, coordination numbers, and chemical compositions of the most abundant local clusters have been analyzed. We found that icosahedral short-range order exists in the liquid, undercooled, and glass states, and it becomes dominant in the glass states. Moreover, we demonstrated the existence of Cu-centered Cu8Zr5 icosahedral clusters as the major local structural unit in the Cu64Zr36 amorphous alloy. This finding agrees well with our previous cluster model of Cu-Zr-based BMG as well as experimental evidences from synchrotron x ray and neutron diffraction measurements.

Ab initio study of II-(VI)2 dichalcogenides.

PubMed

Olsson, P; Vidal, J; Lincot, D

2011-10-12

The structural stabilities of the (Zn,Cd)(S,Se,Te)(2) dichalcogenides have been determined ab initio. These compounds are shown to be stable in the pyrite phase, in agreement with available experiments. Structural parameters for the ZnTe(2) pyrite semiconductor compound proposed here are presented. The opto-electronic properties of these dichalcogenide compounds have been calculated using quasiparticle GW theory. Bandgaps, band structures and effective masses are proposed as well as absorption coefficients and refraction indices. The compounds are all indirect semiconductors with very flat conduction band dispersion and high absorption coefficients. The work functions and surface properties are predicted. The Te and Se based compounds could be of interest as absorber materials in photovoltaic applications.

Inhibition of cholera toxin and other AB toxins by polyphenolic compounds

USDA-ARS?s Scientific Manuscript database

All AB-type protein toxins have intracellular targets despite an initial extracellular location. These toxins use different methods to reach the cytosol and have different effects on the target cell. Broad-spectrum inhibitors against AB toxins are therefore hard to develop because the toxins use dif...

A highly accurate ab initio potential energy surface for methane.

PubMed

Owens, Alec; Yurchenko, Sergei N; Yachmenev, Andrey; Tennyson, Jonathan; Thiel, Walter

2016-09-14

A new nine-dimensional potential energy surface (PES) for methane has been generated using state-of-the-art ab initio theory. The PES is based on explicitly correlated coupled cluster calculations with extrapolation to the complete basis set limit and incorporates a range of higher-level additive energy corrections. These include core-valence electron correlation, higher-order coupled cluster terms beyond perturbative triples, scalar relativistic effects, and the diagonal Born-Oppenheimer correction. Sub-wavenumber accuracy is achieved for the majority of experimentally known vibrational energy levels with the four fundamentals of (12)CH4 reproduced with a root-mean-square error of 0.70 cm(-1). The computed ab initio equilibrium C-H bond length is in excellent agreement with previous values despite pure rotational energies displaying minor systematic errors as J (rotational excitation) increases. It is shown that these errors can be significantly reduced by adjusting the equilibrium geometry. The PES represents the most accurate ab initio surface to date and will serve as a good starting point for empirical refinement.

Theoretical research program to study transition metal trimers and embedded clusters

NASA Technical Reports Server (NTRS)

Walch, Stephen P.

1987-01-01

The results of ab-initio calculations are reported for (1) small transition metal clusters and (2) potential energy surfaces for chemical reactions important in hydrogen combustion and high temperature air chemistry.

Intrinsically High Thermoelectric Performance in AgInSe2 n-Type Diamond-Like Compounds.

PubMed

Qiu, Pengfei; Qin, Yuting; Zhang, Qihao; Li, Ruoxi; Yang, Jiong; Song, Qingfeng; Tang, Yunshan; Bai, Shengqiang; Shi, Xun; Chen, Lidong

2018-03-01

Diamond-like compounds are a promising class of thermoelectric materials, very suitable for real applications. However, almost all high-performance diamond-like thermoelectric materials are p-type semiconductors. The lack of high-performance n-type diamond-like thermoelectric materials greatly restricts the fabrication of diamond-like material-based modules and their real applications. In this work, it is revealed that n-type AgInSe 2 diamond-like compound has intrinsically high thermoelectric performance with a figure of merit ( zT ) of 1.1 at 900 K, comparable to the best p-type diamond-like thermoelectric materials reported before. Such high zT is mainly due to the ultralow lattice thermal conductivity, which is fundamentally limited by the low-frequency Ag-Se "cluster vibrations," as confirmed by ab initio lattice dynamic calculations. Doping Cd at Ag sites significantly improves the thermoelectric performance in the low and medium temperature ranges. By using such high-performance n-type AgInSe 2 -based compounds, the diamond-like thermoelectric module has been fabricated for the first time. An output power of 0.06 W under a temperature difference of 520 K between the two ends of the module is obtained. This work opens a new window for the applications using the diamond-like thermoelectric materials.

Antibacterial Effect of Silver Diamine Fluoride on Cariogenic Organisms.

PubMed

Lou, Yali; Darvell, Brain W; Botelho, Michael G

2018-05-01

To screen the possible antimicrobial activity of a range of clinically used, silver-based compounds on cariogenic organisms: silver diamine fluoride (SDF), silver fluoride, and silver nitrate. Preliminary screening disk-diffusion susceptibility tests were conducted on Mueller-Hinton agar plates inoculated with Streptococcus mutans, Lactobacillus acidophilus, and Actinomyces naeslundii, organisms known to be cariogenic. In order to identify which component of the silver compounds was responsible for any antibacterial (AB) effect, and to provide controls, the following were also investigated at high and low concentrations: sodium fluoride, ammonium fluoride, ammonium chloride, sodium fluoride, sodium chloride, and sodium nitrate, as well as deionized water as control. A volume of 10 pL of a test solution was dispensed onto a paper disk resting on the inoculated agar surface, and the plate incubated anaerobically at 37°C for 48 hours. The zones of inhibition were then measured. Silver diamine fluoride, silver fluoride, silver nitrate, and ammonium fluoride had significant AB effect (p < 0.05) on all three test organisms, although ammonium fluoride had no effect at low concentration; the remaining other compounds had no effect. Silver ions appear to be the principal AB agent at both high and low concentration; fluoride ions only have an AB effect at high concentration, while ammonium, nitrate, chloride and sodium ions have none. The anticaries effect of topical silver solutions appears restricted to that of the silver ions. Silver compounds, such as SDF, silver fluoride, and silver nitrate have AB effect against cariogenic organisms and these may have clinical impact in arresting or preventing dental decay. Sodium fluoride did not have AB effect under the conditions tested.

Hydrogen Ordering in Hexagonal Intermetallic AB5 Type Compounds

NASA Astrophysics Data System (ADS)

Sikora, W.; Kuna, A.

2008-04-01

Intermetallic compounds AB5 type (A = rare-earth atoms, B = transition metal) are known to store reversibly large amounts of hydrogen and as that are discussed in this work. It was shown that the alloy cycling stability can be significantly improved by employing the so-called non-stoichiometric compounds AB5+x and that is why analysis of change of structure turned out to be interesting. A tendency for ordering of hydrogen atoms is one of the most intriguing problems for the unsaturated hydrides. The symmetry analysis method in the frame of the theory of space group and their representation gives opportunity to find all possible transformations of the parent structure. In this work symmetry analysis method was applied for AB5+x structure type (P6/mmm parent symmetry space group). There were investigated all possible ordering types and accompanying atom displacements in positions 1a, 2c, 3g (fully occupied in stoichiometric compounds AB5), in positions 2e, 6l (where atom B could appear in non-stoichiometric compounds) and also 4h, 6m, 6k, 12n, 12o, which could be partly occupied by hydrogen as a result of hydrides. An analysis was carried out of all possible structures of lower symmetry, following from P6/mmm for we k=(0, 0, 0). Also the way of getting the structure described by the P63mc space group with double cell along the z-axiswe k=(0, 0, 0.5), as it is suggested in the work of Latroche et al. is discussed by the symmetry analysis. The analysis was obtained by computer program MODY. The program calculates the so-called basis vectors of irreducible representations of a given symmetry group, which can be used for calculation of possible ordering modes.

The content of compound conditioning.

PubMed

Harris, Justin A; Andrew, Benjamin J; Livesey, Evan J

2012-04-01

In three experiments using Pavlovian conditioning of magazine approach, rats were trained with a compound stimulus, AB, and were concurrently trained with stimulus B on its own. The reinforcement rate of B, rB, was either 1/2, 2/3, or 2/5 of rAB. After extended training, the conditioning strength of A was assessed using probe trials in which A was presented alone. Responding during A was compared with that during AB, B, and a third stimulus, C, for which rC = rAB - rB. In each experiment, the rats' response rate during A was almost identical to that during C (and during B, when rB = 1/2rAB). This suggests that, during AB conditioning, the rats had learned about rA as being equal to [rAB - rB], and implies that the content of their learning was a linear function of r. The findings provide strong support for rate-based models of conditioning (e.g., Gallistel & Gibbon, 2000). They are also consistent with the associative account of learning defined in the Rescorla and Wagner (1972) model, but only if the learning rate during reinforcement equals that during nonreinforcement. (c) 2012 APA, all rights reserved.

Ab Initio Electronic Structure Calculation of [4Fe-3S] Cluster of Hydrogenase as Dihydrogen Dissociation/Production Catalyst

NASA Astrophysics Data System (ADS)

Kim, Jaehyun; Kang, Jiyoung; Nishigami, Hiroshi; Kino, Hiori; Tateno, Masaru

2018-03-01

Hydrogenases catalyze both the dissociation and production of dihydrogen (H2). Most hydrogenases are inactivated rapidly and reactivated slowly (in vitro), in the presence of dioxygen (O2) and H2, respectively. However, membrane-bound [NiFe] hydrogenases (MBHs) sustain their activity even together with O2, which is termed "O2 tolerance". In previous experimental analyses, an MBH was shown to include a hydroxyl ion (OH-) bound to an Fe of the super-oxidized [4Fe-3S]5+ cluster in the proximity of the [NiFe] catalytic cluster. In this study, the functional role of the OH- in the O2 tolerance was investigated by ab initio electronic structure calculation of the [4Fe-3S] proximal cluster. The analysis revealed that the OH- significantly altered the electronic structure, thereby inducing the delocalization of the lowest unoccupied molecular orbital (LUMO) toward the [NiFe] catalytic cluster, which may intermediate the electron transfer between the catalytic and proximal clusters. This can promote the O2-tolerant catalytic cycle in the hydrogenase reaction.

Analysis of Spectral-type A/B Stars in Five Open Clusters

NASA Astrophysics Data System (ADS)

Wilhelm, Ronald J.; Rafuil Islam, M.

2014-01-01

We have obtained low resolution (R = 1000) spectroscopy of N=68, spectral-type A/B stars in five nearby open star clusters using the McDonald Observatory, 2.1m telescope. The sample of blue stars in various clusters were selected to test our new technique for determining interstellar reddening and distances in areas where interstellar reddening is high. We use a Bayesian approach to find the posterior distribution for Teff, Logg and [Fe/H] from a combination of reddened, photometric colors and spectroscopic line strengths. We will present calibration results for this technique using open cluster star data with known reddening and distances. Preliminary results suggest our technique can produce both reddening and distance determinations to within 10% of cluster values. Our technique opens the possibility of determining distances for blue stars at low Galactic latitudes where extinction can be large and differential. We will also compare our stellar parameter determinations to previously reported MK spectral classifications and discuss the probability that some of our stars are not members of their reported clusters.

Ab initio study of the Coulomb interaction in NbxCo clusters: Strong on-site versus weak nonlocal screening

NASA Astrophysics Data System (ADS)

Peters, L.; Şaşıoǧlu, E.; Mertig, I.; Katsnelson, M. I.

2018-01-01

By means of ab initio calculations in conjunction with the random-phase approximation (RPA) within the full-potential linearized augmented plane wave method, we study the screening of the Coulomb interaction in NbxCo (1 ≤x ≤9 ) clusters. In addition, these results are compared with pure bcc Nb bulk. We find that for all clusters the on-site Coulomb interaction in RPA is strongly screened, whereas the intersite nonlocal Coulomb interaction is weakly screened and for some clusters it is unscreened or even antiscreened. This is in strong contrast with pure Nb bulk, where the intersite Coulomb interaction is almost completely screened. Furthermore, constrained RPA calculations reveal that the contribution of the Co 3 d → 3 d channel to the total screening of the Co 3 d electrons is small. Moreover, we find that both the on-site and intersite Coulomb interaction parameters decrease in a reasonable approximation linearly with the cluster size and for clusters having more than 20 Nb atoms a transition from 0D to 3D screening is expected to take place.

Large hydrogen-bonded pre-nucleation (HSO4-)(H2SO4)m(H2O)k and (HSO4-)(NH3)(H2SO4)m(H2O)k clusters in the earth's atmosphere.

PubMed

Herb, Jason; Xu, Yisheng; Yu, Fangqun; Nadykto, A B

2013-01-10

The importance of pre-nucleation cluster stability as the key parameter controlling nucleation of atmospheric airborne ions is well-established. In this Article, large ternary ionic (HSO(4)(-))(H(2)SO(4))(m)(NH(3))(H(2)O)(n) clusters have been studied using Density Functional Theory (DFT) and composite ab initio methods. Twenty classes of clusters have been investigated, and thermochemical properties of common atmospheric (HSO(4)(-))(H(2)SO(4))(m)(NH(3))(0)(H(2)O)(k) and (HSO(4)(-))(H(2)SO(4))(m)(NH(3))(1)(H(2)O)(n) clusters (with m, k, and n up to 3) have been obtained. A large amount of new themochemical and structural data ready-to-use for constraining kinetic nucleation models has been reported. We have performed a comprehensive thermochemical analysis of the obtained data and have investigated the impacts of ammonia and negatively charged bisulfate ion on stability of binary clusters in some detail. The comparison of theoretical predictions and experiments shows that the PW91PW91/6-311++G(3df,3pd) results are in very good agreement with both experimental data and high level ab initio CCSD(T)/CBS values and suggest that the PW91PW91/6-311++G(3df,3pd) method is a viable alternative to higher level ab initio methods in studying large pre-nucleation clusters, for which the higher level computations are prohibitively expensive. The uncertainties in both theory and experiments have been investigated, and possible ways of their reduction have been proposed.

MprAB regulates the espA operon in Mycobacterium tuberculosis and modulates ESX-1 function and host cytokine response.

PubMed

Pang, Xiuhua; Samten, Buka; Cao, Guangxiang; Wang, Xisheng; Tvinnereim, Amy R; Chen, Xiu-Lan; Howard, Susan T

2013-01-01

The ESX-1 secretion system exports the immunomodulatory protein ESAT-6 and other proteins important in the pathogenesis of Mycobacterium tuberculosis. Components and substrates of ESX-1 are encoded at several loci, but the regulation of the encoding genes is only partially understood. In this study, we investigated the role of the MprAB two-component system in the regulation of ESX-1 activity. We determined that MprAB directly regulates the espA gene cluster, a locus necessary for ESX-1 function. Transcript mapping determined that the five genes in the cluster form an operon with two transcriptional start points, and several MprA binding sites were detected in the espA promoter. Expression analyses and promoter constructs indicated that MprAB represses the espA operon. However, the MprAB mutant Rv-D981 secreted lower levels of EspA, ESAT-6, and the ESX-1 substrate EspB than control strains. Secretion of CFP10, which is normally cosecreted with ESAT-6, was similar in Rv-D981 and control strains, further demonstrating aberrant ESX-1 activity in the mutant. ESAT-6 induces proinflammatory cytokines, and macrophages infected with Rv-D981 elicited lower levels of interleukin 1β (IL-1β) and tumor necrosis factor alpha (TNF-α), consistent with the reduced levels of ESAT-6. These findings indicate that MprAB modulates ESX-1 function and reveal a new role for MprAB in host-pathogen interactions.

Investigation of the binding mode of a novel cruzain inhibitor by docking, molecular dynamics, ab initio and MM/PBSA calculations

NASA Astrophysics Data System (ADS)

Martins, Luan Carvalho; Torres, Pedro Henrique Monteiro; de Oliveira, Renata Barbosa; Pascutti, Pedro Geraldo; Cino, Elio A.; Ferreira, Rafaela Salgado

2018-05-01

Chagas disease remains a major health problem in South America, and throughout the world. The two drugs clinically available for its treatment have limited efficacy and cause serious adverse effects. Cruzain is an established therapeutic target of Trypanosoma cruzi, the protozoan that causes Chagas disease. Our group recently identified a competitive cruzain inhibitor (compound 1) with an IC50 = 15 µM that is also more synthetically accessible than the previously reported lead, compound 2. Prior studies, however, did not propose a binding mode for compound 1, hindering understanding of the structure-activity relationship and optimization. Here, the cruzain binding mode of compound 1 was investigated using docking, molecular dynamics (MD) simulations with ab initio derived parameters, ab initio calculations, and MM/PBSA. Two ligand protonation states and four binding poses were evaluated. A careful ligand parameterization method was employed to derive more physically meaningful parameters than those obtained by automated tools. The poses of unprotonated 1 were unstable in MD, showing large conformational changes and diffusing away from the binding site, whereas the protonated form showed higher stability and interaction with negatively charged residues Asp161 and Cys25. MM/PBSA also suggested that these two residues contribute favorably to binding of compound 1. By combining results from MD, ab initio calculations, and MM/PBSA, a binding mode of 1 is proposed. The results also provide insights for further optimization of 1, an interesting lead compound for the development of new cruzain inhibitors.

Investigation of the binding mode of a novel cruzain inhibitor by docking, molecular dynamics, ab initio and MM/PBSA calculations

NASA Astrophysics Data System (ADS)

Martins, Luan Carvalho; Torres, Pedro Henrique Monteiro; de Oliveira, Renata Barbosa; Pascutti, Pedro Geraldo; Cino, Elio A.; Ferreira, Rafaela Salgado

2018-03-01

Chagas disease remains a major health problem in South America, and throughout the world. The two drugs clinically available for its treatment have limited efficacy and cause serious adverse effects. Cruzain is an established therapeutic target of Trypanosoma cruzi, the protozoan that causes Chagas disease. Our group recently identified a competitive cruzain inhibitor (compound 1) with an IC50 = 15 µM that is also more synthetically accessible than the previously reported lead, compound 2. Prior studies, however, did not propose a binding mode for compound 1, hindering understanding of the structure-activity relationship and optimization. Here, the cruzain binding mode of compound 1 was investigated using docking, molecular dynamics (MD) simulations with ab initio derived parameters, ab initio calculations, and MM/PBSA. Two ligand protonation states and four binding poses were evaluated. A careful ligand parameterization method was employed to derive more physically meaningful parameters than those obtained by automated tools. The poses of unprotonated 1 were unstable in MD, showing large conformational changes and diffusing away from the binding site, whereas the protonated form showed higher stability and interaction with negatively charged residues Asp161 and Cys25. MM/PBSA also suggested that these two residues contribute favorably to binding of compound 1. By combining results from MD, ab initio calculations, and MM/PBSA, a binding mode of 1 is proposed. The results also provide insights for further optimization of 1, an interesting lead compound for the development of new cruzain inhibitors.

Investigation of the binding mode of a novel cruzain inhibitor by docking, molecular dynamics, ab initio and MM/PBSA calculations.

PubMed

Martins, Luan Carvalho; Torres, Pedro Henrique Monteiro; de Oliveira, Renata Barbosa; Pascutti, Pedro Geraldo; Cino, Elio A; Ferreira, Rafaela Salgado

2018-05-01

Chagas disease remains a major health problem in South America, and throughout the world. The two drugs clinically available for its treatment have limited efficacy and cause serious adverse effects. Cruzain is an established therapeutic target of Trypanosoma cruzi, the protozoan that causes Chagas disease. Our group recently identified a competitive cruzain inhibitor (compound 1) with an IC 50  = 15 µM that is also more synthetically accessible than the previously reported lead, compound 2. Prior studies, however, did not propose a binding mode for compound 1, hindering understanding of the structure-activity relationship and optimization. Here, the cruzain binding mode of compound 1 was investigated using docking, molecular dynamics (MD) simulations with ab initio derived parameters, ab initio calculations, and MM/PBSA. Two ligand protonation states and four binding poses were evaluated. A careful ligand parameterization method was employed to derive more physically meaningful parameters than those obtained by automated tools. The poses of unprotonated 1 were unstable in MD, showing large conformational changes and diffusing away from the binding site, whereas the protonated form showed higher stability and interaction with negatively charged residues Asp161 and Cys25. MM/PBSA also suggested that these two residues contribute favorably to binding of compound 1. By combining results from MD, ab initio calculations, and MM/PBSA, a binding mode of 1 is proposed. The results also provide insights for further optimization of 1, an interesting lead compound for the development of new cruzain inhibitors.

WIYN OPEN CLUSTER STUDY. LV. ASTROMETRY AND MEMBERSHIP IN NGC 6819

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

Platais, Imants; Gosnell, Natalie M.; Meibom, Soren

2013-08-01

We present proper motions and astrometric membership analysis for 15,750 stars around the intermediate-age open cluster NGC 6819. The accuracy of relative proper motions for well-measured stars ranges from {approx}0.2 mas yr{sup -1} within 10' of the cluster center to 1.1 mas yr{sup -1} outside this radius. In the proper motion vector-point diagram, the separation between the cluster members and field stars is convincing down to V {approx} 18 and within 10' from the cluster center. The formal sum of membership probabilities indicates a total of {approx}2500 cluster members down to V {approx} 22. We confirm the cluster membership ofmore » several variable stars, including some eclipsing binaries. The estimated absolute proper motion of NGC 6819 is {mu}{sub x}{sup abs}=-2.6{+-}0.5 and {mu}{sub y}{sup abs}=-4.2{+-}0.5 mas yr{sup -1}. A cross-identification between the proper motion catalog and a list of X-ray sources in the field of NGC 6819 resulted in a number of new likely optical counterparts, including a candidate CV. For the first time we show that there is significant differential reddening toward NGC 6819.« less

First-principles study of intermetallic phase stability in the ternary Ti-Al-Nb alloy system

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

Asta, M.; Ormeci, A.; Wills, J.M.

The stability of bcc-based phases in the Ti-Al-Nb alloy system has been studied from first-principles using a combination of ab-initio total energy and cluster variation method (CVM) calculations. Total energies have been computed for 18 binary and ternary bcc superstructures in order to determine low temperature ordering tendencies. From the results of these calculations a set of effective cluster interaction parameters have been derived. These interaction parameters are required input for CVM computations of alloy thermodynamic properties. The CVM has been used to study the effect of composition on finite-temperature ordering tendencies and site preferences for bcc-based phases. Strong orderingmore » tendencies are observed for binary Nb-Al and Ti-Al bcc phases as well as for ternary alloys with compositions near Ti{sub 2}AlNb. For selected superstructures we have also analyzed structural stabilities with respect to tetragonal distortions which transform the bcc into an fcc lattice. Instabilities with respect to such distortions are found to exist for binary but not ternary bcc compounds.« less

Thermal behavior of vehicle plastic blends contained acrylonitrile-butadiene-styrene (ABS) in pyrolysis using TG-FTIR.

PubMed

Liu, Guicai; Liao, Yanfen; Ma, Xiaoqian

2017-03-01

As important plastic blends in End-of-Life vehicles (ELV), pyrolysis profiles of ABS/PVC, ABS/PA6 and ABS/PC were investigated using thermogravimetric-Fourier transform infrared spectrometer (TG-FTIR). Also, CaCO 3 was added as plastic filler to discuss its effects on the pyrolysis of these plastics. The results showed that the interaction between ABS and PVC made PVC pyrolysis earlier and HCl emission slightly accelerated. The mixing of ABS and PA6 made their decomposition temperature closer, and ketones in PA6 pyrolysis products were reduced. The presence of ABS made PC pyrolysis earlier, and phenyl compounds in PC pyrolysis products could be transferred into alcohol or H 2 O. The interaction between ABS and other polymers in pyrolysis could be attributed to the intermolecular radical transfer, and free radicals from the polymer firstly decomposed led to a fast initiation the decomposition of the other polymer. As plastic filler, CaCO 3 promoted the thermal decomposition of PA6 and PC, and had no obvious effects on ABS and PVC pyrolysis process. Also, CaCO 3 made the pyrolysis products from PA6 and PC further decomposed into small-molecule compounds like CO 2 . The kinetics analysis showed that isoconversional method like Starink method was more suitable for these polymer blends. Starink method showed the average activation energy of ABS50/PVC50, ABS50/PA50 and ABS50/PC50 was 186.63kJ/mol, 239.61kJ/mol and 248.95kJ/mol, respectively, and the interaction among them could be reflected by the activation energy variation. Copyright © 2017 Elsevier Ltd. All rights reserved.

Derivatized gold clusters and antibody-gold cluster conjugates

DOEpatents

Hainfeld, James F.; Furuya, Frederic R.

1994-11-01

Antibody- or antibody fragment-gold cluster conjugates are shown wherein the conjugate size can be as small as 5.0 nm. Methods and reagents are disclosed in which antibodies, Fab' or F(ab').sub.2 fragments thereof are covalently bound to a stable cluster of gold atoms. The gold clusters may contain 6, 8, 9, 11, 13, 55 or 67 gold atoms in their inner core. The clusters may also contain radioactive gold. The antibody-cluster conjugates are useful in electron microscopy applications as well as in clinical applications that include imaging, diagnosis and therapy.

Multivariable Analysis of Gluten-Free Pasta Elaborated with Non-Conventional Flours Based on the Phenolic Profile, Antioxidant Capacity and Color.

PubMed

Camelo-Méndez, Gustavo A; Flores-Silva, Pamela C; Agama-Acevedo, Edith; Bello-Pérez, Luis A

2017-12-01

The phenolic compounds, color and antioxidant capacity of gluten-free pasta prepared with non-conventional flours such as chickpea (CHF), unripe plantain (UPF), white maize (WMF) and blue maize (BMF) were analyzed. Fifteen phenolic compounds (five anthocyanins, five hydroxybenzoic acids, three hydroxycinnamic acids, one hydroxyphenylacetic acid and one flavonol) were identified in pasta prepared with blue maize, and 10 compounds were identified for samples prepared with white maize. The principal component analysis (PCA) led to results describing 98% of the total variance establishing a clear separation for each pasta. Both the proportion (25, 50 and 75%) and type of maize flour (white and blue) affected the color parameters (L*, C ab *, h ab and ΔE* ab ) and antioxidant properties (DPPH, ABTS and FRAP methods) of samples, thus producing gluten-free products with potential health benefits intended for general consumers (including the population with celiac disease).

Renormalized coupled cluster approaches in the cluster-in-molecule framework: predicting vertical electron binding energies of the anionic water clusters (H2O)(n)(-).

PubMed

Xu, Peng; Gordon, Mark S

2014-09-04

Anionic water clusters are generally considered to be extremely challenging to model using fragmentation approaches due to the diffuse nature of the excess electron distribution. The local correlation coupled cluster (CC) framework cluster-in-molecule (CIM) approach combined with the completely renormalized CR-CC(2,3) method [abbreviated CIM/CR-CC(2,3)] is shown to be a viable alternative for computing the vertical electron binding energies (VEBE). CIM/CR-CC(2,3) with the threshold parameter ζ set to 0.001, as a trade-off between accuracy and computational cost, demonstrates the reliability of predicting the VEBE, with an average percentage error of ∼15% compared to the full ab initio calculation at the same level of theory. The errors are predominantly from the electron correlation energy. The CIM/CR-CC(2,3) approach provides the ease of a black-box type calculation with few threshold parameters to manipulate. The cluster sizes that can be studied by high-level ab initio methods are significantly increased in comparison with full CC calculations. Therefore, the VEBE computed by the CIM/CR-CC(2,3) method can be used as benchmarks for testing model potential approaches in small-to-intermediate-sized water clusters.

MicroRNA-23a/b and microRNA-27a/b suppress Apaf-1 protein and alleviate hypoxia-induced neuronal apoptosis.

PubMed

Chen, Q; Xu, J; Li, L; Li, H; Mao, S; Zhang, F; Zen, K; Zhang, C-Y; Zhang, Q

2014-03-20

Expression of apoptotic protease activating factor-1 (Apaf-1) gradually decreases during brain development, and this decrease is likely responsible for the decreased sensitivity of brain tissue to apoptosis. However, the mechanism by which Apaf-1 expression is decreased remains elusive. In the present study, we found that four microRNAs (miR-23a/b and miR-27a/b) of miR-23a-27a-24 and miR-23b-27b-24 clusters play key roles in modulating the expression of Apaf-1. First, we found that miR-23a/b and miR-27a/b suppressed the expression of Apaf-1 in vitro. Interestingly, the expression of the miR-23-27-24 clusters in the mouse cortex gradually increased in a manner that was inversely correlated with the pattern of Apaf-1 expression. Second, hypoxic injuries during fetal distress caused reduced expression of the miR-23b and miR-27b that was inversely correlated with an elevation of Apaf-1 expression during neuronal apoptosis. Third, we made neuronal-specific transgenic mice and found that overexpressing the miR-23b and miR-27b in mouse neurons inhibited the neuronal apoptosis induced by intrauterine hypoxia. In conclusion, our results demonstrate, in central neural system, that miR-23a/b and miR-27a/b are endogenous inhibitory factors of Apaf-1 expression and regulate the sensitivity of neurons to apoptosis. Our findings may also have implications for the potential target role of microRNAs in the treatment of neuronal apoptosis-related diseases.

Monoclonal antibodies as cancer therapeutics.

PubMed

Elloumi, Jihene; Jellali, Karim; Jemel, Ikram; Aifa, Sami

2012-04-01

Three main targets were subjected for the most approved monoclonal antibodies (mAbs) in cancer therapy: EGFR in solid cancer, the clusters of differentiation in blood cancer and VEGF in angiogenesis. Meanwhile side effects, the elevated costs and resistance problems are limiting the efficiency of mAbs as targeted therapy. The combinatory therapy with chemo or radiotherapy has improved the efficiency of mAbs. The present review aims to shed more light on the immunotherapy and the related patents that were developed for cancer treatment.

Toxicities of emamectin benzoate homologues and photodegradates to Lepidoptera.

PubMed

Argentine, Joseph A; Jansson, Richard K; Starner, Van R; Halliday, W Ross

2002-12-01

The toxicity of a number of emamectin benzoate homologues and photodegradates to five species of Lepidoptera was investigated using diet and foliar bioassays. The emamectin benzoate homologues B1a and B1b were equally toxic in the diet and foliar assays to Spodoptera exigua (Hübner), Heliothis virescens (F.), Tricoplusia ni (Hübner), and Spodoptera frugiperda (J. E. Smith), within each of these species. Plutella xylostella (L.) was the most sensitive species to emamectin benzoate. The AB1a photodegradate of emamectin benzoate was as toxic as the parent compound in the diet assay. However, in the foliage assay AB1a was 4.4-fold less toxic to S. exigua than the parent compound. The MFB1a photodegradate of emamectin benzoate was as toxic as the parent compound to P. xylostella, and 3.1 to 6.2 times as toxic as the parent compound to the other species in the diet assay. The order of toxicity of the photodegradates were AB1a > MFB1a > FAB1a > 8,9-Z-MAB1a > PAB1a.

Production development of organic nonflammable spacecraft potting, encapsulating and conformal coating compounds. Volume 4: Executive summary

NASA Technical Reports Server (NTRS)

Lieberman, S. L.

1974-01-01

The necessity of having nonflammable versions of potting and encapsulating compounds and conformal coatings for space vehicles is discussed. The formulation, EPOCAST 87517 A/B, was found to have the best balance of thermal, electrical, mechanical, physical, and chemical properties of those evaluated. The requirements which this formulation did not meet are listed, and other formulations which were evaluated are summarized. Recommendations for improving EPOCAST 87517 A/B are included.

Characterizing the Promiscuity of LigAB, a Lignin Catabolite Degrading Extradiol Dioxygenase from Sphingomonas paucimobilis SYK-6

PubMed Central

Barry, Kevin P.; Taylor, Erika A.

2014-01-01

LigAB from Sphingomonas paucimobilis SYK-6 is the only structurally characterized dioxygenase of the largely uncharacterized superfamily of Type II extradiol dioxygenases (EDO). This enzyme catalyzes the oxidative ring-opening of protocatechuate (3,4-dihydroxybenzoic acid or PCA) in a pathway allowing the degradation of lignin derived aromatic compounds (LDACs). LigAB has also been shown to utilize two other LDACs from the same metabolic pathway as substrates, gallate, and 3-O-methyl gallate; however, kcat/KM had not been reported for any of these compounds. In order to assess the catalytic efficiency and get insights into the observed promiscuity of this enzyme, steady-state kinetic analyses were performed for LigAB with these and a library of related compounds. The dioxygenation of PCA by LigAB was highly efficient, with a kcat of 51 s−1 and a kcat/KM of 4.26 × 106 M−1s−1. LigAB demonstrated the ability to use a variety of catecholic molecules as substrates beyond the previously identified gallate and 3-O-methyl gallate, including 3,4-dihydroxybenzamide, homoprotocatechuate, catechol, and 3,4-dihydroxybenzonitrile. Interestingly, 3,4-dihydroxybenzamide (DHBAm) behaves in a manner similar to that of the preferred benzoic acid substrates, with a kcat/Km value only ~4-fold lower than that for gallate and ~10-fold higher than that for 3-O-methyl gallate. All of these most active substrates demonstrate mechanistic inactivation of LigAB. Additionally, DHBAm exhibits potent product inhibition that leads to an inactive enzyme, being more highly deactivating at lower substrate concentration, a phenomena that, to our knowledge, has not been reported for another dioxygenase substrate/product pair. These results provide valuable catalytic insight into the reactions catalyzed by LigAB and make it the first Type II EDO that is fully characterized both structurally and kinetically. PMID:23977959

Analysis of the Genes Involved in Thiocyanate Oxidation during Growth in Continuous Culture of the Haloalkaliphilic Sulfur-Oxidizing Bacterium Thioalkalivibrio thiocyanoxidans ARh 2T Using Transcriptomics

PubMed Central

Balkema, Cherel; Sorokin, Dimitry Y.

2017-01-01

ABSTRACT Thiocyanate (N=C−S−) is a moderately toxic, inorganic sulfur compound. It occurs naturally as a by-product of the degradation of glucosinolate-containing plants and is produced industrially in a number of mining processes. Currently, two pathways for the primary degradation of thiocyanate in bacteria are recognized, the carbonyl sulfide pathway and the cyanate pathway, of which only the former has been fully characterized. Use of the cyanate pathway has been shown in only 10 strains of Thioalkalivibrio, a genus of obligately haloalkaliphilic sulfur-oxidizing Gammaproteobacteria found in soda lakes. So far, only the key enzyme in this reaction, thiocyanate dehydrogenase (TcDH), has been purified and studied. To gain a better understanding of the other genes involved in the cyanate pathway, we conducted a transcriptomics experiment comparing gene expression during the growth of Thioalkalivibrio thiocyanoxidans ARh 2T with thiosulfate with that during its growth with thiocyanate. Triplicate cultures were grown in continuous substrate-limited mode, followed by transcriptome sequencing (RNA-Seq) of the total mRNA. Differential expression analysis showed that a cluster of genes surrounding the gene for TcDH were strongly upregulated during growth with thiocyanate. This cluster includes genes for putative copper uptake systems (copCD, ABC-type transporters), a putative electron acceptor (fccAB), and a two-component regulatory system (histidine kinase and a σ54-responsive Fis family transcriptional regulator). Additionally, we observed the increased expression of RuBisCO and some carboxysome shell genes involved in inorganic carbon fixation, as well as of aprAB, genes involved in sulfite oxidation through the reverse sulfidogenesis pathway. IMPORTANCE Thiocyanate is a moderately toxic and chemically stable sulfur compound that is produced by both natural and industrial processes. Despite its significance as a pollutant, knowledge of the microbial degradation of thiocyanate is very limited. Therefore, investigation of thiocyanate oxidation in haloalkaliphiles such as the genus Thioalkalivibrio may lead to improved biotechnological applications in wastewater remediation. PMID:29285524

Impact-parameter dependence of the energy loss of fast molecular clusters in hydrogen

NASA Astrophysics Data System (ADS)

Fadanelli, R. C.; Grande, P. L.; Schiwietz, G.

2008-03-01

The electronic energy loss of molecular clusters as a function of impact parameter is far less understood than atomic energy losses. For instance, there are no analytical expressions for the energy loss as a function of impact parameter for cluster ions. In this work, we describe two procedures to evaluate the combined energy loss of molecules: Ab initio calculations within the semiclassical approximation and the coupled-channels method using atomic orbitals; and simplified models for the electronic cluster energy loss as a function of the impact parameter, namely the molecular perturbative convolution approximation (MPCA, an extension of the corresponding atomic model PCA) and the molecular unitary convolution approximation (MUCA, a molecular extension of the previous unitary convolution approximation UCA). In this work, an improved ansatz for MPCA is proposed, extending its validity for very compact clusters. For the simplified models, the physical inputs are the oscillators strengths of the target atoms and the target-electron density. The results from these models applied to an atomic hydrogen target yield remarkable agreement with their corresponding ab initio counterparts for different angles between cluster axis and velocity direction at specific energies of 150 and 300 keV/u.

Density functional theory calculations of UO2 oxidation: evolution of UO(2+x), U4O(9-y), U3O7, and U3O8.

PubMed

Andersson, D A; Baldinozzi, G; Desgranges, L; Conradson, D R; Conradson, S D

2013-03-04

Formation of hyperstoichiometric uranium dioxide, UO2+x, derived from the fluorite structure was investigated by means of density functional theory (DFT) calculations. Oxidation was modeled by adding oxygen atoms to UO2 fluorite supercells. For each compound ab initio molecular dynamics simulations were performed to allow the ions to optimize their local geometry. A similar approach was used for studying the reduction of U3O8. In agreement with the experimental phase diagram we identify stable line compounds at the U4O9-y and U3O7 stoichiometries. Although the transition from fluorite to the layered U3O8 structure occurs at U3O7 (UO2.333) or U3O7.333 (UO2.444), our calculated low temperature phase diagram indicates that the fluorite derived compounds are favored up to UO2.5, that is, as long as the charge-compensation for adding oxygen atoms occurs via formation of U(5+) ions, after which the U3O8-y phase becomes more stable. The most stable fluorite UO2+x phases at low temperature (0 K) are based on ordering of split quad-interstitial oxygen clusters. Most existing crystallographic models of U4O9 and U3O7, however, apply the cuboctahedral cluster. To better understand these discrepancies, the new structural models are analyzed in terms of existing neutron diffraction data. DFT calculations were also performed on the experimental cuboctahedral based U4O9-y structure, which enable comparisons between the properties of this phase with the quad-interstitial ones in detail.

Myasthenia gravis: past, present, and future

PubMed Central

Conti-Fine, Bianca M.; Milani, Monica; Kaminski, Henry J.

2006-01-01

Myasthenia gravis (MG) is an autoimmune syndrome caused by the failure of neuromuscular transmission, which results from the binding of autoantibodies to proteins involved in signaling at the neuromuscular junction (NMJ). These proteins include the nicotinic AChR or, less frequently, a muscle-specific tyrosine kinase (MuSK) involved in AChR clustering. Much is known about the mechanisms that maintain self tolerance and modulate anti-AChR Ab synthesis, AChR clustering, and AChR function as well as those that cause neuromuscular transmission failure upon Ab binding. This insight has led to the development of improved diagnostic methods and to the design of specific immunosuppressive or immunomodulatory treatments. PMID:17080188

On Mass Polarization Effect in Three-Body Nuclear Systems

NASA Astrophysics Data System (ADS)

Filikhin, I.; Kezerashvili, R. Ya.; Suslov, V. M.; Vlahovic, B.

2018-05-01

The mass polarization effect is considered for different three-body nuclear AAB systems having a strongly bound AB and unbound AA subsystems. We employ the Faddeev equations for calculations and the Schrödinger equation for analysis of the contribution of the mass polarization term of the kinetic-energy operator. For a three-boson system the mass polarization effect is determined by the difference of the doubled binding energy of the AB subsystem 2E2 and the three-body binding energy E3(V_{AA}=0) when the interaction between the identical particles is omitted. In this case: | E3(V_{AA}=0)| >2| E2| . In the case of a system complicated by isospins(spins), such as the kaonic clusters K-K-p and ppK-, a similar evaluation is impossible. For these systems it is found that | E3(V_{AA}=0)| <2| E2| . A model with an AB potential averaged over spin(isospin) variables transforms the latter case to the first one. The mass polarization effect calculated within this model is essential for the kaonic clusters. In addition we have obtained the relation |E_3|≤|2E_2| for the binding energy of the kaonic clusters.

4He+n+n continuum within an ab initio framework

DOE PAGES

Romero-Redondo, Carolina; Quaglioni, Sofia; Navratil, Petr; ...

2014-07-16

In this study, the low-lying continuum spectrum of the 6He nucleus is investigated for the first time within an ab initio framework that encompasses the 4He+n+n three-cluster dynamics characterizing its lowest decay channel. This is achieved through an extension of the no-core shell model combined with the resonating-group method, in which energy-independent nonlocal interactions among three nuclear fragments can be calculated microscopically, starting from realistic nucleon-nucleon interactions and consistent ab initio many-body wave functions of the clusters. The three-cluster Schrödinger equation is solved with three-body scattering boundary conditions by means of the hyperspherical-harmonics method on a Lagrange mesh. Using amore » soft similarity-renormalization-group evolved chiral nucleon-nucleon potential, we find the known J π = 2 + resonance as well as a result consistent with a new low-lying second 2 + resonance recently observed at GANIL at ~2.6 MeV above the He6 ground state. We also find resonances in the 2 –, 1 +, and 0 – channels, while no low-lying resonances are present in the 0 + and 1 – channels.« less

Response to treatment of myasthenia gravis according to clinical subtype.

PubMed

Akaishi, Tetsuya; Suzuki, Yasushi; Imai, Tomihiro; Tsuda, Emiko; Minami, Naoya; Nagane, Yuriko; Uzawa, Akiyuki; Kawaguchi, Naoki; Masuda, Masayuki; Konno, Shingo; Suzuki, Hidekazu; Murai, Hiroyuki; Aoki, Masashi; Utsugisawa, Kimiaki

2016-11-17

We have previously reported using two-step cluster analysis to classify myasthenia gravis (MG) patients into the following five subtypes: ocular MG; thymoma-associated MG; MG with thymic hyperplasia; anti-acetylcholine receptor antibody (AChR-Ab)-negative MG; and AChR-Ab-positive MG without thymic abnormalities. The objectives of the present study were to examine the reproducibility of this five-subtype classification using a new data set of MG patients and to identify additional characteristics of these subtypes, particularly in regard to response to treatment. A total of 923 consecutive MG patients underwent two-step cluster analysis for the classification of subtypes. The variables used for classification were sex, age of onset, disease duration, presence of thymoma or thymic hyperplasia, positivity for AChR-Ab or anti-muscle-specific tyrosine kinase antibody, positivity for other concurrent autoantibodies, and disease condition at worst and current. The period from the start of treatment until the achievement of minimal manifestation status (early-stage response) was determined and then compared between subtypes using Kaplan-Meier analysis and the log-rank test. In addition, between subtypes, the rate of the number of patients who maintained minimal manifestations during the study period/that of patients who only achieved the status once (stability of improved status) was compared. As a result of two-step cluster analysis, 923 MG patients were classified into five subtypes as follows: ocular MG (AChR-Ab-positivity, 77%; histogram of onset age, skewed to older age); thymoma-associated MG (100%; normal distribution); MG with thymic hyperplasia (89%; skewed to younger age); AChR-Ab-negative MG (0%; normal distribution); and AChR-Ab-positive MG without thymic abnormalities (100%, skewed to older age). Furthermore, patients classified as ocular MG showed the best early-stage response to treatment and stability of improved status, followed by those classified as thymoma-associated MG and AChR-Ab-positive MG without thymic abnormalities; by contrast, those classified as AChR-Ab-negative MG showed the worst early-stage response to treatment and stability of improved status. Differences were seen between the five subtypes in demographic characteristics, clinical severity, and therapeutic response. Our five-subtype classification approach would be beneficial not only to elucidate disease subtypes, but also to plan treatment strategies for individual MG patients.

Intrinsically High Thermoelectric Performance in AgInSe2 n‐Type Diamond‐Like Compounds

PubMed Central

Qiu, Pengfei; Qin, Yuting; Zhang, Qihao; Li, Ruoxi; Song, Qingfeng; Tang, Yunshan; Bai, Shengqiang

2017-01-01

Abstract Diamond‐like compounds are a promising class of thermoelectric materials, very suitable for real applications. However, almost all high‐performance diamond‐like thermoelectric materials are p‐type semiconductors. The lack of high‐performance n‐type diamond‐like thermoelectric materials greatly restricts the fabrication of diamond‐like material‐based modules and their real applications. In this work, it is revealed that n‐type AgInSe2 diamond‐like compound has intrinsically high thermoelectric performance with a figure of merit (zT) of 1.1 at 900 K, comparable to the best p‐type diamond‐like thermoelectric materials reported before. Such high zT is mainly due to the ultralow lattice thermal conductivity, which is fundamentally limited by the low‐frequency Ag‐Se “cluster vibrations,” as confirmed by ab initio lattice dynamic calculations. Doping Cd at Ag sites significantly improves the thermoelectric performance in the low and medium temperature ranges. By using such high‐performance n‐type AgInSe2‐based compounds, the diamond‐like thermoelectric module has been fabricated for the first time. An output power of 0.06 W under a temperature difference of 520 K between the two ends of the module is obtained. This work opens a new window for the applications using the diamond‐like thermoelectric materials. PMID:29593972

The influence of radiation-induced vacancy on the formation of thin-film of compound layer during a reactive diffusion process

NASA Astrophysics Data System (ADS)

Akintunde, S. O.; Selyshchev, P. A.

2016-05-01

A theoretical approach is developed that describes the formation of a thin-film of AB-compound layer under the influence of radiation-induced vacancy. The AB-compound layer is formed as a result of a chemical reaction between the atomic species of A and B immiscible layers. The two layers are irradiated with a beam of energetic particles and this process leads to several vacant lattice sites creation in both layers due to the displacement of lattice atoms by irradiating particles. A- and B-atoms diffuse via these lattice sites by means of a vacancy mechanism in considerable amount to reaction interfaces A/AB and AB/B. The reaction interfaces increase in thickness as a result of chemical transformation between the diffusing species and surface atoms (near both layers). The compound layer formation occurs in two stages. The first stage begins as an interfacial reaction controlled process, and the second as a diffusion controlled process. The critical thickness and time are determined at a transition point between the two stages. The influence of radiation-induced vacancy on layer thickness, speed of growth, and reaction rate is investigated under irradiation within the framework of the model presented here. The result obtained shows that the layer thickness, speed of growth, and reaction rate increase strongly as the defect generation rate rises in the irradiated layers. It also shows the feasibility of producing a compound layer (especially in near-noble metal silicide considered in this study) at a temperature below their normal formation temperature under the influence of radiation.

Al7CX (X=Li-Cs) clusters: Stability and the prospect for cluster materials

NASA Astrophysics Data System (ADS)

Ashman, C.; Khanna, S. N.; Pederson, M. R.; Kortus, J.

2000-12-01

Al7C clusters, recently found to have a high-electron affinity and exceptional stability, are shown to form ionic molecules when combined with alkali-metal atoms. Our studies, based on an ab initio gradient-corrected density-functional scheme, show that Al7CX (X=Li-Cs) clusters have a very low-electron affinity and a high-ionization potential. When combined, the two- and four-atom composite clusters of Al7CLi units leave the Al7C clusters almost intact. Preliminary studies indicate that Al7CLi may be suitable to form cluster-based materials.

Derivatized gold clusters and antibody-gold cluster conjugates

DOEpatents

Hainfeld, J.F.; Furuya, F.R.

1994-11-01

Antibody- or antibody fragment-gold cluster conjugates are shown wherein the conjugate size can be as small as 5.0 nm. Methods and reagents are disclosed in which antibodies, Fab' or F(ab')[sub 2] fragments are covalently bound to a stable cluster of gold atoms. The gold clusters may contain 6, 8, 9, 11, 13, 55 or 67 gold atoms in their inner core. The clusters may also contain radioactive gold. The antibody-cluster conjugates are useful in electron microscopy applications as well as in clinical applications that include imaging, diagnosis and therapy. 7 figs.

Outside-in HLA class I signaling regulates ICAM-1 clustering and endothelial cell-monocyte interactions via mTOR in transplant antibody-mediated rejection.

PubMed

Salehi, Sahar; Sosa, Rebecca A; Jin, Yi-Ping; Kageyama, Shoichi; Fishbein, Michael C; Rozengurt, Enrique; Kupiec-Weglinski, Jerzy W; Reed, Elaine F

2018-05-01

Antibody-mediated rejection (AMR) resulting in transplant allograft vasculopathy (TAV) is the major obstacle for long-term survival of solid organ transplants. AMR is caused by donor-specific antibodies to HLA, which contribute to TAV by initiating outside-in signaling transduction pathways that elicit monocyte recruitment to activated endothelium. Mechanistic target of rapamycin (mTOR) inhibitors can attenuate TAV; therefore, we sought to understand the mechanistic underpinnings of mTOR signaling in HLA class I Ab-mediated endothelial cell activation and monocyte recruitment. We used an in vitro model to assess monocyte binding to HLA I Ab-activated endothelial cells and found mTOR inhibition reduced ezrin/radixin/moesin (ERM) phosphorylation, intercellular adhesion molecule 1 (ICAM-1) clustering, and monocyte firm adhesion to HLA I Ab-activated endothelium. Further, in a mouse model of AMR, in which C57BL/6. RAG1 -/- recipients of BALB/c cardiac allografts were passively transferred with donor-specific MHC I antibodies, mTOR inhibition significantly reduced vascular injury, ERM phosphorylation, and macrophage infiltration of the allograft. Taken together, these studies indicate mTOR inhibition suppresses ERM phosphorylation in endothelial cells, which impedes ICAM-1 clustering in response to HLA class I Ab and prevents macrophage infiltration into cardiac allografts. These findings indicate a novel therapeutic application for mTOR inhibitors to disrupt endothelial cell-monocyte interactions during AMR. © 2017 The American Society of Transplantation and the American Society of Transplant Surgeons.

Weighted similarity-based clustering of chemical structures and bioactivity data in early drug discovery.

PubMed

Perualila-Tan, Nolen Joy; Shkedy, Ziv; Talloen, Willem; Göhlmann, Hinrich W H; Moerbeke, Marijke Van; Kasim, Adetayo

2016-08-01

The modern process of discovering candidate molecules in early drug discovery phase includes a wide range of approaches to extract vital information from the intersection of biology and chemistry. A typical strategy in compound selection involves compound clustering based on chemical similarity to obtain representative chemically diverse compounds (not incorporating potency information). In this paper, we propose an integrative clustering approach that makes use of both biological (compound efficacy) and chemical (structural features) data sources for the purpose of discovering a subset of compounds with aligned structural and biological properties. The datasets are integrated at the similarity level by assigning complementary weights to produce a weighted similarity matrix, serving as a generic input in any clustering algorithm. This new analysis work flow is semi-supervised method since, after the determination of clusters, a secondary analysis is performed wherein it finds differentially expressed genes associated to the derived integrated cluster(s) to further explain the compound-induced biological effects inside the cell. In this paper, datasets from two drug development oncology projects are used to illustrate the usefulness of the weighted similarity-based clustering approach to integrate multi-source high-dimensional information to aid drug discovery. Compounds that are structurally and biologically similar to the reference compounds are discovered using this proposed integrative approach.

Rewiring a secondary metabolite pathway towards itaconic acid production in Aspergillus niger.

PubMed

Hossain, Abeer H; Li, An; Brickwedde, Anja; Wilms, Lars; Caspers, Martien; Overkamp, Karin; Punt, Peter J

2016-07-28

The industrially relevant filamentous fungus Aspergillus niger is widely used in industry for its secretion capabilities of enzymes and organic acids. Biotechnologically produced organic acids promise to be an attractive alternative for the chemical industry to replace petrochemicals. Itaconic acid (IA) has been identified as one of the top twelve building block chemicals which have high potential to be produced by biotechnological means. The IA biosynthesis cluster (cadA, mttA and mfsA) has been elucidated in its natural producer Aspergillus terreus and transferred to A. niger to enable IA production. Here we report the rewiring of a secondary metabolite pathway towards further improved IA production through the overexpression of a putative cytosolic citrate synthase citB in a A. niger strain carrying the IA biosynthesis cluster. We have previously shown that expression of cadA from A. terreus results in itaconic acid production in A. niger AB1.13, albeit at low levels. This low-level production is boosted fivefold by the overexpression of mttA and mfsA in itaconic acid producing AB1.13 CAD background strains. Controlled batch cultivations with AB1.13 CAD + MFS + MTT strains showed increased production of itaconic acid compared with AB1.13 CAD strain. Moreover, preliminary RNA-Seq analysis of an itaconic acid producing AB1.13 CAD strain has led to the identification of the putative cytosolic citrate synthase citB which was induced in an IA producing strain. We have overexpressed citB in a AB1.13 CAD + MFS + MTT strain and by doing so hypothesize to have targeted itaconic acid production to the cytosolic compartment. By overexpressing citB in AB1.13 CAD + MFS + MTT strains in controlled batch cultivations we have achieved highly increased titers of up to 26.2 g/L IA with a productivity of 0.35 g/L/h while no CA was produced. Expression of the IA biosynthesis cluster in Aspergillus niger AB1.13 strain enables IA production. Moreover, in the AB1.13 CAD strain IA production resulted in overexpression of a putative cytosolic citrate synthase citB. Upon overexpression of citB we have achieved titers of up to 26.2 g/L IA with a productivity of 0.35 g/L/h in controlled batch cultivations. By overexpressing citB we have also diminished side product formation and optimized the production pathway towards IA.

Magic Numbers in Small Iron Clusters: A First-Principles Study

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

Kim, Eunja; Mohrland, Andrew B.; Weck, Philippe F.

2014-10-03

We perform ab initio spin-polarized density functional calculations of Fen aggregates with n ≤ 17 atoms to reveal the origin of the observed magic numbers, which indicate particularly high stability of clusters with 7, 13 and 15 atoms. Our results clarify the controversy regarding the ground state geometry of clusters such as Fe5and indicate that magnetism plays an important role in determining the stability and magic numbers in small iron clusters.

Ionic liquid-based aqueous biphasic systems as a versatile tool for the recovery of antioxidant compounds.

PubMed

Santos, João H; e Silva, Francisca A; Ventura, Sónia P M; Coutinho, João A P; de Souza, Ranyere L; Soares, Cleide M F; Lima, Álvaro S

2015-01-01

The comparative evaluation of distinct types of ionic liquid-based aqueous biphasic systems (IL-ABS) and more conventional polymer/salt-based ABS to the extraction of two antioxidants, eugenol and propyl gallate, is focused. In a first approach, IL-ABS composed of ILs and potassium citrate (C6H5K3O7/C6H8O7) buffer at pH 7 were applied to the extraction of two antioxidants, enabling the assessment of the impact of IL cation core on the extraction. The second approach uses ABS composed of polyethylene glycol (PEG) and potassium phosphate (K2HPO4/KH2PO4) buffer at pH 7 with imidazolium-based ILs as adjuvants. Their application to the extraction of the compounds allowed the investigation of the impact of the presence/absence of IL, the PEG molecular weight, and the alkyl side chain length of the imidazolium cation on the partition. It is possible to maximize the extractive performance of both antioxidants up to 100% using both types of IL-ABS. The IL enhances the performance of ABS technology. The data puts in evidence the pivotal role of the appropriate selection of the ABS components and design to develop a successful extractive process, from both environmental and performance points of view. © 2014 American Institute of Chemical Engineers.

Solid-State Electrolyte Anchored with a Carboxylated Azo Compound for All-Solid-State Lithium Batteries.

PubMed

Luo, Chao; Ji, Xiao; Chen, Ji; Gaskell, Karen J; He, Xinzi; Liang, Yujia; Jiang, Jianjun; Wang, Chunsheng

2018-05-23

Organic electrode materials are promising for green and sustainable lithium-ion batteries. However, the high solubility of organic materials in the liquid electrolyte results in the shuttle reaction and fast capacity decay. Herein, azo compounds are firstly applied in all-solid-state lithium batteries (ASSLB) to suppress the dissolution challenge. Due to the high compatibility of azobenzene (AB) based compounds to Li 3 PS 4 (LPS) solid electrolyte, the LPS solid electrolyte is used to prevent the dissolution and shuttle reaction of AB. To maintain the low interface resistance during the large volume change upon cycling, a carboxylate group is added into AB to provide 4-(phenylazo) benzoic acid lithium salt (PBALS), which could bond with LPS solid electrolyte via the ionic bonding between oxygen in PBALS and lithium ion in LPS. The ionic bonding between the active material and solid electrolyte stabilizes the contact interface and enables the stable cycle life of PBALS in ASSLB. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Functional Analysis of Alpha-6 Integrin Cytoplasinic Domains.

DTIC Science & Technology

1997-12-01

ßl monoclonal antibody 9EG7 (Lenter et al., 1993), GoH3, mAb 12.2, mAb 24.9 or mAb 22.2. For immunoprecipitation, 9EG7 was covalently coupled to... antibody coupled to horseradish peroxidase (Amersham, Arlington Hts., IL) followed by ECL detection. Biotinylated, immunoprecipitated proteins were...rat immunoglobulin antibody was added to cross-link the bound GoH3, hence clustering the GoH3-bound oc6ßl. In the case of Ln-1, which required oc6ßl

Revisiting the Electronic Structure of FeS Monomers Using ab Initio Ligand Field Theory and the Angular Overlap Model.

PubMed

Chilkuri, Vijay Gopal; DeBeer, Serena; Neese, Frank

2017-09-05

Iron-sulfur (FeS) proteins are universally found in nature with actives sites ranging in complexity from simple monomers to multinuclear sites from two up to eight iron atoms. These sites include mononuclear (rubredoxins), dinuclear (ferredoxins and Rieske proteins), trinuclear (e.g., hydrogenases), and tetranuclear (various ferredoxins and high-potential iron-sulfur proteins). The electronic structure of the higher-nuclearity clusters is inherently extremely complex. Hence, it is reasonable to take a bottom-up approach in which clusters of increasing nuclearity are analyzed in terms of the properties of their lower nuclearity constituents. In the present study, the first step is taken by an in-depth analysis of mononuclear FeS systems. Two different FeS molecules with phenylthiolate and methylthiolate as ligands are studied in their oxidized and reduced forms using modern wave function-based ab initio methods. The ab initio electronic spectra and wave function are presented and analyzed in detail. The very intricate electronic structure-geometry relationship in these systems is analyzed using ab initio ligand field theory (AILFT) in conjunction with the angular overlap model (AOM) parametrization scheme. The simple AOM model is used to explain the effect of geometric variations on the electronic structure. Through a comparison of the ab initio computed UV-vis absorption spectra and the available experimental spectra, the low-energy part of the many-particle spectrum is carefully analyzed. We show ab initio calculated magnetic circular dichroism spectra and present a comparison with the experimental spectrum. Finally, AILFT parameters and the ab initio spectra are compared with those obtained experimentally to understand the effect of the increased covalency of the thiolate ligands on the electronic structure of FeS monomers.

ORBITAL AND PHYSICAL PROPERTIES OF THE σ Ori Aa, Ab, B TRIPLE SYSTEM

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

Simón-Díaz, S.; Caballero, J. A.; Apellániz, J. Maíz

2015-02-01

We provide a complete characterization of the astrophysical properties of the σ Ori Aa, Ab, B hierarchical triple system and an improved set of orbital parameters for the highly eccentric σ Ori Aa, Ab spectroscopic binary. We compiled a spectroscopic data set comprising 90 high-resolution spectra covering a total time span of 1963 days. We applied the Lehman-Filhés method for a detailed orbital analysis of the radial velocity curves and performed a combined quantitative spectroscopic analysis of the σ Ori Aa, Ab, B system by means of the stellar atmosphere code FASTWIND. We used our own plus other available information onmore » photometry and distance to the system for measuring the radii, luminosities, and spectroscopic masses of the three components. We also inferred evolutionary masses and stellar ages using the Bayesian code BONNSAI. The orbital analysis of the new radial velocity curves led to a very accurate orbital solution of the σ Ori Aa, Ab pair. We provided indirect arguments indicating that σ Ori B is a fast-rotating early B dwarf. The FASTWIND+BONNSAI analysis showed that the Aa, Ab pair contains the hottest and most massive components of the triple system while σ Ori B is a bit cooler and less massive. The derived stellar ages of the inner pair are intriguingly younger than the one widely accepted for the σ Orionis cluster, at 3 ± 1 Ma. The outcome of this study will be of key importance for a precise determination of the distance to the σ Orionis cluster, the interpretation of the strong X-ray emission detected for σ Ori Aa, Ab, B, and the investigation of the formation and evolution of multiple massive stellar systems and substellar objects.« less

American foulbrood of the honey bee: occurrence and distribution of different genotypes of Paenibacillus larvae in the administrative district of Arnsberg (North Rhine-Westphalia).

PubMed

Peters, M; Kilwinski, J; Beringhoff, A; Reckling, D; Genersch, E

2006-03-01

Between March 2003 and October 2004, Paenibacillus larvae, the aetiological agent of American foulbrood disease of the honey bee, was isolated from broodcombs and honey samples of 54 apiaries in the administrative district of Arnsberg (North Rhine-Westphalia, Germany). Genotyping of 176 P. larvae isolates with repetitive element polymerase chain reaction fingerprinting (rep-PCR) using BOX A1R and MBO REP1 primers revealed five different genotypes (AB, Ab, ab, ass, Acapital BE, Cyrillic). In samples of three apiaries, more than one genotype was detected. A combination of two genotypes was isolated from honey samples of the same hive two times (ab/ass and Ab/ab). The five genotypes were not randomly distributed in the district, but revealed a certain geographical clustering. Possible factors with impact on the genotype diversity and the distribution pattern are discussed.

Low Temperature Kinetics of the First Steps of Water Cluster Formation

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

Bourgalais, J.; Roussel, V.; Capron, M.

2016-03-01

We present a combined experimental and theoretical low temperature kinetic study of water cluster formation. Water cluster growth takes place in low temperature (23-69 K) supersonic flows. The observed kinetics of formation of water clusters are reproduced with a kinetic model based on theoretical predictions for the first steps of clusterization. The temperature-and pressure-dependent association and dissociation rate coefficients are predicted with an ab initio transition state theory based master equation approach over a wide range of temperatures (20-100 K) and pressures (10(-6) - 10 bar).

Excited states of 4He

NASA Astrophysics Data System (ADS)

Aoyama, Shigeyoshi

2013-04-01

The study of the 4He nucleus is important because it is the most basic sub-unit (cluster) in nuclei. We have investigated the structures and the reaction mechanisms in 4He by using the correlated Gaussian basis function with the global vector representation. In order to treat the boundary condition for the ab-initio calculation of the four nucleons, we employ the Microscopic R-matrix Method (MRM) and the Complex Scaling Method (CSM) . Elastic-scattering phase shifts for four-nucleon systems are studied in an ab-initio type cluster model with MRM in order to clarify the role of the tensor force and to investigate cluster distortions in low energy d+d and t+p scattering. For 1S0, the calculated phase shifts show that the t+p and h+n channels are strongly coupled to the d+d channel for the case of the realistic interaction.

Are trinuclear superhalogens promising candidates for building blocks of novel magnetic materials? A theoretical prospect from combined broken-symmetry density functional theory and ab initio study.

PubMed

Yu, Yang; Li, Chen; Yin, Bing; Li, Jian-Li; Huang, Yuan-He; Wen, Zhen-Yi; Jiang, Zhen-Yi

2013-08-07

The structures, relative stabilities, vertical electron detachment energies, and magnetic properties of a series of trinuclear clusters are explored via combined broken-symmetry density functional theory and ab initio study. Several exchange-correlation functionals are utilized to investigate the effects of different halogen elements and central atoms on the properties of the clusters. These clusters are shown to possess stronger superhalogen properties than previously reported dinuclear superhalogens. The calculated exchange coupling constants indicate the antiferromagnetic coupling between the transition metal ions. Spin density analysis demonstrates the importance of spin delocalization in determining the strengths of various couplings. Spin frustration is shown to occur in some of the trinuclear superhalogens. The coexistence of strong superhalogen properties and spin frustration implies the possibility of trinuclear superhalogens working as the building block of new materials of novel magnetic properties.

Identification of AB-FUBINACA metabolites in authentic urine samples suitable as urinary markers of drug intake using liquid chromatography quadrupole tandem time of flight mass spectrometry.

PubMed

Vikingsson, Svante; Gréen, Henrik; Brinkhagen, Linda; Mukhtar, Shahzabe; Josefsson, Martin

2016-09-01

Synthetic cannabinoids are a group of psychoactive drugs presently widespread among drug users in Europe. Analytical methods to measure these compounds in urine are in demand as urine is a preferred matrix for drug testing. For most synthetic cannabinoids, the parent compounds are rarely detected in urine. Therefore urinary metabolites are needed as markers of drug intake. AB-FUBINACA was one of the top three synthetic cannabinoids most frequently found in seizures and toxicological drug screening in Sweden (2013-2014). Drug abuse is also reported from several other countries such as the USA and Japan. In this study, 28 authentic case samples were used to identify urinary markers of AB-FUBINACA intake using liquid chromatography quadrupole tandem time of flight mass spectrometry and human liver microsomes. Three metabolites suitable as markers of drug intake were identified and at least two of them were detected in all but one case. In total, 15 urinary metabolites of AB-FUBINACA were reported, including hydrolxylations on the indazole ring and the amino-oxobutane moiety, dealkylations and hydrolysis of the primary amide. No modifications on the fluorobenzyl side-chain were observed. The parent compound was detected in 54% of the case samples. Also, after three hours of incubation with human liver microsomes, 77% of the signal from the parent compound remained. Copyright © 2015 John Wiley & Sons, Ltd. Copyright © 2015 John Wiley & Sons, Ltd.

Structure of alcohol cluster ions in the gas phase, according to spectrometry and ab initio calculations

NASA Astrophysics Data System (ADS)

Krisilov, A. V.; Lantsuzskaya, E. V.; Levina, A. M.

2017-01-01

Reduced ion mobility and scattering cross sections are calculated from experimentally obtained spectra of the ion mobility of linear aliphatic alcohols with carbon atom numbers from 2 to 9. A linear increase in the scattering cross sections as the molecular weight grows is found. According to the results from experiments and quantum chemical calculations, alcohol cluster ions do not form a compact structure. Neither are dipole moments compensated for during dimerization, in contrast to the aldehydes and ketones described earlier. It was concluded from ab initio calculations that charge delocalization in monomeric and dimeric ions of alcohols increases the dipole moment many times over.

Prediction of neutral noble gas insertion compounds with heavier pnictides: FNgY (Ng = Kr and Xe; Y = As, Sb and Bi).

PubMed

Ghosh, Ayan; Manna, Debashree; Ghanty, Tapan K

2016-04-28

A novel class of interesting insertion compounds obtained through the insertion of a noble gas atom into the heavier pnictides have been explored by various ab initio quantum chemical techniques. Recently, the first neutral noble gas insertion compounds, FXeY (Y = P, N), were theoretically predicted to be stable; the triplet state was found to be the most stable state, with a high triplet-singlet energy gap, by our group. In this study, we investigated another noble gas inserted compound, FNgY (Ng = Kr and Xe; Y = As, Sb and Bi), with a triplet ground state. Density functional theory (DFT), second order Møller-Plesset perturbation theory (MP2), coupled-cluster theory (CCSD(T)) and multi-reference configuration interaction (MRCI) based techniques have been utilized to investigate the structures, stabilities, harmonic vibrational frequencies, charge distributions and topological properties of these compounds. These predicted species, FNgY (Ng = Kr and Xe; Y = As, Sb and Bi) are found to be energetically stable with respect to all the probable 2-body and 3-body dissociation pathways, except for the 2-body channel leading to the global minimum products (FY + Ng). Nevertheless, the finite barrier height corresponding to the saddle points of the compounds connected to their respective global minima products indicates that these compounds are kinetically stable. The structural parameters, energetics, and charge distribution results as well as atoms-in-molecules (AIM) analysis suggest that these predicted molecules can be best represented as F(-)[(3)NgY](+). Thus, all the aforementioned computed results clearly indicate that it may be possible to experimentally prepare the most stable triplet state of FNgY molecules under cryogenic conditions through a matrix isolation technique.

Distribution Characteristics of Eggs and Neonate Larvae of Codling Moth, Cydia pomonella (L.) (Lepidoptera: Tortricidae)

PubMed Central

Wearing, Christopher H.

2016-01-01

Literature is reviewed on the spatial distribution of the eggs and neonate larvae of codling moth on apple trees in relation to research conducted in Nelson, New Zealand. At Nelson, oviposition increased with height and was greater in the north and east of the trees and in those with greater fruit load in some seasons, which matches published reports. All publications and the research recorded high percentages of eggs laid singly within 10–15 cm of the fruit, with most eggs on leaves even within fruit clusters; oviposition on fruit clusters of different sizes was nonrandom because more eggs were laid on those with more fruit, but the aggregation of both per cluster and within clusters was even greater than that caused by the fruit number alone. Oviposition at random with respect to the fruit occurred only at very low population density. The choice of oviposition site between fruit and the adaxial leaf surface and abaxial leaf surface (AbLS) was variable and cultivar related. Cultivars on which eggs predominated on the AbLS were less frequent and characterized by low trichome density. In the literature, neonate larvae from eggs on the AbLS suffered greater mortality, as did those in Nelson that hatched more distant from the fruit. This review discusses the interaction between these distribution characteristics and species-specific host–plant volatiles, egg adhesion to plant surfaces, oviposition deterrents, predation, and their relevance to pest management. PMID:27429560

Compound formation and melting behavior in the AB compound and rare earth oxide systems

NASA Astrophysics Data System (ADS)

Huang, Z. K.; Yan, D. S.; Yen, T. S.; Tien, T. Y.

1990-03-01

Compound formation in the systems of the covalent compounds BeO, AlN, and SiC with R2O 3(rare earth oxides) is described. Tentative phase diagrams of the AlN sbnd Nd 2O 3 and AlN sbnd Eu 2O 3 systems are presented.

Improved airfield damage assessment System (IADAS) capstone

DTIC Science & Technology

2017-09-01

96  Figure C-1.  Russian RBK-500 BetAB Cluster Bomb . Sources: Jane’s Air Launched Weapons (2007) and Flankers Site (2017...127  Figure C-2.  Russian RBK-500RTM AO Cluster Bomb . Sources: International Campaign to Ban Landmines (2012) and The Fighter...AFCEC Air Force Civil Engineer Center AoA analysis of alternatives CBU cluster bomb unit CCDR combatant commanders COCOMO II Constructive Cost Model

Capillary electrophoresis for rapid identification of monoclonal antibodies for routine application in hospital.

PubMed

Jaccoulet, Emmanuel; Smadja, Claire; Prognon, Patrice; Taverna, Myriam

2015-09-01

mAbs are widely used in cancer therapy. Their compounding, performed just before their administration to patients, is executed in a production unit of the hospital. Identification of these drugs, individually prepared in bags for infusion before patient administration, is of paramount importance to detect potential mistakes during compounding stage. A fast and reliable analytical method based on CZE combined to a cationic capillary coating (hexadimethrine bromide) was developed for identification of the most widely used compounded therapeutic for cancer therapy (bevacizumab, cetuximab, rituximab, and trastuzumab). Considering the high structural and physico-chemical similarities of these mAbs, an extensive optimization of the BGE composition has been performed. The addition of perchlorate ions and polysorbate in the BGE greatly increased the resolution. To validate the method, an internal standard was used and the relative migration times (RTm) were estimated. Very satisfactory RSDs of the RTm for rituximab (0.76%), cetuximab (0.46%), bevacizumab (0.31%), and trastuzumab (0.60%) were obtained. The intraday and interday RSD of the method were less than 0.32 and 1.3%, respectively for RTm. Significant differences between theses RTms have been demonstrated allowing mAbs identification. Finally, accurate mAbs identification has been demonstrated by a blind test. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Comparing ab initio density-functional and wave function theories: the impact of correlation on the electronic density and the role of the correlation potential.

PubMed

Grabowski, Ireneusz; Teale, Andrew M; Śmiga, Szymon; Bartlett, Rodney J

2011-09-21

The framework of ab initio density-functional theory (DFT) has been introduced as a way to provide a seamless connection between the Kohn-Sham (KS) formulation of DFT and wave-function based ab initio approaches [R. J. Bartlett, I. Grabowski, S. Hirata, and S. Ivanov, J. Chem. Phys. 122, 034104 (2005)]. Recently, an analysis of the impact of dynamical correlation effects on the density of the neon atom was presented [K. Jankowski, K. Nowakowski, I. Grabowski, and J. Wasilewski, J. Chem. Phys. 130, 164102 (2009)], contrasting the behaviour for a variety of standard density functionals with that of ab initio approaches based on second-order Møller-Plesset (MP2) and coupled cluster theories at the singles-doubles (CCSD) and singles-doubles perturbative triples [CCSD(T)] levels. In the present work, we consider ab initio density functionals based on second-order many-body perturbation theory and coupled cluster perturbation theory in a similar manner, for a range of small atomic and molecular systems. For comparison, we also consider results obtained from MP2, CCSD, and CCSD(T) calculations. In addition to this density based analysis, we determine the KS correlation potentials corresponding to these densities and compare them with those obtained for a range of ab initio density functionals via the optimized effective potential method. The correlation energies, densities, and potentials calculated using ab initio DFT display a similar systematic behaviour to those derived from electronic densities calculated using ab initio wave function theories. In contrast, typical explicit density functionals for the correlation energy, such as VWN5 and LYP, do not show behaviour consistent with this picture of dynamical correlation, although they may provide some degree of correction for already erroneous explicitly density-dependent exchange-only functionals. The results presented here using orbital dependent ab initio density functionals show that they provide a treatment of exchange and correlation contributions within the KS framework that is more consistent with traditional ab initio wave function based methods.

Network-Forming Nanoclusters in Binary As-S/Se Glasses: From Ab Initio Quantum Chemical Modeling to Experimental Evidences.

PubMed

Hyla, M

2017-12-01

Network-forming As 2 (S/Se) m nanoclusters are employed to recognize expected variations in a vicinity of some remarkable compositions in binary As-Se/S glassy systems accepted as signatures of optimally constrained intermediate topological phases in earlier temperature-modulated differential scanning calorimetry experiments. The ab initio quantum chemical calculations performed using the cation-interlinking network cluster approach show similar oscillating character in tendency to local chemical decomposition but obvious step-like behavior in preference to global phase separation on boundary chemical compounds (pure chalcogen and stoichiometric arsenic chalcogenides). The onsets of stability are defined for chalcogen-rich glasses, these being connected with As 2 Se 5 (Z = 2.29) and As 2 S 6 (Z = 2.25) nanoclusters for As-Se and As-S glasses, respectively. The physical aging effects result preferentially from global phase separation in As-S glass system due to high localization of covalent bonding and local demixing on neighboring As 2 Se m+1 and As 2 Se m-1 nanoclusters in As-Se system. These nanoclusters well explain the lower limits of reversibility windows in temperature-modulated differential scanning calorimetry, but they cannot be accepted as signatures of topological phase transitions in respect to the rigidity theory.

The Pariser-Parr-Pople model for trans-polyenes. I. Ab initio and semiempirical study of the bond alternation in trans-butadiene

NASA Astrophysics Data System (ADS)

Förner, Wolfgang

1992-03-01

Ab initio investigations of the bond alternation in butadiene are presented. The atomic basis sets applied range from minimal to split valence plus polarization quality. With the latter one the Hartree-Fock limit for the bond alternation is reached. Correlation is considered on Møller-Plesset many-body perturbation theory of second order (MP2), linear coupled cluster doubles (L-CCD) and coupled cluster doubles (CCD) level. For the smaller basis sets it is shown that for the bond alternation π-π correlations are essential while the effects of σ-σ and σ-π correlations are, though large, nearly independent of bond alternation. On MP2 level the variation of σ-π correlation with bond alternation is surprisingly large. This is discussed as an artefact of MP2. Comparative Su-Schrieffer-Heeger (SSH) and Pariser-Parr-Pople (PPP) calculations show that these models in their usual parametrizations cannot reproduce the ab initio results.

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

Jian, Tian; Lopez, Gary V.; Wang, Lai-Sheng, E-mail: Lai-Sheng-Wang@brown.edu

We report the observation of a manganese-centered tubular boron cluster (MnB{sub 16}{sup −}), which is characterized by photoelectron spectroscopy and ab initio calculations. The relatively simple pattern of the photoelectron spectrum indicates the cluster to be highly symmetric. Ab initio calculations show that MnB{sub 16}{sup −} has a Mn-centered tubular structure with C{sub 4v} symmetry due to first-order Jahn-Teller effect, while neutral MnB{sub 16} reduces to C{sub 2v} symmetry due to second-order Jahn-Teller effect. In MnB{sub 16}{sup −}, two unpaired electrons are observed, one on the Mn 3d{sub z{sup 2}} orbital and another on the B{sub 16} tube, making itmore » an unusual biradical. Strong covalent bonding is found between the Mn 3d orbitals and the B{sub 16} tube, which helps to stabilize the tubular structure. The current result suggests that there may exist a whole class of metal-stabilized tubular boron clusters. These metal-doped boron clusters provide a new bonding modality for transition metals, as well as a new avenue to design boron-based nanomaterials.« less

Predicting the reactivity of adhesive starting materials

Treesearch

Anthony H. Conner

1999-01-01

Phenolic compounds are important in the production of bonded-wood products. Phenolic compounds in addition to phenol and resorcinol are potential alternative feedstocks for producing adhesives. The reactivity of a wide variety of phenolic compounds with formaldehyde was investigated using semi-empirical and ab initio computational chemistry methods...

Alpha-1 adrenergic antagonists, 5-alpha reductase inhibitors, phosphodiesterase type 5 inhibitors, and phytotherapic compounds in men with lower urinary tract symptoms suggestive of benign prostatic obstruction: A systematic review and meta-analysis of urodynamic studies.

PubMed

Fusco, Ferdinando; Creta, Massimiliano; De Nunzio, Cosimo; Gacci, Mauro; Li Marzi, Vincenzo; Finazzi Agrò, Enrico

2018-03-31

To perform a systematic review and meta-analysis of studies evaluating the urodynamic outcomes of alpha-1 adrenergic antagonists (ABs), 5-alpha reductase inhibitors (5-ARIs), phosphodiesterase type 5 inhibitors (PDE5is), and phytotherapic compounds in patients with lower urinary tract symptoms related to benign prostatic obstruction (LUTS/BPO). A systematic review of PubMed/Medline, ISI Web of Knowledge, and Scopus databases was performed in June 2017. We included full papers that met the following criteria: original research; English language; human studies; enrolling LUTS/BPO patients; reporting maximum urinary flow (Qmax), and detrusor pressure at maximum urinary flow (PdetQmax). The primary endpoint was variation in bladder outlet obstruction index (BOOI). Secondary endpoints were variations in Qmax and PdetQmax. Twenty-three studies involving 1044 patients were included in the final analysis. Eighteen, three, two, and one study evaluated the urodynamic outcomes of ABs, 5-ARIs, PDE5is, and phytotherapic compounds, respectively. BOOI, PdetQmax, and Qmax improved in a statistically significant manner in patients receiving ABs and in those receiving 5-ARIs. The overall pooled data showed a mean BOOI change of -15.40 (P < 0.00001) and of -10.55 (P = 0,004) for ABs and 5-ARIs, respectively. Mean PdetQmax and Qmax changes were:12.30 cm H 2 O (P < 0.00001) and +2.27 ml/s (P < 0.00001) for ABs and -9.63 cm H 2 O (P = 0.05), and +1.18 mL/s (P = 0.04) for 5-ARIs. PDE5is and phytotherapic compounds had no significant effects on urodynamic parameters. ABs and 5-ARIs efficiently improve BOOI in men with LUTS/BPO. Both treatments are associated with a clinically significant decrease in PdetQmax but only marginal improvements in Qmax. © 2018 Wiley Periodicals, Inc.

Synthesis, pharmacological activities and molecular docking studies of pyrazolyltriazoles as anti-bacterial and anti-inflammatory agents.

PubMed

Dayakar, Cherupally; Kumar, Buddana Sudheer; Sneha, Galande; Sagarika, Gudem; Meghana, Koneru; Ramakrishna, Sistla; Prakasham, Reddy Shetty; China Raju, Bhimapaka

2017-10-15

A series of novel pyrazolyl alcohols (5a-h), pyrazolyl azides (6a-h), and pyrazolyltriazoles (8a-h, 10a-p and 12a-l) were prepared and evaluated for their bioactivity (anti-bacterial and anti-inflammatory) profile. The compound 5c displayed the potent anti-bacterial activity against Micrococcus luteus (MIC 3.9 and MBC 7.81µg/mL). In vitro anti-inflammatory activity data denoted that compound 8b is effective among the tested compounds against IL-6 (IC 50 6.23μM). Docking analysis of compounds 5f, 8a-b, 8e-f and 8h displayed high binding energies for the compounds 8a-b and 8h towards TNF-α dimer (2AZ5 protein) and IL-6 (1ALU protein). In vivo anti-inflammatory activity of compounds 8b and 8h with respect to LPS induced mice model indicated that compound 8h showed significant reduction in TNF-α. Copyright © 2017 Elsevier Ltd. All rights reserved.

Visual Field Map Clusters in High-Order Visual Processing: Organization of V3A/V3B and a New Cloverleaf Cluster in the Posterior Superior Temporal Sulcus

PubMed Central

Barton, Brian; Brewer, Alyssa A.

2017-01-01

The cortical hierarchy of the human visual system has been shown to be organized around retinal spatial coordinates throughout much of low- and mid-level visual processing. These regions contain visual field maps (VFMs) that each follows the organization of the retina, with neighboring aspects of the visual field processed in neighboring cortical locations. On a larger, macrostructural scale, groups of such sensory cortical field maps (CFMs) in both the visual and auditory systems are organized into roughly circular cloverleaf clusters. CFMs within clusters tend to share properties such as receptive field distribution, cortical magnification, and processing specialization. Here we use fMRI and population receptive field (pRF) modeling to investigate the extent of VFM and cluster organization with an examination of higher-level visual processing in temporal cortex and compare these measurements to mid-level visual processing in dorsal occipital cortex. In human temporal cortex, the posterior superior temporal sulcus (pSTS) has been implicated in various neuroimaging studies as subserving higher-order vision, including face processing, biological motion perception, and multimodal audiovisual integration. In human dorsal occipital cortex, the transverse occipital sulcus (TOS) contains the V3A/B cluster, which comprises two VFMs subserving mid-level motion perception and visuospatial attention. For the first time, we present the organization of VFMs in pSTS in a cloverleaf cluster. This pSTS cluster contains four VFMs bilaterally: pSTS-1:4. We characterize these pSTS VFMs as relatively small at ∼125 mm2 with relatively large pRF sizes of ∼2–8° of visual angle across the central 10° of the visual field. V3A and V3B are ∼230 mm2 in surface area, with pRF sizes here similarly ∼1–8° of visual angle across the same region. In addition, cortical magnification measurements show that a larger extent of the pSTS VFM surface areas are devoted to the peripheral visual field than those in the V3A/B cluster. Reliability measurements of VFMs in pSTS and V3A/B reveal that these cloverleaf clusters are remarkably consistent and functionally differentiable. Our findings add to the growing number of measurements of widespread sensory CFMs organized into cloverleaf clusters, indicating that CFMs and cloverleaf clusters may both be fundamental organizing principles in cortical sensory processing. PMID:28293182

Accurate ab initio quartic force fields for borane and BeH2

NASA Technical Reports Server (NTRS)

Martin, J. M. L.; Lee, Timothy J.

1992-01-01

The quartic force fields of BH3 and BeH2 have been computed ab initio using an augmented coupled cluster (CCSD(T)) method and basis sets of spdf and spdfg quality. For BH3, the computed spectroscopic constants are in very good agreement with recent experimental data, and definitively confirm misassignments in some older work, in agreement with recent ab initio studies. Using the computed spectroscopic constants, the rovibrational partition function for both molecules has been constructed using a modified direct numerical summation algorithm, and JANAF-style thermochemical tables are presented.

Comparison of methods for determining volatile compounds in milk, cheese, and whey powder

USDA-ARS?s Scientific Manuscript database

Solid phase microextraction (SPME) and gas chromatography-mass spectrometry (GC-MS) are commonly used for qualitative and quantitative analysis of volatile compounds in various dairy products, but conditions have to be adjusted for optimal SPME release while not generating new compounds that are abs...

Structural properties and glass transition in Aln clusters

NASA Astrophysics Data System (ADS)

Sun, D. Y.; Gong, X. G.

1998-02-01

We have studied the structural and dynamical properties of several Aln clusters by the molecular-dynamics method combined with simulated annealing. The well-fitted glue potential is used to describe the interatomic interaction. The obtained atomic structures for n=13, 55, and 147 are in agreement with results from ab initio calculations. Our results have demonstrated that the disordered cluster Al43 can be considered as a glass cluster. The obtained thermal properties of glass cluster Al43 are clearly different from the results for high-symmetry clusters, its melting behavior has properties similar to those of a glass solid. The present studies also show that the surface melting behavior does not exist in the studied Aln clusters.

An Overview of the History of Cluster Conferences

NASA Astrophysics Data System (ADS)

Horiuchi, H.

2017-06-01

An overview is given on the historical development of the cluster conference series which started at Bohum in 1969. I start with the discussion of the philosophy of Karl Wildermuth and then I make a review on the main subjects and topics in cluster conferences. Since the cluster dynamics is a main nuclear dynamics together with the mean-field dynamics, we see that development of the cluster conference has been along with the rises of many new subjects in nuclear physics itself. Examples of them include superheavy nuclei, nuclear astrophysics, neutron-rich nuclei, cluster-gas states and ab initio calculations. Finally I discuss that more activities in and attention to cluster physics are seen in recent days.

Deep eutectic solvents: similia similibus solvuntur?

PubMed

Zahn, Stefan

2017-02-01

Deep eutectic solvents, mixtures of an organic compound and a salt with a deep eutectic melting point, are promising cheap and eco-friendly alternatives to ionic liquids. Ab initio molecular dynamics simulations of reline, a mixture consisting of urea and choline chloride, reveal that not solely hydrogen bonds allow similar interactions between both constituents. The chloride anion and the oxygen atom of urea also show a similar spatial distribution close to the cationic core of choline due to a similar charge located on both atoms. As a result of multiple similar interactions, clusters migrating together cannot be observed in reline which supports the hypothesis similia similibus solvuntur. In contrast to previous suggestions, the interaction of the hydroxyl group of choline with a hydrogen bond acceptor is overall rigid. Fast hydrogen bond acceptor dynamics is facilitated by the hydrogen atoms in the trans position to the carbonyl group of urea which contributes to the low melting point of reline.

Experimental and ab initio molecular dynamics simulation studies of liquid Al60Cu40 alloy

NASA Astrophysics Data System (ADS)

Wang, S. Y.; Kramer, M. J.; Xu, M.; Wu, S.; Hao, S. G.; Sordelet, D. J.; Ho, K. M.; Wang, C. Z.

2009-04-01

X-ray diffraction and ab initio molecular dynamics simulation studies of molten Al60Cu40 have been carried out between 973 and 1323 K. The structures obtained from our simulated atomic models are fully consistent with the experimental results. The local structures of the models analyzed using Honeycutt-Andersen and Voronoi tessellation methods clearly demonstrate that as the temperatures of the liquid is lowered it becomes more ordered. While no one cluster-type dominates the local structure of this liquid, the most prevalent polyhedra in the liquid structure can be described as distorted icosahedra. No obvious correlations between the clusters observed in the liquid and known stable crystalline phases in this system were observed.

Biomimetic synthesis, antimicrobial, antileishmanial and antimalarial activities of euglobals and their analogues.

PubMed

Bharate, Sandip B; Bhutani, Kamlesh K; Khan, Shabana I; Tekwani, Babu L; Jacob, Melissa R; Khan, Ikhlas A; Singh, Inder Pal

2006-03-15

In the present communication, naturally occurring phloroglucinol-monoterpene adducts, euglobals G1-G4 (3b/a and 4a/b) and 16 new analogues (13a/b-18a/b and 19-22) were synthesized by biomimetic approach. These synthetic compounds differ from natural euglobals in the nature of monoterpene and acyl functionality. All of these compounds were evaluated for their antibacterial, antifungal, antileishmanial and antimalarial activities. Analogue 17b possessed good antibacterial activity against methicillin-resistant Staphylococcus aureus, while analogues 19-22 possessed potent antifungal activity against Candida glabrata with IC50s ranging from 1.5 to 2.5 microg/mL. Euglobals along with all synthesized analogues exhibited antileishmanial activity. Amongst these, euglobal G2 (3a), G3 (4a) and analogues 13a and 14a showed potent antileishmanial activity with IC50s ranging from 2.8 to 3.9 microg/mL. Analogue 16a possessed antimalarial activity against chloroquine sensitive D6 clone of Plasmodium falciparum. None of the compounds showed toxicity against mammalian kidney fibroblasts (vero cells) upto the concentration of 4.76 microg/ml.

Low work function, stable compound clusters and generation process

DOEpatents

Dinh, Long N.; Balooch, Mehdi; Schildbach, Marcus A.; Hamza, Alex V.; McLean, II, William

2000-01-01

Low work function, stable compound clusters are generated by co-evaporation of a solid semiconductor (i.e., Si) and alkali metal (i.e., Cs) elements in an oxygen environment. The compound clusters are easily patterned during deposition on substrate surfaces using a conventional photo-resist technique. The cluster size distribution is narrow, with a peak range of angstroms to nanometers depending on the oxygen pressure and the Si source temperature. Tests have shown that compound clusters when deposited on a carbon substrate contain the desired low work function property and are stable up to 600.degree. C. Using the patterned cluster containing plate as a cathode baseplate and a faceplate covered with phosphor as an anode, one can apply a positive bias to the faceplate to easily extract electrons and obtain illumination.

The binding property of a monoclonal antibody against the extracellular domains of aquaporin-4 directs aquaporin-4 toward endocytosis.

PubMed

Huang, Ping; Takai, Yoshiki; Kusano-Arai, Osamu; Ramadhanti, Julia; Iwanari, Hiroko; Miyauchi, Takayuki; Sakihama, Toshiko; Han, Jing-Yan; Aoki, Masashi; Hamakubo, Takao; Fujihara, Kazuo; Yasui, Masato; Abe, Yoichiro

2016-09-01

Neuromyelitis optica (NMO), an autoimmune disease of the central nervous system, is characterized by an autoantibody called NMO-IgG that recognizes the extracellular domains (ECDs) of aquaporin-4 (AQP4). In this study, monoclonal antibodies (mAbs) against the ECDs of mouse AQP4 were established by a baculovirus display method. Two types of mAb were obtained: one (E5415A) recognized both M1 and M23 isoforms, and the other (E5415B) almost exclusively recognized the square-array-formable M23 isoform. While E5415A enhanced endocytosis of both M1 and M23, followed by degradation in cells expressing AQP4, including astrocytes, E5415B did so to a much lesser degree, as determined by live imaging using fluorescence-labeled antibodies and by Western blotting of lysate of cells treated with these mAbs. E5415A promoted cluster formation of AQP4 on the cell surface prior to endocytosis as determined by immunofluorescent microscopic observation of bound mAbs to astrocytes as well as by Blue native PAGE analysis of AQP4 in the cells treated with the mAbs. These observations clearly indicate that an anti-AQP4-ECDs antibody possessing an ability to form a large cluster of AQP4 by cross-linking two or more tetramers outside the AQP4 arrays enhances endocytosis and the subsequent lysosomal degradation of AQP4.

Ba9V3Se15: a novel compound with spin chains

NASA Astrophysics Data System (ADS)

Zhang, Jun; Liu, Min; Wang, Xiancheng; Zhao, Kan; Duan, Lei; Li, Wenmin; Zhao, Jianfa; Cao, Lipeng; Dai, Guangyang; Deng, Zheng; Feng, Shaomin; Zhang, Sijia; Liu, Qingqing; Yang, Yi-feng; Jin, Changqing

2018-05-01

In this work, a novel compound Ba9V3Se15 with one-dimensional (1D) spin chains was synthesized under high-pressure and high-temperature conditions. It was systematically characterized via structural, magnetic, thermodynamic and transport measurements. Ba9V3Se15 crystallizes into a hexagonal structure with a space group of P-6c2 (188) and the lattice constants of a  =  b  =  9.5745(7) Å and c  =  18.7814(4) Å. The crystal structure consists of face-sharing octahedral VSe6 chains along c axis, which are trimeric and arranged in a triangular lattice in ab-plane. Ba9V3Se15 is a semiconductor and undergoes complex magnetic transitions. In the zero-field-cooled (ZFC) process with magnetic field of 10 Oe, Ba9V3Se15 sequentially undergoes ferrimagnetic and spin cluster glass transition at 2.5 K and 3.3 K, respectively. When the magnetic field exceeds 50 Oe, only the ferrimagnetic transition can be observed. Above the transition temperature, the specific heat contains a significant magnetic contribution that is proportional to T 1/2. The calculation suggests that the nearest neighbor (NN) intra-chain antiferromagnetic exchange J 1 is much larger than the next nearest neighbor (NNN) intra-chain ferromagnetic exchange J 2. Therefore, Ba9V3Se15 can be regarded as an effective ferromagnetic chains with effective spin-1/2 by the formation of the V(2)(↓) V(1)(↑) V(2)(↓) cluster.

Synthesis and biological activity of novel series of 4-methoxy, and 4,9-dimethoxy-5-substituted furo[2,3-g]-1,2,3-benzoxathiazine-7,7-dioxide derivatives

PubMed Central

El-Sawy, Eslam R.; Ebaid, Manal S.; Abo-Salem, Heba M.; El-Hallouty, Salwa; Kassem, Emad M.; Mandour, Adel H.

2013-01-01

A novel series of 4-methoxy, and 4,9-dimethoxy-5-substituted furo[2,3-g]-1,2,3-benzoxathiazine-7,7-dioxide derivatives 3a,b, 10a–g and 11a–g were prepared in good yields via the reaction of 4-methoxy (1a) and 4,7-dimethoxy-5-acetyl-6-hydroxybenzofurans (1b) and their α,β-unsaturated keto derivatives 6a–g and 7a–g with chlorosulfonyl isocyanate (CSI). On the other hand, N-chlorosulfonyl carbamate derivatives 4a,b, 12a,b and 13a,b were prepared and allowed to react with piperidine to give the corresponding N-piperidinosulfonyl carbamate derivatives 5a,b, 14a,b and 15a,b, respectively. Sixteen new target compounds 3a,b, 10a–g, and 11a–g were tested for their DPPH radical-scavenging, and in vitro antiproliferative activity against A-549, MCF7 and HCT-116 cancer cell lines. Compounds 10a, 11c, 11e, and 11g showed moderate DPPH radical-scavenging activity compared to ascorbic acid at 100 μg/mL. 4,9-Dimethoxy-5-substituted styrylfuro[3,2-g]-1,2,3-benzoxathiazine-7,7-dioxides 11a, 11b, and 11c were found to be highly active against A-549 and HCT-116 cancer cell lines with IC50 values ranging from 0.02 to 0.08 μmol/mL compared to doxorubicin with IC50 = 0.04 and 0.06 μmol/mL, respectively. PMID:25685501

Synthesis and biological activity of novel series of 4-methoxy, and 4,9-dimethoxy-5-substituted furo[2,3-g]-1,2,3-benzoxathiazine-7,7-dioxide derivatives.

PubMed

El-Sawy, Eslam R; Ebaid, Manal S; Abo-Salem, Heba M; El-Hallouty, Salwa; Kassem, Emad M; Mandour, Adel H

2014-05-01

A novel series of 4-methoxy, and 4,9-dimethoxy-5-substituted furo[2,3-g]-1,2,3-benzoxathiazine-7,7-dioxide derivatives 3a,b, 10a-g and 11a-g were prepared in good yields via the reaction of 4-methoxy (1a) and 4,7-dimethoxy-5-acetyl-6-hydroxybenzofurans (1b) and their α,β-unsaturated keto derivatives 6a-g and 7a-g with chlorosulfonyl isocyanate (CSI). On the other hand, N-chlorosulfonyl carbamate derivatives 4a,b, 12a,b and 13a,b were prepared and allowed to react with piperidine to give the corresponding N-piperidinosulfonyl carbamate derivatives 5a,b, 14a,b and 15a,b, respectively. Sixteen new target compounds 3a,b, 10a-g, and 11a-g were tested for their DPPH radical-scavenging, and in vitro antiproliferative activity against A-549, MCF7 and HCT-116 cancer cell lines. Compounds 10a, 11c, 11e, and 11g showed moderate DPPH radical-scavenging activity compared to ascorbic acid at 100 μg/mL. 4,9-Dimethoxy-5-substituted styrylfuro[3,2-g]-1,2,3-benzoxathiazine-7,7-dioxides 11a, 11b, and 11c were found to be highly active against A-549 and HCT-116 cancer cell lines with IC50 values ranging from 0.02 to 0.08 μmol/mL compared to doxorubicin with IC50 = 0.04 and 0.06 μmol/mL, respectively.

Thiopyridazine-Based Palladium and Platinum Boratrane Complexes.

PubMed

Holler, Stefan; Tüchler, Michael; Steller, Beate G; Belaj, Ferdinand; Veiros, Luis F; Kirchner, Karl; Mösch-Zanetti, Nadia C

2018-06-07

Palladium and platinum boratrane complexes of the type [M{B(Pn Me, tBu ) 3 }(PPh 3 )] (M = Pd 1, Pt 2b) have been prepared via the reaction of the soft scorpionate ligand potassium tris(4-methyl-6- tert-butyl-3-thiopyridazinyl)borate KTn Me, tBu with bis(triphenylphosphine)metal(II) dichloride. While reaction with the Pd precursor allowed direct isolation of a symmetric boratrane complex, the Pt analogue led to the hydrido compound [Pt{B(Pn Me, tBu ) 3 }(PPh 3 )H]Cl (2a), which after reaction with a base gave 2b. Subsequent oxidation with Br 2 and I 2 , respectively, led to the dihalide compounds of the molecular formula [M{B(Pn Me, tBu ) 3 }X 2 ] (3a,b-4a,b). Halide abstraction with Ag(SbF 6 ) further gave interesting cationic compounds of either dimeric [Pd{B(Pn Me, tBu ) 3 }X] 2 (SbF 6 ) 2 (5a,b) or monomeric [Pd{B(Pn Me, tBu ) 3 }(NCMe) 2 ](SbF 6 ) (6) nature. All compounds were spectroscopically and X-ray crystallographically characterized revealing strong metal to boron interactions. DFT calculations of 1, 2a, and 2b confirm the strong M-B interaction and a high positive charge on the metal centers.

Anti-inflammatory potential of ellagic acid, gallic acid and punicalagin A&B isolated from Punica granatum.

PubMed

BenSaad, Lamees A; Kim, Kah Hwi; Quah, Chin Chew; Kim, Wee Ric; Shahimi, Mustafa

2017-01-14

Punica granatum (pomegranate), an edible fruit originating in the Middle East, has been used as a traditional medicine for treatment of pain and inflammatory conditions such as peptic ulcer. The numerous risks associated with nonsteroidal anti-inflammatory drugs (NSAIDs) for treatment of pain and inflammation give rise to using medicinal herbs as alternative therapies. This study aimed to evaluate the anti-inflammatory effect of isolated compounds from the ethyl acetate (EtOAc) fraction of P. granatum by determination of their inhibitory effects on lipopolysaccharide (LPS), stimulated nitric oxide (NO), prostaglandin E2 (PGE-2), interleukin-6 (IL-6) and cyclooxxgenase-2 (COX-2) release from RAW264.7 cells. The compounds ellagic acid, gallic acid and punicalagin A&B were isolated from EtOAc by high performance liquid chromatography (HPLC) and further identified by mass spectrometry (MS). The inhibitory effect of ellagic acid, gallic acid and punicalagin A&B were evaluated on the production of LPS-induced NO by Griess reagent, PGE-2 and IL-6 by immunoassay kit and prostaglandin E2 competitive ELISA kit, and COX-2 by Western blotting. Ellagic acid, gallic acid and punicalagin A&B potentially inhibited LPS-induced NO, PGE-2 and IL-6 production. The results indicate that ellagic acid, gallic acid and punicalagin may be the compounds responsible for the anti-inflammatory potential of P. granatum.

Dehalogenation of persistent halogenated organic compounds: A review of computational studies and quantitative structure-property relationships.

PubMed

Luo, Jin; Hu, Jiwei; Wei, Xionghui; Fu, Liya; Li, Lingyun

2015-07-01

Dehalogenation is one of the highly important degradation reactions for halogenated organic compounds (HOCs) in the environment, which is also being developed as a potential type of the remediation technologies. In combination with the experimental results, intensive efforts have recently been devoted to the development of efficient theoretical methodologies (e.g. multi-scale simulation) to investigate the mechanisms for dehalogenation of HOCs. This review summarizes the structural characteristics of neutral molecules, anionic species and excited states of HOCs as well as their adsorption behavior on the surface of graphene and the Fe cluster. It discusses the key physiochemical properties (e.g. frontier orbital energies and thermodynamic properties) calculated at various levels of theory (e.g. semiempirical, ab initio, density functional theory (DFT) and the periodic DFT) as well as their connections to the reactivity and reaction pathway for the dehalogenation. This paper also reviews the advances in the linear and nonlinear quantitative structure-property relationship models for the dehalogenation kinetics of HOCs and in the mathematical modeling of the dehalogenation processes. Furthermore, prospects of further expansion and exploration of the current research fields are described in this article. Published by Elsevier Ltd.

Introducing ab initio based neural networks for transition-rate prediction in kinetic Monte Carlo simulations

NASA Astrophysics Data System (ADS)

Messina, Luca; Castin, Nicolas; Domain, Christophe; Olsson, Pär

2017-02-01

The quality of kinetic Monte Carlo (KMC) simulations of microstructure evolution in alloys relies on the parametrization of point-defect migration rates, which are complex functions of the local chemical composition and can be calculated accurately with ab initio methods. However, constructing reliable models that ensure the best possible transfer of physical information from ab initio to KMC is a challenging task. This work presents an innovative approach, where the transition rates are predicted by artificial neural networks trained on a database of 2000 migration barriers, obtained with density functional theory (DFT) in place of interatomic potentials. The method is tested on copper precipitation in thermally aged iron alloys, by means of a hybrid atomistic-object KMC model. For the object part of the model, the stability and mobility properties of copper-vacancy clusters are analyzed by means of independent atomistic KMC simulations, driven by the same neural networks. The cluster diffusion coefficients and mean free paths are found to increase with size, confirming the dominant role of coarsening of medium- and large-sized clusters in the precipitation kinetics. The evolution under thermal aging is in better agreement with experiments with respect to a previous interatomic-potential model, especially concerning the experiment time scales. However, the model underestimates the solubility of copper in iron due to the excessively high solution energy predicted by the chosen DFT method. Nevertheless, this work proves the capability of neural networks to transfer complex ab initio physical properties to higher-scale models, and facilitates the extension to systems with increasing chemical complexity, setting the ground for reliable microstructure evolution simulations in a wide range of alloys and applications.

Clustering/anticlustering effects on the GeSi Raman spectra at moderate (Ge,Si) contents: Percolation scheme vs. ab initio calculations

NASA Astrophysics Data System (ADS)

Torres, V. J. B.; Hajj Hussein, R.; Pagès, O.; Rayson, M. J.

2017-02-01

We test a presumed ability behind the phenomenological percolation scheme used for the basic description of the multi-mode Raman spectra of mixed crystals at one dimension along the linear chain approximation, to determine, via the Raman intensities, the nature of the atom substitution, as to whether this is random or due to local clustering/anticlustering. For doing so, we focus on the model percolation-type GeySi1-y system characterized by six oscillators { 1 × ( G e - G e ) , 3 × ( G e - S i ) , 2 × ( S i - S i ) } and place the study around the critical compositions y ˜ (0.16, 0.71, and 0.84) corresponding to nearly matching of intensities between the like Raman modes from a given multiplet ( G e - S i triplet or S i - S i doublet). The interplay between the GeySi1-y Raman intensities predicted by the percolation scheme depending on a suitable order parameter κ of local clustering/anticlustering is found to be consistent with ab initio calculations of the GeySi1-y Raman spectra done with the Ab Initio Modeling PROgram code using large (64-, 216-, and 512-atoms) disordered cubic supercells matching the required ( y , κ ) values. The actual "percolation vs. ab initio" comparative insight at moderate/dilute-(Ge,Si) limits, with an emphasis on the κ -induced intra-bond transfer of oscillator strength, extends a pioneering one earlier achieved at an intermediate composition ( y ˜ 0.50) by using small (32-atom) supercells [O. Pagès et al., J. Appl. Phys. 114, 033513 (2013)], mainly concerned with the inter-bond transfer of oscillator strength, providing altogether a complete picture.

Magnetic and Electrical Transport Properties of Dirac Compound BaMnSb2*

NASA Astrophysics Data System (ADS)

Huang, Silu; Kim, Jisun; Shelton, William. A.; Plummer, Ward; Jin, Rongying

BaMnSb2 is a layered compound containing Sb square nets that is theoretically predicted to host Dirac fermions. We have carried out experimental investigations on electrical transport and magnetic properties of BaMnSb2 single crystals. Both in-plane (ρab) and c-axis (ρc) resistivities show metallic behavior with a small bump in ρc located near 40 K, while there is large anisotropy ρc / ρab ( 100 at 300 K) that increases with decreasing temperature to 1500 at 2 K. Interestingly, Shubnikov-de Hass (SdH) oscillations are observed for both ρab and ρc over a wide temperature and magnetic field range. Quantitative analysis indicates that large amplitude SdH oscillations result from nearly massless Dirac Fermions. Furthermore, our magnetic measurements indicate an A-type antiferromagnetic magnetic ordering below 286 K where ferromagnetic ordering is observed in the ab plane with antiferromagnetic coupling along the c direction. These results indicate that BaMnSb2 is a 2D magnetic Dirac material. This work is supported by NSF through Grant Number DMR-1504226.

Connecting the Particles in the Box - Controlled Fusion of Hexamer Nanocrystal Clusters within an AB6 Binary Nanocrystal Superlattice

PubMed Central

Treml, Benjamin E.; Lukose, Binit; Clancy, Paulette; Smilgies, Detlef-M; Hanrath, Tobias

2014-01-01

Binary nanocrystal superlattices present unique opportunities to create novel interconnected nanostructures by partial fusion of specific components of the superlattice. Here, we demonstrate the binary AB6 superlattice of PbSe and Fe2O3 nanocrystals as a model system to transform the central hexamer of PbSe nanocrystals into a single fused particle. We present detailed structural analysis of the superlattices by combining high-resolution X-ray scattering and electron microscopy. Molecular dynamics simulations show optimum separation of nanocrystals in agreement with the experiment and provide insights into the molecular configuration of surface ligands. We describe the concept of nanocrystal superlattices as a versatile ‘nanoreactor' to create and study novel materials based on precisely defined size, composition and structure of nanocrystals into a mesostructured cluster. We demonstrate ‘controlled fusion' of nanocrystals in the clusters in reactions initiated by thermal treatment and pulsed laser annealing. PMID:25339169

Single-particle cryo-EM-Improved ab initio 3D reconstruction with SIMPLE/PRIME.

PubMed

Reboul, Cyril F; Eager, Michael; Elmlund, Dominika; Elmlund, Hans

2018-01-01

Cryogenic electron microscopy (cryo-EM) and single-particle analysis now enables the determination of high-resolution structures of macromolecular assemblies that have resisted X-ray crystallography and other approaches. We developed the SIMPLE open-source image-processing suite for analysing cryo-EM images of single-particles. A core component of SIMPLE is the probabilistic PRIME algorithm for identifying clusters of images in 2D and determine relative orientations of single-particle projections in 3D. Here, we extend our previous work on PRIME and introduce new stochastic optimization algorithms that improve the robustness of the approach. Our refined method for identification of homogeneous subsets of images in accurate register substantially improves the resolution of the cluster centers and of the ab initio 3D reconstructions derived from them. We now obtain maps with a resolution better than 10 Å by exclusively processing cluster centers. Excellent parallel code performance on over-the-counter laptops and CPU workstations is demonstrated. © 2017 The Protein Society.

Energetics and solvation structure of a dihalogen dopant (I2) in (4)He clusters.

PubMed

Pérez de Tudela, Ricardo; Barragán, Patricia; Valdés, Álvaro; Prosmiti, Rita

2014-08-21

The energetics and structure of small HeNI2 clusters are analyzed as the size of the system changes, with N up to 38. The full interaction between the I2 molecule and the He atoms is based on analytical ab initio He-I2 potentials plus the He-He interaction, obtained from first-principle calculations. The most stable structures, as a function of the number of solvent He atoms, are obtained by employing an evolutionary algorithm and compared with CCSD(T) and MP2 ab initio computations. Further, the classical description is completed by explicitly including thermal corrections and quantum features, such as zero-point-energy values and spatial delocalization. From quantum PIMC calculations, the binding energies and radial/angular probability density distributions of the thermal equilibrium state for selected-size clusters are computed at a low temperature. The sequential formation of regular shell structures is analyzed and discussed for both classical and quantum treatments.

Discovery of phenylsulfonylfuroxan derivatives as gamma globin inducers by histone acetylation.

PubMed

Melo, Thais Regina Ferreira de; Kumkhaek, Chutima; Fernandes, Guilherme Felipe Dos Santos; Lopes Pires, Maria Elisa; Chelucci, Rafael Consolin; Barbieri, Karina Pereira; Coelho, Fernanda; Capote, Ticiana Sidorenko de Oliveira; Lanaro, Carolina; Carlos, Iracilda Zeppone; Marcondes, Sisi; Chegaev, Konstantin; Guglielmo, Stefano; Fruttero, Roberta; Chung, Man Chin; Costa, Fernando Ferreira; Rodgers, Griffin P; Dos Santos, Jean Leandro

2018-05-28

N-oxide derivatives 5(a-b), 8(a-b), and 11(a-c) were designed, synthesized and evaluated in vitro and in vivo as potential drugs that are able to ameliorate sickle cell disease (SCD) symptoms. All of the compounds demonstrated the capacity to releasing nitric oxide at different levels ranging from 0.8 to 30.1%, in vivo analgesic activity and ability to reduce TNF-α levels in the supernatants of monocyte cultures. The most active compound (8b) protected 50.1% against acetic acid-induced abdominal constrictions, while dipyrone, which was used as a control only protected 35%. Compounds 8a and 8b inhibited ADP-induced platelet aggregation by 84% and 76.1%, respectively. Both compounds increased γ-globin in K562 cells at 100 μM. The mechanisms involved in the γ-globin increase are related to the acetylation of histones H3 and H4 that is induced by these compounds. In vitro, the most promising compound (8b) was not cytotoxic, mutagenic and genotoxic. Copyright © 2018 Elsevier Masson SAS. All rights reserved.

X-ray structures of the anticoagulants coumatetralyl and chlorophacinone. Theoretical calculations and SAR investigations on thirteen anticoagulant rodenticides

NASA Astrophysics Data System (ADS)

Dolmella, A.; Gatto, S.; Girardi, E.; Bandoli, G.

1999-12-01

Coumatetralyl and chlorophacinone, two substances related to 4-hydroxycoumarin (HC) and to 1,3-indandione (ID), respectively, show activity as anticoagulant rodenticides. In the present study we have investigated the solid-state structures of coumatetralyl and chlorophacinone by means of X-ray single-crystal and powder diffraction, along with thermal analysis. The crystal structures of the two compounds have been used as input geometries for a series of computational chemistry efforts, involving other anticoagulant derivatives as well. Thus, ab initio, semiempirical molecular orbital, molecular mechanics and molecular dynamics/simulated annealing calculations have been performed on thirteen anticoagulant rodenticides. In particular, the annealing calculations have been made to assess the conformational freedom of the compounds under scrutiny. All the generated conformers have been classified into families. The classification has first been made empirically, and then validated by means of a cluster analysis. A number of structural and physico-chemical parameters derived from the calculations has been used in turn for structure-activity relationships (SARs) investigations. In the latter, we have assessed how the selected parameters affect toxicity. The results seem to be consistent with a three-dimensional biophore model, in which higher toxicity is predicted for the more voluminous rodenticides. We suggest that these compounds better fit the active site of the target enzyme vitamin K 2,3-epoxide reductase (KO-reductase).

Mapping Compound Cosmic Telescopes Containing Multiple Projected Cluster-scale Halos

NASA Astrophysics Data System (ADS)

Ammons, S. Mark; Wong, Kenneth C.; Zabludoff, Ann I.; Keeton, Charles R.

2014-01-01

Lines of sight with multiple projected cluster-scale gravitational lenses have high total masses and complex lens plane interactions that can boost the area of magnification, or étendue, making detection of faint background sources more likely than elsewhere. To identify these new "compound" cosmic telescopes, we have found directions in the sky with the highest integrated mass densities, as traced by the projected concentrations of luminous red galaxies (LRGs). We use new galaxy spectroscopy to derive preliminary magnification maps for two such lines of sight with total mass exceeding ~3 × 1015 M ⊙. From 1151 MMT Hectospec spectra of galaxies down to i AB = 21.2, we identify two to three group- and cluster-scale halos in each beam. These are well traced by LRGs. The majority of the mass in beam J085007.6+360428 (0850) is contributed by Zwicky 1953, a massive cluster at z = 0.3774, whereas beam J130657.5+463219 (1306) is composed of three halos with virial masses of 6 × 1014-2 × 1015 M ⊙, one of which is A1682. The magnification maps derived from our mass models based on spectroscopy and Sloan Digital Sky Survey photometry alone display substantial étendue: the 68% confidence bands on the lens plane area with magnification exceeding 10 for a source plane of zs = 10 are [1.2, 3.8] arcmin2 for 0850 and [2.3, 6.7] arcmin2 for 1306. In deep Subaru Suprime-Cam imaging of beam 0850, we serendipitously discover a candidate multiply imaged V-dropout source at z phot = 5.03. The location of the candidate multiply imaged arcs is consistent with the critical curves for a source plane of z = 5.03 predicted by our mass model. Incorporating the position of the candidate multiply imaged galaxy as a constraint on the critical curve location in 0850 narrows the 68% confidence band on the lens plane area with μ > 10 and zs = 10 to [1.8, 4.2] arcmin2, an étendue range comparable to that of MACS 0717+3745 and El Gordo, two of the most powerful single cluster lenses known. The significant lensing power of our beams makes them powerful probes of reionization and galaxy formation in the early universe.

MacA, a periplasmic membrane fusion protein of the macrolide transporter MacAB-TolC, binds lipopolysaccharide core specifically and with high affinity.

PubMed

Lu, Shuo; Zgurskaya, Helen I

2013-11-01

The Escherichia coli MacAB-TolC transporter has been implicated in efflux of macrolide antibiotics and secretion of enterotoxin STII. In this study, we found that purified MacA, a periplasmic membrane fusion protein, contains one tightly bound rough core lipopolysaccharide (R-LPS) molecule per MacA molecule. R-LPS was bound specifically to MacA protein with affinity exceeding that of polymyxin B. Sequence analyses showed that MacA contains two high-density clusters of positively charged amino acid residues located in the cytoplasmic N-terminal domain and the periplasmic C-terminal domain. Substitutions in the C-terminal cluster reducing the positive-charge density completely abolished binding of R-LPS. At the same time, these substitutions significantly reduced the functionality of MacA in the protection of E. coli against macrolides in vivo and in the in vitro MacB ATPase stimulation assays. Taken together, our results suggest that R-LPS or a similar glycolipid is a physiological substrate of MacAB-TolC.

MacA, a Periplasmic Membrane Fusion Protein of the Macrolide Transporter MacAB-TolC, Binds Lipopolysaccharide Core Specifically and with High Affinity

PubMed Central

Lu, Shuo

2013-01-01

The Escherichia coli MacAB-TolC transporter has been implicated in efflux of macrolide antibiotics and secretion of enterotoxin STII. In this study, we found that purified MacA, a periplasmic membrane fusion protein, contains one tightly bound rough core lipopolysaccharide (R-LPS) molecule per MacA molecule. R-LPS was bound specifically to MacA protein with affinity exceeding that of polymyxin B. Sequence analyses showed that MacA contains two high-density clusters of positively charged amino acid residues located in the cytoplasmic N-terminal domain and the periplasmic C-terminal domain. Substitutions in the C-terminal cluster reducing the positive-charge density completely abolished binding of R-LPS. At the same time, these substitutions significantly reduced the functionality of MacA in the protection of E. coli against macrolides in vivo and in the in vitro MacB ATPase stimulation assays. Taken together, our results suggest that R-LPS or a similar glycolipid is a physiological substrate of MacAB-TolC. PMID:23974027

Structural and electronic transport properties of compound forming HgPb liquid alloy using ab-initio pseudopotential

NASA Astrophysics Data System (ADS)

Sharma, Nalini; Thakur, Anil; Ahluwalia, P. K.

2013-02-01

The electrical resistivity of compound forming liquid alloy HgPb is studied as a function of concentration. Hard sphere diameters of Hg and Pb are obtained through the inter-ionic pair potential evaluated using Troullier and Martins ab initio pseudopotential, which have been used to calculate partial structure factors. Considering the liquid alloy to be a ternary mixture Ziman's formula for calculating the resistivity of binary liquid alloys, modified for complex formation, has been used. The concentration dependence in resistivity occurs due to preferential ordering of unlike atoms as nearest neighbours with help of complex formation model. Though the compound HgiPbi as per structure peaks is found to be less stable. However it contributes significantly to resistivity as compared to bare ions.

Classification of octet AB-type binary compounds using dynamical charges: A materials informatics perspective

DOE PAGES

Pilania, G.; Gubernatis, J. E.; Lookman, T.

2015-12-03

The role of dynamical (or Born effective) charges in classification of octet AB-type binary compounds between four-fold (zincblende/wurtzite crystal structures) and six-fold (rocksalt crystal structure) coordinated systems is discussed. We show that the difference in the dynamical charges of the fourfold and sixfold coordinated structures, in combination with Harrison’s polarity, serves as an excellent feature to classify the coordination of 82 sp–bonded binary octet compounds. We use a support vector machine classifier to estimate the average classification accuracy and the associated variance in our model where a decision boundary is learned in a supervised manner. Lastly, we compare the out-of-samplemore » classification accuracy achieved by our feature pair with those reported previously.« less

An elemental model of retrospective revaluation without within-compound associations.

PubMed

Connor, Patrick C; Lolordo, Vincent M; Trappenberg, Thomas P

2014-03-01

When retrospective revaluation phenomena (e.g., unovershadowing: AB+, then A-, then test B) were discovered, simple elemental models were at a disadvantage because they could not explain such phenomena. Extensions of these models and novel models appealed to within-compound associations to accommodate these new data. Here, we present an elemental, neural network model of conditioning that explains retrospective revaluation apart from within-compound associations. In the model, previously paired stimuli (say, A and B, after AB+) come to activate similar ensembles of neurons, so that revaluation of one stimulus (A-) has the opposite effect on the other stimulus (B) through changes (decreases) in the strength of the inhibitory connections between neurons activated by B. The ventral striatum is discussed as a possible home for the structure and function of the present model.

Ab-initio calculations of the Ruddlesden Popper phases CaMnO3, CaO(CaMnO3) and CaO(CaMnO3)2

NASA Astrophysics Data System (ADS)

Cardoso, C.; Borges, R. P.; Gasche, T.; Godinho, M.

2008-01-01

The present work reports ab-initio density functional theory calculations for the Ruddlesden-Popper phase CaO(CaMnO3)n compounds. In order to study the evolution of the properties with the number of perovskite layers, a detailed analysis of the densities of states calculated for each compound and for several magnetic configurations was performed. The effect of distortions of the crystal structure on the magnetic ground state is also analysed and the exchange constants and transition temperatures are calculated for the three compounds using a mean field model. The calculated magnetic ground state structures and magnetic moments are in good agreement with experimental results and previous calculations.

Synthesis and anti-microbial activity of some 1- substituted amino-4,6-dimethyl-2-oxo-pyridine-3-carbonitrile derivatives.

PubMed

Khidre, Rizk E; Abu-Hashem, Ameen A; El-Shazly, Mohamed

2011-10-01

A new series of 1- substituted amino-4,6-dimethyl-2-oxo-pyridine-3-carbonitrile such as hydrazide hydrazones 3a-h; ethane-1,2-diaminopyridine 6; phthalimidopyridines 8a,b; hydrazides 10a,b; urea 11a and thiourea 11b were synthesized in a good to excellent yield in step efficient process, using 1-amino-4,6-dimethyl-2-oxo-1,2-dihydropyridine-3-carbonitrile (1) as a key intermediate. The antibacterial and antifungal activities of the synthesized compounds were evaluated. The obtained data indicated that the majority of the tested compounds exhibited both antibacterial and antifungal activities, particularly compounds 8a and 8b showed a comparable effect to a well known antibacterial and antifungal agents. Published by Elsevier Masson SAS.

Ab initio study of MF2 (M=Mn, Fe, Co, Ni) rutile-type compounds using the periodic unrestricted Hartree-Fock approach

NASA Astrophysics Data System (ADS)

de P. R. Moreira, Ibério; Dovesi, Roberto; Roetti, Carla; Saunders, Victor R.; Orlando, Roberto

2000-09-01

The ab initio periodic unrestricted Hartree-Fock method has been applied in the investigation of the ground-state structural, electronic, and magnetic properties of the rutile-type compounds MF2 (M=Mn, Fe, Co, and Ni). All electron Gaussian basis sets have been used. The systems turn out to be large band-gap antiferromagnetic insulators; the optimized geometrical parameters are in good agreement with experiment. The calculated most stable electronic state shows an antiferromagnetic order in agreement with that resulting from neutron scattering experiments. The magnetic coupling constants between nearest-neighbor magnetic ions along the [001], [111], and [100] (or [010]) directions have been calculated using several supercells. The resulting ab initio magnetic coupling constants are reasonably satisfactory when compared with available experimental data. The importance of the Jahn-Teller effect in FeF2 and CoF2 is also discussed.

Exploring the speed and performance of molecular replacement with AMPLE using QUARK ab initio protein models.

PubMed

Keegan, Ronan M; Bibby, Jaclyn; Thomas, Jens; Xu, Dong; Zhang, Yang; Mayans, Olga; Winn, Martyn D; Rigden, Daniel J

2015-02-01

AMPLE clusters and truncates ab initio protein structure predictions, producing search models for molecular replacement. Here, an interesting degree of complementarity is shown between targets solved using the different ab initio modelling programs QUARK and ROSETTA. Search models derived from either program collectively solve almost all of the all-helical targets in the test set. Initial solutions produced by Phaser after only 5 min perform surprisingly well, improving the prospects for in situ structure solution by AMPLE during synchrotron visits. Taken together, the results show the potential for AMPLE to run more quickly and successfully solve more targets than previously suspected.

Broad spectrum antibiotic compounds and use thereof

DOEpatents

Koglin, Alexander; Strieker, Matthias

2016-07-05

The discovery of a non-ribosomal peptide synthetase (NRPS) gene cluster in the genome of Clostridium thermocellum that produces a secondary metabolite that is assembled outside of the host membrane is described. Also described is the identification of homologous NRPS gene clusters from several additional microorganisms. The secondary metabolites produced by the NRPS gene clusters exhibit broad spectrum antibiotic activity. Thus, antibiotic compounds produced by the NRPS gene clusters, and analogs thereof, their use for inhibiting bacterial growth, and methods of making the antibiotic compounds are described.

A Computational Study of Rare Gas Clusters: Stepping Stones to the Solid State

ERIC Educational Resources Information Center

Glendening, Eric D.; Halpern, Arthur M.

2012-01-01

An upper-level undergraduate or beginning graduate project is described in which students obtain the Lennard-Jones 6-12 potential parameters for Ne[subscript 2] and Ar[subscript 2] from ab initio calculations and use the results to express pairwise interactions between the atoms in clusters containing up to N = 60 atoms. The students use simulated…

Gd@Au15: A magic magnetic gold cluster for cancer therapy and bioimaging

NASA Astrophysics Data System (ADS)

Yadav, Brahm Deo; Kumar, Vijay

2010-09-01

We report from ab initio calculations a magic magnetic cage cluster of gold, Gd@Au15, obtained by doping of a Gd atom in gold clusters. It has a highest occupied molecular orbital-lowest unoccupied molecular orbital gap of 1.31 eV within the generalized gradient approximation that makes it a potential candidate for cancer therapy with an additional attractive feature that its large magnetic moment of 7 μB could be beneficial for magnetic resonance imaging.

Invasive Species Management on Military Lands: Clustered Regularly Interspaced Short Palindromic Repeat/ CRISPR associated protein 9 (CRISPR/Cas9) based Gene Drives

DTIC Science & Technology

2017-06-30

Clustered Regularly Interspaced Short Palindromic Repeat/ CRISPR -associated protein 9 ( CRISPR /Cas9)-based Gene Drives En vi ro nm en ta l L ab or at...Management on Military Lands Clustered Regularly Interspaced Short Palindromic Repeat/ CRISPR -associated protein 9 ( CRISPR /Cas9)-based Gene Drives Ping... CRISPR /Cas9-based Gene Drives for Invasive Species Management on Military Lands” ERDC/EL SR-17-2 ii Abstract Applications of genetic engineering

Structures and energetics of hydrated deprotonated cis-pinonic acid anion clusters and their atmospheric relevance

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

Hou, Gao-Lei; Zhang, Jun; Valiev, Marat

2017-01-01

Pinonic acid, a C10-monocarboxylic acid with a hydrophilic –CO 2H group and a hydrophobic hydrocarbon backbone, is a key intermediate oxidation product of α-pinene – an important monoterpene compound in biogenic emission processes that influences the atmosphere. Molecular interaction between cis-pinonic acid and water is essential for understanding its role in the formation and growth of pinene-derived secondary organic aerosols. In this work, we studied the structures, energetics, and optical properties of hydrated clusters of cis-pinonate anion (cPA–), the deprotonated form of cis-pinonic acid, by negative ion photoelectron spectroscopy and ab initio theoretical calculations. Our results show that cPA– canmore » adopt two different structural configurations – open and folded. In the absence of waters, the open configuration has the lowest energy and provides the best agreement with the experiment. The addition waters, which mainly interact with the negatively charged -CO 2– group, gradually stabilize the folded configuration and lower its energy difference relative to the most stable open-configured structure. Thermochemical and equilibrium hydrate distribution analysis suggests that the mono- and di- hydrates are likely to exist in humid atmospheric environment with high populations. The detailed molecular description of cPA– hydrated clusters unraveled in this study provides a valuable reference for understanding the initial nucleation process and aerosol formation involving organics containing both hydrophilic and hydrophobic groups, as well as for analyzing the optical properties of those organic aerosols.« less

Superior ab initio identification, annotation and characterisation of TEs and segmental duplications from genome assemblies.

PubMed

Zeng, Lu; Kortschak, R Daniel; Raison, Joy M; Bertozzi, Terry; Adelson, David L

2018-01-01

Transposable Elements (TEs) are mobile DNA sequences that make up significant fractions of amniote genomes. However, they are difficult to detect and annotate ab initio because of their variable features, lengths and clade-specific variants. We have addressed this problem by refining and developing a Comprehensive ab initio Repeat Pipeline (CARP) to identify and cluster TEs and other repetitive sequences in genome assemblies. The pipeline begins with a pairwise alignment using krishna, a custom aligner. Single linkage clustering is then carried out to produce families of repetitive elements. Consensus sequences are then filtered for protein coding genes and then annotated using Repbase and a custom library of retrovirus and reverse transcriptase sequences. This process yields three types of family: fully annotated, partially annotated and unannotated. Fully annotated families reflect recently diverged/young known TEs present in Repbase. The remaining two types of families contain a mixture of novel TEs and segmental duplications. These can be resolved by aligning these consensus sequences back to the genome to assess copy number vs. length distribution. Our pipeline has three significant advantages compared to other methods for ab initio repeat identification: 1) we generate not only consensus sequences, but keep the genomic intervals for the original aligned sequences, allowing straightforward analysis of evolutionary dynamics, 2) consensus sequences represent low-divergence, recently/currently active TE families, 3) segmental duplications are annotated as a useful by-product. We have compared our ab initio repeat annotations for 7 genome assemblies to other methods and demonstrate that CARP compares favourably with RepeatModeler, the most widely used repeat annotation package.

Superior ab initio identification, annotation and characterisation of TEs and segmental duplications from genome assemblies

PubMed Central

Zeng, Lu; Kortschak, R. Daniel; Raison, Joy M.

2018-01-01

Transposable Elements (TEs) are mobile DNA sequences that make up significant fractions of amniote genomes. However, they are difficult to detect and annotate ab initio because of their variable features, lengths and clade-specific variants. We have addressed this problem by refining and developing a Comprehensive ab initio Repeat Pipeline (CARP) to identify and cluster TEs and other repetitive sequences in genome assemblies. The pipeline begins with a pairwise alignment using krishna, a custom aligner. Single linkage clustering is then carried out to produce families of repetitive elements. Consensus sequences are then filtered for protein coding genes and then annotated using Repbase and a custom library of retrovirus and reverse transcriptase sequences. This process yields three types of family: fully annotated, partially annotated and unannotated. Fully annotated families reflect recently diverged/young known TEs present in Repbase. The remaining two types of families contain a mixture of novel TEs and segmental duplications. These can be resolved by aligning these consensus sequences back to the genome to assess copy number vs. length distribution. Our pipeline has three significant advantages compared to other methods for ab initio repeat identification: 1) we generate not only consensus sequences, but keep the genomic intervals for the original aligned sequences, allowing straightforward analysis of evolutionary dynamics, 2) consensus sequences represent low-divergence, recently/currently active TE families, 3) segmental duplications are annotated as a useful by-product. We have compared our ab initio repeat annotations for 7 genome assemblies to other methods and demonstrate that CARP compares favourably with RepeatModeler, the most widely used repeat annotation package. PMID:29538441

Porcine cluster of differentiation (CD) markers 2018 update.

PubMed

Dawson, Harry D; Lunney, Joan K

2018-06-01

Pigs are a major source of food worldwide; preventing and treating their infectious diseases is essential, requiring a thorough understanding of porcine immunity. The use of pigs as models for human physiology is a growing area; progress in this area has been limited because the immune toolkit is not robust. The international community has established cluster of differentiation (CD) markers for assessing cells involved in immunity as well as characterizing numerous other cells like stem cells. Overall, for humans 419 proteins have been designated as CD markers, each reacting with a defined set of antibodies (Abs). This paper summarizes current knowledge of swine CD markers and identifies 359 corresponding CD proteins in pigs. A broad-based literature and vendor search was conducted to identify defined sets of monoclonal (mAbs) and polyclonal Abs (pAbs) reacting with porcine CD markers along with other reagents (fusion proteins, ELISAs, PCR assays, and gene edited cell and pig models). This process identified over 800 reagents that are reportedly reactive with 266 pig CD markers. Despite this number, there is a great need to develop and characterize additional CD marker reagents, particularly mAbs, for pig research. There are numerous high priority targets: reagents for the characterization of porcine innate lymphoid cells, polarized macrophages and T regulatory cells and for the detection of porcine CD45 isoforms. Overall, improved technologies and genomics have contributed to dramatic increases in our knowledge of the pig, its immune system, disease and vaccine responses, and utility as a biomedical model. The development of more CD reagents will clearly advance these initiatives. Published by Elsevier Ltd.

PRN 88-2: Clustering of Quaternary Ammonium Compounds

EPA Pesticide Factsheets

This Notice announces that EPA has clustered the Quaternary Ammonium Compounds into four groups for the purpose of testing chemicals to build a database that will support continued registration of the entire family of quaternary ammonium compounds

Physical conditions in star-forming regions around S235

NASA Astrophysics Data System (ADS)

Kirsanova, M. S.; Wiebe, D. S.; Sobolev, A. M.; Henkel, C.; Tsivilev, A. P.

2014-01-01

Gas density and temperature in star-forming regions around Sh2-235 are derived from ammonia line observations. This information is used to evaluate formation scenarios and to determine evolutionary stages of the young embedded clusters S235 East 1, S235 East 2 and S235 Central. We also estimate the gas mass in the embedded clusters and its ratio to the stellar mass. S235 East 1 appears to be less evolved than S235 East 2 and S235 Central. In S235 East 1 the molecular gas mass exceeds that in the other clusters. Also, this cluster is more embedded in the parent gas cloud than the other two. Comparison with a theoretical model shows that the formation of these three clusters could have been stimulated by the expansion of the Sh2-235 H II region (hereafter S235) via a collect-and-collapse process, provided the density in the surrounding gas exceeds 3 × 103 cm-3, or via collapse of pre-existing clumps. The expansion of S235 cannot be responsible for star formation in the southern S235 A-B region. However, formation of the massive stars in this region might have been triggered by a large-scale supernova shock. Thus, triggered star formation in the studied region may come in three varieties, namely collect-and-collapse and collapse of pre-existing clumps, both initiated by expansion of the local H II regions, and triggered by an external large-scale shock. We argue that the S235 A H II region expands into a highly non-uniform medium with increasing density. It is too young to trigger star formation in its vicinity by a collect-and-collapse process. There is an age spread inside the S235 A-B region. Massive stars in the S235 A-B region are considerably younger than lower mass stars in the same area. This follows from the estimates of their ages and the ages of associated H II regions.

Near infrared overtone (vOH = 2 ← 0) spectroscopy of Ne-H2O clusters

NASA Astrophysics Data System (ADS)

Ziemkiewicz, Michael P.; Pluetzer, Christian; Wojcik, Michael; Loreau, Jérôme; van der Avoird, Ad; Nesbitt, David J.

2017-03-01

Vibrationally state selective overtone spectroscopy and dynamics of weakly bound Ne-H2O complexes (D0(para) = 31.67 cm-1, D0(ortho) = 34.66 cm-1) are reported for the first time, based on near infrared excitation of van der Waals cluster bands correlating with vOH = 2 ← 0 overtone transitions (|02-⟩←|00+⟩ and |02+⟩ ←|00+⟩ ) out of the ortho (101) and para (000) internal rotor states of the H2O moiety. Quantum theoretical calculations for nuclear motion on a high level ab initio potential energy surface (CCSD(T)/VnZ-f12 (n = 3,4), corrected for basis set superposition error and extrapolated to the complete basis set limit) are employed for assignment of Σ ←Σ ,Π ←Σ , and Σ ←Π infrared bands in the overtone spectra, where Σ ( K = 0) and Π (K = 1) represent approximate projections (K) of the body angular momentum along the Ne-H2O internuclear axis. End-over-end tumbling of the ortho Ne-H2O cluster is evident via rotational band contours observed, with band origins and rotational progressions in excellent agreement with ab initio frequency and intensity predictions. A clear Q branch in the corresponding |02+⟩fΠ (111) ←eΣ (000) para Ne-H2O spectrum provides evidence for a novel e/f parity-dependent metastability in these weakly bound clusters, in agreement with ab initio bound state calculations and attributable to the symmetry blocking of an energetically allowed channel for internal rotor predissociation. Finally, Boltzmann analysis of the rotational spectra reveals anomalously low jet temperatures (Trot ≈ 4(1) K), which are attributed to "evaporative cooling" of weakly bound Ne-H2O clusters and provide support for similar cooling dynamics in rare gas-tagging studies.

VizieR Online Data Catalog: Redshift reliability flags (VVDS data) (Jamal+, 2018)

NASA Astrophysics Data System (ADS)

Jamal, S.; Le Brun, V.; Le Fevre, O.; Vibert, D.; Schmitt, A.; Surace, C.; Copin, Y.; Garilli, B.; Moresco, M.; Pozzetti, L.

2017-09-01

The VIMOS VLT Deep Survey (Le Fevre et al. 2013A&A...559A..14L) is a combination of 3 i-band magnitude limited surveys: Wide (17.5<=iAB<=22.5; 8.6deg2), Deep (17.5<=iAB<=24; 0.6deg2) and Ultra-Deep (23<=iAB<=24.75; 512arcmin2), that produced a total of 35526 spectroscopic galaxy redshifts between 0 and 6.7 (22434 in Wide, 12051 in Deep and 1041 in UDeep). We supplement spectra of the VIMOS VLT Deep Survey (VVDS) with newly-defined redshift reliability flags obtained from clustering (unsupervised classification in Machine Learning) a set of descriptors from individual zPDFs. In this paper, we exploit a set of 24519 spectra from the VVDS database. After computing zPDFs for each individual spectrum, a set of (8) descriptors of the zPDF are extracted to build a feature matrix X (dimension = 24519 rows, 8 columns). Then, we use a clustering (unsupervised algorithms in Machine Learning) algorithm to partition the feature space into distinct clusters (5 clusters: C1,C2,C3,C4,C5), each depicting a different level of confidence to associate with the measured redshift zMAP (Maximum-A-Posteriori estimate that corresponds to the maximum of the redshift PDF). The clustering results (C1,C2,C3,C4,C5) reported in the table are those used in the paper (Jamal et al, 2017) to present the new methodology of automating the zspec reliability assessment. In particular, we would like to point out that they were obtained from first tests conducted on the VVDS spectroscopic data (end of 2016). Therefore, the table does not depict immutable results (on-going improvements). Future updates of the VVDS redshift reliability flags can be expected. (1 data file).

Electronic and magnetic properties of magnetoelectric compound Ca2CoSi2O7: An ab initio study

NASA Astrophysics Data System (ADS)

Chakraborty, Jayita

2018-05-01

The detailed first principle density functional theory calculations are carried out to investigate the electronic and magnetic properties of magnetoelectric compound Ca2CoSi2O7. The magnetic properties of this system are analyzed by calculating various hopping integrals as well as exchange interactions and deriving the relevant spin Hamiltonian. The dominant exchange path is visualized with Wannier functions plotting. Only intra planer nearest neighbor exchange interaction is strong in this system. The magnetocrystalline anisotropy is calculated for this system, and the results of the calculation reveal that the spin quantization axis lies in the ab plane.

Identification of FadAB Complexes Involved in Fatty Acid β-Oxidation in Streptomyces coelicolor and Construction of a Triacylglycerol Overproducing strain

PubMed Central

Menendez-Bravo, Simón; Paganini, Julián; Avignone-Rossa, Claudio; Gramajo, Hugo; Arabolaza, Ana

2017-01-01

Oleaginous microorganisms represent possible platforms for the sustainable production of oleochemicals and biofuels due to their metabolic robustness and the possibility to be engineered. Streptomyces coelicolor is among the narrow group of prokaryotes capable of accumulating triacylglycerol (TAG) as carbon and energy reserve. Although the pathways for TAG biosynthesis in this organism have been widely addressed, the set of genes required for their breakdown have remained elusive so far. Here, we identified and characterized three gene clusters involved in the β-oxidation of fatty acids (FA). The role of each of the three different S. coelicolor FadAB proteins in FA catabolism was confirmed by complementation of an Escherichia coliΔfadBA mutant strain deficient in β-oxidation. In S. coelicolor, the expression profile of the three gene clusters showed variation related with the stage of growth and the presence of FA in media. Flux balance analyses using a corrected version of the current S. coelicolor metabolic model containing detailed TAG biosynthesis reactions suggested the relevance of the identified fadAB genes in the accumulation of TAG. Thus, through the construction and analysis of fadAB knockout mutant strains, we obtained an S. coelicolor mutant that showed a 4.3-fold increase in the TAG content compared to the wild type strain grown under the same culture conditions. PMID:28824562

A synthetic cannabinoid FDU-NNEI, two 2H-indazole isomers of synthetic cannabinoids AB-CHMINACA and NNEI indazole analog (MN-18), a phenethylamine derivative N-OH-EDMA, and a cathinone derivative dimethoxy-α-PHP, newly identified in illegal products.

PubMed

Uchiyama, Nahoko; Shimokawa, Yoshihiko; Kikura-Hanajiri, Ruri; Demizu, Yosuke; Goda, Yukihiro; Hakamatsuka, Takashi

Six new psychoactive substances were identified together with two other substances (compounds 1 - 8 ) in illegal products by our ongoing survey in Japan between January and July 2014. A new synthetic cannabinoid, FDU-NNEI [1-(4-fluorobenzyl)- N -(naphthalen-1-yl)-1 H -indole-3-carboxamide, 2 ], was detected with the newly distributed synthetic cannabinoid FDU-PB-22 ( 1 ). Two 2 H -indazole isomers of synthetic cannabinoids, AB-CHMINACA 2 H -indazole analog ( 3 ) and NNEI 2 H -indazole analog ( 4 ), were newly identified with 1 H -indazoles [AB-CHMINACA and NNEI indazole analog (MN-18)]. In addition, 2-methylpropyl N -(naphthalen-1-yl) carbamate ( 5 ) and isobutyl 1-pentyl-1 H -indazole-3-carboxylate ( 6 ) were detected in illegal products. Compound 6 is considered to be a by-product of the preparation of NNEI indazole analog from compound 5 and 1-pentyl-1 H -indazole. A phenethylamine derivative, N -OH-EDMA [ N -hydroxy-3,4-ethylenedioxy- N -methylamphetamine, 7 ], and a cathinone derivative, dimethoxy-α-PHP (dimethoxy-α-pyrrolidinohexanophenone, 8 ), were newly identified in illegal products. Among them, compounds 1 and 8 have been controlled as designated substances (Shitei-Yakubutsu) under the Pharmaceutical Affairs Law in Japan since August and November 2014, respectively.

Reactivity of commercially available monoclonal antibodies to human CD antigens with peripheral blood leucocytes of dromedary camels (Camelus dromedarius)

PubMed Central

Hussen, Jamal; Shawaf, Turke; Al-herz, Abdulkareem Imran; Alturaifi, Hussain R.; Alluwaimi, Ahmed M.

2017-01-01

Monoclonal antibodies (mAbs) to cell surface molecules have been proven as a key tool for phenotypic and functional characterization of the cellular immune response. One of the major difficulties in studying camel cellular immunity consists in the lack of mAbs that dtect their leukocyte differentiation antigens. In the present study two-parameter flow cytometry was used to screen existing commercially available mAbs to human leukocyte antigens and major histocompatibility molecules (MHC) for their reactivity with camel leukocytes. The comparison of patterns of reactivity obtained after labelling human and camel leukocytes have shown that mAbs specific to human cluster of differentiation (CD) 18, CD11a, CD11b and CD14 are predicted to be cross-reactive with homologous camel antigens. PMID:28652982

Endohedral gallide cluster superconductors and superconductivity in ReGa5.

PubMed

Xie, Weiwei; Luo, Huixia; Phelan, Brendan F; Klimczuk, Tomasz; Cevallos, Francois Alexandre; Cava, Robert Joseph

2015-12-22

We present transition metal-embedded (T@Gan) endohedral Ga-clusters as a favorable structural motif for superconductivity and develop empirical, molecule-based, electron counting rules that govern the hierarchical architectures that the clusters assume in binary phases. Among the binary T@Gan endohedral cluster systems, Mo8Ga41, Mo6Ga31, Rh2Ga9, and Ir2Ga9 are all previously known superconductors. The well-known exotic superconductor PuCoGa5 and related phases are also members of this endohedral gallide cluster family. We show that electron-deficient compounds like Mo8Ga41 prefer architectures with vertex-sharing gallium clusters, whereas electron-rich compounds, like PdGa5, prefer edge-sharing cluster architectures. The superconducting transition temperatures are highest for the electron-poor, corner-sharing architectures. Based on this analysis, the previously unknown endohedral cluster compound ReGa5 is postulated to exist at an intermediate electron count and a mix of corner sharing and edge sharing cluster architectures. The empirical prediction is shown to be correct and leads to the discovery of superconductivity in ReGa5. The Fermi levels for endohedral gallide cluster compounds are located in deep pseudogaps in the electronic densities of states, an important factor in determining their chemical stability, while at the same time limiting their superconducting transition temperatures.

Relevance of 4f-3d exchange to finite-temperature magnetism of rare-earth permanent magnets: An ab-initio-based spin model approach for NdFe{sub 12}N

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

Matsumoto, Munehisa; Akai, Hisazumi; Doi, Shotaro

2016-06-07

A classical spin model derived ab initio for rare-earth-based permanent magnet compounds is presented. Our target compound, NdFe{sub 12}N, is a material that goes beyond today's champion magnet compound Nd{sub 2}Fe{sub 14}B in its intrinsic magnetic properties with a simpler crystal structure. Calculated temperature dependence of the magnetization and the anisotropy field agrees with the latest experimental results in the leading order. Having put the realistic observables under our numerical control, we propose that engineering 5d-electron-mediated indirect exchange coupling between 4f-electrons in Nd and 3d-electrons from Fe would most critically help enhance the material's utility over the operation-temperature range.

Testing the Formation Pathway of a Transiting Brown Dwarf in a Middle-aged Cluster

NASA Astrophysics Data System (ADS)

Beatty, Thomas; Curtis, Jason; Morley, Caroline; Burrows, Adam; Montet, Benjamin; Wright, Jason

2018-05-01

We wish to use 15.7 hours of Spitzer time to observe two transits, one each at 3.6um and 4.5um, of the transiting brown dwarf CWW 89Ab (Nowak et al. 2017) to measure its nightside emission. This will allow us to either make the first positive identification of a brown dwarf that has formed through core accretion processes - or will provide a severe challenge to brown dwarf evolution models. CWW 89Ab is a 36.5+/-0.1 MJ, 0.937+/-0.042 RJ, brown dwarf on a 5.3 day orbit about a 5800K dwarf. The brown dwarf is a member of the 3.00+/-0.25 Gyr old open cluster Ruprecht 147 (Curtis et al. 2013). CWW 89Ab is one of two transiting brown dwarfs for which we have an isochronal age - giving us an age, a mass, and a radius that are all independent of evolutionary models. Surprisingly, Spitzer eclipse observations of CWW 89Ab (Beatty et al. 2018) show that the dayside emission requires an internal luminosity is 16 times higher than predicted by evolutionary models. In Beatty et al. (2018) we hypothesized that this is due to a stratospheric temperature inversion on CWW 89Ab's dayside. Atmospheric modeling by Molliere et al. (2015) shows that CWW 89Ab's temperature, an inversion can only happen if the atmospheric carbon-to-oxygen ratio (C/O) is close to one. Since we know that the abundances of Ruprecht 147 and CWW 89A itself (Curtis et al. 2018) are close to the Solar value of C/O 0.54, a super-stellar value of C/O 1 in CWW 89Ab would mean that the material used to form the brown dwarf was processed through CWW 89A's proto-planetary disk (Oberg et al. 2011). It would necessarily follow that CWW 89Ab formed via core accretion within the proto-planetary disk, and not through gravitational collapse. We wish to observe CWW 89Ab to determine if the dayside over-luminosity is caused by a temperature inversion. Since inversions are caused by direct stellar irradiation and impossible at night, the nightside emission should be consistent with Tint=850K if an inversion is the cause of the dayside over-luminosity.

Overexpression of the ABC transporter AvtAB increases avermectin production in Streptomyces avermitilis.

PubMed

Qiu, Jingfan; Zhuo, Ying; Zhu, Dongqing; Zhou, Xiufen; Zhang, Lixin; Bai, Linquan; Deng, Zixin

2011-10-01

Avermectins are 16-membered macrocyclic polyketides with potent antiparasitic activities, produced by Streptomyces avermitilis. Upstream of the avermectin biosynthetic gene cluster, there is the avtAB operon encoding the ABC transporter AvtAB, which is highly homologous to the mammalian multidrug efflux pump P-glycoprotein (Pgp). Inactivation of avtAB had no effect, but increasing the concentration of avtAB mRNA 30-500-fold, using a multi-copy plasmid in S. avermitilis, enhanced avermectin production about two-fold both in the wild-type and in a high-yield producer strain on agar plates. In liquid industrial fermentation medium, the overall productivity of avermectin B1a in the engineered high-yield producer was improved for about 50%, from 3.3 to 4.8 g/l. In liquid YMG medium, moreover, the ratio of intracellular to extracellular accumulation of avermectin B1a was dropped from 6:1 to 4.5:1 in response to multiple copies of avtAB. Additionally, the overexpression of avtAB did not cause any increased expression of the avermectin biosynthetic genes through RT-PCR analysis. We propose that the AvtAB transporter exports avermectin, and thus reduces the feedback inhibition on avermectin production inside the cell. This strategy may be useful for enhancing the production of other antibiotics.

Globular cluster x-ray sources

PubMed Central

Pooley, David

2010-01-01

Globular clusters and x-ray astronomy have a long and fruitful history. Uhuru and OSO-7 revealed highly luminous (> 1036 ergs-1) x-ray sources in globular clusters, and Einstein and ROSAT revealed a larger population of low-luminosity (< 1033 ergs-1) x-ray sources. It was realized early on that the high-luminosity sources were low-mass x-ray binaries in outburst and that they were orders of magnitude more abundant per unit mass in globular clusters than in the rest of the galaxy. However, the low-luminosity sources proved difficult to classify. Many ideas were put forth—low-mass x-ray binaries in quiescence (qLMXBs), cataclysmic variables (CVs), active main-sequence binaries (ABs), and millisecond pulsars (MSPs)—but secure identifications were scarce. In ROSAT observations of 55 clusters, about 25 low-luminosity sources were found. Chandra has now observed over 80 Galactic globular clusters, and these observations have revealed over 1,500 x-ray sources. The superb angular resolution has allowed for many counterpart identifications, providing clues to the nature of this population. It is a heterogeneous mix of qLMXBs, CVs, ABs, and MSPs, and it has been shown that the qLMXBs and CVs are both, in part, overabundant like the luminous LMXBs. The number of x-ray sources in a cluster correlates very well with its encounter frequency. This points to dynamical formation scenarios for the x-ray sources and shows them to be excellent tracers of the complicated internal dynamics. The relation between the encounter frequency and the number of x-ray sources has been used to suggest that we have misunderstood the dynamical states of globular clusters. PMID:20404204

Electronic, magnetic properties and phase diagrams of system with Fe4N compound: An ab initio calculations and Monte Carlo study

NASA Astrophysics Data System (ADS)

Masrour, R.; Jabar, A.; Hlil, E. K.

2018-05-01

Self-consistent ab initio calculations, based on Density Functional Theory (DFT) approach and using Full potential Linear Augmented Plane Wave (FLAPW) method, are performed to investigate the electronic and magnetic properties of the Fe4N compound. Polarized spin and spin-orbit coupling are included in calculations within the framework of the ferromagnetic state between Fe(I) and Fe(II) in Fe4N compound. We have used the obtained data from abinitio calculations as an input in Monte Carlo simulation to calculate the magnetic properties of this compounds such as the ground state phase diagrams, total and partial magnetization of Fe(I) and Fe(II) as well as the transition temperatures are computed. The variation of magnetization with the crystal field are also studied. The magnetic hysteresis cycle of the same Fe4N compound are determined for different values of temperatures and crystal field values. The two-step hysteresis loop are evidenced, which is typical for Fe4N structure. The ferromagnetic and superparamagnetic phase is observed as well.

Heteronuclear Metal Cluster Compounds Synthesis and Reactivity

DTIC Science & Technology

1990-08-10

important role in the formation of complexes with heteronuclear metal - metal bonds. Since this is our Final Report recent results are reported and...DTe FL’ Copy AFOSR-86-0125 Lfl X’ HETERONUCLEAR METAL CLUSTER COMPOUNDS00 SYNTHESIS AND REACTIVITY F. Gordon A. Stone, IDepartment of Inorganic...Security Classification) HETERONUCLEAR METAL CLUSTER COMPOUNDS: SYNTHESIS AND REACTIVITY 12. PERSONAL AUTHOR(S) F. GORDON A. STONE 13a. TYPE OF REPORT

Summary of Research. 1996-1997

DTIC Science & Technology

1997-10-01

the painter. The application on ship hulls and to decrease painter is being exposed to volatile organic compounds environmental pollutants created by...Paper Ab- Sorption Heat Pump Conference, Montreal, No. 296, Corrosion 97, NACE Annual Conference, Canada, pp. 231-236 Sept. 1996. New Orleans, LA...considered. PALMER, Sheila C., Assistant Professor, "Experimental Investigation and Model Verification for a GAX Absorber," International Ab- Sorption Heat

Ge(14)[Ge(SiMe(3))(3)](5)Li(3)(THF)(6): the largest metalloid cluster compound of germanium: on the way to fullerene-like compounds?

PubMed

Schenk, Christian; Schnepf, Andreas

2008-10-14

The reaction of GeBr with LiGe(SiMe(3))(3) yields the largest metalloid cluster compound of germanium Ge(14)[Ge(SiMe(3))(3)](5)Li(3)(THF)(6), in which 14 germanium atoms are arranged as a hollow sphere in the cluster core, showing that in the case of germanium also fullerene-like compounds might be present in the borderland between the molecular and solid states.

Exploring the speed and performance of molecular replacement with AMPLE using QUARK ab initio protein models

PubMed Central

Keegan, Ronan M.; Bibby, Jaclyn; Thomas, Jens; Xu, Dong; Zhang, Yang; Mayans, Olga; Winn, Martyn D.; Rigden, Daniel J.

2015-01-01

AMPLE clusters and truncates ab initio protein structure predictions, producing search models for molecular replacement. Here, an interesting degree of complementarity is shown between targets solved using the different ab initio modelling programs QUARK and ROSETTA. Search models derived from either program collectively solve almost all of the all-helical targets in the test set. Initial solutions produced by Phaser after only 5 min perform surprisingly well, improving the prospects for in situ structure solution by AMPLE during synchrotron visits. Taken together, the results show the potential for AMPLE to run more quickly and successfully solve more targets than previously suspected. PMID:25664744

Predicting the reactivity of phenolic compounds with formaldehyde. II, continuation of an ab initio study.

Treesearch

Tohru Mitsunaga; Anthony H. Conner; Charles G. Jr. Hill

2002-01-01

Phenol–formaldehyde resins are important adhesives used by the forest products industry. The phenolic compounds in these resins are derived primarily from petrochemical sources. Alternate sources of phenolic compounds include tannins, lignins, biomass pyrolysis products, and coal gasification products. Because of variations in their chemical structures, the...

Curved-line search algorithm for ab initio atomic structure relaxation

NASA Astrophysics Data System (ADS)

Chen, Zhanghui; Li, Jingbo; Li, Shushen; Wang, Lin-Wang

2017-09-01

Ab initio atomic relaxations often take large numbers of steps and long times to converge, especially when the initial atomic configurations are far from the local minimum or there are curved and narrow valleys in the multidimensional potentials. An atomic relaxation method based on on-the-flight force learning and a corresponding curved-line search algorithm is presented to accelerate this process. Results demonstrate the superior performance of this method for metal and magnetic clusters when compared with the conventional conjugate-gradient method.

Sensitivity of Breast Cancer Stem Cells to TRA-8 Anti-DR5 Monoclonal Antibody

DTIC Science & Technology

2013-08-01

Janelia Farm , VA, travel award 2010 -­‐ Translational Medicine Symposium, HHMI Peer Cluster Meeting, travel award 2010 -­‐ AACR Annual Conference...lab. Science Education Alliance, Janelia Farm , VA, 2001 3. Londoño-Joshi AI, Forero-Torres A, Fineberg NS, Oliver PG, Zhou T, LoBuglio AF, Buchsbaum...rabbit mAb and cleaved caspase 3 rabbit mAb were purchased from Cell Signaling (Billerica, MA). Secondary antibodies, Alexa fluor 405 goat anti-rabbit

Application of Rhizobacteria for Plant Growth Promotion Effect and Biocontrol of Anthracnose Caused by Colletotrichum acutatum on Pepper

PubMed Central

Lamsal, Kabir; Kim, Sang Woo; Kim, Yun Seok

2012-01-01

In vitro and greenhouse screening of seven rhizobacterial isolates, AB05, AB10, AB11, AB12, AB14, AB15 and AB17, was conducted to investigate the plant growth promoting activities and inhibition against anthracnose caused by Colletotrichum acutatum in pepper. According to identification based on 16S rDNA sequencing, the majority of the isolates are members of Bacillus and a single isolate belongs to the genus Paenibacillus. All seven bacterial isolates were capable of inhibiting C. acutatum to various degrees. The results primarily showed that antibiotic substances produced by the selected bacteria were effective and resulted in strong antifungal activity against the fungi. However, isolate AB15 was the most effective bacterial strain, with the potential to suppress more than 50% mycelial growth of C. acutatum in vitro. Moreover, antibiotics from Paenibacillus polymyxa (AB15) and volatile compounds from Bacillus subtilis (AB14) exerted efficient antagonistic activity against the pathogens in a dual culture assay. In vivo suppression activity of selected bacteria was also analyzed in a greenhouse with the reference to their prominent in vitro antagonism efficacy. Induced systemic resistance in pepper against C. acutatum was also observed under greenhouse conditions. Where, isolate AB15 was found to be the most effective bacterial strain at suppressing pepper anthracnose under greenhouse conditions. Moreover, four isolates, AB10, AB12, AB15, and AB17, were identified as the most effective growth promoting bacteria under greenhouse conditions, with AB17 inducing the greatest enhancement of pepper growth. PMID:23323049

Surface anisotropy of iron oxide nanoparticles and slabs from first principles: Influence of coatings and ligands as a test of the Heisenberg model

NASA Astrophysics Data System (ADS)

Brymora, Katarzyna; Calvayrac, Florent

2017-07-01

We performed ab initio computations of the magnetic properties of simple iron oxide clusters and slabs. We considered an iron oxide cluster functionalized by a molecule or glued to a gold cluster of the same size. We also considered a magnetite slab coated by cobalt oxide or a mixture of iron oxide and cobalt oxide. The changes in magnetic behavior were explored using constrained magnetic calculations. A possible value for the surface anisotropy was estimated from the fit of a classical Heisenberg model on ab initio results. The value was found to be compatible with estimations obtained by other means, or inferred from experimental results. The addition of a ligand, coating, or of a metallic nanoparticle to the systems degraded the quality of the description by the Heisenberg Hamiltonian. Proposing a change in the anisotropies allowing for the proportion of each transition atom we could get a much better description of the magnetism of series of hybrid cobalt and iron oxide systems.

Local structure order in Pd 78Cu 6Si 16 liquid

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

Yue, G. Q.; Zhang, Y.; Sun, Y.

2015-02-05

The short-range order (SRO) in Pd 78Cu 6Si 16 liquid was studied by high energy x-ray diffraction and ab initio molecular dynamics (MD) simulations. The calculated pair correlation functions at different temperatures agree well with the experimental results. The partial pair correlation functions from ab intio MD simulations indicate that Si atoms prefer to be uniformly distributed while Cu atoms tend to aggregate. By performing structure analysis using Honeycutt-Andersen index, Voronoi tessellation, and atomic cluster alignment method, we show that the icosahedron and face-centered cubic SRO increase upon cooling. The dominant SRO is the Pd-centered Pd 9Si 2 motif, namelymore » the structure of which motif is similar to the structure of Pd-centered clusters in the Pd 9Si 2 crystal. The study further confirms the existence of trigonal prism capped with three half-octahedra that is reported as a structural unit in Pd-based amorphous alloys. The majority of Cu-centered clusters are icosahedra, suggesting that the presence of Cu is benefit to promote the glass forming ability.« less

Ab initio study on the structural and electronic properties of water surrounding a multifunctional nanoprobe

NASA Astrophysics Data System (ADS)

Xia, Xiuli; Shao, Yuanzhi

2018-02-01

We report the magneto-electric behavior of a dual-modality biomedical nanoprobe, a ternary nanosystem consisting of gold and gadolinia clusters and water molecules, with the effect of both nanoclusters on the structural and electronic properties of water. The hydrogen-oxygen bond lengths and angles as well as electronic charges of water molecules surrounding both nanoclusters were calculated using Hubbard U corrected density functional theory aided by molecular dynamics approach. The calculations reveal existence of a magneto-electric interaction between gold and gadolinium oxide nanoclusters, which influences the physical properties of surrounding water remarkably. A broader (narrower) distribution of Hsbnd O bond lengths (Hsbnd Osbnd H bond angles) was observed at the presence of either gold or gadolinia nanoclusters. The presence of Gd6O9 cluster leads to the larger charges of neighbour oxygen atoms. The distribution of oxygen atom charges becomes border when both Gd6O9 and Au13 clusters coexist. Ab initio calculation provides a feasible approach to explore the most essential interactions among functional components of a multimodal nanoprobe applied in aqueous environment.

Efficient Organometallic Spin Filter between Single-Wall Carbon Nanotube or Graphene Electrodes

NASA Astrophysics Data System (ADS)

Koleini, Mohammad; Paulsson, Magnus; Brandbyge, Mads

2007-05-01

We present a theoretical study of spin transport in a class of molecular systems consisting of an organometallic benzene-vanadium cluster placed in between graphene or single-wall carbon-nanotube-model contacts. Ab initio modeling is performed by combining spin density functional theory and nonequilibrium Green’s function techniques. We consider weak and strong cluster-contact bonds. Depending on the bonding we find from 73% (strong bonds) up to 99% (weak bonds) spin polarization of the electron transmission, and enhanced polarization with increased cluster length.

Mechanical properties of Fe rich Fe-Si alloys: ab initio local bulk-modulus viewpoint

NASA Astrophysics Data System (ADS)

Bhattacharya, Somesh Kr; Kohyama, Masanori; Tanaka, Shingo; Shiihara, Yoshinori; Saengdeejing, Arkapol; Chen, Ying; Mohri, Tetsuo

2017-11-01

Fe-rich Fe-Si alloys show peculiar bulk-modulus changes depending on the Si concentration in the range of 0-15 at.%Si. In order to clarify the origin of this phenomenon, we have performed density-functional theory calculations of supercells of Fe-Si alloy models with various Si concentrations. We have applied our recent techniques of ab initio local energy and local stress, by which we can obtain a local bulk modulus of each atom or atomic group as a local constituent of the cell-averaged bulk modulus. A2-phase alloy models are constructed by introducing Si substitution into bcc Fe as uniformly as possible so as to prevent mutual neighboring, while higher Si concentrations over 6.25 at.%Si lead to contacts between SiFe8 cubic clusters via sharing corner Fe atoms. For 12.5 at.%Si, in addition to an A2 model, we deal with partial D03 models containing local D03-like layers consisting of edge-shared SiFe8 cubic clusters. For the cell-averaged bulk modulus, we have successfully reproduced the Si-concentration dependence as a monotonic decrease until 11.11 at.%Si and a recovery at 12.5 at.%Si. The analysis of local bulk moduli of SiFe8 cubic clusters and Fe regions is effective to understand the variations of the cell-averaged bulk modulus. The local bulk moduli of Fe regions become lower for increasing Si concentration, due to the suppression of bulk-like d-d bonding states in narrow Fe regions. For higher Si concentrations till 11.11 at.%Si, corner-shared contacts or 1D chains of SiFe8 clusters lead to remarkable reduction of local bulk moduli of the clusters. At 12 at.%Si, on the other hand, two- or three-dimensional arrangements of corner- or edge-shared SiFe8 cubic clusters show greatly enhanced local bulk moduli, due to quite different bonding nature with much stronger p-d hybridization. The relation among the local bulk moduli, local electronic and magnetic structures, and local configurations such as connectivity of SiFe8 clusters and Fe-region sizes has been analyzed. The ab initio local stress has opened the way for obtaining accurate local elastic properties reflecting local valence-electron behaviors.

Ab initio studies on the solvation, electronic structures and intracluster reactions in M(+)L(n), with M(+)=magnesium and calcium singly-charged ions, L=water, methanol, ammonia, and n=1-6, and the elimination of a hydrogen atom in H atom in hydrated sodium clusters

NASA Astrophysics Data System (ADS)

Chan, Ka Wai

The solvation and electronic structures of M+Ln, with M+ = Mg+ and Cat, L = H2O, CH 3OH and NH3, n=1-6 were investigated by ab initio calculations using G03 package and density functional theory based ab initio molecular dynamics (AIMD) simulations with projector augmented-wave (PAW) method and a planewave basis set using Vienna Ab initio Simulation Package (VASP). Furthermore, ab initio studies on the intracluster reactions of Mg+ and Ca+ ions with different solvent molecules, H2O, CH3OH and NH3, were also done using G03 package. Finally, the elimination of a H atom in Na(H2O)n was studied. Such studies on the interactions and reactivity in gas clusters can provide insights into their analogies existing in condense phase. Interactions of Mg+ and Ca+ ions in different solvent molecules, H2O, CH3OH and NH3, were calculated with B3LYP and MP2 methods with basis sets 6-31+g** and 6-311+g**. A systematic comparison on the structures and reactivities of these clusters should provide a better understanding on the interplay of the ion-solvent, solvent-solvent, and electron-solvent interactions. It can provide a better understanding on the structures and bonding of complexes having analogies to those existing in condense phase. For Mg+(CH3OH)n and Ca+(CH 3OH)n, both H-elimination from OH/CH bond and CH3-elimination were investigated. H-elimination from O---H bond becomes more accessible for large cluster due to the diffusion of electron density to O---H bond. Studies on the H-elimination in Mg+(NH3)n and H-elimination from C---H bond in Mg+(CH3OH) n show that the reaction barriers flatten above 20 kcal/mol as n reaches 4 and above. These calculation results prove that the source of loss of H atom in ground state Mg+(CH3OH)n should be through the O---H bond rather than through the C---H bond. Compared to Mg+(CH3OH)n, the reaction barriers for H-elimination in Mg+(NH3)n is much larger, which is in consistent with the experimental observation of little H-elimination for Mg+(NH3)n unless it's photo-excited. The examination of neutral Na(H2O)n clusters, n=4~15 for H-elimination was carried out. The reaction profile for H-elimination was obtained by energy minimization at constrained O---H distance which was successively increased. There was a general trend of decreasing reaction barrier, as the cluster size grows. In contrast to Mg+(H 2O)n, the expected switch-off of H-elimination as in Mg +(H2O)n cannot be observed.

The accuracy of ab initio calculations without ab initio calculations for charged systems: Kriging predictions of atomistic properties for ions in aqueous solutions

NASA Astrophysics Data System (ADS)

Di Pasquale, Nicodemo; Davie, Stuart J.; Popelier, Paul L. A.

2018-06-01

Using the machine learning method kriging, we predict the energies of atoms in ion-water clusters, consisting of either Cl- or Na+ surrounded by a number of water molecules (i.e., without Na+Cl- interaction). These atomic energies are calculated following the topological energy partitioning method called Interacting Quantum Atoms (IQAs). Kriging predicts atomic properties (in this case IQA energies) by a model that has been trained over a small set of geometries with known property values. The results presented here are part of the development of an advanced type of force field, called FFLUX, which offers quantum mechanical information to molecular dynamics simulations without the limiting computational cost of ab initio calculations. The results reported for the prediction of the IQA components of the energy in the test set exhibit an accuracy of a few kJ/mol, corresponding to an average error of less than 5%, even when a large cluster of water molecules surrounding an ion is considered. Ions represent an important chemical system and this work shows that they can be correctly taken into account in the framework of the FFLUX force field.

Endohedral gallide cluster superconductors and superconductivity in ReGa5

PubMed Central

Xie, Weiwei; Luo, Huixia; Phelan, Brendan F.; Klimczuk, Tomasz; Cevallos, Francois Alexandre; Cava, Robert Joseph

2015-01-01

We present transition metal-embedded (T@Gan) endohedral Ga-clusters as a favorable structural motif for superconductivity and develop empirical, molecule-based, electron counting rules that govern the hierarchical architectures that the clusters assume in binary phases. Among the binary T@Gan endohedral cluster systems, Mo8Ga41, Mo6Ga31, Rh2Ga9, and Ir2Ga9 are all previously known superconductors. The well-known exotic superconductor PuCoGa5 and related phases are also members of this endohedral gallide cluster family. We show that electron-deficient compounds like Mo8Ga41 prefer architectures with vertex-sharing gallium clusters, whereas electron-rich compounds, like PdGa5, prefer edge-sharing cluster architectures. The superconducting transition temperatures are highest for the electron-poor, corner-sharing architectures. Based on this analysis, the previously unknown endohedral cluster compound ReGa5 is postulated to exist at an intermediate electron count and a mix of corner sharing and edge sharing cluster architectures. The empirical prediction is shown to be correct and leads to the discovery of superconductivity in ReGa5. The Fermi levels for endohedral gallide cluster compounds are located in deep pseudogaps in the electronic densities of states, an important factor in determining their chemical stability, while at the same time limiting their superconducting transition temperatures. PMID:26644566

Variability in spectrophotometric pyruvate analyses for predicting onion pungency and nutraceutical value.

PubMed

Beretta, Vanesa H; Bannoud, Florencia; Insani, Marina; Galmarini, Claudio R; Cavagnaro, Pablo F

2017-06-01

Onion pyruvate concentration is used as a predictor of flavor intensity and nutraceutical value. The protocol of Schwimmer and Weston (SW) (1961) is the most widespread methodology for estimating onion pyruvate. Anthon and Barret (AB) (2003) proposed modifications to this procedure. Here, we compared these spectrophotometry-based procedures for pyruvate analysis using a diverse collection of onion cultivars. The SW method always led to over-estimation of pyruvate levels in colored, but not in white onions, by up to 65%. Identification of light-absorbance interfering compounds was performed by spectrophotometry and HPLC analysis. Interference by quercetin and anthocyanins, jointly, accounted for more than 90% of the over-estimation of pyruvate. Pyruvate determinations according to AB significantly reduced absorbance interference from compounds other than pyruvate. This study provides evidence about the mechanistic basis underlying differences between the SW and AB methods for indirect assessment of onion flavor and nutraceutical value. Copyright © 2016 Elsevier Ltd. All rights reserved.

(99m)Tc-bioorthogonal click chemistry reagent for in vivo pretargeted imaging.

PubMed

García, María Fernanda; Zhang, Xiuli; Shah, Manankumar; Newton-Northup, Jessica; Cabral, Pablo; Cerecetto, Hugo; Quinn, Thomas

2016-03-15

Metal-free click chemistry has become an important tool for pretargeted approaches in the molecular imaging field. The application of bioorthogonal click chemistry between a pretargeted trans-cyclooctene (TCO) derivatized monoclonal antibody (mAb) and a (99m)Tc-modified 1,2,4,5-tetrazine for tumor imaging was examined in vitro and in vivo. The HYNIC tetrazine compound was synthesized and structurally characterized, confirming its identity. Radiolabeling studies demonstrated that the HYNIC tetrazine was labeled with (99m)Tc at an efficiency of >95% and was radiochemically stable. (99m)Tc-HYNIC tetrazine reacted with the TCO-CC49 mAb in vitro demonstrating its selective reactivity. In vivo biodistribution studies revealed non-specific liver and GI uptake due to the hydrophobic property of the compound, however pretargeted SPECT imaging studies demonstrated tumor visualization confirming the success of the cycloaddition reaction in vivo. These results demonstrated the potential of (99m)Tc-HYNIC-tetrazine for tumor imaging with pretargeted mAbs. Copyright © 2016 Elsevier Ltd. All rights reserved.

Electronic structure and magnetism of titanium substituted Cd3P2: An ab-initio study

NASA Astrophysics Data System (ADS)

Jaiganesh, G.; Jaya, S. Mathi

2018-05-01

Using the ab-initio computations that are based on the density functional theory, we have investigated the magnetism and electronic properties of one and two Ti atom substituted Cd3P2 compound. The magnetic stability of the substituted compounds was obtained by analyzing the minimum total energies in nonmagnetic, ferromagnetic and antiferromagnetic phases. Our results indicated the formation of magnetic order in one and two Ti atom substituted Cd3P2 as well as metallic characteristics in these systems. A significant value of the magnetic moment of Ti atom is observed from our calculations. We further find that the neighboring Cd and P atoms too acquire a small magnetic moment.

Many-body optimization using an ab initio monte carlo method.

PubMed

Haubein, Ned C; McMillan, Scott A; Broadbelt, Linda J

2003-01-01

Advances in computing power have made it possible to study solvated molecules using ab initio quantum chemistry. Inclusion of discrete solvent molecules is required to determine geometric information about solute/solvent clusters. Monte Carlo methods are well suited to finding minima in many-body systems, and ab initio methods are applicable to the widest range of systems. A first principles Monte Carlo (FPMC) method was developed to find minima in many-body systems, and emphasis was placed on implementing moves that increase the likelihood of finding minimum energy structures. Partial optimization and molecular interchange moves aid in finding minima and overcome the incomplete sampling that is unavoidable when using ab initio methods. FPMC was validated by studying the boron trifluoride-water system, and then the method was used to examine the methyl carbenium ion in water to demonstrate its application to solvation problems.

Diterpenes from buds of Wikstroemia chamaedaphne showing anti-hepatitis B virus activities.

PubMed

Li, Shi-Fei; Jiao, Ying-Ying; Zhang, Zhi-Qiang; Chao, Jian-Bin; Jia, Jie; Shi, Xun-Long; Zhang, Li-Wei

2018-07-01

Phytochemical study of the buds of Wikstroemia chamaedaphne Meisn. led to the isolation of seven previously undescribed diterpenes, including one tigliane diterpene (wikstchalide A), two daphnane diterpenes (wikstroelides W-X), and four lathyrane diterpenes (laurifoliosides A-B and 2-epi-laurifoliosides A-B), along with four known diterpenes. The structures of these compounds were established by extensive spectroscopic evidence and electronic circular dichroism (ECD) calculations. Wikstchalide A possesses a 5,6-epoxy ring in the tigliane skeleton. Two compounds exhibited potential anti-hepatitis B virus activities, with IC 50 values of 46.5 and 88.3 μg/mL against hepatitis B virus (HBV) surface antigen (HBsAg), and six compounds showed certain inhibitory effects on HBV-DNA replication with the inhibition ratios ranging from 2.0% to 33.0% at the concentrations ranging from 0.39 to 6.25 μg/mL. Copyright © 2018 Elsevier Ltd. All rights reserved.

Theoretical Study of Indium Compounds of Interest for Organometallic Chemical Vapor Deposition

NASA Technical Reports Server (NTRS)

Cardelino, B. H.; Moore, C. E.; Cardelino, C. A.; Frazier, D. O.; Backmann, K. J.

2000-01-01

The structural. electronic and therinochemical properties of indium compounds which are of interest in halide transport and organometallic chemical vapor deposition processes have been studied by ab initio and statistical mechanics methods. The compounds reported include: indium halides and hydrides (InF, InCl, InCl3, InH, InH2, InH3); indium clusters (In2, In3); methylindium, dimethylindium, and their hydrogen derivatives [In(CH3), In(CH3)H, In(CH3)H2, In(CH3)2, In(CH3)2H]; dimethyl-indium dimer [In2(CH3)4], trimethyl-indium [In(CH3)3]; dehydrogenated methyl, dimethyl and trimethylindium [In(CH3)2CH2, In(CH3)CH2, In(CH2)], trimethylindium adducts with ammonia, trimethylamine and hydrazine [(CH3)3In:NH3, (CH3)3In:N(CH3)3, (CH3)3In:N(H2)N(H2)]; dimethylamino-indium and methylimino-indium [In(CH3)2(NH2), In(CH3)(NH)]; indium nitride and indium nitride dimer (InN, In2N2), indium phosphide, arsenide and antimonide ([InP, InAs, InSb). The predicted electronic properties are based on density functional theory calculations; the calculated thermodynamic properties are reported following the format of the JANAF (Joint Army, Navy, NASA, Air Force) Tables. Equilibrium compositions at two temperatures (298 and 1000 K) have been analyzed for groups of competing simultaneous reactions.

Magnetic properties of a metal-organic porous network [Ni2(BODC)2(TED)

NASA Astrophysics Data System (ADS)

Yuen, Tan; Danilovic, D.; Li, Kunhao; Li, Jing

2008-04-01

A new material [Ni2(BODC)2(TED)], (BODC =4,4'-bicyclo[2.2.2]octane dicarboxylate and TED =triethylene-4,4'-diamine), which is a guest-free, porous metal-organic coordination network, has been successfully synthesized. The crystal structure of this compound is tetragonal with the space group P4/mmm. It is a three-dimensional network that can be deconstructed into rectangular gridlike layers along ab planes. These planes are formed by BODC and Zn2O4 paddle-wheel-like clusters, and the TED ligands from the axial directions of the paddle-wheels connect the layers into a three-dimesional structure. There are no guest molecules found in the pores. The shortest Ni-Ni distance within the paddle wheel is found to be 2.613Å. Magnetic susceptibility χ(T )=M(T)/H and isothermal magnetization M(H ) measurements have been measured on powder samples of this compound. The results of χ(T ) show that there is a rapid increase in the susceptibility below 20K due to a spontaneous ordering of the Ni2+ moments. The effective moment μeff of Ni2+ is about 2.20μB at room temperature. The M(H ) result at 1.8K shows a clear hysteresis with a coercivity of Hcoe≈1700G. The behavior of this compound is discussed in terms of Ni-Ni coupling within the Ni dimers and dimer chains.

Synthesis of bifunctional molecules containing [12]aneN3 and coumarin moieties as effective DNA condensation agents and new non-viral gene vectors.

PubMed

Yue, Pan; Zhang, Ying; Guo, Zhi-Fo; Cao, Ao-Cheng; Lu, Zhong-Lin; Zhai, Yong-Gong

2015-04-21

A series of bifunctional molecules with different combinations of macrocyclic polyamine [12]aneN3 and coumarin moieties, 4a/b and 5a/b, were synthesized by a two-step copper(I)-mediated alkyne–azide click reactions between 1,3,5-tris(azidomethyl)benzene and Boc-protected N-propynyl-[12]aneN3/7-propynyloxycoumarins. Agarose gel electrophoresis experiments indicated that bifunctional molecules 4b and 5b effectively induced complete plasmid DNA condensation at concentrations up to 40 μM. It was found that the structural variation had a major impact on the condensation behavior of these compounds. The electrostatic interaction involving the [12]aneN3 moiety can be compensated by the binding contribution of the coumarin units during the DNA condensation process. These two types of interaction showed different effects on the reversibility of DNA condensation. Results from studies using dynamic laser scattering, atomic force microscopy, and EB replacement assay further supported the above conclusion. Cytotoxicity assays on bifunctional compounds 4a/b and 5a/b indicated their low cytotoxicity. Results from cellular uptake and cell transfection experiments proved that bifunctional compounds 4b and 5b successfully served as non-viral gene vectors. Furthermore, methyl substituents attached to the coumarin unit (4b and 5b) greatly enhanced their DNA condensation capability and gene transfection. These bifunctional molecules, with the advantages of lower cytotoxicity, good water solubility, and potential structural modification, will have great potential for the development of new non-viral gene delivery agents.

The Design and Synthesis of Infrared Flourescent Colorants

DTIC Science & Technology

1974-11-01

VII). The phenazine derivative formed under these conditions reflects the presence of initially high concentrations of unreacted 3-AMF at high...difluoreno[1,9-ab:9’,l’-hi] phenazine (see List of Compounds). (This compound was also obtained merely by heating a solution of 3-aminofluoranthene in

A caged Ab reveals an immediate/instructive effect of BDNF during hippocampal synaptic potentiation

PubMed Central

Kossel, Albrecht H.; Cambridge, Sidney B.; Wagner, Uta; Bonhoeffer, Tobias

2001-01-01

Neurotrophins have been shown to be involved in functional strengthening of central nervous system synapses. Although their general importance in this process is undisputed, it remains unresolved whether neurotrophins are truly mediators of synaptic strengthening or merely important cofactors. To address this question, we have devised a method to inactivate endogenous brain-derived neurotrophic factor (BDNF) with high time resolution by “caging” a function-blocking mAb against BDNF with a photosensitive protecting compound. Different assays were used to show that this inactivation of the Ab is reversible by UV light. Synaptic potentiation after τ-burst stimulation in the CA1 region of acute hippocampal slices was significantly less when applying the unmodified Ab compared with the caged Ab. Importantly, photoactivation of the caged Ab during the time of induction of synaptic enhancement led to a marked decrease in potentiation. Our experiments therefore strengthen the view that endogenous BDNF has fast effects during induction of synaptic plasticity. The results additionally show that caged Abs can provide a tool for precise spatiotemporal control over endogenous protein levels. PMID:11724927

Immunoglobulin Gene Insertions and Deletions in the Affinity Maturation of HIV-1 Broadly Reactive Neutralizing Antibodies

PubMed Central

Kepler, Thomas B.; Liao, Hua-Xin; Alam, S. Munir; Bhaskarabhatla, Rekha; Zhang, Ruijun; Stewart, Shelley; Anasti, Kara; Kelsoe, Garnett; Parks, Robert; Lloyd, Krissey E.; Stolarchuk, Christina; Pritchett, Jamie; Solomon, Erika; Friberg, Emma; Morris, Lynn; Karim, Salim S. Abdool; Cohen, Myron S.; Walter, Emmanuel; Moody, M. Anthony; Wu, Xueling; Altae-Tran, Han R.; Georgiev, Ivelin S.; Kwong, Peter D.; Boyd, Scott D.; Fire, Andrew Z.; Mascola, John R.; Haynes, Barton F.

2014-01-01

Summary Induction of HIV-1 broad neutralizing antibodies (bnAbs) is a goal of HIV-1 vaccine development but has remained challenging partially due to unusual traits of bnAbs, including high somatic hypermutation (SHM) frequencies and in-frame insertions and deletions (indels). Here we examined the propensity and functional requirement for indels within HIV-1 bnAbs. High-throughput sequencing of the immunoglobulin (Ig) VHDJH genes in HIV-1 infected and uninfected individuals revealed that the indel frequency was elevated among HIV-1-infected subjects, with no unique properties attributable to bnAb-producing individuals. This increased indel occurrence depended only on the frequency of SHM point-mutations. Indel-encoded regions were generally proximal to antigen binding sites. Additionally, reconstruction of a HIV-1 CD4-binding site bnAb clonal lineage revealed that a large compound VHDJH indel was required for bnAb activity. Thus, vaccine development should focus on designing regimens targeted at sustained activation of bnAb lineages to achieve the required SHM and indel events. PMID:25211073

Sulfur in Cometary Dust

NASA Technical Reports Server (NTRS)

Fomenkova, M. N.

1997-01-01

The computer-intensive project consisted of the analysis and synthesis of existing data on composition of comet Halley dust particles. The main objective was to obtain a complete inventory of sulfur containing compounds in the comet Halley dust by building upon the existing classification of organic and inorganic compounds and applying a variety of statistical techniques for cluster and cross-correlational analyses. A student hired for this project wrote and tested the software to perform cluster analysis. The following tasks were carried out: (1) selecting the data from existing database for the proposed project; (2) finding access to a standard library of statistical routines for cluster analysis; (3) reformatting the data as necessary for input into the library routines; (4) performing cluster analysis and constructing hierarchical cluster trees using three methods to define the proximity of clusters; (5) presenting the output results in different formats to facilitate the interpretation of the obtained cluster trees; (6) selecting groups of data points common for all three trees as stable clusters. We have also considered the chemistry of sulfur in inorganic compounds.

Gene signatures and expression of miRNAs associated with efficacy of panitumumab in a head and neck cancer phase II trial.

PubMed

Siano, Marco; Espeli, Vittoria; Mach, Nicolas; Bossi, Paolo; Licitra, Lisa; Ghielmini, Michele; Frattini, Milo; Canevari, Silvana; De Cecco, Loris

2018-07-01

Platinum-based chemotherapy plus the anti-EGFR monoclonal antibody (mAb) cetuximab is used to treat recurrent/metastatic (RM) head-neck squamous cell carcinoma (HNSCC). Recently, we defined Cluster3 gene-expression signature as a potential predictor of favorable progression-free survival (PFS) in cetuximab-treated RM-HNSCC patients and predictor of partial metabolic FDG-PET response in an afatinib window-of-opportunity trial. Another anti-EGFR-mAb (panitumumab) was used as the treatment agent in RM-HNSCC patients in the phase II PANI01trial. PANI01 tumor samples were analyzed using functional genomics to explore response predictors to anti-EGFR therapy. Whole-gene expression and real-time PCR analyses were applied to pre-treatment samples from 25 PANI01 patients. Three gene signatures (Cluster3 score, RAS onco-signature, microenvironment score) and seven selected miRNAs were separately analyzed for association with panitumumab efficacy. Cluster3 expression levels had a profile with a significant bimodal separation of samples (P =  3.08 E-13). Higher RAS activation, microenvironment score, and miRNA expression were associated with low-Cluster3 patients. The same biomarkers were separately associated with PFS. Patients with high-Cluster3 had significantly longer PFS than patients with low-Cluster3 (median PFS: 174 versus 51 days; log-rank P = 0.0021). ROC analysis demonstrated accuracy in predicting PFS (AUC = 0.877). Despite differences in clinical settings and anti-EGFR inhibitors used for treatment, response prediction by the Cluster3 signature and selected miRNAs was essentially the same. Translation into a useful clinical assay requires validation in a broader setting. Copyright © 2018 Elsevier Ltd. All rights reserved.

{beta}-K{sub 4}La{sub 6}I{sub 14}Os: A new structure type for rare-earth-metal cluster compounds that contains discrete tetrahedral K{sub 4}I{sup 3+} units

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

Uma, S.; Corbett, J.D.

1999-08-23

Suitable reactions of KI, La, LaI{sub 3}, and Os in niobium tubes at 800--850 C result in black, air- and moisture-sensitive crystals of the quaternary title phase. Isostructural K{sub 4}Pr{sub 6}I{sub 14}Z also exist for Z = Fe, Ru. The title phase was characterized by single-crystal X-ray diffraction (tetragonal, P4/ncc (No. 130), Z = 4; a = 13.117(3), c = 25.17(1) {angstrom} at 23 C). The important structural feature is the constitution (K{sub 4}I){sup 3+}(La{sub 6}I{sub 13}Os{sup 3{minus}}) with a new type of 3D anion network of [(La{sub 6}Os)I{sub 8}{sup i}I{sub 4/2}{sup i{minus}a}I{sub 4/2}{sup a{minus}i}I{sub 2/2}{sup a{minus}a}] clusters that aremore » connected into puckered layers through I{sup i{minus}a} and I{sup a{minus}i} atom pairs that bridge diagonally in the a-b plane. These cluster layers are further interlinked along {rvec c} at trans-vertexes through simple bridging I{sup a{minus}a}. The 14th iodine atom occurs in the unique K{sub 4}I{sup 3+} ions which lie in columns that interpenetrate the La{sub 6}OsI{sub 13} network along c. The present 16-e{sup {minus}} clusters, in contrast with the optimal 18-e{sup {minus}} octahedral cluster configuration, exhibit an uncommon tetragonal elongation and evidently become closed shell, with only a small temperature-independent (van Vleck-like) paramagnetism, {approximately}4 x 10{sup {minus}4} emu mol{sup {minus}1}.« less

Structure and Stability of GeAu{sub n}, n = 1-10 clusters: A Density Functional Study

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

Priyanka,; Dharamvir, Keya; Sharma, Hitesh

2011-12-12

The structures of Germanium doped gold clusters GeAu{sub n} (n = 1-10) have been investigated using ab initio calculations based on density functional theory (DFT). We have obtained ground state geometries of GeAu{sub n} clusters and have it compared with Silicon doped gold clusters and pure gold clusters. The ground state geometries of the GeAu{sub n} clusters show patterns similar to silicon doped gold clusters except for n = 5, 6 and 9. The introduction of germanium atom increases the binding energy of gold clusters. The binding energy per atom of germanium doped cluster is smaller than the corresponding siliconmore » doped gold cluster. The HUMO-LOMO gap for Au{sub n}Ge clusters have been found to vary between 0.46 eV-2.09 eV. The mullikan charge analysis indicates that charge of order of 0.1e always transfers from germanium atom to gold atom.« less

Pleiotropic regulatory genes bldA, adpA and absB are implicated in production of phosphoglycolipid antibiotic moenomycin.

PubMed

Makitrynskyy, Roman; Ostash, Bohdan; Tsypik, Olga; Rebets, Yuriy; Doud, Emma; Meredith, Timothy; Luzhetskyy, Andriy; Bechthold, Andreas; Walker, Suzanne; Fedorenko, Victor

2013-10-23

Unlike the majority of actinomycete secondary metabolic pathways, the biosynthesis of peptidoglycan glycosyltransferase inhibitor moenomycin in Streptomyces ghanaensis does not involve any cluster-situated regulators (CSRs). This raises questions about the regulatory signals that initiate and sustain moenomycin production. We now show that three pleiotropic regulatory genes for Streptomyces morphogenesis and antibiotic production-bldA, adpA and absB-exert multi-layered control over moenomycin biosynthesis in native and heterologous producers. The bldA gene for tRNA(Leu)UAA is required for the translation of rare UUA codons within two key moenomycin biosynthetic genes (moe), moeO5 and moeE5. It also indirectly influences moenomycin production by controlling the translation of the UUA-containing adpA and, probably, other as-yet-unknown repressor gene(s). AdpA binds key moe promoters and activates them. Furthermore, AdpA interacts with the bldA promoter, thus impacting translation of bldA-dependent mRNAs-that of adpA and several moe genes. Both adpA expression and moenomycin production are increased in an absB-deficient background, most probably because AbsB normally limits adpA mRNA abundance through ribonucleolytic cleavage. Our work highlights an underappreciated strategy for secondary metabolism regulation, in which the interaction between structural genes and pleiotropic regulators is not mediated by CSRs. This strategy might be relevant for a growing number of CSR-free gene clusters unearthed during actinomycete genome mining.

Genetically based location from triploid populations and gene ontology of a 3.3-mb genome region linked to Alternaria brown spot resistance in citrus reveal clusters of resistance genes.

PubMed

Cuenca, José; Aleza, Pablo; Vicent, Antonio; Brunel, Dominique; Ollitrault, Patrick; Navarro, Luis

2013-01-01

Genetic analysis of phenotypical traits and marker-trait association in polyploid species is generally considered as a challenge. In the present work, different approaches were combined taking advantage of the particular genetic structures of 2n gametes resulting from second division restitution (SDR) to map a genome region linked to Alternaria brown spot (ABS) resistance in triploid citrus progeny. ABS in citrus is a serious disease caused by the tangerine pathotype of the fungus Alternaria alternata. This pathogen produces ACT-toxin, which induces necrotic lesions on fruit and young leaves, defoliation and fruit drop in susceptible genotypes. It is a strong concern for triploid breeding programs aiming to produce seedless mandarin cultivars. The monolocus dominant inheritance of susceptibility, proposed on the basis of diploid population studies, was corroborated in triploid progeny. Bulk segregant analysis coupled with genome scan using a large set of genetically mapped SNP markers and targeted genetic mapping by half tetrad analysis, using SSR and SNP markers, allowed locating a 3.3 Mb genomic region linked to ABS resistance near the centromere of chromosome III. Clusters of resistance genes were identified by gene ontology analysis of this genomic region. Some of these genes are good candidates to control the dominant susceptibility to the ACT-toxin. SSR and SNP markers were developed for efficient early marker-assisted selection of ABS resistant hybrids.

Genetically Based Location from Triploid Populations and Gene Ontology of a 3.3-Mb Genome Region Linked to Alternaria Brown Spot Resistance in Citrus Reveal Clusters of Resistance Genes

PubMed Central

Cuenca, José; Aleza, Pablo; Vicent, Antonio; Brunel, Dominique; Ollitrault, Patrick; Navarro, Luis

2013-01-01

Genetic analysis of phenotypical traits and marker-trait association in polyploid species is generally considered as a challenge. In the present work, different approaches were combined taking advantage of the particular genetic structures of 2n gametes resulting from second division restitution (SDR) to map a genome region linked to Alternaria brown spot (ABS) resistance in triploid citrus progeny. ABS in citrus is a serious disease caused by the tangerine pathotype of the fungus Alternaria alternata. This pathogen produces ACT-toxin, which induces necrotic lesions on fruit and young leaves, defoliation and fruit drop in susceptible genotypes. It is a strong concern for triploid breeding programs aiming to produce seedless mandarin cultivars. The monolocus dominant inheritance of susceptibility, proposed on the basis of diploid population studies, was corroborated in triploid progeny. Bulk segregant analysis coupled with genome scan using a large set of genetically mapped SNP markers and targeted genetic mapping by half tetrad analysis, using SSR and SNP markers, allowed locating a 3.3 Mb genomic region linked to ABS resistance near the centromere of chromosome III. Clusters of resistance genes were identified by gene ontology analysis of this genomic region. Some of these genes are good candidates to control the dominant susceptibility to the ACT-toxin. SSR and SNP markers were developed for efficient early marker-assisted selection of ABS resistant hybrids. PMID:24116149

The structural diversity of ABS{sub 3} compounds with d{sup 0} electronic configuration for the B-cation

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

Brehm, John A., E-mail: brehmj@sas.upenn.edu; Bennett, Joseph W.; Schoenberg, Michael Rutenberg

2014-06-14

We use first-principles density functional theory within the local density approximation to ascertain the ground state structure of real and theoretical compounds with the formula ABS{sub 3} (A = K, Rb, Cs, Ca, Sr, Ba, Tl, Sn, Pb, and Bi; and B = Sc, Y, Ti, Zr, V, and Nb) under the constraint that B must have a d{sup 0} electronic configuration. Our findings indicate that none of these AB combinations prefer a perovskite ground state with corner-sharing BS{sub 6} octahedra, but that they prefer phases with either edge- or face-sharing motifs. Further, a simple two-dimensional structure field map createdmore » from A and B ionic radii provides a neat demarcation between combinations preferring face-sharing versus edge-sharing phases for most of these combinations. We then show that by modifying the common Goldschmidt tolerance factor with a multiplicative term based on the electronegativity difference between A and S, the demarcation between predicted edge-sharing and face-sharing ground state phases is enhanced. We also demonstrate that, by calculating the free energy contribution of phonons, some of these compounds may assume multiple phases as synthesis temperatures are altered, or as ambient temperatures rise or fall.« less

Ab initio calculation of the deprotonation constants of an atomistically defined nanometer-sized, aluminium hydroxide oligomer

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

Wander, Matthew C. F.; Shuford, Kevin L.; Rustad, James R.

Aluminium possesses significant and diverse chemistry. Numerous compounds have been defined, and the elucidation of their chemistry is of significant geochemical interest. In this paper, a brucite-like, eight-aluminium aqueous cluster is modelled with density functional theory to identify its primary site of deprotonation and the associated pK(a) constant using both explicit (a full first solvent shell) and implicit solvent. Two methods for calculating the pK(a) are compared. We found that a bond density approach is better than a direct energy calculation for ions with large charge and high symmetry. The terminal aluminium atoms have equatorial ligated waters that in solventmore » have one long O-H bond. This site is more reactive than any of the other protons on the particle. Insights into the experimental crystal structure and Bader's Atoms in Molecules density analysis are presented as routes to reduce the computational time required for the identification of protonation sites.« less

A Systematic Theoretical Study of UC6: Structure, Bonding Nature, and Spectroscopy.

PubMed

Du, Jiguang; Jiang, Gang

2017-11-20

The study of uranium carbides has received renewed attention in recent years due to the potential use of these compounds as fuels in new generations of nuclear reactors. The isomers of the UC 6 cluster were determined by DFT and ab initio methods. The structures obtained using SC-RECP for U were generally consistent with those obtained using an all-electron basis set (ZORA-SARC). The CCSD(T) calculations indicated that two isomers had similar energies and may coexist in laser evaporation experiments. The nature of the U-C bonds in the different isomers was examined via a topological analysis of the electron density, and the results indicated that the U-C bonds are predominantly closed-shell (ionic) interactions with a certain degree of covalent character in all cases, particularly in the linear species. The IR and UV-vis spectra of the isomers were theoretically simulated to provide information that can be used to identify the isomers of UC 6 in future experiments.

Antibodies causing thrombocytopenia in patients treated with RGD-mimetic platelet inhibitors recognize ligand-specific conformers of αIIb/β3 integrin

PubMed Central

Rasmussen, Mark; Zhu, Jieqing; Aster, Richard H.

2012-01-01

Arginine-glycine-aspartic acid (RGD)–mimetic platelet inhibitors act by occupying the RGD recognition site of αIIb/β3 integrin (GPIIb/IIIa), thereby preventing the activated integrin from reacting with fibrinogen. Thrombocytopenia is a well-known side effect of treatment with this class of drugs and is caused by Abs, often naturally occurring, that recognize αIIb/β3 in a complex with the drug being administered. RGD peptide and RGD-mimetic drugs are known to induce epitopes (ligand-induced binding sites [LIBS]) in αIIb/β3 that are recognized by certain mAbs. It has been speculated, but not shown experimentally, that Abs from patients who develop thrombocytopenia when treated with an RGD-mimetic inhibitor similarly recognize LIBS determinants. We addressed this question by comparing the reactions of patient Abs and LIBS-specific mAbs against αIIb/β3 in a complex with RGD and RGD-mimetic drugs, and by examining the ability of selected non-LIBS mAbs to block binding of patient Abs to the liganded integrin. Findings made provide evidence that the patient Abs recognize subtle, drug-induced structural changes in the integrin head region that are clustered about the RGD recognition site. The target epitopes differ from classic LIBS determinants, however, both in their location and by virtue of being largely drug-specific. PMID:22490676

EIN3-like gene expression during fruit ripening of Cavendish banana (Musa acuminata cv. Grande naine).

PubMed

Mbéguié-A-Mbéguié, Didier; Hubert, Olivier; Fils-Lycaon, Bernard; Chillet, Marc; Baurens, Franc-Christophe

2008-06-01

Ethylene signal transduction initiates with ethylene binding at receptor proteins and terminates in a transcription cascade involving the EIN3/EIL transcription factors. Here, we have isolated four cDNAs homologs of the Arabidopsis EIN3/EIN3-like gene, MA-EILs (Musa acuminata ethylene insensitive 3-like) from banana fruit. Sequence comparison with other banana EIL gene already registered in the database led us to conclude that, at this day, at least five different genes namely MA-EIL1, MA-EIL2/AB266318, MA-EIL3/AB266319, MA-EIL4/AB266320 and AB266321 exist in banana. Phylogenetic analyses included all banana EIL genes within a same cluster consisting of rice OsEILs, a monocotyledonous plant as banana. However, MA-EIL1, MA-EIL2/AB266318, MA-EIL4/AB266320 and AB266321 on one side, and MA-EIL3/AB266319 on the other side, belong to two distant subclusters. MA-EIL mRNAs were detected in all examined banana tissues but at lower level in peel than in pulp. According to tissues, MA-EIL genes were differentially regulated by ripening and ethylene in mature green fruit and wounding in old and young leaves. MA-EIL2/AB266318 was the unique ripening- and ethylene-induced gene; MA-EIL1, MA-EIL4/Ab266320 and AB266321 genes were downregulated, while MA-EIL3/AB266319 presented an unusual pattern of expression. Interestingly, a marked change was observed mainly in MA-EIL1 and MA-EIL3/Ab266319 mRNA accumulation concomitantly with changes in ethylene responsiveness of fruit. Upon wounding, the main effect was observed in MA-EIL4/AB266320 and AB266321 mRNA levels, which presented a markedly increase in both young and old leaves, respectively. Data presented in this study suggest the importance of a transcriptionally step control in the regulation of EIL genes during banana fruit ripening.

An ab initio cluster study of the chemisorption of atomic cesium and hydrogen on reconstructed surfaces of gallium rich gallium arsenide

NASA Astrophysics Data System (ADS)

Schailey, Ronald

1999-11-01

Chemisorption properties of cesium and hydrogen atoms on the Ga-rich GaAs (100) (2 x 1), (2 x 2), and β(4 x 2) surfaces are investigated using ab initio self-consistent restricted open shell Hartree-Fock (ROHF) total energy calculations with Hay- Wadt effective core potentials. The effects of electron correlation have been included using many-body perturbation theory through second order, with the exception of β(4 x 2) symmetry due to computational limitations. The semiconductor surface is modeled by finite sized hydrogen saturated clusters. The effects of surface relaxation and reconstruction have been investigated in detail. Results are given for the energetics of chemisorption, charge population analysis, HOMO-LUMO gaps, and consequent possibilities of metallization for atomic cesium adsorption. For the chemisorption of atomic hydrogen, the experimentally verified mechanism of surface dimer bond breaking is investigated in detail.

Trends in magnetism of free Rh clusters via relativistic ab-initio calculations.

PubMed

Šipr, O; Ebert, H; Minár, J

2015-02-11

A fully relativistic ab-initio study on free Rh clusters of 13-135 atoms is performed to identify general trends concerning their magnetism and to check whether concepts which proved to be useful in interpreting magnetism of 3d metals are applicable to magnetism of 4d systems. We found that there is no systematic relation between local magnetic moments and coordination numbers. On the other hand, the Stoner model appears well-suited both as a criterion for the onset of magnetism and as a guide for the dependence of local magnetic moments on the site-resolved density of states at the Fermi level. Large orbital magnetic moments antiparallel to spin magnetic moments were found for some sites. The intra-atomic magnetic dipole Tz term can be quite large at certain sites but as a whole it is unlikely to affect the interpretation of x-ray magnetic circular dichroism experiments based on the sum rules.

AB INITIO Molecular Dynamics Simulations on Local Structure and Electronic Properties in Liquid Sb from 913 K to 1193 K

NASA Astrophysics Data System (ADS)

Hao, Qing-Hai; Li, Y. D.; Kong, Xiang-Shan; Liu, C. S.

2013-02-01

Ab initio molecular dynamics simulations on liquid Sb have been carried out at five different temperatures from 913 K to 1193 K. We have investigated the temperature dependence of structure properties including structural factor S(Q), pair correlation function g(r), bond-angle distribution function g3(θ), cluster properties and bond order parameter Q4 and Q6. A shoulder was reproduced in the high wave number side of the first peak in the S(Q) implying that the residual structure units of crystalline Sb remain in liquid Sb. There is a noticeable bend at around 1023 K in the temperature dependence of the first-peak height of S(Q), the cluster properties and bond order parameter Q4, respectively, indicating that an abnormal structural change may occur at 973-1023 K.

Dioxonaphthoimidazoliums AB1 and YM155 disrupt phosphorylation of p50 in the NF-κB pathway

PubMed Central

Chin, Tan Min; Go, Mei Lin

2016-01-01

The NF-κB pathway is overexpressed in non-small cell lung cancers (NSCLC) and contributes to the poor prognosis and high mortality characterizing this malignancy. Silencing the p50 and p65 NF-κB subunits in the NSCLC H1299 cell line led to profound loss in cell viability and downregulated anti-apoptotic proteins survivin and Mcl1. We also showed that a survivin suppressant, the dioxonaphthoimidazolium YM155, and its structural analog AB1 arrested the growth of H1299 cells at nanomolar concentrations. Both compounds were apoptogenic and suppressed survivin and other anti-apoptotic proteins (Mcl1, Bcl-2, Bcl-xl) in a dose- and/or time-dependent manner. YM155 and AB1 did not affect the expression of key proteins (IκBα, p65, p50) involved in NF-κB signaling. Stable IκBα levels suggest that the NF-κB/IκB complex and proteins upstream of IκBα, were not targeted. Neither did the compounds intercept the nuclear translocation of the p50 and p65 subunits. On the other hand, YM155 and AB1 suppressed the phosphorylation of the p50 subunit at Ser337 which is critical in promoting the binding of NF-κB dimers to DNA. Both compounds duly impeded the binding of NF-κB dimers to DNA and attenuated transcriptional activity of luciferase-transfected HEK293 cells controlled by NF-κB response elements. We propose that the “silencing” the NF-κB pathway effected by these compounds contributed to their potent apoptogenic effects on H1299. Notwithstanding, the mechanism(s) involved in their ability to abolish phosphorylation of p50 remains to be elucidated. Taken together, these results disclose a novel facet of functionalized dioxonaphthoimidazoliums that could account for their potent cell killing property. PMID:26872379

Blocked inverted indices for exact clustering of large chemical spaces.

PubMed

Thiel, Philipp; Sach-Peltason, Lisa; Ottmann, Christian; Kohlbacher, Oliver

2014-09-22

The calculation of pairwise compound similarities based on fingerprints is one of the fundamental tasks in chemoinformatics. Methods for efficient calculation of compound similarities are of the utmost importance for various applications like similarity searching or library clustering. With the increasing size of public compound databases, exact clustering of these databases is desirable, but often computationally prohibitively expensive. We present an optimized inverted index algorithm for the calculation of all pairwise similarities on 2D fingerprints of a given data set. In contrast to other algorithms, it neither requires GPU computing nor yields a stochastic approximation of the clustering. The algorithm has been designed to work well with multicore architectures and shows excellent parallel speedup. As an application example of this algorithm, we implemented a deterministic clustering application, which has been designed to decompose virtual libraries comprising tens of millions of compounds in a short time on current hardware. Our results show that our implementation achieves more than 400 million Tanimoto similarity calculations per second on a common desktop CPU. Deterministic clustering of the available chemical space thus can be done on modern multicore machines within a few days.

Enhanced hydrogen release by catalyzed hydrolysis of sodium borohydride-ammonia borane mixtures: a solution-state 11B NMR study.

PubMed

Hannauer, J; Demirci, U B; Geantet, C; Herrmann, J M; Miele, P

2011-03-07

Hydrolysis of mixtures consisting of sodium borohydride NaBH(4) (SB) and ammonia borane NH(3)BH(3) (AB) was studied in the absence/presence of a Co catalyst. The kinetics of the H(2) evolutions was measured. The reactions were followed in situ by solution-state (11)B NMR and the hydrolysis by-products characterized by NMR, XRD and IR. It is demonstrated that the combination of the two compounds gives a synergetic effect. SB rapidly reduces the Co catalyst precursor and the NH(4)(+) ions from AB contribute in the dispersion of the in situ formed Co nanoparticles. As a result, the kinetics of H(2) evolution is greatly improved. For instance, a hydrogen generation rate of 29.6 L min(-1) g(-1)(Co) was found for a mixture consisting of 81 wt% NH(3)BH(3), 9 wt% NaBH(4) and 10 wt% CoCl(2). By (11)B NMR, it was showed that the reaction mechanisms are quite trivial. As soon as the Co catalyst forms in situ, SB, rather than AB, hydrolyzes until it is totally converted. Then, the overall hydrolysis continues with that of AB. Both reactions follow a bimolecular Langmuir-Hinshelwood mechanism; no reaction intermediates were observed during the process. In fact, SB and AB convert directly into B(OH)(4)(-), which comes in equilibrium with a polyborate compound identified as B(3)O(3)(OH)(4)(-). All of these results are discussed herein.

Biocontrol of Bacterial Fruit Blotch by Bacillus subtilis 9407 via Surfactin-Mediated Antibacterial Activity and Colonization

PubMed Central

Fan, Haiyan; Zhang, Zhanwei; Li, Yan; Zhang, Xun; Duan, Yongming; Wang, Qi

2017-01-01

In this study, Bacillus subtilis 9407 showed a strong antibacterial activity against Acidovorax citrulli in vitro and 61.7% biocontrol efficacy on melon seedlings 4 days post inoculation under greenhouse conditions. To understand the biocontrol mechanism of B. subtilis 9407, identify the primary antibacterial compound and determine its role in controlling bacterial fruit blotch (BFB), a srfAB deletion mutant (ΔsrfAB) was constructed. The ΔsrfAB which was deficient in production of surfactin, not only showed almost no ability to inhibit growth of A. citrulli but also decreased biofilm formation and reduced swarming motility. Colonization assay demonstrated that B. subtilis 9407 could conlonize on melon roots and leaves in a large population, while ΔsrfAB showed a four- to ten-fold reduction in colonization of melon roots and leaves. Furthermore, a biocontrol assay showed that ΔsrfAB lost the biocontrol efficacy. In summary, our results indicated that surfactin, which consists of C13- to C16-surfactin A was the primary antibacterial compound of B. subtilis 9407, and it played a major role in biofilm formation, swarming motility, colonization and suppressing BFB. We propose that the biocontrol activity of B. subtilis 9407 is the results of the coordinated action of surfactin-mediated antibacterial activity and colonization. This study reveals for the first time that the use of a B. subtilis strain as a potential biological control agent could efficiently control BFB by producing surfactin. PMID:29075242

Biocontrol of Bacterial Fruit Blotch by Bacillus subtilis 9407 via Surfactin-Mediated Antibacterial Activity and Colonization.

PubMed

Fan, Haiyan; Zhang, Zhanwei; Li, Yan; Zhang, Xun; Duan, Yongming; Wang, Qi

2017-01-01

In this study, Bacillus subtilis 9407 showed a strong antibacterial activity against Acidovorax citrulli in vitro and 61.7% biocontrol efficacy on melon seedlings 4 days post inoculation under greenhouse conditions. To understand the biocontrol mechanism of B. subtilis 9407, identify the primary antibacterial compound and determine its role in controlling bacterial fruit blotch (BFB), a srfAB deletion mutant (Δ srfAB ) was constructed. The Δ srfAB which was deficient in production of surfactin, not only showed almost no ability to inhibit growth of A. citrulli but also decreased biofilm formation and reduced swarming motility. Colonization assay demonstrated that B. subtilis 9407 could conlonize on melon roots and leaves in a large population, while Δ srfAB showed a four- to ten-fold reduction in colonization of melon roots and leaves. Furthermore, a biocontrol assay showed that Δ srfAB lost the biocontrol efficacy. In summary, our results indicated that surfactin, which consists of C13- to C16-surfactin A was the primary antibacterial compound of B. subtilis 9407, and it played a major role in biofilm formation, swarming motility, colonization and suppressing BFB. We propose that the biocontrol activity of B. subtilis 9407 is the results of the coordinated action of surfactin-mediated antibacterial activity and colonization. This study reveals for the first time that the use of a B. subtilis strain as a potential biological control agent could efficiently control BFB by producing surfactin.

Pollution characteristics and health risk assessment of volatile organic compounds emitted from different plastic solid waste recycling workshops.

PubMed

He, Zhigui; Li, Guiying; Chen, Jiangyao; Huang, Yong; An, Taicheng; Zhang, Chaosheng

2015-04-01

The pollution profiles of volatile organic compounds (VOCs) emitted from different recycling workshops processing different types of plastic solid waste (PSW) and their health risks were investigated. A total of 64 VOCs including alkanes, alkenes, monoaromatics, oxygenated VOCs (OVOCs), chlorinated VOCs (ClVOCs) and acrylonitrile during the melting extrusion procedure were identified and quantified. The highest concentration of total VOCs (TVOC) occurred in the poly(acrylonitrile-butadiene styrene) (ABS) recycling workshop, followed by the polystyrene (PS), polypropylene (PP), polyamide (PA), polyvinyl chloride (PVC), polyethylene (PE) and polycarbonate (PC) workshops. Monoaromatics were found as the major component emitted from the ABS and PS recycling workshops, while alkanes were mainly emitted from the PE and PP recycling processes, and OVOCs from the PVC and PA recycling workshops. According to the occupational exposure limits' (OEL) assessment, the workers suffered acute and chronic health risks in the ABS and PS recycling workshops. Meanwhile, it was found that most VOCs in the indoor microenvironments were originated from the melting extrusion process, while the highest TVOC concentration was observed in the PS rather than in the ABS recycling workshop. Non-cancer hazard indices (HIs) of all individual VOCs were <1.0, whereas the total HI in the PS recycling workshop was 1.9, posing an adverse chronic health threat. Lifetime cancer risk assessment suggested that the residents also suffered from definite cancer risk in the PS, PA, ABS and PVC recycling workshops. Copyright © 2015 Elsevier Ltd. All rights reserved.

Improving olefin tolerance and production in E. coli using native and evolved AcrB

DOE PAGES

Mingardon, Florence; Clement, Camille; Hirano, Kathleen; ...

2015-01-20

Microorganisms can be engineered for the production of chemicals utilized in the polymer industry. However many such target compounds inhibit microbial growth and might correspondingly limit production levels. Here, we focus on compounds that are precursors to bioplastics, specifically styrene and representative alpha-olefins; 1-hexene, 1-octene, and 1-nonene. We evaluated the role of the Escherichia coli efflux pump, AcrAB-TolC, in enhancing tolerance towards these olefin compounds. AcrAB-TolC is involved in the tolerance towards all four compounds in E. coli. Both styrene and 1-hexene are highly toxic to E. coli. Styrene is a model plastics precursor with an established route for productionmore » in E. coli (McKenna and Nielsen, 2011). Though our data indicates that AcrAB-TolC is important for its optimal production, we observed a strong negative selection against the production of styrene in E. coli. Thus we used 1-hexene as a model compound to implement a directed evolution strategy to further improve the tolerance phenotype towards this alpha-olefin. We focused on optimization of AcrB, the inner membrane domain known to be responsible for substrate binding, and found several mutations (A279T, Q584R, F617L, L822P, F927S, and F1033Y) that resulted in improved tolerance. Several of these mutations could also be combined in a synergistic manner. Our study shows efflux pumps to be an important mechanism in host engineering for olefins, and one that can be further improved using strategies such as directed evolution, to increase tolerance and potentially production.« less

Electron detachment energies in high-symmetry alkali halide solvated-electron anions

NASA Astrophysics Data System (ADS)

Anusiewicz, Iwona; Berdys, Joanna; Simons, Jack; Skurski, Piotr

2003-07-01

We decompose the vertical electron detachment energies (VDEs) in solvated-electron clusters of alkali halides in terms of (i) an electrostatic contribution that correlates with the dipole moment (μ) of the individual alkali halide molecule and (ii) a relaxation component that is related to the polarizability (α) of the alkali halide molecule. Detailed numerical ab initio results for twelve species (MX)n- (M=Li,Na; X=F,Cl,Br; n=2,3) are used to construct an interpolation model that relates the clusters' VDEs to their μ and α values as well as a cluster size parameter r that we show is closely related to the alkali cation's ionic radius. The interpolation formula is then tested by applying it to predict the VDEs of four systems [i.e., (KF)2-, (KF)3-, (KCl)2-, and (KCl)3-] that were not used in determining the parameters of the model. The average difference between the model's predicted VDEs and the ab initio calculated electron binding energies is less than 4% (for the twelve species studied). It is concluded that one can easily estimate the VDE of a given high-symmetry solvated electron system by employing the model put forth here if the α, μ and cation ionic radii are known. Alternatively, if VDEs are measured for an alkali halide cluster and the α and μ values are known, one can estimate the r parameter, which, in turn, determines the "size" of the cluster anion.

Predicting the points of interaction of small molecules in the NF-κB pathway

PubMed Central

2011-01-01

Background The similarity property principle has been used extensively in drug discovery to identify small compounds that interact with specific drug targets. Here we show it can be applied to identify the interactions of small molecules within the NF-κB signalling pathway. Results Clusters that contain compounds with a predominant interaction within the pathway were created, which were then used to predict the interaction of compounds not included in the clustering analysis. Conclusions The technique successfully predicted the points of interactions of compounds that are known to interact with the NF-κB pathway. The method was also shown to be successful when compounds for which the interaction points were unknown were included in the clustering analysis. PMID:21342508

Ab Initio Prediction of the Structural, Electronic, Elastic, and Thermoelectric Properties of Half-Heusler Ternary Compounds TiIrX (X = As and Sb)

NASA Astrophysics Data System (ADS)

Chibani, S.; Arbouche, O.; Zemouli, M.; Amara, K.; Benallou, Y.; Azzaz, Y.; Belgoumène, B.; Bentayeb, A.; Ameri, M.

2018-01-01

The structural, electronic, elastic, and thermoelectric properties of TiIrX (X = As and Sb) half-Heusler compounds with 18 valence electrons were studied using density functional theory. The generalized gradient approximation of Perdew-Burke and Ernzerhof used for calculation of the structural parameters and elastic properties of TiIrAs and TiIrSb denotes that the computed lattice constants were in excellent agreement with the available experimental data and previous theoretical works. Furthermore, the calculated elastic constants for both compounds satisfy the Born criteria indicating their mechanical stabilities. The modified Becke-Johnson potential (TB-mBJ) was used to provide a better description of the electronic structures, which indicate that both compounds are narrow-gap semiconductors. Additionally, the investigations of thermoelectric performance were carried out using the results of ab initio band-structure calculations and the semi-classical Boltzmann theory within the constant relaxation time approximations. The predicted values of the figure of merit ZT e are close to unity at room temperature. This reveals that TiIrAs and TiIrSb compounds are excellent candidates for practical applications in the thermoelectric devices.

Ab initio Thermal Transport in Compound Semiconductors

DTIC Science & Technology

2013-04-02

upper bound to the thermal conductivities of cubic aluminum-V, gallium -V, and indium-V compounds as limited by anharmonic phonon scattering. The effects...and GaP [red circles (Ref. 51) and red triangles (Ref. 52)]. B. Gallium -V compounds We previously presented results for κL and P for wurtzite GaN and...data was found. We used this approach to examine κL in aluminum-V, gallium -V, and indium-V compounds as well as the technologically important materials

Specificity and biologic activities of novel anti-membrane IgM antibodies

PubMed Central

Welt, Rachel S.; Welt, Jonathan A.; Kostyal, David; Gangadharan, Yamuna D; Raymond, Virginia; Welt, Sydney

2016-01-01

The concept that the B-cell Receptor (BCR) initiates a driver pathway in lymphoma-leukemia has been clinically validated. Previously described unique BCR Ig-class-specific sequences (proximal domains (PDs)), are not expressed in serum Ig (sIg). As a consequence of sequence and structural differences in the membrane IgM (mIgM) μ-Constant Domain 4, additional epitopes distinguish mIgM from sIgM. mAbs generated to linear and conformational epitopes, restricted to mIgM and not reacting with sIgM, were generated despite the relative hydrophobicity of the PDm sequence. Anti-PD mAbs (mAb1, mAb2, and mAb3) internalize mIgM. Anti-mIgM mAb4, which recognizes a distinct non-ligand binding site epitope, mediates mIgM internalization, and in low-density cultures, growth inhibition, anti-clonogenic activity, and apoptosis. We show that mAb-mediated mIgM internalization generally does not interrupt BCR-directed cell growth, however, mAb4 binding to a non-ligand binding site in the mIgM PDm-μC4 domain induces both mIgM internalization and anti-tumor effects. BCR micro-clustering in many B-cell leukemia and lymphoma lines is demonstrated by SEM micrographs using these new mAb reagents. mAb4 is a clinical candidate as a mediator of inhibition of the BCR signaling pathway. As these agents do not bind to non-mIgM B-cells, nor cross-react to non-lymphatic tissues, they may spare B-cell/normal tissue destruction as mAb-drug conjugates. PMID:27732950

Specificity and biologic activities of novel anti-membrane IgM antibodies.

PubMed

Welt, Rachel S; Welt, Jonathan A; Kostyal, David; Gangadharan, Yamuna D; Raymond, Virginia; Welt, Sydney

2016-11-15

The concept that the B-cell Receptor (BCR) initiates a driver pathway in lymphoma-leukemia has been clinically validated. Previously described unique BCR Ig-class-specific sequences (proximal domains (PDs)), are not expressed in serum Ig (sIg). As a consequence of sequence and structural differences in the membrane IgM (mIgM) µ-Constant Domain 4, additional epitopes distinguish mIgM from sIgM. mAbs generated to linear and conformational epitopes, restricted to mIgM and not reacting with sIgM, were generated despite the relative hydrophobicity of the PDm sequence. Anti-PD mAbs (mAb1, mAb2, and mAb3) internalize mIgM. Anti-mIgM mAb4, which recognizes a distinct non-ligand binding site epitope, mediates mIgM internalization, and in low-density cultures, growth inhibition, anti-clonogenic activity, and apoptosis. We show that mAb-mediated mIgM internalization generally does not interrupt BCR-directed cell growth, however, mAb4 binding to a non-ligand binding site in the mIgM PDm-μC4 domain induces both mIgM internalization and anti-tumor effects. BCR micro-clustering in many B-cell leukemia and lymphoma lines is demonstrated by SEM micrographs using these new mAb reagents. mAb4 is a clinical candidate as a mediator of inhibition of the BCR signaling pathway. As these agents do not bind to non-mIgM B-cells, nor cross-react to non-lymphatic tissues, they may spare B-cell/normal tissue destruction as mAb-drug conjugates.

Electronic and molecular structure of carbon grains

NASA Technical Reports Server (NTRS)

Almloef, Jan; Luethi, Hans-Peter

1990-01-01

Clusters of carbon atoms have been studied with large-scale ab initio calculations. Planar, single-sheet graphite fragments with 6 to 54 atoms were investigated, as well as the spherical C(sub 60) Buckminsterfullerene molecule. Polycyclic aromatic hydrocarbons (PAHs) have also been considered. Thermodynamic differences between diamond- and graphite-like grains have been studied in particular. Saturation of the peripheral bonds with hydrogen is found to provide a smooth and uniform convergence of the properties with increasing cluster size. For the graphite-like clusters the convergence to bulk values is much slower than for the three-dimensional complexes.

Application of the AMPLE cluster-and-truncate approach to NMR structures for molecular replacement

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

Bibby, Jaclyn; Keegan, Ronan M.; Mayans, Olga

2013-11-01

Processing of NMR structures for molecular replacement by AMPLE works well. AMPLE is a program developed for clustering and truncating ab initio protein structure predictions into search models for molecular replacement. Here, it is shown that its core cluster-and-truncate methods also work well for processing NMR ensembles into search models. Rosetta remodelling helps to extend success to NMR structures bearing low sequence identity or high structural divergence from the target protein. Potential future routes to improved performance are considered and practical, general guidelines on using AMPLE are provided.

Sample Integrity Evaluation and EPA Method 325b Interlaboratory Comparison for Select Volatile Organic Compounds Collected Diffusively on Carbopack X Sorbent Tubes

EPA Science Inventory

Sample integrity evaluations and inter-laboratory comparisons were conducted in application of U.S. Environmental Protection Agency (EPA) Methods 325A/B for monitoring benzene and additional selected volatile organic compounds (VOCs) usingpassive-diffusive Carbopack X tube sample...

Lowest-energy structures and electronic properties of Na-Si binary clusters from ab initio global search.

PubMed

Sai, Linwei; Tang, Lingli; Zhao, Jijun; Wang, Jun; Kumar, Vijay

2011-11-14

The ground state structures of neutral and anionic clusters of Na(n)Si(m) (1 ≤ n ≤ 3, 1 ≤ m ≤ 11) have been determined using genetic algorithm incorporated in first principles total energy code. The size dependence of the structural and electronic properties is discussed in detail. It is found that the lowest-energy structures of Na(n)Si(m) clusters resemble those of the pure Si clusters. Interestingly, Na atoms in neutral Na(n)Si(m) clusters are usually well separated by the Si(m) skeleton, whereas Na atoms can form Na-Na bonds in some anionic clusters. The ionization potentials, adiabatic electron affinities, and photoelectron spectra are also calculated and the results compare well with the experimental data. © 2011 American Institute of Physics

Immunoaffinity Knockout of Saponin Glycosides from Asparagus racemosus to Assess Anti-lipid Peroxidation.

PubMed

Onlom, Churanya; Phrompittayarat, Watoo; Putalun, Waraporn; Waranuch, Neti; Ingkaninan, Kornkanok

2017-07-01

Asparagus racemosus Willd (Asparagaceae family), known as Shatavari, is important in Ayurveda and traditional Thai medicines. The saponin glycosides, shatavarin I and IV are major constituents in its roots and may be responsible for their actions including protection against lipid peroxidation and carcinogenesis. To develop an immunoaffinity column for isolating compounds with structures related to shatavarin IV from crude extracts of A. racemosus root. The monoclonal antibody recognising shatavarin IV (mAbShavIV) was coupled to an Affi-Gel Hz gel to isolate compounds with structures related to shatavarin IV from the other components of crude extracts of A. racemosus root. The saponin glycosides in each fraction were analysed by mAbShavIV ELISA and LC-MS/MS. The pooled wash-through fractions contained 3% of loaded mAbShavIV reactive saponin glycosides, while eluted fractions released ~ 90% of shatavarin saponin glycosides in a single step. Using thiobarbiturate (TBARs) to measure lipid-peroxidation, the extract, and the pooled wash-through fractions showed moderate protection against Cu + -induced oxidation of human low density lipoprotein (LDL) (IC 50 11.3 ± 1.4 and 12.6 ± 0.9 μg/mL, respectively). In contrast, the saponin glycosides eluted from the mAbShavIV-column had weaker protectant (IC 50 29.7 ± 1.8 μg/mL) suggesting that A. racemosus shatavarins do not inhibit carcinogenesis through preventing lipid peroxidation. The strategy described here demonstrates its utility for isolating a group of related compounds from the rest of the extract with selectivity and recovery rate. Pharmacological efficacy and synergistic effects of the components obtained can be further investigated. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

On the bonding mechanism of CO to Pt(111) and its effect on the vibrational frequency of chemisorbed CO

NASA Astrophysics Data System (ADS)

Illas, F.; Zurita, S.; Márquez, A. M.; Rubio, J.

1997-04-01

The chemisorption of CO on the atop site of Pt(111) has been simulated by a Pt4 cluster model. Ab initio self consistent field (SCF) and complete active space self consistent field (CASSCF) cluster model wave functions have been obtained for the electronic ground state. Likewise, ab initio SCF wavefunctions have been obtained for two other electronic states. The optimum geometry and vibrational frequencies of chemisorbed CO are reported for the three states. The interaction energy and vibrational shift of chemisorbed CO, with respect to free gas phase CO, have been analyzed for the three electronic states. This analysis is carried out by means of the constrained space orbital variation (CSOV) method. In all cases the bond is found to be dominated by σ donation and π back-donation, known as Blyholder's mechanism. This mechanism is further supported by SCF calculations on a larger, Pt13, cluster model. For both clusters, the CSOV analysis of the vibrational frequency definitely shows that, contrary to previous recent studies, a major contribution to the experimentally observed vibrational shift comes from the π back-donation mechanism. However, we found that, contrary to common belief, σ donation also acts to lower the CO frequency and not to increase it. Physical reasons for such unexpected behaviour are given.

A combined photoelectron spectroscopy and ab initio study of the quasi-planar B24(-) cluster.

PubMed

Popov, Ivan A; Piazza, Zachary A; Li, Wei-Li; Wang, Lai-Sheng; Boldyrev, Alexander I

2013-10-14

The structure and chemical bonding of the 24-atom boron cluster are investigated using photoelectron spectroscopy and ab initio calculations. The joint experimental and theoretical investigation shows that B24(-) possesses a quasi-planar structure containing fifteen outer and nine inner atoms with six of the inner atoms forming a filled pentagonal moiety. The central atom of the pentagonal moiety is puckered out of plane by 0.9 Å, reminiscent of the six-atom pentagonal caps of the well-known B12 icosahedral unit. The next closest isomer at the ROCCSD(T) level of theory has a tubular double-ring structure. Comparison of the simulated spectra with the experimental data shows that the global minimum quasi-planar B24(-) isomer is the major contributor to the observed photoelectron spectrum, while the tubular isomer has no contribution to the experiment. Chemical bonding analyses reveal that the periphery of the quasi-planar B24 constitutes 15 classical 2c-2e B-B σ-bonds, whereas delocalized σ- and π-bonds are found in the interior of the cluster with one unique 6c-2e π-bond responsible for bonding in the B-centered pentagon. The current work suggests that the 24-atom boron cluster continues to be quasi-2D, albeit the tendency to form filled pentagonal units, characteristic of 3D cage-like structures of bulk boron, is observed.

Probing the Early Stages of Solvation of cis-Pinate Dianions by Water, Acetonitrile, and Methanol: A Photoelectron Spectroscopy and Theoretical Study

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

Hou, Gao-Lei; Kong, Xiang-Tao; Valiev, Marat

2016-01-01

Cis-pinic acid is one of the most important oxidation products of α-pinene – a key monoterpene compound in biogenic emission processes affecting the atmosphere. Molecular level understanding of interactions involved in the cluster formations around cis-pinic acid is an important and necessary prerequisite toward ascertaining its role in the aerosol formation processes. In this work, we studied the structures and energetics of the solvated clusters of cis-pinate (cis-PA²⁻), the doubly deprotonated dicarboxylate of cis-pinic acid, with H₂O, CH₃OH, and CH₃CN by negative ion photoelectron spectroscopy and ab initio theoretical calculations. We found that cis-PA²⁻ prefers being solvated alternately on themore » two -CO₂⁻ groups with increase of solvent coverage, a well-known solvation pattern that has been observed in microhydrated linear dicarboxylate dianion (DC n²⁻) clusters. Experiments and calculations further reveal an intriguing feature for the existence of the asymmetric type isomers for cis-PA2–(H2O)2 and cis-PA²⁻(CH₃OH)₂, in which both solvent molecules interact with only one of the -CO²⁻ groups – a phenomena that has not been observed in DCn²⁻ water clusters and exhibits the subtle effect of the rigid four-membered carbon ring brought in on the cis-PA²⁻ solvation. The dominant interactions between cis-PA²⁻ and solvent molecules are forming bidentate O–···H–O H-bonds for H₂O, O–···H–O and O–···H–C H-bonds for CH₃OH, and tridentate O–···H–C H-bonds for CH₃CN. The formation of inter-solvent H-bonds between H₂O and CH₃CN is found to be favorable in mixed solvent clusters, distinctly different from that between H₂O and CH₃OH. These findings have important implications for understanding the mechanism of cluster growth and nucleation of atmospheric organic aerosols and the nature of structure-function relationship of proteins containing carboxylate groups under various solvent environments.« less

Probing the early stages of solvation of cis-pinate dianions by water, acetonitrile, and methanol: a photoelectron spectroscopy and theoretical study.

PubMed

Hou, Gao-Lei; Kong, Xiang-Tao; Valiev, Marat; Jiang, Ling; Wang, Xue-Bin

2016-02-07

cis-Pinic acid is one of the most important oxidation products of α-pinene--a key monoterpene compound in biogenic emission processes. Molecular level understanding of its interaction with water in cluster formation is an important and necessary prerequisite for ascertaining its role in the aerosol formation processes. In this work, we studied the structures and energetics of the solvated clusters of cis-pinate (cis-PA(2-)), the doubly deprotonated dicarboxylate of cis-pinic acid, with H2O, CH3OH, and CH3CN by negative ion photoelectron spectroscopy and ab initio theoretical calculations. We found that cis-PA(2-) prefers being solvated alternately on the two -CO2(-) groups with increase of solvent coverage, a well-known solvation pattern that has been observed in microhydrated linear dicarboxylate dianion (DCn(2-)) clusters. Experiments and calculations further reveal an intriguing feature for the existence of the asymmetric type isomers for cis-PA(2-)(H2O)2 and cis-PA(2-)(CH3OH)2, in which both solvent molecules interact with only one of the -CO2(-) groups, a phenomenon that has not been observed in DCn(2-) water clusters and exhibits that the subtle effect of the rigid four-membered carbon ring brought on the cis-PA(2-) solvation. The dominant interactions between cis-PA(2-) and solvent molecules form bidentate O(-)...H-O H-bonds for H2O, O(-)...H-O and O(-)...H-C H-bonds for CH3OH, and tridentate O(-)...H-C H-bonds for CH3CN. The formation of inter-solvent H-bonds between H2O and CH3CN is found to be favorable in mixed solvent clusters, different from that between H2O and CH3OH. These findings have important implications for understanding the mechanism of cluster growth and the formation of atmospheric organic aerosols, as well as for rationalizing the nature of structure-function relationship of proteins containing carboxylate groups in various solvent environments.

Ab initio study of Pd carbonyls and CO/Pd(110)

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

Ramprasad, R.; Glassford, K.M.; Adams, J.B.

1994-12-31

Carbon monoxide chemisorption on transition metal surfaces has been one of the most extensively studied in surface science in past years due to its importance in a variety of catalytic processes, especially, automotive catalytic converters using Pt or Pd. The authors have performed ab initio studies to understand the electronic and geometric aspects of the Pd-CO bond in small carbonyl clusters and the CO covered (2 x 1)p2mg superstructure of the Pd(110) surface. They have used the standard quantum chemistry package Gaussian to study the former system and a LDA (local density approximation) formalism using ab initio pseudopotentials and amore » plane wave basis to study the latter. The latter results are preliminary; the authors intended to study thicker slabs in the future. The organization of the paper is as follows. The authors describe the methods used in their calculation in Sec. 2. In Sec. 3, they present results and discussion; here, they first look at the smallest possible clusters, viz, Pd{sub 2} and PdCO, take a brief look at the orbital chemistry involved and then move on to the study of the CO covered Pd(110) surface and examine the geometry of the near equilibrium structure.« less

Molecular identification of disk abalone (Haliotis discus discus) tetraspanin 33 and CD63: Insights into potent players in the disk abalone host defense system.

PubMed

Priyathilaka, Thanthrige Thiunuwan; Bathige, S D N K; Herath, H M L P B; Lee, Sukkyoung; Lee, Jehee

2017-10-01

Tetraspanins are a superfamily of transmembrane proteins involved in a diverse range of physiological processes including differentiation, adhesion, signal transduction, cell motility, and immune responses. In the present study, two tetraspanins, CD63 and tetraspanin 33 (TSPAN33) from disk abalone (AbCD63 and AbTSPAN33), were identified and characterized at the molecular level. The coding sequences for AbCD63 and AbTSPAN33 encoded polypeptides of 234 and 290 amino acids (aa) with predicted molecular mass of 25.3 and 32.5 kDa, respectively. The deduced AbCD63 and AbTSPAN33 protein sequences were also predicted to have a typical tetraspanin domain architecture, including four transmembrane domains (TM), short N- and C- terminal regions, a short intracellular loop, as well as a large and small extracellular loop. A characteristic CCG motif and cysteine residues, which are highly conserved across CD63 and TSPAN33 proteins of different species, were present in the large extracellular loop of both abalone tetraspanins. Phylogenetic analysis revealed that the AbCD63 and AbTSPAN33 clustered in the invertebrate subclade of tetraspanins, thus exhibiting a close relationship with tetraspanins of other mollusks. The AbCD63 and AbTSPAN33 mRNA transcripts were detected at early embryonic development stages of disk abalone with significantly higher amounts at the trochophore stage, suggesting the involvement of these proteins in embryonic development. Both AbCD63 and AbTSPAN33 were ubiquitously expressed in all the tissues of unchallenged abalones analyzed, with the highest expression levels found in hemocytes. Moreover, significant induction of AbCD63 and AbTSPAN33 mRNA expression was observed in immunologically important tissues, such as hemocytes and gills, upon stimulation with live bacteria (Vibrio parahaemolyticus and Listeria monocytogenes), virus (viral hemorrhagic septicemia virus), and two potent immune stimulators [polyinosinic:polycytidylic acid (poly I:C) and lipopolysaccharide (LPS)]. Collectively, these findings suggest that AbCD63 and AbTSPAN33 are involved in innate immune responses in disk abalone during pathogenic stress. Copyright © 2017 Elsevier Ltd. All rights reserved.

Ab initio dynamics and photoionization mass spectrometry reveal ion-molecule pathways from ionized acetylene clusters to benzene cation

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

Stein, Tamar; Bandyopadhyay, Biswajit; Troy, Tyler P.

The growth mechanism of hydrocarbons in ionizing environments, such as the interstellar medium (ISM), and some combustion conditions remains incompletely understood. Ab initio molecular dynamics (AIMD) simulations and molecular beam vacuum-UV (VUV) photoionization mass spectrometry experiments were performed to understand the ion-molecule growth mechanism of small acetylene clusters (up to hexamers). A dramatic dependence of product distribution on the ionization conditions is demonstrated experimentally and understood from simulations. The products change from reactive fragmentation products in a higher temperature, higher density gas regime toward a very cold collision-free cluster regime that is dominated by products whose empirical formula is (Cmore » 2H 2) n +, just like ionized acetylene clusters. The fragmentation products result from reactive ion- molecule collisions in a comparatively higher pressure and temperature regime followed by unimolecular decomposition. The isolated ionized clusters display rich dynamics that contain bonded C 4H 4 + and C 6H 6 + structures solvated with one or more neutral acetylene molecules. Such species contain large amounts ( > 2 eV) of excess internal energy. The role of the solvent acetylene molecules is to affect the barrier crossing dynamics in the potential energy surface (PES) between (C 2H 2) n + isomers and provide evaporative cooling to dissipate the excess internal energy and stabilize products including the aromatic ring of the benzene cation. Formation of the benzene cation is demonstrated in AIMD simulations of acetylene clusters with n > 3, as well as other metastable C 6H 6 + isomers. Lastly, these results suggest a path for aromatic ring formation in cold acetylene-rich environments such as parts of the ISM.« less

Ab initio dynamics and photoionization mass spectrometry reveal ion–molecule pathways from ionized acetylene clusters to benzene cation

PubMed Central

Stein, Tamar; Bandyopadhyay, Biswajit; Troy, Tyler P.; Fang, Yigang; Kostko, Oleg

2017-01-01

The growth mechanism of hydrocarbons in ionizing environments, such as the interstellar medium (ISM), and some combustion conditions remains incompletely understood. Ab initio molecular dynamics (AIMD) simulations and molecular beam vacuum-UV (VUV) photoionization mass spectrometry experiments were performed to understand the ion–molecule growth mechanism of small acetylene clusters (up to hexamers). A dramatic dependence of product distribution on the ionization conditions is demonstrated experimentally and understood from simulations. The products change from reactive fragmentation products in a higher temperature, higher density gas regime toward a very cold collision-free cluster regime that is dominated by products whose empirical formula is (C2H2)n+, just like ionized acetylene clusters. The fragmentation products result from reactive ion–molecule collisions in a comparatively higher pressure and temperature regime followed by unimolecular decomposition. The isolated ionized clusters display rich dynamics that contain bonded C4H4+ and C6H6+ structures solvated with one or more neutral acetylene molecules. Such species contain large amounts (>2 eV) of excess internal energy. The role of the solvent acetylene molecules is to affect the barrier crossing dynamics in the potential energy surface (PES) between (C2H2)n+ isomers and provide evaporative cooling to dissipate the excess internal energy and stabilize products including the aromatic ring of the benzene cation. Formation of the benzene cation is demonstrated in AIMD simulations of acetylene clusters with n > 3, as well as other metastable C6H6+ isomers. These results suggest a path for aromatic ring formation in cold acetylene-rich environments such as parts of the ISM. PMID:28484019

Ab initio dynamics and photoionization mass spectrometry reveal ion-molecule pathways from ionized acetylene clusters to benzene cation.

PubMed

Stein, Tamar; Bandyopadhyay, Biswajit; Troy, Tyler P; Fang, Yigang; Kostko, Oleg; Ahmed, Musahid; Head-Gordon, Martin

2017-05-23

The growth mechanism of hydrocarbons in ionizing environments, such as the interstellar medium (ISM), and some combustion conditions remains incompletely understood. Ab initio molecular dynamics (AIMD) simulations and molecular beam vacuum-UV (VUV) photoionization mass spectrometry experiments were performed to understand the ion-molecule growth mechanism of small acetylene clusters (up to hexamers). A dramatic dependence of product distribution on the ionization conditions is demonstrated experimentally and understood from simulations. The products change from reactive fragmentation products in a higher temperature, higher density gas regime toward a very cold collision-free cluster regime that is dominated by products whose empirical formula is (C 2 H 2 ) n + , just like ionized acetylene clusters. The fragmentation products result from reactive ion-molecule collisions in a comparatively higher pressure and temperature regime followed by unimolecular decomposition. The isolated ionized clusters display rich dynamics that contain bonded C 4 H 4 + and C 6 H 6 + structures solvated with one or more neutral acetylene molecules. Such species contain large amounts (>2 eV) of excess internal energy. The role of the solvent acetylene molecules is to affect the barrier crossing dynamics in the potential energy surface (PES) between (C 2 H 2 ) n + isomers and provide evaporative cooling to dissipate the excess internal energy and stabilize products including the aromatic ring of the benzene cation. Formation of the benzene cation is demonstrated in AIMD simulations of acetylene clusters with n > 3, as well as other metastable C 6 H 6 + isomers. These results suggest a path for aromatic ring formation in cold acetylene-rich environments such as parts of the ISM.

Ab initio dynamics and photoionization mass spectrometry reveal ion-molecule pathways from ionized acetylene clusters to benzene cation

DOE PAGES

Stein, Tamar; Bandyopadhyay, Biswajit; Troy, Tyler P.; ...

2017-05-08

The growth mechanism of hydrocarbons in ionizing environments, such as the interstellar medium (ISM), and some combustion conditions remains incompletely understood. Ab initio molecular dynamics (AIMD) simulations and molecular beam vacuum-UV (VUV) photoionization mass spectrometry experiments were performed to understand the ion-molecule growth mechanism of small acetylene clusters (up to hexamers). A dramatic dependence of product distribution on the ionization conditions is demonstrated experimentally and understood from simulations. The products change from reactive fragmentation products in a higher temperature, higher density gas regime toward a very cold collision-free cluster regime that is dominated by products whose empirical formula is (Cmore » 2H 2) n +, just like ionized acetylene clusters. The fragmentation products result from reactive ion- molecule collisions in a comparatively higher pressure and temperature regime followed by unimolecular decomposition. The isolated ionized clusters display rich dynamics that contain bonded C 4H 4 + and C 6H 6 + structures solvated with one or more neutral acetylene molecules. Such species contain large amounts ( > 2 eV) of excess internal energy. The role of the solvent acetylene molecules is to affect the barrier crossing dynamics in the potential energy surface (PES) between (C 2H 2) n + isomers and provide evaporative cooling to dissipate the excess internal energy and stabilize products including the aromatic ring of the benzene cation. Formation of the benzene cation is demonstrated in AIMD simulations of acetylene clusters with n > 3, as well as other metastable C 6H 6 + isomers. Lastly, these results suggest a path for aromatic ring formation in cold acetylene-rich environments such as parts of the ISM.« less

Drosophila small heat shock protein CryAB ensures structural integrity of developing muscles, and proper muscle and heart performance.

PubMed

Wójtowicz, Inga; Jabłońska, Jadwiga; Zmojdzian, Monika; Taghli-Lamallem, Ouarda; Renaud, Yoan; Junion, Guillaume; Daczewska, Malgorzata; Huelsmann, Sven; Jagla, Krzysztof; Jagla, Teresa

2015-03-01

Molecular chaperones, such as the small heat shock proteins (sHsps), maintain normal cellular function by controlling protein homeostasis in stress conditions. However, sHsps are not only activated in response to environmental insults, but also exert developmental and tissue-specific functions that are much less known. Here, we show that during normal development the Drosophila sHsp CryAB [L(2)efl] is specifically expressed in larval body wall muscles and accumulates at the level of Z-bands and around myonuclei. CryAB features a conserved actin-binding domain and, when attenuated, leads to clustering of myonuclei and an altered pattern of sarcomeric actin and the Z-band-associated actin crosslinker Cheerio (filamin). Our data suggest that CryAB and Cheerio form a complex essential for muscle integrity: CryAB colocalizes with Cheerio and, as revealed by mass spectrometry and co-immunoprecipitation experiments, binds to Cheerio, and the muscle-specific attenuation of cheerio leads to CryAB-like sarcomeric phenotypes. Furthermore, muscle-targeted expression of CryAB(R120G), which carries a mutation associated with desmin-related myopathy (DRM), results in an altered sarcomeric actin pattern, in affected myofibrillar integrity and in Z-band breaks, leading to reduced muscle performance and to marked cardiac arrhythmia. Taken together, we demonstrate that CryAB ensures myofibrillar integrity in Drosophila muscles during development and propose that it does so by interacting with the actin crosslinker Cheerio. The evidence that a DRM-causing mutation affects CryAB muscle function and leads to DRM-like phenotypes in the fly reveals a conserved stress-independent role of CryAB in maintaining muscle cell cytoarchitecture. © 2015. Published by The Company of Biologists Ltd.

Preparation and characterization of mechanically alloyed AB3-type based material LaMg2Ni5Al4 and its solid-gaz hydrogen storage reaction

NASA Astrophysics Data System (ADS)

Jaafar, Hassen; Aymard, Luc; Dachraoui, Walid; Demortière, Arnaud; Abdellaoui, Mohieddine

2018-04-01

We developed in the present paper the synthesis of a new AB3-type compound LaMg2Ni5Al4 by mechanical alloying (MA) process. ​​X-ray diffraction analysis (XRD) was used to determine the structural properties and the phase evolution of the powder mixtures. Two different synthesis pathways have been investigated. The first starting from elemental metals and the second from a mixture of two binary compounds LaNi5 (CaCu5-type structure, P6/mmm space group) and Al(Mg) solid solution (cubic Fm-3 m space group). The results show multiphase alloys which contain LaMg2Ni5Al4 main phase with hexagonal PuNi3-type structure (R-3 m space group). Rietveld analysis shows that using a planetary ball mill, we obtain a good yield of LaMg2Ni5Al4 compound after 5 h of mechanical alloying for both synthesis pathways. TEM analysis confirmed XRD results. SEM-EDX analysis of the final product was in agreement with the nominal chemical formula. A setup of possible solid-gaz hydrogenation reaction will be described so far at the end of this work. Electrochemical results demonstrate evidence on hydrogen absorption in the AB3 material and the discharge capacity was equal to 5.9 H/f.u.

Volatile organic compounds at oil and natural gas production well pads in Colorado and Texas using passive samplers

EPA Science Inventory

A pilot study was conducted in application of the U.S. Environmental Protection Agency (EPA) Methods 325A/B variant for monitoring volatile organic compounds (VOCs) near two oil and natural gas (ONG) production well pads in the Texas Barnett Shale formation and Colorado Denver&nd...

Application of passive sorbent tube and canister samplers for volatile organic compounds at refinery fenceline locations in Whiting, Indiana

EPA Science Inventory

Select volatile organic compounds (VOCs) in ambient air were measured at four fenceline sites at a petroleum refinery in Whiting, Indiana, USA using modified EPA Method 325 A/B with passive tubes and EPA Compendium Method TO-15 with canister samplers. One-week, time-integrated s...

Color evaluation of seventeen European unifloral honey types by means of spectrophotometrically determined CIE L*Cab*h(ab)° chromaticity coordinates.

PubMed

Tuberoso, Carlo Ignazio Giovanni; Jerković, Igor; Sarais, Giorgia; Congiu, Francesca; Marijanović, Zvonimir; Kuś, Piotr Marek

2014-02-15

CIE (Commission Internationale de l'Eclairage) L(*)Cab(*)h(ab)° color coordinates for 305 samples of 17 unifloral honeys types (asphodel, buckwheat, black locust, sweet chestnut, citrus, eucalyptus, Garland thorn, honeydew, heather, lime, mint, rapeseed, sage, strawberry tree, sulla flower, savory and thistle) from different geographic locations in Europe were spectrophotometrically assessed and statistically evaluated. Preliminary separation of unifloral honeys was obtained by means of L(*)-C(ab)(*) color coordination correlation. Hierarchical Cluster Analysis (HCA) revealed an expected segregation of the honeys types according to their chromatic characteristics. Principal Component Analysis (PCA) allowed to obtain a more defined distinction of the 17 unifloral honey types, particularly when using 3D graphics. CIE L(*)C(ab)(*)hab(*) color coordinates were useful for the identification of several honey types. The proposed method represents a simple and efficient procedure that can be used as a basis for the authentication of unifloral honeys worldwide. Copyright © 2013 Elsevier Ltd. All rights reserved.

Modeling Organochlorine Compounds and the σ-Hole Effect Using a Polarizable Multipole Force Field

PubMed Central

2015-01-01

The charge distribution of halogen atoms on organochlorine compounds can be highly anisotropic and even display a so-called σ-hole, which leads to strong halogen bonds with electron donors. In this paper, we have systematically investigated a series of chloromethanes with one to four chloro substituents using a polarizable multipole-based molecular mechanics model. The atomic multipoles accurately reproduced the ab initio electrostatic potential around chloromethanes, including CCl4, which has a prominent σ-hole on the Cl atom. The van der Waals parameters for Cl were fitted to the experimental density and heat of vaporization. The calculated hydration free energy, solvent reaction fields, and interaction energies of several homo- and heterodimer of chloromethanes are in good agreement with experimental and ab initio data. This study suggests that sophisticated electrostatic models, such as polarizable atomic multipoles, are needed for accurate description of electrostatics in organochlorine compounds and halogen bonds, although further improvement is necessary for better transferability. PMID:24484473

Novel Carbonyl Analogues of Tamoxifen: Design, Synthesis, and Biological Evaluation

NASA Astrophysics Data System (ADS)

Kasiotis, Konstantinos M.; Lambrinidis, George; Fokialakis, Nikolas; Tzanetou, Evangelia N.; Mikros, Emmanuel; Haroutounian, Serkos A.

2017-09-01

Aim of this work was to provide tamoxifen analogues with enhanced estrogen receptor binding affinity. Hence, several derivatives were prepared using an efficient triarylethylenes synthetic protocol. The novel compounds bioactivity was evaluated through the determination of their receptor binding affinity and their agonist/antagonist activity against breast cancer tissue using a MCF-7 cell-based assay. Phenyl esters 6a,b and 8a,b exhibited binding affinity to both ERα and ERβ higher than 4-hydroxytamoxifen while compounds 13 and 14 have shown cellular antiestrogenic activity similar to 4-hydroxytamoxifen and the known estrogen receptor inhibitor ICI182,780. Theoretical calculations and molecular modelling were applied to investigate, support and explain the biological profile of the new compounds. The relevant data indicated an agreement between calculations and demonstrated biological activity allowing to extract useful structure-activity relationships. Results herein underline that modifications of tamoxifen structure still provide molecules with substantial activity, as portrayed in the inhibition of MCF-7 cells proliferation.

Proteomic Analysis of Host Cell Protein Dynamics in the Culture Supernatants of Antibody-Producing CHO Cells

PubMed Central

Park, Jin Hyoung; Jin, Jong Hwa; Lim, Myung Sin; An, Hyun Joo; Kim, Jong Won; Lee, Gyun Min

2017-01-01

Chinese hamster ovary (CHO) cells are the most common cell line used for the production of therapeutic proteins including monoclonal antibodies (mAbs). Host cell proteins (HCPs), secreted and released from lysed cells, accumulate extracellularly during the cultures of recombinant CHO (rCHO) cells, potentially impairing product quality. In an effort to maintain good mAb quality during the cultures, HCPs accumulated extracellularly in batch and fed-batch cultures of a mAb-producing rCHO cell line were identified and quantified by nanoflow liquid chromatography-tandem mass spectrometry, followed by their gene ontology and functional analysis. Due to higher cell concentration and longer culture duration, more HCPs were identified and quantitated in fed-batch culture (2145 proteins identified and 1673 proteins quantified) than in batch culture (1934 proteins identified and 1486 proteins quantified). Clustering analysis of HCPs showed that the concentration profiles of HCPs affecting mAb quality (Lgmn, Ctsd, Gbl1, and B4galt1) correlated with changes in mAb quality attributes such as aggregation, charge variants, and N-glycosylation during the cultures. Taken together, the dataset of HCPs obtained in this study provides insights into determining the appropriate target proteins to be removed during both the cultures and purification steps for ensuring good mAb quality. PMID:28281648

IgG and complement deposition and neuronal loss in cats and humans with epilepsy and voltage-gated potassium channel complex antibodies.

PubMed

Klang, Andrea; Schmidt, Peter; Kneissl, Sibylle; Bagó, Zoltán; Vincent, Angela; Lang, Bethan; Moloney, Teresa; Bien, Christian G; Halász, Péter; Bauer, Jan; Pákozdy, Akos

2014-05-01

Voltage-gated potassium channel complex (VGKC-complex) antibody (Ab) encephalitis is a well-recognized form of limbic encephalitis in humans, usually occurring in the absence of an underlying tumor. The patients have a subacute onset of seizures, magnetic resonance imaging findings suggestive of hippocampal inflammation, and high serum titers of Abs against proteins of the VGKC-complex, particularly leucine-rich, glioma-inactivated 1 (LGI1). Most patients are diagnosed promptly and recover substantially with immunotherapies; consequently, neuropathological data are limited. We have recently shown that feline complex partial cluster seizures with orofacial involvement (FEPSO) in cats can also be associated with Abs against VGKC-complexes/LGI1. Here we examined the brains of cats with FEPSO and compared the neuropathological findings with those in a human with VGKC-complex-Ab limbic encephalitis. Similar to humans, cats with VGKC-complex-Ab and FEPSO have hippocampal lesions with only moderate T-cell infiltrates but with marked IgG infiltration and complement C9neo deposition on hippocampal neurons, associated with neuronal loss. These findings provide further evidence that FEPSO is a feline form of VGKC-complex-Ab limbic encephalitis and provide a model for increasing understanding of the human disease.

Modulation of the Acetone/Butanol Ratio during Fermentation of Corn Stover-Derived Hydrolysate by Clostridium beijerinckii Strain NCIMB 8052.

PubMed

Liu, Zi-Yong; Yao, Xiu-Qing; Zhang, Quan; Liu, Zhen; Wang, Ze-Jie; Zhang, Yong-Yu; Li, Fu-Li

2017-04-01

Producing biobutanol from lignocellulosic biomass has shown promise to ultimately reduce greenhouse gases and alleviate the global energy crisis. However, because of the recalcitrance of a lignocellulosic biomass, a pretreatment of the substrate is needed which in many cases releases soluble lignin compounds (SLCs), which inhibit growth of butanol-producing clostridia. In this study, we found that SLCs changed the acetone/butanol ratio (A/B ratio) during butanol fermentation. The typical A/B molar ratio during Clostridium beijerinckii NCIMB 8052 batch fermentation with glucose as the carbon source is about 0.5. In the present study, the A/B molar ratio during batch fermentation with a lignocellulosic hydrolysate as the carbon source was 0.95 at the end of fermentation. Structural and redox potential changes of the SLCs were characterized before and after fermentation by using gas chromatography/mass spectrometry and electrochemical analyses, which indicated that some exogenous SLCs were involved in distributing electron flow to C. beijerinckii , leading to modulation of the redox balance. This was further demonstrated by the NADH/NAD + ratio and trxB gene expression profile assays at the onset of solventogenic growth. As a result, the A/B ratio of end products changed significantly during C. beijerinckii fermentation using corn stover-derived hydrolysate as the carbon source compared to glucose as the carbon source. These results revealed that SLCs not only inhibited cell growth but also modulated the A/B ratio during C. beijerinckii butanol fermentation. IMPORTANCE Bioconversion of lignocellulosic feedstocks to butanol involves pretreatment, during which hundreds of soluble lignin compounds (SLCs) form. Most of these SLCs inhibit growth of solvent-producing clostridia. However, the mechanism by which these compounds modulate electron flow in clostridia remains elusive. In this study, the results revealed that SLCs changed redox balance by producing oxidative stress and modulating electron flow as electron donors. Production of H 2 and acetone was stimulated, while butanol production remained unchanged, which led to a high A/B ratio during C. beijerinckii fermentation using corn stover-derived hydrolysate as the carbon source. These observations provide insight into utilizing C. beijerinckii to produce butanol from a lignocellulosic biomass. Copyright © 2017 American Society for Microbiology.

Modulation of the Acetone/Butanol Ratio during Fermentation of Corn Stover-Derived Hydrolysate by Clostridium beijerinckii Strain NCIMB 8052

PubMed Central

Liu, Zi-Yong; Yao, Xiu-Qing; Zhang, Quan; Liu, Zhen; Wang, Ze-Jie; Zhang, Yong-Yu

2017-01-01

ABSTRACT Producing biobutanol from lignocellulosic biomass has shown promise to ultimately reduce greenhouse gases and alleviate the global energy crisis. However, because of the recalcitrance of a lignocellulosic biomass, a pretreatment of the substrate is needed which in many cases releases soluble lignin compounds (SLCs), which inhibit growth of butanol-producing clostridia. In this study, we found that SLCs changed the acetone/butanol ratio (A/B ratio) during butanol fermentation. The typical A/B molar ratio during Clostridium beijerinckii NCIMB 8052 batch fermentation with glucose as the carbon source is about 0.5. In the present study, the A/B molar ratio during batch fermentation with a lignocellulosic hydrolysate as the carbon source was 0.95 at the end of fermentation. Structural and redox potential changes of the SLCs were characterized before and after fermentation by using gas chromatography/mass spectrometry and electrochemical analyses, which indicated that some exogenous SLCs were involved in distributing electron flow to C. beijerinckii, leading to modulation of the redox balance. This was further demonstrated by the NADH/NAD+ ratio and trxB gene expression profile assays at the onset of solventogenic growth. As a result, the A/B ratio of end products changed significantly during C. beijerinckii fermentation using corn stover-derived hydrolysate as the carbon source compared to glucose as the carbon source. These results revealed that SLCs not only inhibited cell growth but also modulated the A/B ratio during C. beijerinckii butanol fermentation. IMPORTANCE Bioconversion of lignocellulosic feedstocks to butanol involves pretreatment, during which hundreds of soluble lignin compounds (SLCs) form. Most of these SLCs inhibit growth of solvent-producing clostridia. However, the mechanism by which these compounds modulate electron flow in clostridia remains elusive. In this study, the results revealed that SLCs changed redox balance by producing oxidative stress and modulating electron flow as electron donors. Production of H2 and acetone was stimulated, while butanol production remained unchanged, which led to a high A/B ratio during C. beijerinckii fermentation using corn stover-derived hydrolysate as the carbon source. These observations provide insight into utilizing C. beijerinckii to produce butanol from a lignocellulosic biomass. PMID:28130305

Two worlds collide: Image analysis methods for quantifying structural variation in cluster molecular dynamics

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

Steenbergen, K. G., E-mail: kgsteen@gmail.com; Gaston, N.

2014-02-14

Inspired by methods of remote sensing image analysis, we analyze structural variation in cluster molecular dynamics (MD) simulations through a unique application of the principal component analysis (PCA) and Pearson Correlation Coefficient (PCC). The PCA analysis characterizes the geometric shape of the cluster structure at each time step, yielding a detailed and quantitative measure of structural stability and variation at finite temperature. Our PCC analysis captures bond structure variation in MD, which can be used to both supplement the PCA analysis as well as compare bond patterns between different cluster sizes. Relying only on atomic position data, without requirement formore » a priori structural input, PCA and PCC can be used to analyze both classical and ab initio MD simulations for any cluster composition or electronic configuration. Taken together, these statistical tools represent powerful new techniques for quantitative structural characterization and isomer identification in cluster MD.« less

Two worlds collide: image analysis methods for quantifying structural variation in cluster molecular dynamics.

PubMed

Steenbergen, K G; Gaston, N

2014-02-14

Inspired by methods of remote sensing image analysis, we analyze structural variation in cluster molecular dynamics (MD) simulations through a unique application of the principal component analysis (PCA) and Pearson Correlation Coefficient (PCC). The PCA analysis characterizes the geometric shape of the cluster structure at each time step, yielding a detailed and quantitative measure of structural stability and variation at finite temperature. Our PCC analysis captures bond structure variation in MD, which can be used to both supplement the PCA analysis as well as compare bond patterns between different cluster sizes. Relying only on atomic position data, without requirement for a priori structural input, PCA and PCC can be used to analyze both classical and ab initio MD simulations for any cluster composition or electronic configuration. Taken together, these statistical tools represent powerful new techniques for quantitative structural characterization and isomer identification in cluster MD.

Composition Formulas of Inorganic Compounds in Terms of Cluster Plus Glue Atom Model.

PubMed

Ma, Yanping; Dong, Dandan; Wu, Aimin; Dong, Chuang

2018-01-16

The present paper attempts to identify the molecule-like structural units in inorganic compounds, by applying the so-called "cluster plus glue atom model". This model, originating from metallic glasses and quasi-crystals, describes any structure in terms of a nearest-neighbor cluster and a few outer-shell glue atoms, expressed in the cluster formula [cluster](glue atoms). Similar to the case for normal molecules where the charge transfer occurs within the molecule to meet the commonly known octet electron rule, the octet state is reached after matching the nearest-neighbor cluster with certain outer-shell glue atoms. These kinds of structural units contain information on local atomic configuration, chemical composition, and electron numbers, just as for normal molecules. It is shown that the formulas of typical inorganic compounds, such as fluorides, oxides, and nitrides, satisfy a similar octet electron rule, with the total number of valence electrons per unit formula being multiples of eight.

Effects of hydrostatic pressure on the thermoelectric properties of the ɛ-polytype of InSe, GaSe, and InGaSe2 semiconductor compounds: an ab initio study

NASA Astrophysics Data System (ADS)

Elsayed, H.; Olguín, D.; Cantarero, A.

2017-12-01

This work presents an ab initio study of the effects of hydrostatic pressure on the Seebeck coefficients and thermoelectric power factors of the ɛ-polytype of InSe, GaSe, and InGaSe2 semiconductor compounds. Our study is performed using the semi-classical Boltzmann theory and the rigid band approach. The electronic band structures of these materials are calculated using the full-potential linearized augmented plane-wave method. The obtained thermoelectric properties are discussed in terms of the results of the electronic structure calculations. As we will show, our calculated Seebeck coefficient values indicate that these materials are good alternatives to other well-studied thermoelectric systems.

Formation Dynamics of Potassium-Based Graphite Intercalation Compounds: An Ab Initio Study

NASA Astrophysics Data System (ADS)

Jiang, Xiankai; Song, Bo; Tománek, David

2018-04-01

This paper is a contribution to the Physical Review Applied collection in memory of Mildred S. Dresselhaus. We use ab initio molecular dynamics simulations to study the microscopic dynamics of potassium intercalation in graphite. Upon adsorbing on graphite from the vapor phase, K atoms transfer their valence charge to the substrate. K atoms adsorbed on the surface diffuse rapidly along the graphene basal plane and eventually enter the interlayer region following a "U -turn" across the edge, gaining additional energy. This process is promoted at higher coverages associated with higher K pressure, leading to the formation of a stable intercalation compound. We find that the functionalization of graphene edges is an essential prerequisite for intercalation since bare edges reconstruct and reconnect, closing off the entry channels for the atoms.

Quantum chemical calculation of the equilibrium structures of small metal atom clusters

NASA Technical Reports Server (NTRS)

Kahn, L. R.

1982-01-01

Metal atom clusters are studied based on the application of ab initio quantum mechanical approaches. Because these large 'molecular' systems pose special practical computational problems in the application of the quantum mechanical methods, there is a special need to find simplifying techniques that do not compromise the reliability of the calculations. Research is therefore directed towards various aspects of the implementation of the effective core potential technique for the removal of the metal atom core electrons from the calculations.

Size-induced chemical and magnetic ordering in individual Fe-Au nanoparticles.

PubMed

Mukherjee, Pinaki; Manchanda, Priyanka; Kumar, Pankaj; Zhou, Lin; Kramer, Matthew J; Kashyap, Arti; Skomski, Ralph; Sellmyer, David; Shield, Jeffrey E

2014-08-26

Formation of chemically ordered compounds of Fe and Au is inhibited in bulk materials due to their limited mutual solubility. However, here we report the formation of chemically ordered L12-type Fe3Au and FeAu3 compounds in Fe-Au sub-10 nm nanoparticles, suggesting that they are equilibrium structures in size-constrained systems. The stability of these L12-ordered Fe3Au and FeAu3 compounds along with a previously discovered L10-ordered FeAu has been explained by a size-dependent equilibrium thermodynamic model. Furthermore, the spin ordering of these three compounds has been computed using ab initio first-principle calculations. All ordered compounds exhibit a substantial magnetization at room temperature. The Fe3Au had a high saturation magnetization of about 143.6 emu/g with a ferromagnetic spin structure. The FeAu3 nanoparticles displayed a low saturation magnetization of about 11 emu/g. This suggests a antiferromagnetic spin structure, with the net magnetization arising from uncompensated surface spins. First-principle calculations using the Vienna ab initio simulation package (VASP) indicate that ferromagnetic ordering is energetically most stable in Fe3Au, while antiferromagnetic order is predicted in FeAu and FeAu3, consistent with the experimental results.

Binding site feature description of 2-substituted benzothiazoles as potential AcrAB-TolC efflux pump inhibitors in E. coli.

PubMed

Yilmaz, S; Altinkanat-Gelmez, G; Bolelli, K; Guneser-Merdan, D; Ufuk Over-Hasdemir, M; Aki-Yalcin, E; Yalcin, I

2015-01-01

The resistance-nodulation-division (RND) family efflux pumps are important in the antibiotic resistance of Gram-negative bacteria. However, although a number of bacterial RND efflux pump inhibitors have been developed, there has been no clinically available RND efflux pump inhibitor to date. A set of BSN-coded 2-substituted benzothiazoles were tested alone and in combinations with ciprofloxacin (CIP) against the AcrAB-TolC overexpressor Escherichia coli AG102 clinical strain. The results indicated that the BSN compounds did not show intrinsic antimicrobial activity when tested alone. However, when used in combinations with CIP, a reversal in the antibacterial activity of CIP with up to 10-fold better MIC values was observed. In order to describe the binding site features of these BSN compounds with AcrB, docking studies were performed using the CDocker method. The performed docking poses and the calculated binding energy scores revealed that the tested compounds BSN-006, BSN-023, and BSN-004 showed significant binding interactions with the phenylalanine-rich region in the distal binding site of the AcrB binding monomer. Moreover, the tested compounds BSN-006 and BSN-023 possessed stronger binding energies than CIP, verifying that BSN compounds are acting as the putative substrates of AcrB.

Ab initio calculations of ionic hydrocarbon compounds with heptacoordinate carbon.

PubMed

Wang, George; Rahman, A K Fazlur; Wang, Bin

2018-04-25

Ionic hydrocarbon compounds that contain hypercarbon atoms, which bond to five or more atoms, are important intermediates in chemical synthesis and may also find applications in hydrogen storage. Extensive investigations have identified hydrocarbon compounds that contain a five- or six-coordinated hypercarbon atom, such as the pentagonal-pyramidal hexamethylbenzene, C 6 (CH 3 ) 6 2+ , in which a hexacoordinate carbon atom is involved. It remains challenging to search for further higher-coordinated carbon in ionic hydrocarbon compounds, such as seven- and eight-coordinated carbon. Here, we report ab initio density functional calculations that show a stable 3D hexagonal-pyramidal configuration of tropylium trication, (C 7 H 7 ) 3+ , in which a heptacoordinate carbon atom is involved. We show that this tropylium trication is stable against deprotonation, dissociation, and structural deformation. In contrast, the pyramidal configurations of ionic C 8 H 8 compounds, which would contain an octacoordinate carbon atom, are unstable. These results provide insights for developing new molecular structures containing hypercarbon atoms, which may have potential applications in chemical synthesis and in hydrogen storage. Graphical abstract Possible structural transformations of stable configurations of (C 7 H 7 ) 3+ , which may result in the formation of the pyramidal structure that involves a heptacoordinate hypercarbon atom.

Energetics of defects formation and oxygen migration in pyrochlore compounds from first principles calculations

NASA Astrophysics Data System (ADS)

Li, Yan; Kowalski, Piotr M.

2018-07-01

In order to get better understanding of the selective order-disorder transition in pyrochlore compounds, using ab initio methods we calculated the formation energies of coupled cation anti-site and anion Frenkel pair defects and the energy barriers for the oxygen migration for number of families of A2B2 O7 pyrochlore-type compounds. While these parameters have been previously computed with force field-based methods, the ab initio results provide more reliable values that can be confidently used in subsequent analysis. We found a fairly good correlation between the formation energies of the coupled defects and the stability field of pyrochlores. In line with previous studies, the compounds that crystallize in defect fluorite structure are found to have smaller values of coupled defect formation energies than those crystallizing in the pyrochlore phase, although the correlation is not that sharp as in the case of isolated anion Frenkel pair defect. The investigation of the energy barriers for the oxygen migration shows that it is not a good, sole indicator of the tendency of the order-disorder phase transition in pyrochlores. However, we found that the oxygen migration barrier is reduced in the presence of the cation antisite defect. This points at disordering-induced enhancement of oxygen diffusion in pyrochlore compounds.

Infrared laser spectroscopy of jet-cooled carbon clusters: structure of triplet C6

NASA Technical Reports Server (NTRS)

Hwang, H. J.; Van Orden, A.; Tanaka, K.; Kuo, E. W.; Heath, J. R.; Saykally, R. J.

1993-01-01

We report the first structural characterization of the triplet isomer of C6. Forty-one rovibrational/fine structure transitions in the nu 4(sigma u) antisymmetric stretch fundamental of the C6 cluster have been measured by diode laser absorption spectroscopy of a supersonic carbon cluster beam. The observed spectrum is characteristic of a centrosymmetric linear triplet state with cumulene-type bonding. The measured ground state rotational constant B0 = 0.048 479 (10)cm-1 and the effective bond length r(eff) = 1.2868 (1) angstroms are in good agreement with ab initio predictions for the linear triplet (3 sigma g-) state of C6.

Topological defect clustering and plastic deformation mechanisms in functionalized graphene

NASA Astrophysics Data System (ADS)

Nunes, Ricardo; Araujo, Joice; Chacham, Helio

2011-03-01

We present ab initio results suggesting that strain plays a central role in the clustering of topological defects in strained and functionalized graphene models. We apply strain onto the topological-defect graphene networks from our previous work, and obtain topological-defect clustering patterns which are in excellent agreement with recent observations in samples of reduced graphene oxide. In our models, the graphene layer, containing an initial concentration of isolated topological defects, is covered by hydrogen or hydroxyl groups. Our results also suggest a rich variety of plastic deformation mechanism in functionalized graphene systems. We acknowledge support from the Brazilian agencies: CNPq, Fapemig, and INCT-Materiais de Carbono.

The HCO+-H2 van der Waals interaction: Potential energy and scattering

NASA Astrophysics Data System (ADS)

Massó, H.; Wiesenfeld, L.

2014-11-01

We compute the rigid-body, four-dimensional interaction potential between HCO+ and H2. The ab initio energies are obtained at the coupled-cluster single double triple level of theory, corrected for Basis Set Superposition Errors. The ab initio points are fit onto the spherical basis relevant for quantum scattering. We present elastic and rotationally inelastic coupled channels scattering between low lying rotational levels of HCO+ and para-/ortho-H2. Results are compared with similar earlier computations with He or isotropic para-H2 as the projectile. Computations agree with earlier pressure broadening measurements.

The HCO⁺-H₂ van der Waals interaction: potential energy and scattering.

PubMed

Massó, H; Wiesenfeld, L

2014-11-14

We compute the rigid-body, four-dimensional interaction potential between HCO(+) and H2. The ab initio energies are obtained at the coupled-cluster single double triple level of theory, corrected for Basis Set Superposition Errors. The ab initio points are fit onto the spherical basis relevant for quantum scattering. We present elastic and rotationally inelastic coupled channels scattering between low lying rotational levels of HCO(+) and para-/ortho-H2. Results are compared with similar earlier computations with He or isotropic para-H2 as the projectile. Computations agree with earlier pressure broadening measurements.

Site occupancy trend of Co in Ni{sub 2}MnIn: Ab initio approach

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

Pal, Soumyadipta, E-mail: soumyadipta.pal@gmail.com; Mahadevan, Priya; Biswas, C.

2015-06-24

The trend of site occupation of Co at Ni sites of Ni{sub 2}MnIn system is studied in austenitic phase having L2{sub 1} structure by ab initio density functional theory (DFT) calculation. The Co atoms prefer to be at Ni sites rather than Mn site and are ferromagetically coupled with Ni and Mn. The ground state has tetragonal structure for Ni{sub 1.5}Co{sub 0.5}MnIn and Ni{sub 1.25}Co{sub 0.75}MnIn. The Co tends to form cluster.

Stabilization of flat aromatic Si6 rings analogous to benzene: ab initio theoretical prediction.

PubMed

Zdetsis, Aristides D

2007-12-07

It is shown by ab initio calculations, based on density functional (DFT/B3LYP), and high level coupled-cluster [CCSD(T)] and quadratic CI [QCISD(T)] methods, that flat aromatic silicon structures analogous to benzene (C6H6) can be stabilized in the presence of lithium. The resulting planar Si6Li6 structure is both stable and aromatic, sharing many key characteristics with benzene. To facilitate possible synthesis and characterization of these species, routes of formation with high exothermicity are suggested and several spectral properties (including optical absorption, infrared, and Raman) are calculated.

Multiple time step integrators in ab initio molecular dynamics.

PubMed

Luehr, Nathan; Markland, Thomas E; Martínez, Todd J

2014-02-28

Multiple time-scale algorithms exploit the natural separation of time-scales in chemical systems to greatly accelerate the efficiency of molecular dynamics simulations. Although the utility of these methods in systems where the interactions are described by empirical potentials is now well established, their application to ab initio molecular dynamics calculations has been limited by difficulties associated with splitting the ab initio potential into fast and slowly varying components. Here we present two schemes that enable efficient time-scale separation in ab initio calculations: one based on fragment decomposition and the other on range separation of the Coulomb operator in the electronic Hamiltonian. We demonstrate for both water clusters and a solvated hydroxide ion that multiple time-scale molecular dynamics allows for outer time steps of 2.5 fs, which are as large as those obtained when such schemes are applied to empirical potentials, while still allowing for bonds to be broken and reformed throughout the dynamics. This permits computational speedups of up to 4.4x, compared to standard Born-Oppenheimer ab initio molecular dynamics with a 0.5 fs time step, while maintaining the same energy conservation and accuracy.

Localization and orientation of heavy-atom cluster compounds in protein crystals using molecular replacement

PubMed Central

Dahms, Sven O.; Kuester, Miriam; Streb, Carsten; Roth, Christian; Sträter, Norbert; Than, Manuel E.

2013-01-01

Heavy-atom clusters (HA clusters) containing a large number of specifically arranged electron-dense scatterers are especially useful for experimental phase determination of large complex structures, weakly diffracting crystals or structures with large unit cells. Often, the determination of the exact orientation of the HA cluster and hence of the individual heavy-atom positions proves to be the critical step in successful phasing and subsequent structure solution. Here, it is demonstrated that molecular replacement (MR) with either anomalous or isomorphous differences is a useful strategy for the correct placement of HA cluster compounds. The polyoxometallate cluster hexasodium α-metatungstate (HMT) was applied in phasing the structure of death receptor 6. Even though the HA cluster is bound in alternate partially occupied orientations and is located at a special position, its correct localization and orientation could be determined at resolutions as low as 4.9 Å. The broad applicability of this approach was demonstrated for five different derivative crystals that included the compounds tantalum tetradeca­bromide and trisodium phosphotungstate in addition to HMT. The correct placement of the HA cluster depends on the length of the intramolecular vectors chosen for MR, such that both a larger cluster size and the optimal choice of the wavelength used for anomalous data collection strongly affect the outcome. PMID:23385464

Proton affinity of the histidine-tryptophan cluster motif from the influenza A virus from ab initio molecular dynamics

NASA Astrophysics Data System (ADS)

Bankura, Arindam; Klein, Michael L.; Carnevale, Vincenzo

2013-08-01

Ab initio molecular dynamics calculations have been used to compare and contrast the deprotonation reaction of a histidine residue in aqueous solution with the situation arising in a histidine-tryptophan cluster. The latter is used as a model of the proton storage unit present in the pore of the M2 proton conducting ion channel. We compute potentials of mean force for the dissociation of a proton from the Nδ and Nɛ positions of the imidazole group to estimate the pKas. Anticipating our results, we will see that the estimated pKa for the first protonation event of the M2 channel is in good agreement with experimental estimates. Surprisingly, despite the fact that the histidine is partially desolvated in the M2 channel, the affinity for protons is similar to that of a histidine in aqueous solution. Importantly, the electrostatic environment provided by the indoles is responsible for the stabilization of the charged imidazolium.

Igs expressed by chronic lymphocytic leukemia B cells show limited binding-site structure variability.

PubMed

Marcatili, Paolo; Ghiotto, Fabio; Tenca, Claudya; Chailyan, Anna; Mazzarello, Andrea N; Yan, Xiao-Jie; Colombo, Monica; Albesiano, Emilia; Bagnara, Davide; Cutrona, Giovanna; Morabito, Fortunato; Bruno, Silvia; Ferrarini, Manlio; Chiorazzi, Nicholas; Tramontano, Anna; Fais, Franco

2013-06-01

Ag selection has been suggested to play a role in chronic lymphocytic leukemia (CLL) pathogenesis, but no large-scale analysis has been performed so far on the structure of the Ag-binding sites (ABSs) of leukemic cell Igs. We sequenced both H and L chain V(D)J rearrangements from 366 CLL patients and modeled their three-dimensional structures. The resulting ABS structures were clustered into a small number of discrete sets, each containing ABSs with similar shapes and physicochemical properties. This structural classification correlates well with other known prognostic factors such as Ig mutation status and recurrent (stereotyped) receptors, but it shows a better prognostic value, at least in the case of one structural cluster for which clinical data were available. These findings suggest, for the first time, to our knowledge, on the basis of a structural analysis of the Ab-binding sites, that selection by a finite quota of antigenic structures operates on most CLL cases, whether mutated or unmutated.

Phosphorus vacancy cluster model for phosphorus diffusion gettering of metals in Si

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

Chen, Renyu; Trzynadlowski, Bart; Dunham, Scott T.

2014-02-07

In this work, we develop models for the gettering of metals in silicon by high phosphorus concentration. We first performed ab initio calculations to determine favorable configurations of complexes involving phosphorus and transition metals (Fe, Cu, Cr, Ni, Ti, Mo, and W). Our ab initio calculations found that the P{sub 4}V cluster, a vacancy surrounded by 4 nearest-neighbor phosphorus atoms, which is the most favorable inactive P species in heavily doped Si, strongly binds metals such as Cu, Cr, Ni, and Fe. Based on the calculated binding energies, we build continuum models to describe the P deactivation and Fe getteringmore » processes with model parameters calibrated against experimental data. In contrast to previous models assuming metal-P{sub 1}V or metal-P{sub 2}V as the gettered species, the binding of metals to P{sub 4}V satisfactorily explains the experimentally observed strong gettering behavior at high phosphorus concentrations.« less

Ab initio simulations of the structure, energetics and mobility of radiation-induced point defects in bcc Nb

NASA Astrophysics Data System (ADS)

Cerdeira, M. A.; Palacios, S. L.; González, C.; Fernández-Pello, D.; Iglesias, R.

2016-09-01

The formation, binding and migration energetics of helium clusters inside a niobium crystal have been analysed via ab initio simulations. The effect of placing several He atoms within an n-vacancy previously formed or as interstitials inside the initial perfect bulk matrix has been studied. DFT-based results show that He atoms prefer to aggregate forming small clusters at n-vacancy sites rather than at interstitial positions in the perfect crystal. The minimum formation energy is found when NHe is equal to the number of vacancies, n. It follows that vacancies act as almost perfect traps for He atoms, as is well known for other metals. The migration barriers of He atoms inside vacancies increase considerably when compared to what happens for vacancies alone. A secondary consequence is that the full set of energies obtained will be highly relevant as an input for new approaches to KMC simulations of defects in Nb.

Effect of myasthenic patient sera on the number and distribution of acetylcholine receptors in muscle and nerve-muscle cultures from rat. Correlations with clinical state.

PubMed

Eymard, B; de la Porte, S; Pannier, C; Berrih-Aknin, S; Morel, E; Fardeau, M; Bach, J F; Koenig, J

1988-08-01

We studied the functional activities (FA) of sera obtained from 83 myasthenic patients on rat muscle cultures. Using the same sets of cultures, two parameters were evaluated after exposure to sera: residual fraction (RF) of acetylcholine receptors (AChR) coupled to 125I-labelled alpha-bungarotoxin (alpha Bgt) (81 sera) and the number of rhodamine labelled clusters (56 sera). Two types of culture were assayed: muscle alone and nerve-muscle cocultures (12 cases). In all combinations (fluorescence, radiolabelling, muscle alone and nerve-muscle cocultures), we found a significant correlation between FA and antibody (Ab) titre, and no correlation between FA and clinical severity: only sera with a high or intermediate Ab titre were effective, whatever the clinical severity of disease. With active sera, AChR loss was about 50% whereas the disappearance of AChR clusters was quite complete, which suggests AChR redistribution induced by MG sera.

Two Zn coordination polymers with meso-helical chains based on mononuclear or dinuclear cluster units

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

Qin, Ling, E-mail: qinling@hfut.edu.cn; Jiangsu Engineering Technology Research Center of Environmental Cleaning Materials; State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing National Laboratory of Microstructures, Nanjing University, Nanjing 210093

2016-07-15

Two zinc coordination polymers {[Zn_2(TPPBDA)(oba)_2]·DMF·1.5H_2O}{sub n} (1), {[Zn(TPPBDA)_1_/_2(tpdc)]·DMF}{sub n} (2) have been synthesized by zinc metal salt, nanosized tetradentate pyridine ligand with flexible or rigid V-shaped carboxylate co-ligands. These complexes were characterized by elemental analyses and X-ray single-crystal diffraction analyses. Compound 1 is a 2-fold interpenetrated 3D framework with [Zn{sub 2}(CO{sub 2}){sub 4}] clusters. Compound 2 can be defined as a five folded interpenetrating bbf topology with mononuclear Zn{sup 2+}. These mononuclear or dinuclear cluster units are linked by mix-ligands, resulting in various degrees of interpenetration. In addition, the photoluminescent properties for TPPBDA ligand under different state and coordination polymersmore » have been investigated in detail. - Graphical abstract: Two zinc coordination polymers have been synthesized by zinc metal salt, nanosized tetradentate pyridine ligand with flexible or rigid V-shaped carboxylate co-ligands. Compound 1 is a 2-fold interpenetrated 3D framework with [Zn{sub 2}(CO{sub 2}){sub 4}] clusters. Compound 2 can be defined as a five folded interpenetrating bbf topology with mononuclear Zn{sup 2+}. In addition, the photoluminescent properties for TPPBDA ligand under different status and coordination polymers have been investigated in detail. Display Omitted - Highlights: • Two Zn coordination polymers based on mononuclear or dinuclear cluster units have been synthesized. • Compound 1 is a 2-fold interpenetrated 3D framework with [Zn{sub 2}(CO{sub 2}){sub 4}] clusters. • Compound 2 is a five folded interpenetrating bbf topology with mononuclear Zn{sup 2+}. • The photoluminescent properties for TPPBDA with different state and two coordination polymers have been investigated.« less

Nanostructure of and structural defects in a Mo2BC hard coating investigated by transmission electron microscopy and atom probe tomography

NASA Astrophysics Data System (ADS)

Gleich, Stephan; Fager, Hanna; Bolvardi, Hamid; Achenbach, Jan-Ole; Soler, Rafael; Pradeep, Konda Gokuldoss; Schneider, Jochen M.; Dehm, Gerhard; Scheu, Christina

2017-08-01

In this work, the nanostructure of a Mo2BC hard coating was determined by several transmission electron microscopy methods and correlated with the mechanical properties. The coating was deposited on a Si (100) wafer by bipolar pulsed direct current magnetron sputtering from a Mo2BC compound target in Ar at a substrate temperature of 630 °C. Transmission electron microscopy investigations revealed structural features at various length scales: bundles (30 nm to networks of several micrometers) consisting of columnar grains (˜10 nm in diameter), grain boundary regions with a less ordered atomic arrangement, and defects including disordered clusters (˜1.5 nm in diameter) as well as stacking faults within the grains. The most prominent defect with a volume fraction of ˜0.5% is the disordered clusters, which were investigated in detail by electron energy loss spectroscopy and atom probe tomography. The results provide conclusive evidence that Ar is incorporated into the Mo2BC film as disordered Ar-rich Mo-B-C clusters of approximately 1.5 nm in diameter. Hardness values of 28 ± 1 GPa were obtained by nanoindentation tests. The Young's modulus of the Mo2BC coating exhibits a value of 462 ± 9 GPa, which is consistent with ab initio calculations for crystalline and defect free Mo2BC and measurements of combinatorically deposited Mo2BC thin films at a substrate temperature of 900 °C. We conclude that a reduction of the substrate temperature of 270 °C has no significant influence on hardness and Young's modulus of the Mo2BC hard coating, even if its nanostructure exhibits defects.

The Novel Bacterial N-Demethylase PdmAB Is Responsible for the Initial Step of N,N-Dimethyl-Substituted Phenylurea Herbicide Degradation

PubMed Central

Gu, Tao; Zhou, Chaoyang; Sørensen, Sebastian R.; Zhang, Ji; He, Jian; Yu, Peiwen; Li, Shunpeng

2013-01-01

The environmental fate of phenylurea herbicides has received considerable attention in recent decades. The microbial metabolism of N,N-dimethyl-substituted phenylurea herbicides can generally be initiated by mono-N-demethylation. In this study, the molecular basis for this process was revealed. The pdmAB genes in Sphingobium sp. strain YBL2 were shown to be responsible for the initial mono-N-demethylation of commonly used N,N-dimethyl-substituted phenylurea herbicides. PdmAB is the oxygenase component of a bacterial Rieske non-heme iron oxygenase (RO) system. The genes pdmAB, encoding the α subunit PdmA and the β subunit PdmB, are organized in a transposable element flanked by two direct repeats of an insertion element resembling ISRh1. Furthermore, this transposable element is highly conserved among phenylurea herbicide-degrading sphingomonads originating from different areas of the world. However, there was no evidence of a gene for an electron carrier (a ferredoxin or a reductase) located in the immediate vicinity of pdmAB. Without its cognate electron transport components, expression of PdmAB in Escherichia coli, Pseudomonas putida, and other sphingomonads resulted in a functional enzyme. Moreover, coexpression of a putative [3Fe-4S]-type ferredoxin from Sphingomonas sp. strain RW1 greatly enhanced the catalytic activity of PdmAB in E. coli. These data suggested that PdmAB has a low specificity for electron transport components and that its optimal ferredoxin may be the [3Fe-4S] type. PdmA exhibited low homology to the α subunits of previously characterized ROs (less than 37% identity) and did not cluster with the RO group involved in O- or N-demethylation reactions, indicating that PdmAB is a distinct bacterial RO N-demethylase. PMID:24123738

Revealing isomerism in sodium-water clusters: Photoionization spectra of Na(H2O)n (n = 2-90)

NASA Astrophysics Data System (ADS)

Dierking, Christoph W.; Zurheide, Florian; Zeuch, Thomas; Med, Jakub; Parez, Stanislav; Slavíček, Petr

2017-06-01

Soft ionization of sodium tagged polar clusters is increasingly used as a powerful technique for sizing and characterization of small aerosols with possible application, e.g., in atmospheric chemistry or combustion science. Understanding the structure and photoionization of the sodium doped clusters is critical for such applications. In this work, we report on measurements of photoionization spectra for sodium doped water clusters containing 2-90 water molecules. While most of the previous studies focused on the ionization threshold of the Na(H2O)n clusters, we provide for the first time full photoionization spectra, including the high-energy region, which are used as reference for a comparison with theory. As reported in previous work, we have seen an initial drop of the appearance ionization energy with cluster size to values of about 3.2 eV for n <5 . In the size range from n = 5 to n = 15, broad ion yield curves emerge; for larger clusters, a constant range between signal appearance (˜2.8 eV) and signal saturation (˜4.1 eV) has been observed. The measurements are interpreted with ab initio calculations and ab initio molecular dynamics simulations for selected cluster sizes (n ≤ 15). The simulations revealed theory shortfalls when aiming at quantitative agreement but allowed us identifying structural motifs consistent with the observed ionization energy distributions. We found a decrease in the ionization energy with increasing coordination of the Na atom and increasing delocalization of the Na 3s electron cloud. The appearance ionization energy is determined by isomers with fully solvated sodium and a highly delocalized electron cloud, while both fully and incompletely solvated isomers with localized electron clouds can contribute to the high energy part of the photoionization spectrum. Simulations at elevated temperatures show an increased abundance of isomers with low ionization energies, an entropic effect enabling size selective infrared action spectroscopy, based on near threshold photoionization of Na(H2O)n clusters. In addition, simulations of the sodium pick-up process were carried out to study the gradual formation of the hydrated electron which is the basis of the sodium-tagging sizing.

Revealing isomerism in sodium-water clusters: Photoionization spectra of Na(H2O)n (n = 2-90).

PubMed

Dierking, Christoph W; Zurheide, Florian; Zeuch, Thomas; Med, Jakub; Parez, Stanislav; Slavíček, Petr

2017-06-28

Soft ionization of sodium tagged polar clusters is increasingly used as a powerful technique for sizing and characterization of small aerosols with possible application, e.g., in atmospheric chemistry or combustion science. Understanding the structure and photoionization of the sodium doped clusters is critical for such applications. In this work, we report on measurements of photoionization spectra for sodium doped water clusters containing 2-90 water molecules. While most of the previous studies focused on the ionization threshold of the Na(H 2 O) n clusters, we provide for the first time full photoionization spectra, including the high-energy region, which are used as reference for a comparison with theory. As reported in previous work, we have seen an initial drop of the appearance ionization energy with cluster size to values of about 3.2 eV for n<5. In the size range from n = 5 to n = 15, broad ion yield curves emerge; for larger clusters, a constant range between signal appearance (∼2.8 eV) and signal saturation (∼4.1 eV) has been observed. The measurements are interpreted with ab initio calculations and ab initio molecular dynamics simulations for selected cluster sizes (n≤ 15). The simulations revealed theory shortfalls when aiming at quantitative agreement but allowed us identifying structural motifs consistent with the observed ionization energy distributions. We found a decrease in the ionization energy with increasing coordination of the Na atom and increasing delocalization of the Na 3s electron cloud. The appearance ionization energy is determined by isomers with fully solvated sodium and a highly delocalized electron cloud, while both fully and incompletely solvated isomers with localized electron clouds can contribute to the high energy part of the photoionization spectrum. Simulations at elevated temperatures show an increased abundance of isomers with low ionization energies, an entropic effect enabling size selective infrared action spectroscopy, based on near threshold photoionization of Na(H 2 O) n clusters. In addition, simulations of the sodium pick-up process were carried out to study the gradual formation of the hydrated electron which is the basis of the sodium-tagging sizing.

Two Host-Induced Ralstonia solanacearum Genes, acrA and dinF, Encode Multidrug Efflux Pumps and Contribute to Bacterial Wilt Virulence▿ †

PubMed Central

Brown, Darby G.; Swanson, Jill K.; Allen, Caitilyn

2007-01-01

Multidrug efflux pumps (MDRs) are hypothesized to protect pathogenic bacteria from toxic host defense compounds. We created mutations in the Ralstonia solanacearum acrA and dinF genes, which encode putative MDRs in the broad-host-range plant pathogen. Both mutations reduced the ability of R. solanacearum to grow in the presence of various toxic compounds, including antibiotics, phytoalexins, and detergents. Both acrAB and dinF mutants were significantly less virulent on the tomato plant than the wild-type strain. Complementation restored near-wild-type levels of virulence to both mutants. Addition of either dinF or acrAB to Escherichia coli MDR mutants KAM3 and KAM32 restored the resistance of these strains to several toxins, demonstrating that the R. solanacearum genes can function heterologously to complement known MDR mutations. Toxic and DNA-damaging compounds induced expression of acrA and dinF, as did growth in both susceptible and resistant tomato plants. Carbon limitation also increased expression of acrA and dinF, while the stress-related sigma factor RpoS was required at a high cell density (>107 CFU/ml) to obtain wild-type levels of acrA expression both in minimal medium and in planta. The type III secretion system regulator HrpB negatively regulated dinF expression in culture at high cell densities. Together, these results show that acrAB and dinF encode MDRs in R. solanacearum and that they contribute to the overall aggressiveness of this phytopathogen, probably by protecting the bacterium from the toxic effects of host antimicrobial compounds. PMID:17337552

Two host-induced Ralstonia solanacearum genes, acrA and dinF, encode multidrug efflux pumps and contribute to bacterial wilt virulence.

PubMed

Brown, Darby G; Swanson, Jill K; Allen, Caitilyn

2007-05-01

Multidrug efflux pumps (MDRs) are hypothesized to protect pathogenic bacteria from toxic host defense compounds. We created mutations in the Ralstonia solanacearum acrA and dinF genes, which encode putative MDRs in the broad-host-range plant pathogen. Both mutations reduced the ability of R. solanacearum to grow in the presence of various toxic compounds, including antibiotics, phytoalexins, and detergents. Both acrAB and dinF mutants were significantly less virulent on the tomato plant than the wild-type strain. Complementation restored near-wild-type levels of virulence to both mutants. Addition of either dinF or acrAB to Escherichia coli MDR mutants KAM3 and KAM32 restored the resistance of these strains to several toxins, demonstrating that the R. solanacearum genes can function heterologously to complement known MDR mutations. Toxic and DNA-damaging compounds induced expression of acrA and dinF, as did growth in both susceptible and resistant tomato plants. Carbon limitation also increased expression of acrA and dinF, while the stress-related sigma factor RpoS was required at a high cell density (>10(7) CFU/ml) to obtain wild-type levels of acrA expression both in minimal medium and in planta. The type III secretion system regulator HrpB negatively regulated dinF expression in culture at high cell densities. Together, these results show that acrAB and dinF encode MDRs in R. solanacearum and that they contribute to the overall aggressiveness of this phytopathogen, probably by protecting the bacterium from the toxic effects of host antimicrobial compounds.

Ab initio Kinetics and Thermal Decomposition Mechanism of Mononitrobiuret and 1,5-Dinitrobiuret

DTIC Science & Technology

2016-03-14

Journal Article 3. DATES COVERED (From - To) Feb 2015-May 2015 4. TITLE AND SUBTITLE Ab initio Kinetics and Thermal Decomposition Mechanism of 5a...tetrazole-free, nitrogen-rich, energetic compounds. For the first time, the thermal decomposition mechanisms of MNB and DNB have been investigated...potential energy surfaces for thermal decomposition of MNB and DNB were characterized at the RCCSD(T)/cc-pV∞Z//M06-2X/aug- cc-pVTZ level of theory

Humans seem to produce arsenobetaine and dimethylarsinate after a bolus dose of seafood.

PubMed

Molin, M; Ulven, S M; Dahl, L; Telle-Hansen, V H; Holck, M; Skjegstad, G; Ledsaak, O; Sloth, J J; Goessler, W; Oshaug, A; Alexander, J; Fliegel, D; Ydersbond, T A; Meltzer, H M

2012-01-01

Seafood is the predominant food source of several organoarsenic compounds. Some seafood species, like crustaceans and seaweed, also contain inorganic arsenic (iAs), a well-known toxicant. It is unclear whether human biotransformation of ingested organoarsenicals from seafood result in formation of arsenicals of health concern. The present controlled dietary study examined the urinary excretion of arsenic compounds (total arsenic (tAs), iAs, AB (arsenobetaine), dimethylarsinate (DMA) and methylarsonate (MA)) following ingestion of a single test meal of seafood (cod, 780 μg tAs, farmed salmon, 290 μg tAs or blue mussel, 690 μg tAs or potato (control, 110 μg tAs)) in 38 volunteers. The amount of ingested tAs excreted via the urine within 0-72 h varied significantly among the groups: Cod, 74% (52-92%), salmon 56% (46-82%), blue mussel 49% (37-78%), control 45% (30-60%). The estimated total urinary excretion of AB was higher than the amount of ingested AB in the blue mussel group (112%) and also ingestion of cod seemed to result in more AB, indicating possible endogenous formation of AB from other organoarsenicals. Excretion of iAs was lower than ingested (13-22% of the ingested iAs was excreted in the different groups). Although the ingested amount of iAs+DMA+MA was low for all seafood groups (1.2-4.5% of tAs ingested), the urinary DMA excretion was high in the blue mussel and salmon groups, counting for 25% and 11% of the excreted tAs respectively. In conclusion our data indicate a possible formation of AB as a result of biotransformation of other organic arsenicals. The considerable amount of DMA excreted is probably not only due to methylation of ingested iAs, but due to biotransformation of organoarsenicals making it an inappropriate biomarker of iAs exposure in populations with a high seafood intake. Copyright © 2011 Elsevier Inc. All rights reserved.

Endothelial miR-17∼92 cluster negatively regulates arteriogenesis via miRNA-19 repression of WNT signaling.

PubMed

Landskroner-Eiger, Shira; Qiu, Cong; Perrotta, Paola; Siragusa, Mauro; Lee, Monica Y; Ulrich, Victoria; Luciano, Amelia K; Zhuang, Zhen W; Corti, Federico; Simons, Michael; Montgomery, Rusty L; Wu, Dianqing; Yu, Jun; Sessa, William C

2015-10-13

The contribution of endothelial-derived miR-17∼92 to ischemia-induced arteriogenesis has not been investigated in an in vivo model. In the present study, we demonstrate a critical role for the endothelial-derived miR-17∼92 cluster in shaping physiological and ischemia-triggered arteriogenesis. Endothelial-specific deletion of miR-17∼92 results in an increase in collateral density limbs and hearts and in ischemic limbs compared with control mice, and consequently improves blood flow recovery. Individual cluster components positively or negatively regulate endothelial cell (EC) functions in vitro, and, remarkably, ECs lacking the cluster spontaneously form cords in a manner rescued by miR-17a, -18a, and -19a. Using both in vitro and in vivo analyses, we identified FZD4 and LRP6 as targets of miR-19a/b. Both of these targets were up-regulated in 17∼92 KO ECs compared with control ECs, and both were shown to be targeted by miR-19 using luciferase assays. We demonstrate that miR-19a negatively regulates FZD4, its coreceptor LRP6, and WNT signaling, and that antagonism of miR-19a/b in aged mice improves blood flow recovery after ischemia and reduces repression of these targets. Collectively, these data provide insights into miRNA regulation of arterialization and highlight the importance of vascular WNT signaling in maintaining arterial blood flow.

D-A type sensor array for differentiation and identification of white wine varieties based on specific solvent effect activated by CT-LE transition

NASA Astrophysics Data System (ADS)

Han, Jingqi; Zhang, Xin; Li, Hao; Hou, Yue; Hou, Jingdan; Li, Zhongfeng; Yang, Feng; Liu, Yang; Han, Tianyu

2018-02-01

In this work, we synthesize a series of compounds with electron donor (D) and acceptor (A) units. They show general solvent effect in aprotic solvents, suggesting a charge transfer (CT) process. While in protic solvents including water, ethanol and methanol, the spectra exert no polarity-dependence but a remarkable hypochromatic shift together with the fading of CT band. Dynamic analysis implies that intermolecular hydrogen bond will be formed between carboxylic acid and protic solvent, boosting another deactivation pathway that jumps off a bigger energy gap, in other words, favoring the locally excited (LE) state emission. The CT-LE transition involves variations in both absorption and emission spectra, and further poses competition with other mechanisms including activated/restricted intramolecular rotation (IR/RIR). Inspired by the cross-reactivity, we turn our attention to the development of sensor array, in order to identify white wine varieties. The differential spectral responses are recorded, generating multiple factors including absorption wavelength (λab), emission wavelength (λem), absorbance (Abs.) and emission intensity (Int.). These factors are processed with principal component analysis (PCA), creating a three-dimensional fingerprint data base for white wines. The data points in the coordinate system are clustered into 10 different groups, demonstrating a clear differentiation of all the white wines. More importantly, as our final test for whether the sensor array can identify the counterfeits, an adulterated liquor sample, which is provided by police officers, is fingerprinted on the three-dimensional diagram. Its canonical factors fall into an area distinct from the adulterated wine, indicating a clear identification.

Fine-Scale Community Structure Analysis of ANME in Nyegga Sediments with High and Low Methane Flux

PubMed Central

Roalkvam, Irene; Dahle, Håkon; Chen, Yifeng; Jørgensen, Steffen Leth; Haflidason, Haflidi; Steen, Ida Helene

2012-01-01

To obtain knowledge on how regional variations in methane seepage rates influence the stratification, abundance, and diversity of anaerobic methanotrophs (ANME), we analyzed the vertical microbial stratification in a gravity core from a methane micro-seeping area at Nyegga by using 454-pyrosequencing of 16S rRNA gene tagged amplicons and quantitative PCR. These data were compared with previously obtained data from the more active G11 pockmark, characterized by higher methane flux. A down core stratification and high relative abundance of ANME were observed in both cores, with transition from an ANME-2a/b dominated community in low-sulfide and low methane horizons to ANME-1 dominance in horizons near the sulfate-methane transition zone. The stratification was over a wider spatial region and at greater depth in the core with lower methane flux, and the total 16S rRNA copy numbers were two orders of magnitude lower than in the sediments at G11 pockmark. A fine-scale view into the ANME communities at each location was achieved through operational taxonomical units (OTU) clustering of ANME-affiliated sequences. The majority of ANME-1 sequences from both sampling sites clustered within one OTU, while ANME-2a/b sequences were represented in unique OTUs. We suggest that free-living ANME-1 is the most abundant taxon in Nyegga cold seeps, and also the main consumer of methane. The observation of specific ANME-2a/b OTUs at each location could reflect that organisms within this clade are adapted to different geochemical settings, perhaps due to differences in methane affinity. Given that the ANME-2a/b population could be sustained in less active seepage areas, this subgroup could be potential seed populations in newly developed methane-enriched environments. PMID:22715336

The biosynthetic gene cluster for the cyanogenic glucoside dhurrin in Sorghum bicolor contains its co-expressed vacuolar MATE transporter

PubMed Central

Darbani, Behrooz; Motawia, Mohammed Saddik; Olsen, Carl Erik; Nour-Eldin, Hussam H.; Møller, Birger Lindberg; Rook, Fred

2016-01-01

Genomic gene clusters for the biosynthesis of chemical defence compounds are increasingly identified in plant genomes. We previously reported the independent evolution of biosynthetic gene clusters for cyanogenic glucoside biosynthesis in three plant lineages. Here we report that the gene cluster for the cyanogenic glucoside dhurrin in Sorghum bicolor additionally contains a gene, SbMATE2, encoding a transporter of the multidrug and toxic compound extrusion (MATE) family, which is co-expressed with the biosynthetic genes. The predicted localisation of SbMATE2 to the vacuolar membrane was demonstrated experimentally by transient expression of a SbMATE2-YFP fusion protein and confocal microscopy. Transport studies in Xenopus laevis oocytes demonstrate that SbMATE2 is able to transport dhurrin. In addition, SbMATE2 was able to transport non-endogenous cyanogenic glucosides, but not the anthocyanin cyanidin 3-O-glucoside or the glucosinolate indol-3-yl-methyl glucosinolate. The genomic co-localisation of a transporter gene with the biosynthetic genes producing the transported compound is discussed in relation to the role self-toxicity of chemical defence compounds may play in the formation of gene clusters. PMID:27841372

A Simple ab initio Model for the Hydrated Electron that Matches Experiment

PubMed Central

Kumar, Anil; Walker, Jonathan A.; Bartels, David M.; Sevilla, Michael D.

2015-01-01

Since its discovery over 50 years ago, the “structure” and properties of the hydrated electron has been a subject for wonderment and also fierce debate. In the present work we seriously explore a minimal model for the aqueous electron, consisting of a small water anion cluster embedded in a polarized continuum, using several levels of ab initio calculation and basis set. The minimum energy zero “Kelvin” structure found for any 4-water (or larger) anion cluster, at any post-Hartree-Fock theory level, is very similar to a recently reported embedded-DFT-in-classical-water-MD simulation (UMJ: Uhlig, Marsalek, and Jungwirth, Journal of Physical Chemistry Letters 2012, 3, 3071-5), with four OH bonds oriented toward the maximum charge density in a small central “void”. The minimum calculation with just four water molecules does a remarkably good job of reproducing the resonance Raman properties, the radius of gyration derived from the optical spectrum, the vertical detachment energy, and the hydration free energy. For the first time we also successfully calculate the EPR g-factor and (low temperature ice) hyperfine couplings. The simple tetrahedral anion cluster model conforms very well to experiment, suggesting it does in fact represent the dominant structural motif of the hydrated electron. PMID:26275103

Edge functionalised & Li-intercalated 555-777 defective bilayer graphene for the adsorption of CO2 and H2O

NASA Astrophysics Data System (ADS)

Lalitha, Murugan; Lakshmipathi, Senthilkumar; Bhatia, Suresh K.

2017-04-01

The adsorption of CO2 and H2O on divacanacy (DV) defected graphene cluster, and its bilayer counterpart is investigated using first-principles calculations. Both single and bilayer DV graphene cluster, are functionalised with H and F atoms. On these sheets the gas molecules are physisorbed, and the divacancy defect effectively improves the adsorption of CO2, while fluorination enhances the hydrophobicity of the graphene cluster. Among the convex and concave curvature regions induced due to the DV defect, the adsorption of the gas molecules on the concave meniscus is more favourable. Fluorine termination induces 73% reduction in Henry law constants for H2O, while for the CO2 molecule it increases by 8%, which indicates the DV defective sheet is a better candidate for CO2 capture compared to the STW defective sheet. Besides, both AA and AB divacant defect bilayer sheets are equally stable, wherein AA stacking results in a cavity between the sheets, while in AB stacking, the layers slide one over the other. Nevertheless, both these bilayer sheets are comparatively stabler than the monolayer. However, intercalation of lithium decreases the interlayer separation, particularly in AA stacking, which enhances the CO2 adsorption, but in the Bernal stacking enhances it hydrophobicity.

Ab initio many-body calculations of nucleon scattering on ^16O

NASA Astrophysics Data System (ADS)

Navratil, Petr; Quaglioni, Sofia; Roth, Robert

2008-10-01

We develop a new ab initio many-body approachootnotetextS. Quaglioni and P. Navratil, arXiv:0804.1560. capable of describing simultaneously both bound and scattering states in light nuclei, by combining the resonating-group methodootnotetextY. C. Tang et al., Phys. Rep. 47, 167 (1978); K. Langanke and H. Friedrich, Advances in Nuclear Physics, Plenum, New York, 1987. with the ab initio no-core shell model (NCSM).ootnotetextP. Navratil, J. P. Vary, and B. R. Barrett, Phys. Rev. Lett. 84, 5728 (2000); Phys. Rev. C 62, 054311 (2000). In this way, we complement a microscopic-cluster technique with the use of realistic interactions, and a microscopic and consistent description of the nucleon clusters, while preserving Pauli principle and translational symmetry. We will present results for low-energy nucleon scattering on ^16O and for A=17 bound states obtained using realistic nucleon-nucleon potentials. The ^16O wave functions are calculated within the importance-truncated NCSMootnotetextR. Roth and P. Navratil, Phys. Rev. Lett. 99, 092501 (2007). that allows the use of model spaces up to 18φ and ultimately enables to reach convergence of phase-shifts and other observables. Prepared by LLNL under Contract DE-AC52-07NA27344. Support from the U.S. DOE/SC/NP (Work Proposal No. SCW0498), and from the U. S. Department of Energy Grant DE-FC02-07ER41457 is acknowledged.

Highly sensitive sites for guanine-O6 ethylation in rat brain DNA exposed to N-ethyl-N-nitrosourea in vivo.

PubMed Central

Nehls, P; Rajewsky, M F; Spiess, E; Werner, D

1984-01-01

Brain chromosomal DNA isolated from fetal BDIX-rats 1 h after i.v. administration of the ethylating N-nitroso carcinogen N-ethyl-N-nitrosourea (75 micrograms/g body weight), statistically contained one molecule of O6-ethyl-2'-deoxyguanosine (O6-EtdGuo) per 81 micron of DNA, as determined in enzymatic DNA hydrolysates by competitive radio-immunoassay using a high-affinity anti-(O6-EtdGuo) monoclonal antibody (ER-6). After fragmentation of the DNA by the restriction enzyme AluI (average fragment length, Lav = 0.28 micron = 970 bp; length range, Lr = 1.87-0.02 micron = 6540 - 60 bp), a small (approximately 2%) fraction of DNA enriched in specific polypeptides tightly associated with DNA was separated from the bulk DNA by a glass fiber binding technique. As analyzed by immune electron microscopy, approximately 1% of the DNA molecules in this fraction contained clusters of 2-10 (O6-EtdGuo)-antibody binding sites (ABS). On the cluster-bearing fragments (Lav, 0.85 micron +/- 0.50 micron S.D.; corresponding to 2970 +/- 1760 bp) the average ABS-ABS interspace distance was 110 nm (= 390 bp; range approximately 9-600 nm), indicating a highly non-random distribution of O6-EtdGuo in target cell DNA. Images Fig. 2. PMID:6370677

Novel Acetone Metabolism in a Propane-Utilizing Bacterium, Gordonia sp. Strain TY-5▿

PubMed Central

Kotani, Tetsuya; Yurimoto, Hiroya; Kato, Nobuo; Sakai, Yasuyoshi

2007-01-01

In the propane-utilizing bacterium Gordonia sp. strain TY-5, propane was shown to be oxidized to 2-propanol and then further oxidized to acetone. In this study, the subsequent metabolism of acetone was studied. Acetone-induced proteins were found in extracts of cells induced by acetone, and a gene cluster designated acmAB was cloned on the basis of the N-terminal amino acid sequences of acetone-induced proteins. The acmA and acmB genes encode a Baeyer-Villiger monooxygenase (BVMO) and esterase, respectively. The BVMO encoded by acmA was purified from acetone-induced cells of Gordonia sp. strain TY-5 and characterized. The BVMO exhibited NADPH-dependent oxidation activity for linear ketones (C3 to C10) and cyclic ketones (C4 to C8). Escherichia coli expressing the acmA gene oxidized acetone to methyl acetate, and E. coli expressing the acmB gene hydrolyzed methyl acetate. Northern blot analyses revealed that polycistronic transcription of the acmAB gene cluster was induced by propane, 2-propanol, and acetone. These results indicate that the acmAB gene products play an important role in the metabolism of acetone derived from propane oxidation and clarify the propane metabolism pathway of strain TY-5 (propane → 2-propanol → acetone → methyl acetate → acetic acid + methanol). This paper provides the first evidence for BVMO-dependent acetone metabolism. PMID:17071761

Magnetic properties of the surface layer and its magnetic interaction with the interior of Nd-Fe-B sintered magnets

NASA Astrophysics Data System (ADS)

Kobayashi, Kurima; Nakamura, Michi-hide; Urushibata, Kimiko

2015-05-01

The magnetization and demagnetization mechanisms in the mechanically polished surface layers (SL) of the c-plane and a-b plane of Nd-Fe-B sintered magnets were investigated. The magnetic interaction between the SL and the interior of the magnet was clarified by using vibrating sample magnetometer measurements of a whole sample and magneto-force microscopy observations of the domain structure of the SL layer. The polishing eliminated the Nd-rich grain boundary phases, which was only about 2 nm thick, from the SL crystal grains in the sintered magnets. The a-b plane polishing caused the independent magnetic reversal of the a-b plane SL, which was about 5.5 μm thick, as in the platy samples. The coercivities (μ0Hc) of the SL were less than 0.3 T. In contrast, the c-plane polishing did not produce independent magnetic reversal of the SL, although the coercivity of bulk samples was clearly decreased by the formation of the c-plane SL. The grains in the SL should form clusters that alter the demagnetizing factors, depending on the shape of cluster as a magnetic unit. The magnetic interaction among the SL crystal grains is expected to play an important role in the coercivity mechanism of Nd-Fe-B sintered magnets.

Emergent properties of nuclei from ab initio coupled-cluster calculations

NASA Astrophysics Data System (ADS)

Hagen, G.; Hjorth-Jensen, M.; Jansen, G. R.; Papenbrock, T.

2016-06-01

Emergent properties such as nuclear saturation and deformation, and the effects on shell structure due to the proximity of the scattering continuum and particle decay channels are fascinating phenomena in atomic nuclei. In recent years, ab initio approaches to nuclei have taken the first steps towards tackling the computational challenge of describing these phenomena from Hamiltonians with microscopic degrees of freedom. This endeavor is now possible due to ideas from effective field theories, novel optimization strategies for nuclear interactions, ab initio methods exhibiting a soft scaling with mass number, and ever-increasing computational power. This paper reviews some of the recent accomplishments. We also present new results. The recently optimized chiral interaction NNLO{}{{sat}} is shown to provide an accurate description of both charge radii and binding energies in selected light- and medium-mass nuclei up to 56Ni. We derive an efficient scheme for including continuum effects in coupled-cluster computations of nuclei based on chiral nucleon-nucleon and three-nucleon forces, and present new results for unbound states in the neutron-rich isotopes of oxygen and calcium. The coupling to the continuum impacts the energies of the {J}π =1/{2}-,3/{2}-,7/{2}-,3/{2}+ states in {}{17,23,25}O, and—contrary to naive shell-model expectations—the level ordering of the {J}π =3/{2}+,5/{2}+,9/{2}+ states in {}{53,55,61}Ca. ).

Functionalizing graphene by embedded boron clusters

NASA Astrophysics Data System (ADS)

Quandt, Alexander; Kunstmann, Jens; Ozdogan, Cem; Fehske, Holger

2010-03-01

We present results from an ab initio study of B7 clusters implanted into graphene [1,2]. Our model system consists of an alternating chain of quasiplanar B7 clusters. We show that graphene easily accepts these alternating B7-C6 chains and that the implanted boron components may dramatically modify the electronic properties. This suggests that our model system might serve as a blueprint for the controlled layout of graphene based nanodevices, where the semiconducting properties are supplemented by parts of the graphene matrix itself, and the basic metallic wiring is provided by alternating chains of implanted boron clusters. [1] A. Quandt, C. "Ozdogan, J. Kunstmann, and H. Fehske, Nanotechnology 19, 335707 (2008). [2] A. Quandt, C. "Ozdogan, J. Kunstmann, and H. Fehske, phys. stat. solidi (b) 245, 2077 (2008).

A density functional global optimisation study of neutral 8-atom Cu-Ag and Cu-Au clusters

NASA Astrophysics Data System (ADS)

Heard, Christopher J.; Johnston, Roy L.

2013-02-01

The effect of doping on the energetics and dimensionality of eight atom coinage metal subnanometre particles is fully resolved using a genetic algorithm in tandem with on the fly density functional theory calculations to determine the global minima (GM) for Cu n Ag(8- n) and Cu n Au(8- n) clusters. Comparisons are made to previous ab initio work on mono- and bimetallic clusters, with excellent agreement found. Charge transfer and geometric arguments are considered to rationalise the stability of the particular permutational isomers found. An interesting transition between three dimensional and two dimensional GM structures is observed for copper-gold clusters, which is sharper and appears earlier in the doping series than is known for gold-silver particles.

CuNi Nanoparticles Assembled on Graphene for Catalytic Methanolysis of Ammonia Borane and Hydrogenation of Nitro/Nitrile Compounds

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

Yu, Chao; Fu, Jiaju; Muzzio, Michelle

Here we report a solution phase synthesis of 16 nm CuNi nanoparticles (NPs) with the Cu/Ni composition control. These NPs are assembled on graphene (G) and show Cu/Ni composition-dependent catalysis for methanolysis of ammonia borane (AB) and hydrogenation of aromatic nitro (nitrile) compounds to primary amines in methanol at room temperature. Among five different CuNi NPs studied, the G-Cu 36Ni 64 NPs are the best catalyst for both AB methanolysis (TOF = 49.1 mol H2 mol CuNi -1 min -1 and E a = 24.4 kJ/mol) and hydrogenation reactions (conversion yield >97%). In conclusion, the G-CuNi represents a unique noble-metal-freemore » catalyst for hydrogenation reactions in a green environment without using pure hydrogen.« less

Ab initio structure determination of nanocrystals of organic pharmaceutical compounds by electron diffraction at room temperature using a Timepix quantum area direct electron detector.

PubMed

van Genderen, E; Clabbers, M T B; Das, P P; Stewart, A; Nederlof, I; Barentsen, K C; Portillo, Q; Pannu, N S; Nicolopoulos, S; Gruene, T; Abrahams, J P

2016-03-01

Until recently, structure determination by transmission electron microscopy of beam-sensitive three-dimensional nanocrystals required electron diffraction tomography data collection at liquid-nitrogen temperature, in order to reduce radiation damage. Here it is shown that the novel Timepix detector combines a high dynamic range with a very high signal-to-noise ratio and single-electron sensitivity, enabling ab initio phasing of beam-sensitive organic compounds. Low-dose electron diffraction data (∼ 0.013 e(-) Å(-2) s(-1)) were collected at room temperature with the rotation method. It was ascertained that the data were of sufficient quality for structure solution using direct methods using software developed for X-ray crystallography (XDS, SHELX) and for electron crystallography (ADT3D/PETS, SIR2014).

CuNi Nanoparticles Assembled on Graphene for Catalytic Methanolysis of Ammonia Borane and Hydrogenation of Nitro/Nitrile Compounds

DOE PAGES

Yu, Chao; Fu, Jiaju; Muzzio, Michelle; ...

2017-01-12

Here we report a solution phase synthesis of 16 nm CuNi nanoparticles (NPs) with the Cu/Ni composition control. These NPs are assembled on graphene (G) and show Cu/Ni composition-dependent catalysis for methanolysis of ammonia borane (AB) and hydrogenation of aromatic nitro (nitrile) compounds to primary amines in methanol at room temperature. Among five different CuNi NPs studied, the G-Cu 36Ni 64 NPs are the best catalyst for both AB methanolysis (TOF = 49.1 mol H2 mol CuNi -1 min -1 and E a = 24.4 kJ/mol) and hydrogenation reactions (conversion yield >97%). In conclusion, the G-CuNi represents a unique noble-metal-freemore » catalyst for hydrogenation reactions in a green environment without using pure hydrogen.« less

Products derived from waste plastics (PC, HIPS, ABS, PP and PA6) via hydrothermal treatment: Characterization and potential applications.

PubMed

Zhao, Xuyuan; Zhan, Lu; Xie, Bing; Gao, Bin

2018-09-01

In this study, hydrothermal method was applied for the treatment of five typical waste plastics (PC, HIPS, ABS, PP and PA6). The hydrothermal products of oils and solid residues were analyzed for the product slate and combustion behaviors. Some predominant chemical feedstock were detected in the oils, such as phenolic compounds and bisphenol A (BPA) in PC oils, single-ringed aromatic compounds and diphenyl-sketetons compounds in HIPS and ABS oils, alkanes in PP oils, and caprolactam (CPL) in PA6 oils. The hydrothermal solid residues were subjected to DSC analysis. Except the solid residues of PA6, all the solid residues had enormous improvement on the enthalpy of combustion. The solid residues of PC had the maximum promotion up to 576.03% compared to the raw material. The hydrothermal treatment significantly improved the energy density and facilitated effective combustion. Meanwhile, the glass fiber was recovered from the PA6 plastics. In addition, the combustion behaviors of the uplifting residues were investigated to provide the theoretical foundation for further study of combustion optimization. All the results indicated that the oils of waste plastics after hydrothermal treatment could be used as chemical feedstock; the solid residues of waste plastics after hydrothermal treatment could be used as potentially clean and efficient solid fuels. The hydrothermal treatment for various waste plastics was verified as a novel waste-to-energy technique. Copyright © 2018 Elsevier Ltd. All rights reserved.

Comparative genomics reveals phylogenetic distribution patterns of secondary metabolites in Amycolatopsis species.

PubMed

Adamek, Martina; Alanjary, Mohammad; Sales-Ortells, Helena; Goodfellow, Michael; Bull, Alan T; Winkler, Anika; Wibberg, Daniel; Kalinowski, Jörn; Ziemert, Nadine

2018-06-01

Genome mining tools have enabled us to predict biosynthetic gene clusters that might encode compounds with valuable functions for industrial and medical applications. With the continuously increasing number of genomes sequenced, we are confronted with an overwhelming number of predicted clusters. In order to guide the effective prioritization of biosynthetic gene clusters towards finding the most promising compounds, knowledge about diversity, phylogenetic relationships and distribution patterns of biosynthetic gene clusters is necessary. Here, we provide a comprehensive analysis of the model actinobacterial genus Amycolatopsis and its potential for the production of secondary metabolites. A phylogenetic characterization, together with a pan-genome analysis showed that within this highly diverse genus, four major lineages could be distinguished which differed in their potential to produce secondary metabolites. Furthermore, we were able to distinguish gene cluster families whose distribution correlated with phylogeny, indicating that vertical gene transfer plays a major role in the evolution of secondary metabolite gene clusters. Still, the vast majority of the diverse biosynthetic gene clusters were derived from clusters unique to the genus, and also unique in comparison to a database of known compounds. Our study on the locations of biosynthetic gene clusters in the genomes of Amycolatopsis' strains showed that clusters acquired by horizontal gene transfer tend to be incorporated into non-conserved regions of the genome thereby allowing us to distinguish core and hypervariable regions in Amycolatopsis genomes. Using a comparative genomics approach, it was possible to determine the potential of the genus Amycolatopsis to produce a huge diversity of secondary metabolites. Furthermore, the analysis demonstrates that horizontal and vertical gene transfer play an important role in the acquisition and maintenance of valuable secondary metabolites. Our results cast light on the interconnections between secondary metabolite gene clusters and provide a way to prioritize biosynthetic pathways in the search and discovery of novel compounds.

Biodegradation of 3-methyldiphenylether (MDE) by Hydrogenophaga atypical strain QY7-2 and cloning of the methy-oxidation gene mdeABCD

NASA Astrophysics Data System (ADS)

Yang, Qian; Cai, Shu; Dong, Shaowei; Chen, Lulu; Chen, Jifei; Cai, Tianming

2016-12-01

3-Methyldiphenylether (MDE) is an important alkyl-substituted diphenyl ether compound that is widely used as an intermediate in the synthesis of pyrethroid insecticides. An efficient MDE-degrading strain QY7-2, identified as Hydrogenophaga atypical, was isolated from activated sludge for the first time. Strain QY7-2 can utilize MDE as the sole carbon and energy source and completely mineralize MDE. The degradation pathway of MDE was proposed in the strain through metabolites identification. A gene cluster involving in methy-oxidation of MDE was cloned from QY7-2 and expressed in Escherichia coli BL21 (DE3), and the products were purified by SDS-PAGE. The specific activities of the recombinant enzymes MdeAB, MdeC and MdeD were 113.8 ± 3.5, 274.5 ± 6.2 and 673.4 ± 8.7 nmol min-1 mg-1, respectively. These results provide the biochemical and genetic foundation of microbial degradation pathway of MDE and benefit the bioremediation of MDE-contaminated environments.

Features of Electron Density Distribution in Delafossite Cualo2

NASA Astrophysics Data System (ADS)

Pogoreltsev, A. I.; Schmidt, S. V.; Gavrilenko, A. N.; Shulgin, D. A.; Korzun, B. V.; Matukhin, V. L.

2015-07-01

We have used pulsed 63,65Cu nuclear quadrupole resonance at room temperature to study the semiconductor compound CuAlO2 with a delafossite crystal structure, and we have determined the quadrupole frequency νQ = 28.12 MHz and the asymmetry parameter η ~ 0, which we used to study the features of the electron density distribution in the vicinity of the quadrupolar nucleus. In order to take into account the influence of correlation effects on the electric field gradient, we carried out ab initio calculations within the density functional theory (DFT) approximation using a set of correlation functionals VWN1RPA, VWN5, PW91LDA, CPW91, and B3LYP1. We mapped the electron density distribution in the vicinity of the quadrupolar copper nucleus for the Cu7Al6o{14/- 1} cluster and we calculated the size of the LUMO-HOMO gap, Δ ~ 3.33 eV. We established the anisotropy of the spatial electron density distribution. Based on analysis of the electron density distribution obtained, we suggest that the bond in CuAlO2 is not purely covalent.

Biodegradation of 3-methyldiphenylether (MDE) by Hydrogenophaga atypical strain QY7-2 and cloning of the methy-oxidation gene mdeABCD

PubMed Central

Yang, Qian; Cai, Shu; Dong, Shaowei; Chen, Lulu; Chen, Jifei; Cai, Tianming

2016-01-01

3-Methyldiphenylether (MDE) is an important alkyl-substituted diphenyl ether compound that is widely used as an intermediate in the synthesis of pyrethroid insecticides. An efficient MDE-degrading strain QY7-2, identified as Hydrogenophaga atypical, was isolated from activated sludge for the first time. Strain QY7-2 can utilize MDE as the sole carbon and energy source and completely mineralize MDE. The degradation pathway of MDE was proposed in the strain through metabolites identification. A gene cluster involving in methy-oxidation of MDE was cloned from QY7-2 and expressed in Escherichia coli BL21 (DE3), and the products were purified by SDS-PAGE. The specific activities of the recombinant enzymes MdeAB, MdeC and MdeD were 113.8 ± 3.5, 274.5 ± 6.2 and 673.4 ± 8.7 nmol min−1 mg−1, respectively. These results provide the biochemical and genetic foundation of microbial degradation pathway of MDE and benefit the bioremediation of MDE-contaminated environments. PMID:27995977

Grape cluster microclimate influences the aroma composition of Sauvignon blanc wine.

PubMed

Martin, Damian; Grose, Claire; Fedrizzi, Bruno; Stuart, Lily; Albright, Abby; McLachlan, Andrew

2016-11-01

New Zealand Sauvignon blanc (SB) wines are characterised by a distinctive combination of tropical-fruity and green-herbaceous aromatic compounds. The influence of sunlight exposure of grape clusters on juice and wine composition was investigated, with the aim of manipulating aromatic compounds in SB wine. In the absence of basal leaf removal SB clusters naturally exposed to sunlight were riper than shaded clusters, evidenced by higher total soluble solids (TSS) and proline, and lower malic acid, 3-isobutyl-2-methoxypyrazine (IBMP) and arginine. Volatile thiols in wines did not differ between shaded and exposed clusters. At equivalent TSS, cluster exposure had little or no effect on malic acid concentration. Conversely, wine from shaded clusters had almost double the IBMP concentration of wine from exposed clusters at equivalent TSS. The effects on SB juice and wine composition of natural variations in cluster microclimate are not comparable with the effects of cluster exposure created through leaf removal. Copyright © 2016 Elsevier Ltd. All rights reserved.

Crystal structure of the new A2SnTa6X18 (A = K, Rb, Cs; X = Cl, Br) cluster compounds

NASA Astrophysics Data System (ADS)

Lemoine, P.; Wilmet, M.; Malaman, B.; Paofai, S.; Dumait, N.; Cordier, S.

2018-01-01

The crystal structure of the new cluster compounds A2SnTa6X18 (with A = K, Rb, Cs, and X = Cl, Br) was determined by using single-crystal and powder X-ray diffraction, and 119Sn Mössbauer spectroscopy. Those compounds crystallize in the Cs2EuNb6Br18-type structure of space group R 3 ̅. This type of structure is built up on discrete edge-bridged [M6Xi12Xa6]4- cluster units arranged according to a pseudo face-centered cubic stacking, where the octahedral and tetrahedral vacancies are fully occupied by divalent tin cations and monovalent alkaline cations, respectively. The tin cations influence on the halogen matrix and the electronic effects on the cluster units in the Cs2EuNb6Br18-type structure are discussed by comparison with isotype compounds. From those analyses, the ionic radius of Sn2+ in coordination number VI is estimated to be 1.14(1) Å. Finally, K2SnTa6Br18 might be considered as a new example of compound containing a quite bare stannous ion (5 s2 configuration).

Conformation and tautomerism of methoxy-substituted 4-phenyl-4-thiazoline-2-thiones: a combined crystallographic and ab initio investigation.

PubMed

Balti, Monaem; Norberg, Bernadette; Efrit, Mohamed Lotfi; Lanners, Steve; Wouters, Johan

2016-05-01

4-Phenyl-4-thiazoline-2-thiol is an active pharmaceutical compound, one of whose activities is as a human indolenamine dioxygenase inhibitor. It has been shown recently that in both the solid state and the gas phase, the thiazolinethione tautomer should be preferred. As part of both research on this lead compound and a medicinal chemistry program, a series of substituted arylthiazolinethiones have been synthesized. The molecular conformations and tautomerism of 4-(2-methoxyphenyl)-4-thiazoline-2-thione and 4-(4-methoxyphenyl)-4-thiazoline-2-thione, both C10H9NOS2, are reported and compared with the geometry deduced from ab initio calculations [PBE/6-311G(d,p)]. Both the crystal structure analyses and the calculations establish the thione tautomer for the two substituted arylthiazolinethiones. In the crystal structure of the 2-methoxyphenyl regioisomer, the thiazolinethione unit was disordered over two conformations. Both isomers exhibit similar hydrogen-bond patterns [R2(2)(8) motif] and form dimers. The crystal packing is further reinforced by short S...S interactions in the 2-methoxyphenyl isomer. The conformations of the two regioisomers correspond to stable geometries calculated from an ab initio energy-relaxed scan.

New mechanisms of cluster diffusion on metal fcc(100) surfaces

NASA Astrophysics Data System (ADS)

Trushin, Oleg; Salo, Petri; Alatalo, Matti; Ala-Nissila, Tapio

2001-03-01

We have studied atomic mechanisms of the diffusion of small clusters on the fcc(100) metal surfaces using semi-empirical and ab-initio molecular static calculations. Primary goal of these studies was to investigate possible many-body mechanisms of cluster motion which can contribute to low temperature crystal growth. We used embedded atom and Glue potentials in semi-empirical simulations of Cu and Al. Combination of the Nudged Elastic Band and Eigenvector Following methods allowed us to find all the possible transition paths for cluster movements on flat terrace. In case of Cu(001) we have found several new mechanisms for diffusion of clusters, including mechanisms called row-shearing and dimer-rotating in which a whole row inside an island moves according to a concerted jump and a dimer rotates at the periphery of an island, respectively. In some cases these mechanisms yield a lower energy barrier than the standard mechanisms.

Ground-state geometries and stability of impurity doped clusters: LinBe and LinMg (n=1-12)

NASA Astrophysics Data System (ADS)

Deshpande, M.; Dhavale, A.; Zope, R. R.; Chacko, S.; Kanhere, D. G.

2000-12-01

We have investigated the ground-state geometries of LinBe and LinMg (n=1-12) clusters using ab initio molecular dynamics. These divalent impurities Be and Mg induce different geometries and follow a different growth path for n>5. LinMg clusters are significantly different from the host geometries while LinBe clusters can be approximately viewed as Be occupying an interstitial site in the host. Our results indicate that Be gets trapped inside the Li cage, while Mg remains on the surface of the cluster. Mg-induced geometries become three-dimensional earlier at n=4 as compared to the Be system. In spite of a distinct arrangement of atoms in both cases the character of the wave functions in the d manifold is remarkably similar. In both cases an eight valence electron system has been found to be the most stable, in conformity with the spherical jellium model.

Atomic structure of a decagonal Al-Pd-Mn phase

NASA Astrophysics Data System (ADS)

Mihalkovič, Marek; Roth, Johannes; Trebin, Hans-Rainer

2017-12-01

We present a detailed structure solution for the 16 -Å decagonal quasicrystal in the Al-Pd-Mn system by means of cluster decoration and ab initio energy minimization. It is based on structure models of the ɛ and other approximant phases. The ɛ phases can be represented as subsets of a hexagon-boat-star (HBS) tiling. The decagonal phase comprises further HBS tiles. We have constructed several fictitious HBS approximants and optimized their structures individually. All tiles are decorated by two types of atomic clusters: the pseudo-Mackay icosahedron (PMI) and the large bicapped pentagonal prism (LBPP). It turns out that, whereas the PMI clusters can be kept essentially unchanged, the LBPP clusters must be adjusted in occupancy with Al atoms depending on their positions in the various tiles. In this way we obtain cluster decorations for all tiles of the decagonal quasicrystal. The calculations were confirmed by evaluation of an effective tile Hamiltonian.

Liver disease among polyvinyl chloride production workers.

PubMed

Creech, J L; Makk, L

1975-01-31

A protocol for systematic testing of all employees of a chemical plant is presented. This factory manufactures polyvinyl chloride compounds and resins, ABS compounds and resins, and synthetic rubber. The results were reviewed, which led to the discovery of 2 additional cases of angiosarcoma and 11 cases of portal fibrosis. Two of the 11 cases were found to have developed in employees other than polyvinyl chloride production workers.

The Globular Cluster NGC 6402 (M14). II. Variable Stars

NASA Astrophysics Data System (ADS)

Contreras Peña, C.; Catelan, M.; Grundahl, F.; Stephens, A. W.; Smith, H. A.

2018-03-01

We present time-series BVI photometry for the Galactic globular cluster NGC 6402 (M14). The data consist of ∼137 images per filter, obtained using the 0.9 and 1.0 m SMARTS telescopes at the Cerro Tololo Inter-American Observatory. The images were obtained during two observing runs in 2006–2007. The image-subtraction package ISIS, along with DAOPHOT II/ALLFRAME, was used to perform crowded-field photometry and search for variable stars. We identified 130 variables, eight of which are new discoveries. The variable star population is comprised of 56 ab-type RR Lyrae stars, 54 c-type RR Lyrae, 6 type II Cepheids, 1 W UMa star, 1 detached eclipsing binary, and 12 long-period variables. We provide Fourier decomposition parameters for the RR Lyrae, and discuss the physical parameters and photometric metallicity derived therefrom. The M14 distance modulus is also discussed, based on different approaches for the calibration of the absolute magnitudes of RR Lyrae stars. The possible presence of second-overtone RR Lyrae in M14 is critically addressed, with our results arguing against this possibility. By considering all of the RR Lyrae stars as members of the cluster, we derive < {P}ab > =0.589 {{d}}{{a}}{{y}}{{s}}. This, together with the position of the RR Lyrae stars of both Bailey types in the period–amplitude diagram, suggests an Oosterhoff-intermediate classification for the cluster. Such an intermediate Oosterhoff type is much more commonly found in nearby extragalactic systems, and we critically discuss several other possible indications that may point to an extragalactic origin for this cluster. Based on observations obtained with the 0.9 m and 1 m telescopes at the Cerro Tololo Inter-American Observatory, Chile, operated by the SMARTS consortium.

The rates and time-delay distribution of multiply imaged supernovae behind lensing clusters

NASA Astrophysics Data System (ADS)

Li, Xue; Hjorth, Jens; Richard, Johan

2012-11-01

Time delays of gravitationally lensed sources can be used to constrain the mass model of a deflector and determine cosmological parameters. We here present an analysis of the time-delay distribution of multiply imaged sources behind 17 strong lensing galaxy clusters with well-calibrated mass models. We find that for time delays less than 1000 days, at z = 3.0, their logarithmic probability distribution functions are well represented by P(log Δt) = 5.3 × 10-4Δttilde beta/M2502tilde beta, with tilde beta = 0.77, where M250 is the projected cluster mass inside 250 kpc (in 1014M⊙), and tilde beta is the power-law slope of the distribution. The resultant probability distribution function enables us to estimate the time-delay distribution in a lensing cluster of known mass. For a cluster with M250 = 2 × 1014M⊙, the fraction of time delays less than 1000 days is approximately 3%. Taking Abell 1689 as an example, its dark halo and brightest galaxies, with central velocity dispersions σ>=500kms-1, mainly produce large time delays, while galaxy-scale mass clumps are responsible for generating smaller time delays. We estimate the probability of observing multiple images of a supernova in the known images of Abell 1689. A two-component model of estimating the supernova rate is applied in this work. For a magnitude threshold of mAB = 26.5, the yearly rate of Type Ia (core-collapse) supernovae with time delays less than 1000 days is 0.004±0.002 (0.029±0.001). If the magnitude threshold is lowered to mAB ~ 27.0, the rate of core-collapse supernovae suitable for time delay observation is 0.044±0.015 per year.

Collision-Induced Dissociation Study of Strong Hydrogen-Bonded Cluster Ions Y−(HF)n (Y=F, O2) Using Atmospheric Pressure Corona Discharge Ionization Mass Spectrometry Combined with a HF Generator

PubMed Central

Sakamoto, Kenya; Sekimoto, Kanako; Takayama, Mitsuo

2017-01-01

Hydrogen fluoride (HF) was produced by a homemade HF generator in order to investigate the properties of strong hydrogen-bonded clusters such as (HF)n. The HF molecules were ionized in the form of complex ions associated with the negative core ions Y− produced by atmospheric pressure corona discharge ionization (APCDI). The use of APCDI in combination with the homemade HF generator led to the formation of negative-ion HF clusters Y−(HF)n (Y=F, O2), where larger clusters with n≥4 were not detected. The mechanisms for the formation of the HF, F−(HF)n, and O2−(HF)n species were discussed from the standpoints of the HF generator and APCDI MS. By performing energy-resolved collision-induced dissociation (CID) experiments on the cluster ions F−(HF)n (n=1–3), the energies for the loss of HF from F−(HF)3, F−(HF)2, and F−(HF) were evaluated to be 1 eV or lower, 1 eV or higher, and 2 eV, respectively, on the basis of their center-of-mass energy (ECM). These ECM values were consistent with the values of 0.995, 1.308, and 2.048 eV, respectively, obtained by ab initio calculations. The stability of [O2(HF)n]− (n=1–4) was discussed on the basis of the bond lengths of O2H–F−(HF)n and O2−H–F(HF)n obtained by ab initio calculations. The calculations indicated that [O2(HF)4]− separated into O2H and F−(HF)3. PMID:28966900

Collision-Induced Dissociation Study of Strong Hydrogen-Bonded Cluster Ions Y-(HF) n (Y=F, O2) Using Atmospheric Pressure Corona Discharge Ionization Mass Spectrometry Combined with a HF Generator.

PubMed

Sakamoto, Kenya; Sekimoto, Kanako; Takayama, Mitsuo

2017-01-01

Hydrogen fluoride (HF) was produced by a homemade HF generator in order to investigate the properties of strong hydrogen-bonded clusters such as (HF) n . The HF molecules were ionized in the form of complex ions associated with the negative core ions Y - produced by atmospheric pressure corona discharge ionization (APCDI). The use of APCDI in combination with the homemade HF generator led to the formation of negative-ion HF clusters Y - (HF) n (Y=F, O 2 ), where larger clusters with n ≥4 were not detected. The mechanisms for the formation of the HF, F - (HF) n , and O 2 - (HF) n species were discussed from the standpoints of the HF generator and APCDI MS. By performing energy-resolved collision-induced dissociation (CID) experiments on the cluster ions F - (HF) n ( n =1-3), the energies for the loss of HF from F - (HF) 3 , F - (HF) 2 , and F - (HF) were evaluated to be 1 eV or lower, 1 eV or higher, and 2 eV, respectively, on the basis of their center-of-mass energy ( E CM ). These E CM values were consistent with the values of 0.995, 1.308, and 2.048 eV, respectively, obtained by ab initio calculations. The stability of [O 2 (HF) n ] - ( n =1-4) was discussed on the basis of the bond lengths of O 2 H-F - (HF) n and O 2 - H-F(HF) n obtained by ab initio calculations. The calculations indicated that [O 2 (HF) 4 ] - separated into O 2 H and F - (HF) 3 .

Theoretical studies on the coupling interactions in H2SO4···HOO˙···(H2O)n (n = 0-2) clusters: toward understanding the role of water molecules in the uptake of HOO˙ radical by sulfuric acid aerosols.

PubMed

Li, Ping; Ma, Zhiying; Wang, Weihua; Zhai, Yazhou; Sun, Haitao; Bi, Siwei; Bu, Yuxiang

2011-01-21

A detailed knowledge of coupling interactions among sulfuric acid (H(2)SO(4)), the hydroperoxyl radical (HOO˙), and water molecules (H(2)O) is crucial for the better understanding of the uptake of HOO˙ radicals by sulfuric acid aerosols at different atmospheric humidities. In the present study, the equilibrium structures, binding energies, equilibrium distributions, and the nature of the coupling interactions in H(2)SO(4)···HOO˙···(H(2)O)(n) (n = 0-2) clusters have been systematically investigated at the B3LYP/6-311++G(3df,3pd) level of theory in combination with the atoms in molecules (AIM) theory, natural bond orbital (NBO) method, energy decomposition analyses, and ab initio molecular dynamics. Two binary, five ternary, and twelve tetramer clusters possessing multiple intermolecular H-bonds have been located on their potential energy surfaces. Two different modes for water molecules have been observed to influence the coupling interactions between H(2)SO(4) and HOO˙ through the formations of intermolecular H-bonds with or without breaking the original intermolecular H-bonds in the binary H(2)SO(4)···HOO˙ cluster. It was found that the introduction of one or two water molecules can efficiently enhance the interactions between H(2)SO(4) and HOO˙, implying the positive role of water molecules in the uptake of the HOO˙ radical by sulfuric acid aerosols. Additionally, the coupling interaction modes of the most stable clusters under study have been verified by the ab initio molecular dynamics.

Chandra studies of the globular cluster 47 Tucanae: A deeper X-ray source catalogue, five new X-ray counterparts to millisecond radio pulsars, and new constraints to r-mode instability window

NASA Astrophysics Data System (ADS)

Bhattacharya, Souradeep; Heinke, Craig O.; Chugunov, Andrey I.; Freire, Paulo C. C.; Ridolfi, Alessandro; Bogdanov, Slavko

2017-12-01

We combined Chandra ACIS observations of the globular cluster 47 Tucanae (47 Tuc) from 2000, 2002 and 2014-2015 to create a deeper X-ray source list, and study some of the faint radio millisecond pulsars (MSPs) present in this cluster. We have detected 370 X-ray sources within the half-mass radius (2.79 arcsec) of the cluster, 81 of which are newly identified, by including new data and using improved source detection techniques. The majority of the newly identified sources are in the crowded core region, indicating cluster membership. We associate five of the new X-ray sources with chromospherically active BY Dra or W UMa variables identified by Albrow et al. We present alternative positions derived from two methods, centroiding and image reconstruction, for faint, crowded sources. We are able to extract X-ray spectra of the recently discovered MSPs 47 Tuc aa, 47 Tuc ab, the newly timed MSP 47 Tuc Z, and the newly resolved MSPs 47 Tuc S and 47 Tuc F. Generally, they are well fitted by blackbody or neutron star atmosphere models, with temperatures, luminosities and emitting radii similar to those of other known MSPs in 47 Tuc, though 47 Tuc aa and 47 Tuc ab reach lower X-ray luminosities. We limit X-ray emission from the full surface of the rapidly spinning (542 Hz) MSP 47 Tuc aa, and use this limit to put an upper bound for amplitude of r-mode oscillations in this pulsar as α < 2.5 × 10-9 and constrain the shape of the r-mode instability window.

Mid-infrared signatures of hydroxyl containing water clusters: Infrared laser Stark spectroscopy of OH–H{sub 2}O and OH(D{sub 2}O){sub n} (n = 1-3)

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

Hernandez, Federico J.; INFIQC, Dpto. de Fisicoquímica, Facultad de Ciencias Químicas, Centro Láser de Ciencias Moleculares, Universidad Nacional de Córdoba, Ciudad Universitaria, Pabellón, X5000HUA Córdoba; Brice, Joseph T.

2015-10-28

Small water clusters containing a single hydroxyl radical are synthesized in liquid helium droplets. The OH–H{sub 2}O and OH(D{sub 2}O){sub n} clusters (n = 1-3) are probed with infrared laser spectroscopy in the vicinity of the hydroxyl radical OH stretch vibration. Experimental band origins are qualitatively consistent with ab initio calculations of the global minimum structures; however, frequency shifts from isolated OH are significantly over-predicted by both B3LYP and MP2 methods. An effective Hamiltonian that accounts for partial quenching of electronic angular momentum is used to analyze Stark spectra of the OH–H{sub 2}O and OH–D{sub 2}O binary complexes, revealing amore » 3.70(5) D permanent electric dipole moment. Computations of the dipole moment are in good agreement with experiment when large-amplitude vibrational averaging is taken into account. Polarization spectroscopy is employed to characterize two vibrational bands assigned to OH(D{sub 2}O){sub 2}, revealing two nearly isoenergetic cyclic isomers that differ in the orientation of the non-hydrogen-bonded deuterium atoms relative to the plane of the three oxygen atoms. The dipole moments for these clusters are determined to be approximately 2.5 and 1.8 D for “up-up” and “up-down” structures, respectively. Hydroxyl stretching bands of larger clusters containing three or more D{sub 2}O molecules are observed shifted approximately 300 cm{sup −1} to the red of the isolated OH radical. Pressure dependence studies and ab initio calculations imply the presence of multiple cyclic isomers of OH(D{sub 2}O){sub 3}.« less

Spatial event cluster detection using an approximate normal distribution.

PubMed

Torabi, Mahmoud; Rosychuk, Rhonda J

2008-12-12

In geographic surveillance of disease, areas with large numbers of disease cases are to be identified so that investigations of the causes of high disease rates can be pursued. Areas with high rates are called disease clusters and statistical cluster detection tests are used to identify geographic areas with higher disease rates than expected by chance alone. Typically cluster detection tests are applied to incident or prevalent cases of disease, but surveillance of disease-related events, where an individual may have multiple events, may also be of interest. Previously, a compound Poisson approach that detects clusters of events by testing individual areas that may be combined with their neighbours has been proposed. However, the relevant probabilities from the compound Poisson distribution are obtained from a recursion relation that can be cumbersome if the number of events are large or analyses by strata are performed. We propose a simpler approach that uses an approximate normal distribution. This method is very easy to implement and is applicable to situations where the population sizes are large and the population distribution by important strata may differ by area. We demonstrate the approach on pediatric self-inflicted injury presentations to emergency departments and compare the results for probabilities based on the recursion and the normal approach. We also implement a Monte Carlo simulation to study the performance of the proposed approach. In a self-inflicted injury data example, the normal approach identifies twelve out of thirteen of the same clusters as the compound Poisson approach, noting that the compound Poisson method detects twelve significant clusters in total. Through simulation studies, the normal approach well approximates the compound Poisson approach for a variety of different population sizes and case and event thresholds. A drawback of the compound Poisson approach is that the relevant probabilities must be determined through a recursion relation and such calculations can be computationally intensive if the cluster size is relatively large or if analyses are conducted with strata variables. On the other hand, the normal approach is very flexible, easily implemented, and hence, more appealing for users. Moreover, the concepts may be more easily conveyed to non-statisticians interested in understanding the methodology associated with cluster detection test results.

Ab initio Bogoliubov coupled cluster theory for open-shell nuclei

DOE PAGES

Signoracci, Angelo J.; Duguet, Thomas; Hagen, Gaute; ...

2015-06-29

Background: Ab initio many-body methods have been developed over the past 10 yr to address closed-shell nuclei up to mass A≈130 on the basis of realistic two- and three-nucleon interactions. A current frontier relates to the extension of those many-body methods to the description of open-shell nuclei. Several routes to address open-shell nuclei are currently under investigation, including ideas that exploit spontaneous symmetry breaking. Purpose: Singly open-shell nuclei can be efficiently described via the sole breaking of U(1) gauge symmetry associated with particle-number conservation as a way to account for their superfluid character. While this route was recently followed withinmore » the framework of self-consistent Green's function theory, the goal of the present work is to formulate a similar extension within the framework of coupled cluster theory. Methods: We formulate and apply Bogoliubov coupled cluster (BCC) theory, which consists of representing the exact ground-state wave function of the system as the exponential of a quasiparticle excitation cluster operator acting on a Bogoliubov reference state. Equations for the ground-state energy and the cluster amplitudes are derived at the singles and doubles level (BCCSD) both algebraically and diagrammatically. The formalism includes three-nucleon forces at the normal-ordered two-body level. The first BCC code is implemented in m scheme, which will permit the treatment of doubly open-shell nuclei via the further breaking of SU(2) symmetry associated with angular momentum conservation. Results: Proof-of-principle calculations in an N max=6 spherical harmonic oscillator basis for 16,18O and 18Ne in the BCCD approximation are in good agreement with standard coupled cluster results with the same chiral two-nucleon interaction, while 20O and 20Mg display underbinding relative to experiment. The breaking of U(1) symmetry, monitored by computing the variance associated with the particle-number operator, is relatively constant for all five nuclei, in both the Hartree-Fock-Bogoliubov and BCCD approximations. Conclusions: The newly developed many-body formalism increases the potential span of ab initio calculations based on single-reference coupled cluster techniques tremendously, i.e., potentially to reach several hundred additional midmass nuclei. The new formalism offers a wealth of potential applications and further extensions dedicated to the description of ground and excited states of open-shell nuclei. Short-term goals include the implementation of three-nucleon forces at the normal-ordered two-body level. Midterm extensions include the approximate treatment of triples corrections and the development of the equation-of-motion methodology to treat both excited states and odd nuclei. Long-term extensions include exact restoration of U(1) and SU(2) symmetries.« less

A "First Principles" Potential Energy Surface for Liquid Water from VRT Spectroscopy of Water Clusters

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

Goldman, N; Leforestier, C; Saykally, R J

We present results of gas phase cluster and liquid water simulations from the recently determined VRT(ASP-W)III water dimer potential energy surface. VRT(ASP-W)III is shown to not only be a model of high ''spectroscopic'' accuracy for the water dimer, but also makes accurate predictions of vibrational ground-state properties for clusters up through the hexamer. Results of ambient liquid water simulations from VRT(ASP-W)III are compared to those from ab initio Molecular Dynamics, other potentials of ''spectroscopic'' accuracy, and to experiment. The results herein represent the first time that a ''spectroscopic'' potential surface is able to correctly model condensed phase properties of water.

Molecular Networking and Pattern-Based Genome Mining Improves Discovery of Biosynthetic Gene Clusters and their Products from Salinispora Species

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

Duncan, Katherine R.; Crüsemann, Max; Lechner, Anna

Genome sequencing has revealed that bacteria contain many more biosynthetic gene clusters than predicted based on the number of secondary metabolites discovered to date. While this biosynthetic reservoir has fostered interest in new tools for natural product discovery, there remains a gap between gene cluster detection and compound discovery. In this paper, we apply molecular networking and the new concept of pattern-based genome mining to 35 Salinispora strains, including 30 for which draft genome sequences were either available or obtained for this study. The results provide a method to simultaneously compare large numbers of complex microbial extracts, which facilitated themore » identification of media components, known compounds and their derivatives, and new compounds that could be prioritized for structure elucidation. Finally, these efforts revealed considerable metabolite diversity and led to several molecular family-gene cluster pairings, of which the quinomycin-type depsipeptide retimycin A was characterized and linked to gene cluster NRPS40 using pattern-based bioinformatic approaches.« less

Molecular Networking and Pattern-Based Genome Mining Improves Discovery of Biosynthetic Gene Clusters and their Products from Salinispora Species

DOE PAGES

Duncan, Katherine R.; Crüsemann, Max; Lechner, Anna; ...

2015-04-09

Genome sequencing has revealed that bacteria contain many more biosynthetic gene clusters than predicted based on the number of secondary metabolites discovered to date. While this biosynthetic reservoir has fostered interest in new tools for natural product discovery, there remains a gap between gene cluster detection and compound discovery. In this paper, we apply molecular networking and the new concept of pattern-based genome mining to 35 Salinispora strains, including 30 for which draft genome sequences were either available or obtained for this study. The results provide a method to simultaneously compare large numbers of complex microbial extracts, which facilitated themore » identification of media components, known compounds and their derivatives, and new compounds that could be prioritized for structure elucidation. Finally, these efforts revealed considerable metabolite diversity and led to several molecular family-gene cluster pairings, of which the quinomycin-type depsipeptide retimycin A was characterized and linked to gene cluster NRPS40 using pattern-based bioinformatic approaches.« less

Molecular Networking and Pattern-Based Genome Mining Improves discovery of biosynthetic gene clusters and their products from Salinispora species

PubMed Central

Duncan, Katherine R.; Crüsemann, Max; Lechner, Anna; Sarkar, Anindita; Li, Jie; Ziemert, Nadine; Wang, Mingxun; Bandeira, Nuno; Moore, Bradley S.; Dorrestein, Pieter C.; Jensen, Paul R.

2015-01-01

Summary Genome sequencing has revealed that bacteria contain many more biosynthetic gene clusters than predicted based on the number of secondary metabolites discovered to date. While this biosynthetic reservoir has fostered interest in new tools for natural product discovery, there remains a gap between gene cluster detection and compound discovery. Here we apply molecular networking and the new concept of pattern-based genome mining to 35 Salinispora strains including 30 for which draft genome sequences were either available or obtained for this study. The results provide a method to simultaneously compare large numbers of complex microbial extracts, which facilitated the identification of media components, known compounds and their derivatives, and new compounds that could be prioritized for structure elucidation. These efforts revealed considerable metabolite diversity and led to several molecular family-gene cluster pairings, of which the quinomycin-type depsipeptide retimycin A was characterized and linked to gene cluster NRPS40 using pattern-based bioinformatic approaches. PMID:25865308

A discrete Cu cluster and a 3D MnII-CuII framework based on assembly of Mn2Cu4 clusters: synthesis, structure and magnetic properties.

PubMed

Chakraborty, Anindita; Escuer, Albert; Ribas, Joan; Maji, Tapas Kumar

2016-10-04

The synthesis, single-crystal structure characterization and detailed magnetic study of a homometallic hexanuclear Cu II cluster [Cu 6 (μ 3 -OH) 2 (ppk) 6 (H 2 O) 2 (NO 3 ) 4 ] (1) and a three-dimensional (3D) compound [{MnCu 2 (dpkO 2 H) 2 (dpkO 2 )N 3 }·(NO 3 )·H 2 O] n (2) (ppk = phenyl-2-pyridyl ketoxime; dpk = di-2-pyridyl ketone) consisting of heterometallic Mn II -Cu II hexanuclear cores as secondary building units are reported in this paper. In compound 1, two symmetry-related Cu 3 triangles consisting of a hydroxido-bridged trinuclear unit, [Cu 3 (μ 3 -OH)(ppk) 3 (H 2 O)(NO 3 )] + , are assembled through nitrate bridging giving rise to the homometallic Cu 6 cluster. Compound 2 contains heterometallic {MnCu} cores, which are further connected to each other through an azido bridging ligand in all the crystallographic directions, resulting in a 3D metal-organic framework. Construction of such a heterometallic 3D framework from {MnCu} units is until now, unknown. Magnetic studies of both 1 and 2 were performed in detail and both compounds show dominant antiferromagnetic interaction in the respective clusters. Compound 1 reveals significant spin frustration and anti-symmetric exchange interaction in the trinuclear cores, with a significantly high value of J av (-655 cm -1 ). Furthermore, compound 2 exhibits a dominant antiferromagnetic interaction, which is also supported by an extensive magneto-structural correlation which considers the different magnetic pathways.

Isolated lymphoid follicles are not IgA inductive sites for recombinant Salmonella

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

Hashizume, Tomomi; Momoi, Fumiki; Kurita-Ochiai, Tomoko

2007-08-24

In this study, we investigated whether isolated lymphoid follicles (ILF) play a role in the regulation of intestinal IgA antibody (Ab) responses. The transfer of wild type (WT) bone marrow (BM) to lymphotoxin-{alpha}-deficient (LT{alpha}{sup -/-}) mice resulted in the formation of mature ILF containing T cells, B cells, and FDC clusters in the absence of mesenteric lymph nodes and Peyer's patches. Although the ILF restored total IgA Abs in the intestine, antigen (Ag)-specific IgA responses were not induced after oral immunization with recombinant Salmonella expressing fragment C of tetanus toxin. Moreover, Ag-specific cell proliferation was not detected in the ILF.more » Interestingly, no IgA anti-LPS Abs were detected in the fecal extracts of LT{alpha}{sup -/-} mice reconstituted with WT BM. On the basis of these findings, ILF can be presumed to play a role in the production of IgA Abs, but lymphoid nodules are not inductive sites for the regulation of Ag-specific intestinal IgA responses to recombinant Salmonella.« less

Identification and quantification of major maillard cross-links in human serum albumin and lens protein. Evidence for glucosepane as the dominant compound.

PubMed

Biemel, Klaus M; Friedl, D Alexander; Lederer, Markus O

2002-07-12

Glycation reactions leading to protein modifications (advanced glycation end products) contribute to various pathologies associated with the general aging process and long term complications of diabetes. However, only few relevant compounds have so far been detected in vivo. We now report on the first unequivocal identification of the lysine-arginine cross-links glucosepane 5, DOGDIC 6, MODIC 7, and GODIC 8 in human material. For their accurate quantification by coupled liquid chromatography-electrospray ionization mass spectrometry, (13)C-labeled reference compounds were synthesized independently. Compounds 5-8 are formed via the alpha-dicarbonyl compounds N(6)-(2,3-dihydroxy-5,6-dioxohexyl)-l-lysinate (1a,b), 3-deoxyglucosone (), methylglyoxal (), and glyoxal (), respectively. The protein-bound dideoxyosone 1a,b seems to be of prime significance for cross-linking because it presumably is not detoxified by mammalian enzymes as readily as 2-4. Hence, the follow-up product glucosepane 5 was found to be the dominant compound. Up to 42.3 pmol of 5/mg of protein was identified in human serum albumin of diabetics; the level of 5 correlates markedly with the glycated hemoglobin HbA(1c). In the water-insoluble fraction of lens proteins from normoglycemics, concentration of 5 ranges between 132.3 and 241.7 pmol/mg. The advanced glycoxidation end product GODIC 8 is elevated significantly in brunescent lenses, indicating enhanced oxidative stress in this material. Compounds 5-8 thus appear predestined as markers for pathophysiological processes.

PPL2ab neurons restore sexual responses in aged Drosophila males through dopamine.

PubMed

Kuo, Shu-Yun; Wu, Chia-Lin; Hsieh, Min-Yen; Lin, Chen-Ta; Wen, Rong-Kun; Chen, Lien-Cheng; Chen, Yu-Hui; Yu, Yhu-Wei; Wang, Horng-Dar; Su, Yi-Ju; Lin, Chun-Ju; Yang, Cian-Yi; Guan, Hsien-Yu; Wang, Pei-Yu; Lan, Tsuo-Hung; Fu, Tsai-Feng

2015-06-30

Male sexual desire typically declines with ageing. However, our understanding of the neurobiological basis for this phenomenon is limited by our knowledge of the brain circuitry and neuronal pathways controlling male sexual desire. A number of studies across species suggest that dopamine (DA) affects sexual desire. Here we use genetic tools and behavioural assays to identify a novel subset of DA neurons that regulate age-associated male courtship activity in Drosophila. We find that increasing DA levels in a subset of cells in the PPL2ab neuronal cluster is necessary and sufficient for increased sustained courtship in both young and aged male flies. Our results indicate that preventing the age-related decline in DA levels in PPL2ab neurons alleviates diminished courtship behaviours in male Drosophila. These results may provide the foundation for deciphering the circuitry involved in sexual motivation in the male Drosophila brain.

A global ab initio potential for HCN/HNC, exact vibrational energies, and comparison to experiment

NASA Technical Reports Server (NTRS)

Bentley, Joseph A.; Bowman, Joel M.; Gazdy, Bela; Lee, Timothy J.; Dateo, Christopher E.

1992-01-01

An ab initio (i.e., from first principles) calculation of vibrational energies of HCN and HNC is reported. The vibrational calculations were done with a new potential derived from a fit to 1124 ab initio electronic energies which were calculated using the highly accurate CCSD(T) coupled-cluster method in conjunction with a large atomic natural orbital basis set. The properties of this potential are presented, and the vibrational calculations are compared to experiment for 54 vibrational transitions, 39 of which are for zero total angular momentum, J = 0, and 15 of which are for J = 1. The level of agreement with experiment is unprecedented for a triatomic with two nonhydrogen atoms, and demonstrates the capability of the latest computational methods to give reliable predictions on a strongly bound triatomic molecule at very high levels of vibrational excitation.

Amino acid anions in organic ionic compounds. An ab initio study of selected ion pairs.

PubMed

Benedetto, A; Bodo, E; Gontrani, L; Ballone, P; Caminiti, R

2014-03-06

The combination of amino acids in their deprotonated and thus anionic form with a choline cation gives origin to a new and potentially important class of organic ionic compounds. A series of such neutral ion pairs has been investigated by first principle methods. The results reveal intriguing structural motives as well as regular patterns in the charge distribution and predict a number of vibrational and optical properties that could guide the experimental investigation of these compounds. The replacement of choline with its phosphocholine analogue causes the spontaneous reciprocal neutralization of cations and anions, taking place through the transfer of a proton between the two ions. Systems of this kind, therefore, provide a wide and easily accessible playground to probe the ionic/polar transition in organic systems, while the easy transfer of H(+) among neutral and ionic species points to their potential application as proton conductors. The analysis of the ab initio data highlights similarities as well as discrepancies from the rigid-ions force-field picture and suggests directions for the improvement of empirical models.

Vibrational spectrum and assignments of 2-(4-methoxyphenyl)-1 H-benzo[ d]imidazole by ab initio Hartree-Fock and density functional methods

NASA Astrophysics Data System (ADS)

Arslan, Hakan; Algül, Öztekin

2008-06-01

The room temperature attenuated total reflection Fourier transform infrared spectrum of the 2-(4-methoxyphenyl)-1 H-benzo[ d]imidazole has been recorded with diamond/ZnSe prism. The conformational behaviour, structural stability of optimized geometry, frequency and intensity of the vibrational bands of the title compound were investigated by utilizing ab initio calculations with 6-311G** basis set at HF, B3LYP, BLYP, B3PW91 and mPW1PW91 levels. The harmonic vibrational frequencies were calculated and scaled values have been compared with experimental IR spectrum. The observed and the calculated frequencies are found to be in good agreement. The theoretical vibrational spectra of the title compound were interpreted by means of potential energy distributions using VEDA 4 program. Furthermore, the optimal uniform scaling factors calculated for the title compound are 0.9120, 0.9596, 0.9660, 0.9699, and 0.9993 for HF, mPW1PW91, B3PW91, B3LYP and BLYP methods, respectively.

Ab initio structure determination of nanocrystals of organic pharmaceutical compounds by electron diffraction at room temperature using a Timepix quantum area direct electron detector

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

Genderen, E. van; Clabbers, M. T. B.; Center for Cellular Imaging and NanoAnalytics

A specialized quantum area detector for electron diffraction studies makes it possible to solve the structure of small organic compound nanocrystals in non-cryo conditions by direct methods. Until recently, structure determination by transmission electron microscopy of beam-sensitive three-dimensional nanocrystals required electron diffraction tomography data collection at liquid-nitrogen temperature, in order to reduce radiation damage. Here it is shown that the novel Timepix detector combines a high dynamic range with a very high signal-to-noise ratio and single-electron sensitivity, enabling ab initio phasing of beam-sensitive organic compounds. Low-dose electron diffraction data (∼0.013 e{sup −} Å{sup −2} s{sup −1}) were collected at roommore » temperature with the rotation method. It was ascertained that the data were of sufficient quality for structure solution using direct methods using software developed for X-ray crystallography (XDS, SHELX) and for electron crystallography (ADT3D/PETS, SIR2014)« less

Ab initio quantum chemistry: methodology and applications.

PubMed

Friesner, Richard A

2005-05-10

This Perspective provides an overview of state-of-the-art ab initio quantum chemical methodology and applications. The methods that are discussed include coupled cluster theory, localized second-order Moller-Plesset perturbation theory, multireference perturbation approaches, and density functional theory. The accuracy of each approach for key chemical properties is summarized, and the computational performance is analyzed, emphasizing significant advances in algorithms and implementation over the past decade. Incorporation of a condensed-phase environment by means of mixed quantum mechanical/molecular mechanics or self-consistent reaction field techniques, is presented. A wide range of illustrative applications, focusing on materials science and biology, are discussed briefly.

Long range intermolecular interactions between the alkali diatomics Na2, K2, and NaK

NASA Astrophysics Data System (ADS)

Zemke, Warren T.; Byrd, Jason N.; Michels, H. Harvey; Montgomery, John A.; Stwalley, William C.

2010-06-01

Long range interactions between the ground state alkali diatomics Na2-Na2, K2-K2, Na2-K2, and NaK-NaK are examined. Interaction energies are first determined from ab initio calculations at the coupled-cluster with singles, doubles, and perturbative triples [CCSD(T)] level of theory, including counterpoise corrections. Long range energies calculated from diatomic molecular properties (polarizabilities and dipole and quadrupole moments) are then compared with the ab initio energies. A simple asymptotic model potential ELR=Eelec+Edisp+Eind is shown to accurately represent the intermolecular interactions for these systems at long range.

Long range intermolecular interactions between the alkali diatomics Na(2), K(2), and NaK.

PubMed

Zemke, Warren T; Byrd, Jason N; Michels, H Harvey; Montgomery, John A; Stwalley, William C

2010-06-28

Long range interactions between the ground state alkali diatomics Na(2)-Na(2), K(2)-K(2), Na(2)-K(2), and NaK-NaK are examined. Interaction energies are first determined from ab initio calculations at the coupled-cluster with singles, doubles, and perturbative triples [CCSD(T)] level of theory, including counterpoise corrections. Long range energies calculated from diatomic molecular properties (polarizabilities and dipole and quadrupole moments) are then compared with the ab initio energies. A simple asymptotic model potential E(LR)=E(elec)+E(disp)+E(ind) is shown to accurately represent the intermolecular interactions for these systems at long range.

Solving local structure around dopants in metal nanoparticles with ab initio modeling of X-ray absorption near edge structure

DOE PAGES

Timoshenko, J.; Shivhare, A.; Scott, R. W.; ...

2016-06-30

We adopted ab-initio X-ray Absorption Near Edge Structure (XANES) modelling for structural refinement of local environments around metal impurities in a large variety of materials. Our method enables both direct modelling, where the candidate structures are known, and the inverse modelling, where the unknown structural motifs are deciphered from the experimental spectra. We present also estimates of systematic errors, and their influence on the stability and accuracy of the obtained results. We illustrate our approach by following the evolution of local environment of palladium atoms in palladium-doped gold thiolate clusters upon chemical and thermal treatments.

The stability of vacancy clusters and their effect on helium behaviors in 3C-SiC

NASA Astrophysics Data System (ADS)

Sun, Jingjing; Li, B. S.; You, Yu-Wei; Hou, Jie; Xu, Yichun; Liu, C. S.; Fang, Q. F.; Wang, Z. G.

2018-05-01

We have carried out systematical ab initio calculations to study the stability of vacancy clusters and their effect on helium behaviors in 3C-SiC. It is found that the formation energies of vacancy clusters containing only carbon vacancies are the lowest although the vacancies are not closest to each other, while the binding energies of vacancy clusters composed of both silicon and carbon vacancies in the closest neighbors to each other are the highest. Vacancy clusters can provide with free space for helium atoms to aggregate, while interstitial sites are not favorable for helium atoms to accumulate. The binding energies of vacancy clusters with helium atoms increase almost linearly with the ratio of helium to vacancy, n/m. The binding strength of vacancy cluster having the participation of the silicon vacancy with helium is relatively stronger than that without silicon vacancy. The vacancy clusters with more vacancies can trap helium atoms more tightly. With the presence of vacancy clusters in the material, the diffusivity of helium will be significantly reduced. Moreover, the three-dimension electron density is calculated to analyze the interplay of vacancy clusters with helium.

Unsupervised Cryo-EM Data Clustering through Adaptively Constrained K-Means Algorithm

PubMed Central

Xu, Yaofang; Wu, Jiayi; Yin, Chang-Cheng; Mao, Youdong

2016-01-01

In single-particle cryo-electron microscopy (cryo-EM), K-means clustering algorithm is widely used in unsupervised 2D classification of projection images of biological macromolecules. 3D ab initio reconstruction requires accurate unsupervised classification in order to separate molecular projections of distinct orientations. Due to background noise in single-particle images and uncertainty of molecular orientations, traditional K-means clustering algorithm may classify images into wrong classes and produce classes with a large variation in membership. Overcoming these limitations requires further development on clustering algorithms for cryo-EM data analysis. We propose a novel unsupervised data clustering method building upon the traditional K-means algorithm. By introducing an adaptive constraint term in the objective function, our algorithm not only avoids a large variation in class sizes but also produces more accurate data clustering. Applications of this approach to both simulated and experimental cryo-EM data demonstrate that our algorithm is a significantly improved alterative to the traditional K-means algorithm in single-particle cryo-EM analysis. PMID:27959895

Unsupervised Cryo-EM Data Clustering through Adaptively Constrained K-Means Algorithm.

PubMed

Xu, Yaofang; Wu, Jiayi; Yin, Chang-Cheng; Mao, Youdong

2016-01-01

In single-particle cryo-electron microscopy (cryo-EM), K-means clustering algorithm is widely used in unsupervised 2D classification of projection images of biological macromolecules. 3D ab initio reconstruction requires accurate unsupervised classification in order to separate molecular projections of distinct orientations. Due to background noise in single-particle images and uncertainty of molecular orientations, traditional K-means clustering algorithm may classify images into wrong classes and produce classes with a large variation in membership. Overcoming these limitations requires further development on clustering algorithms for cryo-EM data analysis. We propose a novel unsupervised data clustering method building upon the traditional K-means algorithm. By introducing an adaptive constraint term in the objective function, our algorithm not only avoids a large variation in class sizes but also produces more accurate data clustering. Applications of this approach to both simulated and experimental cryo-EM data demonstrate that our algorithm is a significantly improved alterative to the traditional K-means algorithm in single-particle cryo-EM analysis.

DOES THE OOSTERHOFF DICHOTOMY EXIST IN THE ANDROMEDA GALAXY? I. THE CASE OF G11

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

Contreras Ramos, Rodrigo; Clementini, Gisella; Federici, Luciana, E-mail: rodrigo.contreras@oabo.inaf.it, E-mail: gisella.clementini@oabo.inaf.it, E-mail: luciana.federici@oabo.inaf.it

We present the first evidence that Oosterhoff type II globular clusters exist in the Andromeda galaxy (M31). On the basis of time-series photometry of the moderately metal-poor ([Fe/H] {approx}-1.6 dex) M31 globular cluster G11, obtained with the Wide Field Planetary Camera 2 on board the Hubble Space Telescope, we detected and derived periods for 14 RR Lyrae stars, of which five are found to lie inside the cluster tidal radius. They include three fundamental-mode (RRab) and two first-overtone (RRc) pulsators, with average periods (P{sub ab} ) = 0.70 days, and (P{sub c} ) = 0.40 days, respectively. These mean periodsmore » and the position of the cluster variable stars in the period-amplitude and period-metallicity diagrams all suggest that G11 is likely to be an Oosterhoff type II globular cluster. This appears to be in agreement with the general behavior of Milky Way globular clusters with similar metallicity and horizontal branch morphology.« less

[Cloning and expression of Tbx3 gene in Siberian sturgeon, Acipenser baerii].

PubMed

Zhang, Hao; Fan, Chun-Xin; Song, Jia-Kun

2012-04-01

Tbx3, a member of the TBX2 subfamily of T-box gene family, encodes a transcription factor with a highly conserved DNA-binding domain, which called T-domain. Tbx3 is involved in morphogenesis and organogenesis in vertebrates, such as limb development, heart remodeling, and neural placode differentiation. In the present study, a full-length 2 908 bp Tbx3 cDNA from Acipenser baerii (AbTbx3) was obtained using RT-PCR and RACE technique, which includes a 2 166 bp complete open reading frame encoding a putative peptide of 721 amino acids. AbTbx3 shares 73.5% identity with its human homolog. Particularly, the DNA-binding domain of AbTbx3 shared 95.2% identity with human Tbx3. Phylogenetic analysis revealed that AbTbx3 was grouped with Tbx3s in other vertebrates, which were clustered with Tbx2s and separated from Tbx4/5s. The predicted secondary and three-dimensional structures of the T-domain of AbTbx3 were remarkably similar to human Tbx3. Through semi-quantity RT-PCR, the expression of AbTbx3 was first detected at blastula stage during Siberian sturgeon embryonic development, increased gradually, reached its peak at early tail-bud stage and then decreased slightly. In adult sturgeon, AbTbx3 was strongly expressed in eye, brain, gill, intestines, pectoral fin and pelvic fin, but not in liver, blood, heart, kidney and muscle. The whole mount in situ hybridization showed that AbTbx3 was mainly expressed in the otic vesicle, hindbrain, dorsal notochord, pineal organ and dorsal fin bud in the larvae of stage 37 and 43.

Uncovering production of specialized metabolites by Streptomyces argillaceus: Activation of cryptic biosynthesis gene clusters using nutritional and genetic approaches.

PubMed

Becerril, Adriana; Álvarez, Susana; Braña, Alfredo F; Rico, Sergio; Díaz, Margarita; Santamaría, Ramón I; Salas, José A; Méndez, Carmen

2018-01-01

Sequencing of Streptomyces genomes has revealed they harbor a high number of biosynthesis gene cluster (BGC), which uncovered their enormous potentiality to encode specialized metabolites. However, these metabolites are not usually produced under standard laboratory conditions. In this manuscript we report the activation of BGCs for antimycins, carotenoids, germicidins and desferrioxamine compounds in Streptomyces argillaceus, and the identification of the encoded compounds. This was achieved by following different strategies, including changing the growth conditions, heterologous expression of the cluster and inactivating the adpAa or overexpressing the abrC3 global regulatory genes. In addition, three new carotenoid compounds have been identified.

Semiconductor nanocrystals covalently bound to solid inorganic surfaces using self-assembled monolayers

DOEpatents

Alivisatos, A. Paul; Colvin, Vicki L.

1998-01-01

Methods are described for attaching semiconductor nanocrystals to solid inorganic surfaces, using self-assembled bifunctional organic monolayers as bridge compounds. Two different techniques are presented. One relies on the formation of self-assembled monolayers on these surfaces. When exposed to solutions of nanocrystals, these bridge compounds bind the crystals and anchor them to the surface. The second technique attaches nanocrystals already coated with bridge compounds to the surfaces. Analyses indicate the presence of quantum confined clusters on the surfaces at the nanolayer level. These materials allow electron spectroscopies to be completed on condensed phase clusters, and represent a first step towards synthesis of an organized assembly of clusters. These new products are also disclosed.

A hierarchical clustering methodology for the estimation of toxicity.

PubMed

Martin, Todd M; Harten, Paul; Venkatapathy, Raghuraman; Das, Shashikala; Young, Douglas M

2008-01-01

ABSTRACT A quantitative structure-activity relationship (QSAR) methodology based on hierarchical clustering was developed to predict toxicological endpoints. This methodology utilizes Ward's method to divide a training set into a series of structurally similar clusters. The structural similarity is defined in terms of 2-D physicochemical descriptors (such as connectivity and E-state indices). A genetic algorithm-based technique is used to generate statistically valid QSAR models for each cluster (using the pool of descriptors described above). The toxicity for a given query compound is estimated using the weighted average of the predictions from the closest cluster from each step in the hierarchical clustering assuming that the compound is within the domain of applicability of the cluster. The hierarchical clustering methodology was tested using a Tetrahymena pyriformis acute toxicity data set containing 644 chemicals in the training set and with two prediction sets containing 339 and 110 chemicals. The results from the hierarchical clustering methodology were compared to the results from several different QSAR methodologies.

Ionothermal synthesis of discrete supertetrahedral Tn (n = 4, 5) clusters with tunable components, band gaps, and fluorescence properties.

PubMed

Yang, Dan-Dan; Li, Wei; Xiong, Wei-Wei; Li, Jian-Rong; Huang, Xiao-Ying

2018-05-01

The preparation of crystalline molecularly supertetrahedral Tn clusters with variable sizes and components is of vital importance for the fundamental study of their physicochemical properties. However, setting up an efficient method to stabilize large discrete Tn clusters is a challenge due to their high negative charges and polymerization nature. In this work, we report on the ionothermal synthesis of three discrete T4 cluster compounds, namely [Bmmim]5[(CH3)2NH2]4[NH4][M4In16S31(SH)4]·6H2O (M = Mn (1), Zn (2), Cd (3), Bmmim = 1-buty-2,3-dimethyl-imidazolium), and four discrete T5 cluster compounds, namely [Bmmim]10[NH4]3[Cu5Ga30-xInxS52(SH)4] (x = 6.6 (5), 14.5 (6), 23.8 (7), and 30 (8)). The compound [Bmmim]10[NH4]3[Cu5Ga30S52(SH)4] (4) previously reported by us features a discrete T5 cluster. The steep UV-Vis absorption edges indicate band gaps of 2.20 eV for 1, 2.64 eV for 2, 2.69 eV for 3, 3.04 eV for 4, 2.65 eV for 5, 2.48 eV for 6, 2.32 eV for 7, and 2.30 eV for 8. The compositions of T5 clusters could be varied with the ratios of Ga : In in the starting reagents, providing an opportunity to systematically control the band gaps and fluorescence performances of T5 cluster-based compounds. This research might advance the understanding of the ionothermal preparation and functionality tuning of crystalline chalcogenides.

Metabolic Clustering Analysis as a Strategy for Compound Selection in the Drug Discovery Pipeline for Leishmaniasis.

PubMed

Armitage, Emily G; Godzien, Joanna; Peña, Imanol; López-Gonzálvez, Ángeles; Angulo, Santiago; Gradillas, Ana; Alonso-Herranz, Vanesa; Martín, Julio; Fiandor, Jose M; Barrett, Michael P; Gabarro, Raquel; Barbas, Coral

2018-05-18

A lack of viable hits, increasing resistance, and limited knowledge on mode of action is hindering drug discovery for many diseases. To optimize prioritization and accelerate the discovery process, a strategy to cluster compounds based on more than chemical structure is required. We show the power of metabolomics in comparing effects on metabolism of 28 different candidate treatments for Leishmaniasis (25 from the GSK Leishmania box, two analogues of Leishmania box series, and amphotericin B as a gold standard treatment), tested in the axenic amastigote form of Leishmania donovani. Capillary electrophoresis-mass spectrometry was applied to identify the metabolic profile of Leishmania donovani, and principal components analysis was used to cluster compounds on potential mode of action, offering a medium throughput screening approach in drug selection/prioritization. The comprehensive and sensitive nature of the data has also made detailed effects of each compound obtainable, providing a resource to assist in further mechanistic studies and prioritization of these compounds for the development of new antileishmanial drugs.

Mercury methylation by novel microorganisms from new environments

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

Gilmour, C C; Podar, Mircea; Bullock, Allyson L

2013-01-01

Microbial mercury (Hg) methylation transforms a toxic trace metal into the highly bioaccumulated neurotoxin methylmercury (MeHg). The lack of a genetic marker for microbial MeHg production has prevented a clear understanding of Hg-methylating organism distribution in nature. Recently, a specific gene cluster (hgcAB) was linked to Hg methylation in two bacteria.1 Here we test if the presence of hgcAB orthologues is a reliable predictor of Hg methylation capability in microorganisms, a necessary confirmation for the development of molecular probes for Hg-methylation in nature. Although hgcAB orthologues are rare among all available microbial genomes, organisms are much more phylogenetically and environmentallymore » diverse than previously thought. By directly measuring MeHg production in several bacterial and archaeal strains encoding hgcAB, we confirmed that possessing hgcAB predicts Hg methylation capability. For the first time, we demonstrated Hg methylation in a number of species other than sulfate- (SRB) and iron- (FeRB) reducing bacteria, including methanogens, and syntrophic, acetogenic, and fermentative Firmicutes. Several of these species occupy novel environmental niches for Hg methylation, including methanogenic habitats such as rice paddies, the animal gut, and extremes of pH and salinity. Identification of these organisms as Hg methylators now links methylation to discrete gene markers in microbial communities.« less

Mercury methylation by novel microorganisms from new environments.

PubMed

Gilmour, Cynthia C; Podar, Mircea; Bullock, Allyson L; Graham, Andrew M; Brown, Steven D; Somenahally, Anil C; Johs, Alex; Hurt, Richard A; Bailey, Kathryn L; Elias, Dwayne A

2013-10-15

Microbial mercury (Hg) methylation transforms a toxic trace metal into the highly bioaccumulated neurotoxin methylmercury (MeHg). The lack of a genetic marker for microbial MeHg production has prevented a clear understanding of Hg-methylating organism distribution in nature. Recently, a specific gene cluster (hgcAB) was linked to Hg methylation in two bacteria.1 Here we test if the presence of hgcAB orthologues is a reliable predictor of Hg methylation capability in microorganisms, a necessary confirmation for the development of molecular probes for Hg-methylation in nature. Although hgcAB orthologues are rare among all available microbial genomes, organisms are much more phylogenetically and environmentally diverse than previously thought. By directly measuring MeHg production in several bacterial and archaeal strains encoding hgcAB, we confirmed that possessing hgcAB predicts Hg methylation capability. For the first time, we demonstrated Hg methylation in a number of species other than sulfate- (SRB) and iron- (FeRB) reducing bacteria, including methanogens, and syntrophic, acetogenic, and fermentative Firmicutes. Several of these species occupy novel environmental niches for Hg methylation, including methanogenic habitats such as rice paddies, the animal gut, and extremes of pH and salinity. Identification of these organisms as Hg methylators now links methylation to discrete gene markers in microbial communities.

Synthesis and antiviral evaluation of novel 2,3-dihydroxypropyl nucleosides from 2- and 4-thiouracils.

PubMed

Abdel-Rahman, Adel A-H; El-Etrawy, Abd-Allah Sh; Abdel-Megied, Ahmed E-S; Zeid, Ibrahim F; El Ashry, El Sayed H

2008-12-01

Regioselective alkylation of 2-thiouracils 1a-c and 4-thiouracils 7a,b with 2,3-O-isopropylidene-2,3-dihydroxypropyl chloride (2) afforded 2-[[(2,2-Dimethyl-1,3-dioxolan-4-yl) methyl]thio]pyrimidin-4(1H)-ones 3a-c and 4-[[(2,2-Dimethyl-1,3-dioxolan-4-yl)methyl]thio] pyrimidin-2(1H)-ones 8a,b, respectively. Further alkylation with 2 and/or 2,3-O-isopropylidine-1-O-(4-toluenesulfonyl)-glycerol (4) gave the acyclo N-nucleosides 5a-c and 9a,b whose deprotection afforded 6a-c and 10a,b. 2-(Methylthio)pyrimidin-4(1H)-ones 11a-c and 4-(methylthio)pyrimidin-2(1H)-ones 14a,b were treated with 2 and/or 4 to give 12a-c and 15a,b which were deprotected to give 13a-c and 16a,b. Pyrimidine-2,4(1H,3H)-dithiones 17a-c were treated with two equivalents of 2 to give 2,4-bis[[(2,2-dimethyl-1,3-dioxolan-4-yl)methyl]thio] pyrimidines 18a-c. Deprotection of compounds 18a-c gave 2,4-bis[(2,3-dihydroxypropyl)thio]pyrimidines 19a-c. The activity of the deprotected nucleosides against Hepatitis B virus was evaluated and showed moderate inhibition activity against HBV with mild cytotoxicity.

Influence of Winemaking Processing Steps on the Amounts of (E)-2-Decenal and Tridecane as Off-Odorants Caused by Brown Marmorated Stink Bug (Halyomorpha halys).

PubMed

Mohekar, Pallavi; Osborne, James; Wiman, Nik G; Walton, Vaughn; Tomasino, Elizabeth

2017-02-01

Brown marmorated stink bugs (BMSB) release stress compounds, tridecane and (E)-2-decenal, that affect final wine quality. This study focuses on determining the effect of wine processing on (E)-2-decenal and tridecane release in both red and white wines. Wines were produced by adding live BMSB to grape clusters at densities of 0, 0.3, 1, and 3 bugs/cluster. Compound concentrations were measured using headspace solid phase microextraction with multidimensional gas chromatography and mass spectrometry. For red wines, the highest levels of stress compounds were found using 3 BMSB/cluster [tridecane, 614 μg/L; (E)-2-decenal, 2.0 μg/L]. Pressing was found to be the critical process point for stress compound release, and additional pressing processes, press types, and press fractions were investigated. BMSB taint for white wines was not found to be problematic with respect to wine quality. An action control of 3 BMSB/cluster is recommended as this was related to the known consumption rejection threshold for (E)-2-decenal.

Aromaticity and Antiaromaticity in Zintl Clusters

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

Sun, Zhong -Ming; Liu, Chao; Popov, Ivan Aleksandrovich

Originally, the concepts of aromaticity and antiaromaticity were introduced to explain the stability and reactivity of unsaturated organic compounds. Since then, they have been extended to other species with delocalized electrons including various saturated systems, organometallic compounds, and even inorganic clusters and molecules. In this study, we focus on the most recent progress of using these concepts to guide experimental synthesis and rationalize geometrical and electronic structures of a particular family of polyanions composed of Group 14 and 15 elements, namely Zintl clusters.

Aromaticity and Antiaromaticity in Zintl Clusters

DOE PAGES

Sun, Zhong -Ming; Liu, Chao; Popov, Ivan Aleksandrovich; ...

2018-05-18

Originally, the concepts of aromaticity and antiaromaticity were introduced to explain the stability and reactivity of unsaturated organic compounds. Since then, they have been extended to other species with delocalized electrons including various saturated systems, organometallic compounds, and even inorganic clusters and molecules. In this study, we focus on the most recent progress of using these concepts to guide experimental synthesis and rationalize geometrical and electronic structures of a particular family of polyanions composed of Group 14 and 15 elements, namely Zintl clusters.

Improvement of the ab initio embedded cluster method for luminescence properties of doped materials by taking into account impurity induced distortions: the example of Y2O3:Bi(3+).

PubMed

Réal, Florent; Ordejón, Belén; Vallet, Valérie; Flament, Jean-Pierre; Schamps, Joël

2009-11-21

New ab initio embedded-cluster calculations devoted to simulating the electronic spectroscopy of Bi(3+) impurities in Y(2)O(3) sesquioxide for substitutions in either S(6) or C(2) cationic sites have been carried out taking special care of the quality of the environment. A considerable quantitative improvement with respect to previous studies [F. Real et al. J. Chem. Phys. 125, 174709 (2006); F. Real et al. J. Chem. Phys. 127, 104705 (2007)] is brought by using environments of the impurities obtained via supercell techniques that allow the whole (pseudo) crystal to relax (WCR geometries) instead of environments obtained from local relaxation of the first coordination shell only (FSR geometries) within the embedded cluster approach, as was done previously. In particular the uniform 0.4 eV discrepancy of absorption energies found previously with FSR environments disappears completely when the new WCR environments of the impurities are employed. Moreover emission energies and hence Stokes shifts are in much better agreement with experiment. These decisive improvements are mainly due to a lowering of the local point-group symmetry (S(6)-->C(3) and C(2)-->C(1)) when relaxing the geometry of the emitting (lowest) triplet state. This symmetry lowering was not observed in FSR embedded cluster relaxations because the crystal field of the embedding frozen at the genuine pure crystal positions seems to be a more important driving force than the interactions within the cluster, thus constraining the overall symmetry of the system. Variations of the doping rate are found to have negligible influence on the spectra. In conclusion, the use of WCR environments may be crucial to render the structural distortions occurring in a doped crystal and it may help to significantly improve the embedded-cluster methodology to reach the quantitative accuracy necessary to interpret and predict luminescence properties of doped materials of this type.

Preparation of new Schiff bases derived from beta-enaminonitriles and hetarylcarboxaldehydes. Anti-inflammatory and ulcerogenic activities.

PubMed

Atta, S M; Ameen, A

1993-12-01

Schiff bases 3a-j were prepared by reacting the beta-enaminonitriles (1a,b) with the appropriate hetarylcarboxaldehyde, in boiling ethanol. Structural elucidations for the new compounds (3a-j) were based upon compatible analytical and spectroscopic results. Compounds 1a, 1b, 3a, 3c, 3d and 3i were tested for their anti-inflammatory and ulcerogenic activities.

Mechanical and magneto-opto-electronic investigation of transition metal based fluoro-perovskites: An ab-initio DFT study

NASA Astrophysics Data System (ADS)

Erum, Nazia; Azhar Iqbal, Muhammad

2017-09-01

Detailed ab-initio calculations are performed to investigate structural, elastic, mechanical, magneto-electronic and optical properties of the KXF3 (X = V, Fe, Co, Ni) fluoro-perovskites using Full Potential Linearized Augmented Plane Wave (FP-LAPW) method within the framework of density functional theory (DFT). The calculated structural parameters by DFT and analytical methods are found consistent with the experimental results. From the elastic and mechanical properties, it can be inferred that these compounds are elastically stable and anisotropic while KCoF3 is harder than rest of the compounds. Furthermore, thermal behavior of these compounds is analyzed by calculating Debye temperature (θD). The calculated spin dependent magneto-electronic properties in these compounds reveal that exchange splitting is dominated by N-3d orbital. The stable magnetic phase optimizations verify the experimental observations at low temperature. Type of chemical bonding is analyzed with the help of variations in electron density difference distribution that is induced due to changes of the second cation. The linear optical properties are also discussed in terms of optical spectra. The present methodology represents an influential approach to calculate the whole set of mechanical and magneto-opto-electronic parameters, which would support to understand various physical phenomena and empower device engineers for implementing these materials in spintronic applications.

Anharmonic effects in the quantum cluster equilibrium method

NASA Astrophysics Data System (ADS)

von Domaros, Michael; Perlt, Eva

2017-03-01

The well-established quantum cluster equilibrium (QCE) model provides a statistical thermodynamic framework to apply high-level ab initio calculations of finite cluster structures to macroscopic liquid phases using the partition function. So far, the harmonic approximation has been applied throughout the calculations. In this article, we apply an important correction in the evaluation of the one-particle partition function and account for anharmonicity. Therefore, we implemented an analytical approximation to the Morse partition function and the derivatives of its logarithm with respect to temperature, which are required for the evaluation of thermodynamic quantities. This anharmonic QCE approach has been applied to liquid hydrogen chloride and cluster distributions, and the molar volume, the volumetric thermal expansion coefficient, and the isobaric heat capacity have been calculated. An improved description for all properties is observed if anharmonic effects are considered.

Exploring N-Rich Phases in Li(x)N(y) Clusters for Hydrogen Storage at Nanoscale.

PubMed

Bhattacharya, Amrita; Bhattacharya, Saswata

2015-09-17

We have performed cascade genetic algorithm and ab initio atomistic thermodynamics under the framework of first-principles-based hybrid density functional theory to study the (meta-)stability of a wide range of Li(x)N(y) clusters. We found that hybrid xc-functional is essential to address this problem as a local/semilocal functional simply fails even to predict a qualitative prediction. Most importantly, we find that though in bulk lithium nitride, the Li-rich phase, that is, Li3N, is the stable stoichiometry; in small Li(x)N(y) clusters, N-rich phases are more stable at thermodynamic equilibrium. We further show that these N-rich clusters are promising hydrogen storage material because of their easy adsorption and desorption ability at respectively low (≤300 K) and moderately high temperature (≥600 K).

Pseudopotential for ab initio calculations of uranium compounds

NASA Astrophysics Data System (ADS)

Smirnov, G. S.; Pisarev, V. V.; Stegailov, V. V.

2018-01-01

The density functional theory (DFT) is a research tool of the highest importance for electronic structure calculations. It is often the only affordable method for ab initio calculations of complex materials. The pseudopotential approach allows reducing the total number of electrons in the model that speeds up calculations. However, there is a lack of pseudopotentials for heavy elements suitable for condensed matter DFT models. In this work, we present a pseudopotential for uranium developed in the Goedecker-Teter-Hutter form. Its accuracy is illustrated using several molecular and solid-state calculations.

Ab initio study of the alkaline hydrolysis of a thio-β-lactam structure

NASA Astrophysics Data System (ADS)

Coll, Miguel; Frau, Juan; Vilanova, Bartolomé; Donoso, Josefa; Muñoz, Francisco

2000-08-01

The alkaline hydrolysis of a thio-β-lactam in the gas phase was examined in the light of RHF and DFT ab initio calculations. The solvent effect was considered via IPCM computations. The tetrahedral intermediate for the thio-β-lactam studied is unstable, so the compound evolves directly to the corresponding thio-azethidin-2-one open ring with cleavage of the C-S bond. The end-products obtained bear a carbamate group, which suggests that the thio-β-lactam might be an effective inhibitor for β-lactamases.

The First Example of an Organogallium Compound Containing a Ga-Te Bond: Synthesis, Properties and Molecular Structure of ((Me3CCH2)2GaTePh)2

DTIC Science & Technology

1989-06-12

Government *This document has been approved for public release and sale ; its distribution is unlimited S v r DL/1113/89/1 TECHNICAL REPORT DISTRIBUTION LIST...thermal parameter defined as (4/3) (a2B(1,1) + b2B (2,2) + c 2B(3,3) + ab(cos Y)B(1,2) + ac(cos B)B(1,3) + bc(cos a)B(2,3)]. -16- Captions for Figures

Solid-state NMR/NQR and first-principles study of two niobium halide cluster compounds.

PubMed

Perić, Berislav; Gautier, Régis; Pickard, Chris J; Bosiočić, Marko; Grbić, Mihael S; Požek, Miroslav

2014-01-01

Two hexanuclear niobium halide cluster compounds with a [Nb6X12](2+) (X=Cl, Br) diamagnetic cluster core, have been studied by a combination of experimental solid-state NMR/NQR techniques and PAW/GIPAW calculations. For niobium sites the NMR parameters were determined by using variable Bo field static broadband NMR measurements and additional NQR measurements. It was found that they possess large positive chemical shifts, contrary to majority of niobium compounds studied so far by solid-state NMR, but in accordance with chemical shifts of (95)Mo nuclei in structurally related compounds containing [Mo6Br8](4+) cluster cores. Experimentally determined δiso((93)Nb) values are in the range from 2,400 to 3,000 ppm. A detailed analysis of geometrical relations between computed electric field gradient (EFG) and chemical shift (CS) tensors with respect to structural features of cluster units was carried out. These tensors on niobium sites are almost axially symmetric with parallel orientation of the largest EFG and the smallest CS principal axes (Vzz and δ33) coinciding with the molecular four-fold axis of the [Nb6X12](2+) unit. Bridging halogen sites are characterized by large asymmetry of EFG and CS tensors, the largest EFG principal axis (Vzz) is perpendicular to the X-Nb bonds, while intermediate EFG principal axis (Vyy) and the largest CS principal axis (δ11) are oriented in the radial direction with respect to the center of the cluster unit. For more symmetrical bromide compound the PAW predictions for EFG parameters are in better correspondence with the NMR/NQR measurements than in the less symmetrical chlorine compound. Theoretically predicted NMR parameters of bridging halogen sites were checked by (79/81)Br NQR and (35)Cl solid-state NMR measurements. Copyright © 2014 Elsevier Inc. All rights reserved.

Discovering chemistry with an ab initio nanoreactor

DOE PAGES

Wang, Lee-Ping; Titov, Alexey; McGibbon, Robert; ...

2014-11-02

Chemical understanding is driven by the experimental discovery of new compounds and reactivity, and is supported by theory and computation that provides detailed physical insight. While theoretical and computational studies have generally focused on specific processes or mechanistic hypotheses, recent methodological and computational advances harken the advent of their principal role in discovery. Here we report the development and application of the ab initio nanoreactor – a highly accelerated, first-principles molecular dynamics simulation of chemical reactions that discovers new molecules and mechanisms without preordained reaction coordinates or elementary steps. Using the nanoreactor we show new pathways for glycine synthesis frommore » primitive compounds proposed to exist on the early Earth, providing new insight into the classic Urey-Miller experiment. Ultimately, these results highlight the emergence of theoretical and computational chemistry as a tool for discovery in addition to its traditional role of interpreting experimental findings.« less

Discovering chemistry with an ab initio nanoreactor

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

Wang, Lee-Ping; Titov, Alexey; McGibbon, Robert

Chemical understanding is driven by the experimental discovery of new compounds and reactivity, and is supported by theory and computation that provides detailed physical insight. While theoretical and computational studies have generally focused on specific processes or mechanistic hypotheses, recent methodological and computational advances harken the advent of their principal role in discovery. Here we report the development and application of the ab initio nanoreactor – a highly accelerated, first-principles molecular dynamics simulation of chemical reactions that discovers new molecules and mechanisms without preordained reaction coordinates or elementary steps. Using the nanoreactor we show new pathways for glycine synthesis frommore » primitive compounds proposed to exist on the early Earth, providing new insight into the classic Urey-Miller experiment. Ultimately, these results highlight the emergence of theoretical and computational chemistry as a tool for discovery in addition to its traditional role of interpreting experimental findings.« less

Conformational analysis of a trihydroxylated derivative of cinnamic acid—a combined Raman spectroscopy and Ab initio study

NASA Astrophysics Data System (ADS)

Fiuza, S. M.; Van Besien, E.; Milhazes, N.; Borges, F.; Marques, M. P. M.

2004-05-01

A conformational analysis of 3-(3,4,5-trihydroxyphenyl)-2-propenoic acid (3,4,5-trihydroxycinnamic acid, THPPE), a trihydroxylated cinnamic acid analogous to caffeic acid (a natural compound often present in diet), was carried out by Raman spectroscopy coupled to Ab initio MO calculations. Apart from the optimised geometrical parameters for the most stable conformers of this compound, and for one of its dimeric species, the corresponding harmonic vibrational frequencies, as well as potential-energy profiles for rotation around several bonds within the molecule, were obtained. Twenty one distinct conformers were found for THPPE, the lowest energy ones—THPPE 1 and THPPE 2—displaying a completely planar geometry. The conformational preferences of this system were thus found to be mainly ruled by the stabilising effect of π-electron delocalisation. At the light of these results, a complete assignment of the corresponding solid state Raman spectra was performed.

Mean-field theory on mixed ferro-ferrimagnetic compounds with (A aB bC c) yD

NASA Astrophysics Data System (ADS)

Wei, Guo-Zhu; Xin, Zihua; Liang, Yaqiu; Zhang, Qi

2004-01-01

The magnetic properties of the mixed ferro-ferrimagnetic compounds with (A aB bC c) yD, in which A, B, C and D are four different magnetic ions and form four different sublattices, are studied by using the Ising model. And the Ising model was dealt with standard mean-field approximation. The regions of concentration in which two compensation points or one compensation point exit are given in c- a, b- c and a- b planes. The phase diagrams of the transition temperature Tc and compensation temperature Tcomp are obtained. The temperature dependences of the magnetization are also investigated. Some of the result can be used to explain the experimental work of the molecule-based ferro-ferrimagnet (Ni IIaMn IIbFe IIc) 1.5[Cr III(CN) 6]· zH 2O.

Exploration of phase transition in Th2C under pressure: An Ab-initio investigation

NASA Astrophysics Data System (ADS)

Sahoo, B. D.; Joshi, K. D.; Kaushik, T. C.

2018-05-01

With the motivation of searching for new compounds in the Th-C system, we have performed ab initio evolutionary searches for all the stable compounds in this binary system in the pressure range of 0-100 GPa. We have found previously unknown, thermodynamically stable, composition Th2C along with experimentally known ThC, ThC2 and Th2C3 phases at 0 GPa. Interestingly at pressure of 13 GPa the predicted ground state orthorhombic (SG no. 59, Pmmn) phase of Th2C transforms to trigonal (SG no. 164, P-3m1) phase. We also find the mechanical and dynamical stability of both the phases. Further, the theoretically determined equation of state has been utilized to derive various physical quantities such as zero pressure equilibrium volume, bulk modulus, and pressure derivative of bulk modulus of Pmmn phase at ambient conditions.

Investigation of electronic structure and chemical bonding of intermetallic Pd2HfIn: An ab-initio study

NASA Astrophysics Data System (ADS)

Bano, Amreen; Gaur, N. K.

2018-05-01

Ab-initio calculations are carried out to study the electronic and chemical bonding properties of Intermetallic full Heusler compound Pd2HfIn which crystallizes in F-43m structure. All calculations are performed by using density functional theory (DFT) based code Quantum Espresso. Generalized gradient approximations (GGA) of Perdew- Burke- Ernzerhof (PBE) have been adopted for exchange-correlation potential. Calculated electronic band structure reveals the metallic character of the compound. From partial density of states (PDoS), we found the presence of relatively high intensity electronic states of 4d-Pd atom at Fermi level. We have found a pseudo-gap just abouve the Fermi level and N(E) at Fermi level is observed to be 0.8 states/eV, these finding indicates the existence of superconducting character in Pd2HfIn.

Ab initio structure determination of nanocrystals of organic pharmaceutical compounds by electron diffraction at room temperature using a Timepix quantum area direct electron detector

PubMed Central

van Genderen, E.; Clabbers, M. T. B.; Das, P. P.; Stewart, A.; Nederlof, I.; Barentsen, K. C.; Portillo, Q.; Pannu, N. S.; Nicolopoulos, S.; Gruene, T.; Abrahams, J. P.

2016-01-01

Until recently, structure determination by transmission electron microscopy of beam-sensitive three-dimensional nanocrystals required electron diffraction tomography data collection at liquid-nitrogen temperature, in order to reduce radiation damage. Here it is shown that the novel Timepix detector combines a high dynamic range with a very high signal-to-noise ratio and single-electron sensitivity, enabling ab initio phasing of beam-sensitive organic compounds. Low-dose electron diffraction data (∼0.013 e− Å−2 s−1) were collected at room temperature with the rotation method. It was ascertained that the data were of sufficient quality for structure solution using direct methods using software developed for X-ray crystallography (XDS, SHELX) and for electron crystallography (ADT3D/PETS, SIR2014). PMID:26919375

Magneto-optical spectroscopy of Co{sub 2}FeSi Heusler compound

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

Veis, M., E-mail: veis@karlov.mff.cuni.cz; Beran, L.; Antos, R.

2014-05-07

Magneto-optical and electronic properties of the Co{sub 2}FeSi Heusler compound were studied by polar Kerr magneto-optical spectroscopy and ab-initio calculations. The thin-film samples were grown by dc/rf magnetron co-sputtering on MgO(100) substrates. A Cr seed layer was deposited prior to the Co{sub 2}FeSi layer to achieve its epitaxial growth. The magneto-optical spectroscopy was carried out using generalized magneto-optical ellipsometry with rotating analyzer in the photon energy range from 1.4 to 5.5 eV with an applied magnetic field of up to 1.2 T. The polar Kerr spectra showed a smooth spectral behavior up to 5.5 eV indicating nearly free charge carriers. Experimental data weremore » compared with ab-initio calculations based on density functional theory employing the full-potential linearized augmented plane wave method.« less

Effect of regulated deficit irrigation on quality parameters, carotenoids and phenolics of diverse tomato varieties (Solanum lycopersicum L.).

PubMed

Coyago-Cruz, Elena; Corell, Mireia; Stinco, Carla M; Hernanz, Dolores; Moriana, Alfonso; Meléndez-Martínez, Antonio J

2017-06-01

This study aims to evaluate the effects of regulated deficit irrigation (RDI) and of cluster position (CI: first and second cluster; CII: third and fourth cluster; CIII: fifth and sixth cluster) on fruit quality parameters, carotenoids and phenolics in tomatoes. Three common ('Tigerella', 'Palamós' and 'Byelsa') and two cherry varieties ('Lazarino' and 'Summerbrix') were studied. The results showed that the regulated deficit irrigation with reduction of 40 and 50% in the leaf water potential in common and cherry tomatoes did not affect greatly the organoleptic quality of common tomatoes and 'Summerbrix', while cherry varieties were significantly affected with the cluster position. In most case, significant changes in the levels of carotenoids were observed depending on the treatment and the cluster position in all varieties. Significant changes with the treatment and no change with the cluster position were observed in phenolic compounds. Thus, in general, increased total carotenoid levels and reduced the content of phenolic compounds were observed. Considering the significance of changes in the levels of these groups of compounds it was concluded that 'Lazarino' was more susceptible to water deficit, whereas 'Summerbrix' and 'Palamós' were more resistant. On the other hand, the organoleptic and functional quality changed with the variety. Copyright © 2017 Elsevier Ltd. All rights reserved.

Phase stability and electronic structure of UMo2Al20: A first-principles study

NASA Astrophysics Data System (ADS)

Liu, Peng-Chuang; Xian, Ya-Jiang; Wang, Xin; Zhang, Yu-Ting; Zhang, Peng-Cheng

2017-09-01

In this paper, the phase stability of UMo2Al20 was explored using cluster formula in combination with first-principles calculations. Cluster formula analysis uncovered that the compound was composed of two principal clusters, i.e. [Mo-Al12] and [U-Al16]. The electronic interactions between U, Mo and Al atoms in this compound were discussed using elastic property, Bader charges and energy-resolved local bonding analysis, as well as the electronic interactions between Mo and Al atoms in [Mo-Al12] cluster and between U and Al atoms in [U-Al16] cluster. It revealed that UMo2Al20 satisfied the mechanical stability criterion for cubic system, and exhibited near ionic bonding character with weak bonding directionality. The calculations within both standard DFT and HSE frameworks demonstrated that U and Al atoms acted as an electron donor while Mo atoms acted as electron acceptor. The intrinsic stability of UMo2Al20 mainly stemmed from the bonding states of Mo-Al bonds and Al-Al bonds in [Mo-Al12] cluster. These calculations provide a further insight on the CeCr2Al20-type ternary compounds.

Theoretical study on the spectroscopic properties of CO3(*-).nH2O clusters: extrapolation to bulk.

PubMed

Pathak, Arup K; Mukherjee, Tulsi; Maity, Dilip K

2008-10-24

Vertical detachment energies (VDE) and UV/Vis absorption spectra of hydrated carbonate radical anion clusters, CO(3)(*-).nH(2)O (n=1-8), are determined by means of ab initio electronic structure theory. The VDE values of the hydrated clusters are calculated with second-order Moller-Plesset perturbation (MP2) and coupled cluster theory using the 6-311++G(d,p) set of basis functions. The bulk VDE value of an aqueous carbonate radical anion solution is predicted to be 10.6 eV from the calculated weighted average VDE values of the CO(3)(*-).nH(2)O clusters. UV/Vis absorption spectra of the hydrated clusters are calculated by means of time-dependent density functional theory using the Becke three-parameter nonlocal exchange and the Lee-Yang-Parr nonlocal correlation functional (B3LYP). The simulated UV/Vis spectrum of the CO(3)(*-).8H(2)O cluster is in excellent agreement with the reported experimental spectrum for CO(3)(*-) (aq), obtained based on pulse radiolysis experiments.

Properties of Polyhydroxyalkanoate Granules and Bioemulsifiers from Pseudomonas sp. and Burkholderia sp. Isolates Growing on Glucose.

PubMed

Sacco, Laís Postai; Castellane, Tereza Cristina Luque; Lopes, Erica Mendes; de Macedo Lemos, Eliana Gertrudes; Alves, Lúcia Maria Carareto

2016-03-01

A Burkholderia and Pseudomonas species designated as AB4 and AS1, respectively, were isolated from soil containing decomposing straw or sugar cane bagasse collected from Brazil. This study sought to evaluate the capacities of culture media, cell-free medium, and crude lysate preparations (containing PHB inclusion bodies) from bacterial cell cultures to stabilize emulsions with several hydrophobic compounds. Four conditions showed good production of bioemulsifiers (E24 ≥ 50 %), headed by substantially cell-free media from bacterial cell cultures in which bacterial isolates from Burkholderia sp. strain AB4 and Pseudomonas sp. strain AS1 were grown. Our results revealed that the both isolates (AB4 and AS1 strains) exhibited high emulsification indices (indicating usefulness in bioremediation) and good stabilities.

Cn(n=2-4): current status

NASA Astrophysics Data System (ADS)

Varandas, A. J. C.; Rocha, C. M. R.

2018-03-01

The major aspects of the C2, C3 and C4 elemental carbon clusters are surveyed. For C2, a brief analysis of its current status is presented. Regarding C3, the most recent results obtained in our group are reviewed with emphasis on modelling its potential energy surface which is particularly complicated due to the presence of multiple conical intersections. As for C4, the most stable isomeric forms of both triplet and singlet spin states and their possible interconversion pathways are examined afresh by means of accurate ab initio calculations. The main strategies for modelling the ground triplet C4 potential are also discussed. Starting from a truncated cluster expansion and a previously reported DMBE form for C3, an approximate four-body term is calibrated from the ab initio energies. The final six-dimensional global DMBE form so obtained reproduces all known topographical aspects while providing an accurate description of the C4 linear-rhombic isomerization pathway. It is therefore commended for both spectroscopic and reaction dynamics studies. This article is part of the theme issue `Modern theoretical chemistry'.

Initial hydration processes of magnesium chloride: size-selected anion photoelectron spectroscopy and ab initio calculations.

PubMed

Feng, Gang; Liu, Cheng-Wen; Zeng, Zhen; Hou, Gao-Lei; Xu, Hong-Guang; Zheng, Wei-Jun

2017-06-14

To understand the initial hydration processes of MgCl 2 , we measured photoelectron spectra of MgCl 2 (H 2 O) n - (n = 0-6) and conducted ab initio calculations on MgCl 2 (H 2 O) n - and their neutral counterparts up to n = 7. A dramatic drop in the vertical detachment energy (VDE) was observed upon addition of the first water molecule to bare MgCl 2 - . This large variation in VDE can be associated with the charge-transfer-to-solvent (CTTS) effect occurring in the MgCl 2 (H 2 O) n - clusters, as hydration induces transfer of the excess electron of MgCl 2 - to the water molecules. Investigation of the separation of Cl - -Mg 2+ ion pair shows that, in MgCl 2 (H 2 O) n - anions, breaking of the first Mg-Cl bond occurs at n = 4, while breaking of the second Mg-Cl bond takes place at n = 6. For neutral MgCl 2 (H 2 O) n clusters, breaking of the first Mg-Cl bond starts at n = 7.

Ab initio structural and spectroscopic study of HPS{sup x} and HSP{sup x} (x = 0,+1,−1) in the gas phase

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

Yaghlane, Saida Ben; Cotton, C. Eric; Francisco, Joseph S., E-mail: francisc@purdue.edu, E-mail: hochlaf@univ-mlv.fr

2013-11-07

Accurate ab initio computations of structural and spectroscopic parameters for the HPS/HSP molecules and corresponding cations and anions have been performed. For the electronic structure computations, standard and explicitly correlated coupled cluster techniques in conjunction with large basis sets have been adopted. In particular, we present equilibrium geometries, rotational constants, harmonic vibrational frequencies, adiabatic ionization energies, electron affinities, and, for the neutral species, singlet-triplet relative energies. Besides, the full-dimensional potential energy surfaces (PESs) for HPS{sup x} and HSP{sup x} (x = −1,0,1) systems have been generated at the standard coupled cluster level with a basis set of augmented quintuple-zeta quality.more » By applying perturbation theory to the calculated PESs, an extended set of spectroscopic constants, including τ, first-order centrifugal distortion and anharmonic vibrational constants has been obtained. In addition, the potentials have been used in a variational approach to deduce the whole pattern of vibrational levels up to 4000 cm{sup −1} above the minima of the corresponding PESs.« less

Wide Distribution of Foxicin Biosynthetic Gene Clusters in Streptomyces Strains – An Unusual Secondary Metabolite with Various Properties

PubMed Central

Greule, Anja; Marolt, Marija; Deubel, Denise; Peintner, Iris; Zhang, Songya; Jessen-Trefzer, Claudia; De Ford, Christian; Burschel, Sabrina; Li, Shu-Ming; Friedrich, Thorsten; Merfort, Irmgard; Lüdeke, Steffen; Bisel, Philippe; Müller, Michael; Paululat, Thomas; Bechthold, Andreas

2017-01-01

Streptomyces diastatochromogenes Tü6028 is known to produce the polyketide antibiotic polyketomycin. The deletion of the pokOIV oxygenase gene led to a non-polyketomycin-producing mutant. Instead, novel compounds were produced by the mutant, which have not been detected before in the wild type strain. Four different compounds were identified and named foxicins A–D. Foxicin A was isolated and its structure was elucidated as an unusual nitrogen-containing quinone derivative using various spectroscopic methods. Through genome mining, the foxicin biosynthetic gene cluster was identified in the draft genome sequence of S. diastatochromogenes. The cluster spans 57 kb and encodes three PKS type I modules, one NRPS module and 41 additional enzymes. A foxBII gene-inactivated mutant of S. diastatochromogenes Tü6028 ΔpokOIV is unable to produce foxicins. Homologous fox biosynthetic gene clusters were found in more than 20 additional Streptomyces strains, overall in about 2.6% of all sequenced Streptomyces genomes. However, the production of foxicin-like compounds in these strains has never been described indicating that the clusters are expressed at a very low level or are silent under fermentation conditions. Foxicin A acts as a siderophore through interacting with ferric ions. Furthermore, it is a weak inhibitor of the Escherichia coli aerobic respiratory chain and shows moderate antibiotic activity. The wide distribution of the cluster and the various properties of the compound indicate a major role of foxicins in Streptomyces strains. PMID:28270798

Ab initio Studies of Magnetism in the Iron Chalcogenides FeTe and FeSe

NASA Astrophysics Data System (ADS)

Hirayama, Motoaki; Misawa, Takahiro; Miyake, Takashi; Imada, Masatoshi

2015-09-01

The iron chalcogenides FeTe and FeSe belong to the family of iron-based superconductors. We study the magnetism in these compounds in the normal state using the ab initio downfolding scheme developed for strongly correlated electron systems. In deriving ab initio low-energy effective models, we employ the constrained GW method to eliminate the double counting of electron correlations originating from the exchange correlations already taken into account in the density functional theory. By solving the derived ab initio effective models, we reveal that the elimination of the double counting is important in reproducing the bicollinear antiferromagnetic order in FeTe, as is observed in experiments. We also show that the elimination of the double counting induces a unique degeneracy of several magnetic orders in FeSe, which may explain the absence of the magnetic ordering. We discuss the relationship between the degeneracy and the recently found puzzling phenomena in FeSe as well as the magnetic ordering found under pressure.

Under the Microscope: Single-Domain Antibodies for Live-Cell Imaging and Super-Resolution Microscopy.

PubMed

Traenkle, Bjoern; Rothbauer, Ulrich

2017-01-01

Single-domain antibodies (sdAbs) have substantially expanded the possibilities of advanced cellular imaging such as live-cell or super-resolution microscopy to visualize cellular antigens and their dynamics. In addition to their unique properties including small size, high stability, and solubility in many environments, sdAbs can be efficiently functionalized according to the needs of the respective imaging approach. Genetically encoded intrabodies fused to fluorescent proteins (chromobodies) have become versatile tools to study dynamics of endogenous proteins in living cells. Additionally, sdAbs conjugated to organic dyes were shown to label cellular structures with high density and minimal fluorophore displacement making them highly attractive probes for super-resolution microscopy. Here, we review recent advances of the chromobody technology to visualize localization and dynamics of cellular targets and the application of chromobody-based cell models for compound screening. Acknowledging the emerging importance of super-resolution microscopy in cell biology, we further discuss advantages and challenges of sdAbs for this technology.

Regional-dependent intestinal permeability and BCS classification: elucidation of pH-related complexity in rats using pseudoephedrine.

PubMed

Fairstein, Moran; Swissa, Rotem; Dahan, Arik

2013-04-01

Based on its lower Log P value relative to metoprolol, a marker for the low/high-permeability (P(eff)) class boundary, pseudoephedrine was provisionally classified as BCS low-permeability compound. On the other hand, following oral administration, pseudoephedrine fraction dose absorbed (F(abs)) and systemic bioavailability approaches 100%. This represents a challenge to the generally recognized P(eff)-F(abs) correlation. The purpose of this study was to elucidate the underlying mechanisms behind the confusion in pseudoephedrine's BCS classification. Pseudoephedrine's BCS solubility class was determined, and its physicochemical properties and intestinal permeability were thoroughly investigated, both in vitro and in vivo in rats, considering the complexity of the whole of the small intestine. Pseudoephedrine was found to be unequivocally a high-solubility compound. All of the permeability studies revealed similar phenomenon; at any given intestinal segment/pH, the permeability of metoprolol was higher than that of pseudoephedrine, however, as the intestinal region becomes progressively distal, and the pH gradually increases, pseudoephedrine's permeability rises above that of metoprolol in the former segment. This unique permeability pattern likely explains pseudoephedrine's complete absorption. In conclusion, pseudoephedrine is a BCS Class I compound; no discrepancy between P(eff) and F(abs) is involved in its absorption. Rather, it reflects the complexity behind P(eff) when considering the whole of the intestine. We propose to allow high-permeability classification to drugs with P(eff) that matches/exceeds the low/high class benchmark anywhere throughout the intestinal tract and not restricted necessarily to the jejunum.

X-Ray source populations in old open clusters: Collinder 261

NASA Astrophysics Data System (ADS)

Vats, Smriti; van den Berg, Maureen; Wijnands, Rudy

2014-09-01

We are carrying out an X-ray survey of old open clusters with the Chandra X-ray Observatory. Single old stars, being slow rotators, are very faint in X-rays (L_X < 1×10^27 erg/s). Hence, X-rays produced by mass transfer in cataclysmic variables (CVs) or by rapid rotation of the stars in tidally locked, detached binaries (active binaries; ABs) can be detected, without contamination from single stars. By comparing the properties of various types of interacting binaries in different environments (the Galactic field, old open clusters, globular clusters), we aim to study binary evolution and how it may be affected by dynamical encounters with other cluster stars. Stellar clusters are good targets to study binaries, as age, distance, chemical composition, are well constrained. Collinder (Cr) 261 is an old open cluster (age ~ 7 Gyr), with one of the richest populations inferred of close binaries and blue stragglers of all open clusters and is therefore an obvious target to study the products of close encounters in open clusters. We will present the first results of this study, detailing the low-luminosity X-ray population of Cr 261, in conjunction with other open clusters in our survey (NGC 188, Berkeley 17, NGC 6253, M67, NGC 6791) and in comparison with populations in globular clusters.

Ligand combination strategy for the preparation of novel low-dimensional and open-framework metal cluster materials

NASA Astrophysics Data System (ADS)

Anokhina, Ekaterina V.

Low-dimensional and open-framework materials containing transition metals have a wide range of applications in redox catalysis, solid-state batteries, and electronic and magnetic devices. This dissertation reports on research carried out with the goal to develop a strategy for the preparation of low-dimensional and open-framework materials using octahedral metal clusters as building blocks. Our approach takes its roots from crystal engineering principles where the desired framework topologies are achieved through building block design. The key idea of this work is to induce directional bonding preferences in the cluster units using a combination of ligands with a large difference in charge density. This investigation led to the preparation and characterization of a new family of niobium oxychloride cluster compounds with original structure types exhibiting 1ow-dimensional or open-framework character. Most of these materials have framework topologies unprecedented in compounds containing octahedral clusters. Comparative analysis of their structural features indicates that the novel cluster connectivity patterns in these systems are the result of complex interplay between the effects of anisotropic ligand arrangement in the cluster unit and optimization of ligand-counterion electrostatic interactions. The important role played by these factors sets niobium oxychloride systems apart from cluster compounds with one ligand type or statistical ligand distribution where the main structure-determining factor is the total number of ligands. These results provide a blueprint for expanding the ligand combination strategy to other transition metal cluster systems and for the future rational design of cluster-based materials.

Semiconductor nanocrystals covalently bound to solid inorganic surfaces using self-assembled monolayers

DOEpatents

Alivisatos, A.P.; Colvin, V.L.

1998-05-12

Methods are described for attaching semiconductor nanocrystals to solid inorganic surfaces, using self-assembled bifunctional organic monolayers as bridge compounds. Two different techniques are presented. One relies on the formation of self-assembled monolayers on these surfaces. When exposed to solutions of nanocrystals, these bridge compounds bind the crystals and anchor them to the surface. The second technique attaches nanocrystals already coated with bridge compounds to the surfaces. Analyses indicate the presence of quantum confined clusters on the surfaces at the nanolayer level. These materials allow electron spectroscopies to be completed on condensed phase clusters, and represent a first step towards synthesis of an organized assembly of clusters. These new products are also disclosed. 10 figs.

A method for topological analysis of high nuclearity coordination clusters and its application to Mn coordination compounds.

PubMed

Kostakis, George E; Blatov, Vladislav A; Proserpio, Davide M

2012-04-21

A novel method for the topological description of high nuclearity coordination clusters (CCs) was improved and applied to all compounds containing only manganese as a metal center, the data on which are collected in the CCDC (CCDC 5.33 Nov. 2011). Using the TOPOS program package that supports this method, we identified 539 CCs with five or more Mn centers adopting 159 topologically different graphs. In the present database all the Mn CCs are collected and illustrated in such a way that can be searched by cluster topological symbol and nuclearity, compound name and Refcode. The main principles for such an analysis are described herein as well as useful applications of this method.

Polymer-coated nanoparticles: Carrier platforms for hydrophobic water- and air-sensitive metallo-organic compounds.

PubMed

Valdeperez, Daniel; Wang, Tianqiang; Eußner, Jens P; Weinert, Bastian; Hao, Jianyuan; Parak, Wolfgang J; Dehnen, Stefanie; Pelaz, Beatriz

2017-03-01

Many of the relevant compounds for anticancer therapy are metal-based compounds (metallodrugs), being platinum-based drugs such as cisplatin, carboplatin (Paraplatin ® ), and oxaliplatin (Eloxatin ® ) the most widely used. Despite this, their application is limited by issues such as cell-acquired platinum resistance and manifold side effects following systemic delivery. Thus, the development of new metal-based compounds is highly needed. The catalytic properties of a variety of metal-based compounds are nowadays very well known, which opens new opportunities to take advantage of them inside living cells or organisms. However, many of these compounds are hydrophobic and thus not soluble in aqueous solution, as they lack stability against water or oxygen presence. Thus, versatile platforms capable of enhancing the features of these compounds in aqueous solutions are of importance in the development of new drugs. Surface engineered nanoparticles may render metallodrugs with good colloidal stability in water and in complex media containing high salt concentration and/or proteins. Herein, polymer coated nanoparticles are proposed as a platform to link insoluble and water/oxygen sensitive drugs. The linkage of insoluble and oxygen sensitive tin clusters to nanoparticles is presented, aiming to enhance both, the solubility and the stability of these compounds in water, which may be an alternative approach in the development of metal-based drugs. The formation of the cluster-nanoparticle system was confirmed via inductively coupled plasma mass spectrometry experiments. The catalytic activity and the stability of the cluster in water were studied through the reduction of methylene blue. Results demonstrate that in fact the tin clusters could be transferred into aqueous solution and retained their catalytic activity. Copyright © 2016 Elsevier Ltd. All rights reserved.

High-Level ab initio electronic structure calculations of Water Clusters (H2O)16 and (H2O)17: a new global minimum for (H2O)16

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

Yoo, Soohaeng; Apra, Edoardo; Zeng, Xiao Cheng

The lowest-energy structures of water clusters (H2O)16 and (H2O)17 were revisited at the MP2 and CCSD(T) levels of theory. A new global minimum structure for (H2O)16 was found at the MP2 and CCSD(T) levels of theory and the effect of zero-point energy corrections on the relative stability of the low-lying minimum energy structures was assessed. For (H2O)17 the CCSD(T) calculations confirm the previously found at the MP2 level of theory "interior" arrangement (fully coordinated water molecule inside a spherical cluster) as the global minimum.

High-Level ab-initio Electronic Structure Calculations of Water Clusters (H2O)16 and (H2O)17 : a New Global Minimum for (H2O)16

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

Yoo, Soohaeng; Apra, Edoardo; Zeng, X.C.

The lowest-energy structures of water clusters (H2O)16 and (H2O)17 were revisited at the MP2 and CCSD(T) levels of theory. A new global minimum structure for (H2O)16 was found at both the MP2 and CCSD(T) levels of theory, and the effect of zero-point energy corrections on the relative stability of the low-lying minimum energy structures was assessed. For (H2O)17, the CCSD(T) calculations confirm the previously found at the MP2 level of theory interior arrangement (fully coordinated water molecule inside a spherical cluster) as the global minimum

A Hundred-Year-Old Experiment Re-evaluated: Accurate Ab-Initio Monte-Carlo Simulations of the Melting of Radon.

PubMed

Schwerdtfeger, Peter; Smits, Odile; Pahl, Elke; Jerabek, Paul

2018-06-12

State-of-the-art relativistic coupled-cluster theory is used to construct many-body potentials for the rare gas element radon in order to determine its bulk properties including the solid-to-liquid phase transition from parallel tempering Monte Carlo simulations through either direct sampling of the bulk or from a finite cluster approach. The calculated melting temperature are 201(3) K and 201(6) K from bulk simulations and from extrapolation of finite cluster values, respectively. This is in excellent agreement with the often debated (but widely cited) and only available value of 202 K, dating back to measurements by Gray and Ramsay in 1909. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Correlation study of sodium-atom chemisorption on the GaAs(110) surface

NASA Astrophysics Data System (ADS)

Song, K. M.; Khan, D. C.; Ray, A. K.

1994-01-01

Different possible adsorption sites of sodium atoms on a gallium arsenide surface have been investigated using ab initio self-consistent unrestricted Hartree-Fock total-energy cluster calculations with Hay-Wadt effective core potentials. The effects of electron correlation have been included by invoking the concepts of many-body perturbation theory and are found to be highly significant. We find that the Na-atom adsorption at a site modeled with an NaGa5As4H12 cluster is most favored energetically followed by Na adsorption at the site modeled with the NaGa4As5H12 cluster. The effects of charge transfer from Na to the GaAs surface as also possibilities of metallization are also analyzed and discussed.

Applying the Coupled-Cluster Ansatz to Solids and Surfaces in the Thermodynamic Limit

NASA Astrophysics Data System (ADS)

Gruber, Thomas; Liao, Ke; Tsatsoulis, Theodoros; Hummel, Felix; Grüneis, Andreas

2018-04-01

Modern electronic structure theories can predict and simulate a wealth of phenomena in surface science and solid-state physics. In order to allow for a direct comparison with experiment, such ab initio predictions have to be made in the thermodynamic limit, substantially increasing the computational cost of many-electron wave-function theories. Here, we present a method that achieves thermodynamic limit results for solids and surfaces using the "gold standard" coupled cluster ansatz of quantum chemistry with unprecedented efficiency. We study the energy difference between carbon diamond and graphite crystals, adsorption energies of water on h -BN, as well as the cohesive energy of the Ne solid, demonstrating the increased efficiency and accuracy of coupled cluster theory for solids and surfaces.

Type A-B carbonate chlorapatite synthesized at high pressure

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

Fleet, Michael E.; Liu, Xi

2008-09-15

Sodium-bearing type A-B carbonate chlorapatites {l_brace}CCLAP; Ca{sub 10-(y+z)}Na{sub y}{open_square}{sub z}[(PO{sub 4}){sub 6-(y+2z)}(CO{sub 3}){sub y+2z}][Cl{sub 2-=} 2{sub x}(CO{sub 3}){sub x}], with x{approx}y{approx}4z{approx}0.4{r_brace} have been synthesized from carbonate-rich melts at 1350-1000 deg. C and 1.0 GPa, and investigated by single-crystal X-ray structure and FTIR spectroscopy. Typical crystal and compositional data are: a=9.5321(4) A, c=6.8448(3) A, space group P6{sub 3}/m, R=0.027, R{sub w}=0.025, x=0.37(3), y=0.57(2). Crystal-chemical features and FTIR spectra are similar to Na-bearing type A-B carbonate hydroxyapatites (CHAP) and fluorapatites (CFAP) reported recently. The molar amounts of Na and channel (type A) carbonate maintain a near 1:1 ratio in all three compositionmore » series, confirming that the Na cation and A and B carbonate ion substituents exist as a defect cluster within the apatite matrix, to facilitate charge compensation and spatial accommodation. Uptake of carbonate is significantly lower in CCLAP than in CHAP for similar conditions of crystal synthesis. - Graphical abstract: Defect cluster (blue) of A carbonate ion in apatite channel, Na{sup +} cation, and B carbonate ion replacing phosphate group, in carbonate chlorapatite synthesized at high pressure.« less

Emergent properties of nuclei from ab initio coupled-cluster calculations

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

Hagen, G.; Hjorth-Jensen, M.; Jansen, G. R.

Emergent properties such as nuclear saturation and deformation, and the effects on shell structure due to the proximity of the scattering continuum and particle decay channels are fascinating phenomena in atomic nuclei. In recent years, ab initio approaches to nuclei have taken the first steps towards tackling the computational challenge of describing these phenomena from Hamiltonians with microscopic degrees of freedom. Our endeavor is now possible due to ideas from effective field theories, novel optimization strategies for nuclear interactions, ab initio methods exhibiting a soft scaling with mass number, and ever-increasing computational power. We review some of the recent accomplishments. We also present new results. The recently optimized chiral interaction NNLOmore » $${}_{{\\rm{sat}}}$$ is shown to provide an accurate description of both charge radii and binding energies in selected light- and medium-mass nuclei up to 56Ni. We derive an efficient scheme for including continuum effects in coupled-cluster computations of nuclei based on chiral nucleon–nucleon and three-nucleon forces, and present new results for unbound states in the neutron-rich isotopes of oxygen and calcium. Finally, the coupling to the continuum impacts the energies of the $${J}^{\\pi }=1/{2}^{-},3/{2}^{-},7/{2}^{-},3/{2}^{+}$$ states in $${}^{\\mathrm{17,23,25}}$$O, and—contrary to naive shell-model expectations—the level ordering of the $${J}^{\\pi }=3/{2}^{+},5/{2}^{+},9/{2}^{+}$$ states in $${}^{\\mathrm{53,55,61}}$$Ca.« less

Emergent properties of nuclei from ab initio coupled-cluster calculations

DOE PAGES

Hagen, G.; Hjorth-Jensen, M.; Jansen, G. R.; ...

2016-05-17

Emergent properties such as nuclear saturation and deformation, and the effects on shell structure due to the proximity of the scattering continuum and particle decay channels are fascinating phenomena in atomic nuclei. In recent years, ab initio approaches to nuclei have taken the first steps towards tackling the computational challenge of describing these phenomena from Hamiltonians with microscopic degrees of freedom. Our endeavor is now possible due to ideas from effective field theories, novel optimization strategies for nuclear interactions, ab initio methods exhibiting a soft scaling with mass number, and ever-increasing computational power. We review some of the recent accomplishments. We also present new results. The recently optimized chiral interaction NNLOmore » $${}_{{\\rm{sat}}}$$ is shown to provide an accurate description of both charge radii and binding energies in selected light- and medium-mass nuclei up to 56Ni. We derive an efficient scheme for including continuum effects in coupled-cluster computations of nuclei based on chiral nucleon–nucleon and three-nucleon forces, and present new results for unbound states in the neutron-rich isotopes of oxygen and calcium. Finally, the coupling to the continuum impacts the energies of the $${J}^{\\pi }=1/{2}^{-},3/{2}^{-},7/{2}^{-},3/{2}^{+}$$ states in $${}^{\\mathrm{17,23,25}}$$O, and—contrary to naive shell-model expectations—the level ordering of the $${J}^{\\pi }=3/{2}^{+},5/{2}^{+},9/{2}^{+}$$ states in $${}^{\\mathrm{53,55,61}}$$Ca.« less

Solvent induced conformational fluctuation of alanine dipeptide studied by using vibrational probes

NASA Astrophysics Data System (ADS)

Cai, Kaicong; Du, Fenfen; Liu, Jia; Su, Tingting

2015-02-01

The solvation effect on the three dimensional structure and the vibrational feature of alanine dipeptide (ALAD) was evaluated by applying the implicit solvents from polarizable continuum solvent model (PCM) through ab initio calculations, by using molecular dynamic (MD) simulations with explicit solvents, and by combining these two approaches. The implicit solvent induced potential energy fluctuations of ALAD in CHCl3, DMSO and H2O are revealed by means of ab initio calculations, and a global view of conformational and solvation environmental dependence of amide I frequencies is achieved. The results from MD simulations with explicit solvents show that ALAD trends to form PPII, αL, αR, and C5 in water, PPII and C5 in DMSO, and C5 in CHCl3, ordered by population, and the demonstration of the solvated structure, the solute-solvent interaction and hydrogen bonding is therefore enhanced. Representative ALAD-solvent clusters were sampled from MD trajectories and undergone ab initio calculations. The explicit solvents reveal the hydrogen bonding between ALAD and solvents, and the correlation between amide I frequencies and the Cdbnd O bond length is built. The implicit solvents applied to the ALAD-solvent clusters further compensate the solvation effect from the bulk, and thus enlarge the degree of structural distortion and the amide I frequency red shift. The combination of explicit solvent in the first hydration shell and implicit solvent in the bulk is helpful for our understanding about the conformational fluctuation of solvated polypeptides through vibrational probes.

Lithium formate ion clusters formation during electrospray ionization: Evidence of magic number clusters by mass spectrometry and ab initio calculations

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

Shukla, Anil; Bogdanov, Bogdan

2015-02-14

Small cationic and anionic clusters of lithium formate were generated by electrospray ionization and their fragmentations were studied by tandem mass spectrometry. Singly as well as multiply charged clusters were formed with the general formulae, (HCOOLi)nLi+, (HCOOLi)nLimm+, (HCOOLi)nHCOO- and (HCOOLi)n(HCOO)mm-. Several magic number cluster ions were observed in both the positive and negative ion modes although more predominant in the positive ion mode with (HCOOLi)3Li+ being the most abundant and stable cluster ions. Fragmentations of singly charged clusters proceed first by the loss of a dimer unit ((HCOOLi)2) followed by sequential loss of monomer units (HCOOLi). In the case ofmore » positive cluster ions, all fragmentations lead to the magic cluster (HCOOLi)3Li+ at higher collision energies which later fragments to dimer and monomer ions in lower abundance. Quantum mechanical calculations performed for smaller cluster ions showed that the trimer ion has a closed ring structure similar to the phenalenylium structure with three closed rings connected to the lithium ion. Further additions of monomer units result in similar symmetric structures for hexamer and nonamer cluster ions. Thermochemical calculations show that trimer cluster ion is relatively more stable than neighboring cluster ions, supporting the experimental observation of a magic number cluster with enhanced stability.« less

Adhesion between liposomes mediated by the chlorophyll a/b light- harvesting complex isolated from chloroplast membranes

PubMed Central

1980-01-01

A highly purified chlorophyll a/b light-harvesting complex (chl a/b LHC; chl a/b ratio 1.2) was obtained from Triton-solubilized chloroplast membranes of pea and barley according to the method of Burke et al. (1978, Arch. Biochem. Biophys. 187: 252--263). Gel electrophoresis of the cation-precipitated chl a/b LHC from peas reveals the presence of four polypeptides in the 23- to 28-kdalton size range. Three of these peptides appear to be identical to those derived from re-electrophoresed CPII and CPII* bands. In freeze-fracture replicas, the cation-precipitated chl a/b LHC appears as a semicrystalline aggregate of membranous sheets containing closely spaced granules. Upon removal of the cations by dialysis, the aggregates break up into their constituent membranous sheets without changing their granular substructure. These membranous sheets can be resolubilized in 1.5% Triton X-100, and the chl a/b LHC particles then reconstituted into soybean lecithin liposomes. Freeze-fracture micrographs of the reconstituted chl a/b LHC vesicles suspended in a low salt medium reveal randomly dispersed approximately 80-A particles on both concave and convex fracture faces as well as some crystalline particle arrays, presumably resulting from incompletely solubilized fragments of the membranous sheets. Based on the approximately 80-A diameter of the particles, and on the assumption that one freeze- fracture particle represents the structural unit of one chl a/b LHC aggregate, a theoretical mol wt of approximately 200 kdalton has been calculated for the chl a/b LHC. Deep-etching and negative-staining techniques reveal that the chl a/b LHC particles are also exposed on the surface of the bilayer membranes. Addition of greater than or equal to 2 mM MgCl2 or greater than or equal to 60 mM NaCl to the reconstituted vesicles leads to their aggregation and, with divalent cations, to the formation of extensive membrane stacks. At the same time, the chl a/b LHC particles become clustered into the adhering membrane regions. Under these conditions the particles in adjacent membranes usually become precisely aligned. Evidence is presented to aupport the hypothesis that adhesion between the chl a/b LHC particles is mediated by hydrophobic interactions, and that the cations are needed to neutralize surface charges on the particles. PMID:7350170

Electronic structure of shandite Co3Sn2S2

NASA Astrophysics Data System (ADS)

Dedkov, Y. S.; Holder, M.; Molodtsov, S. L.; Rosner, H.

2008-03-01

The electronic structure of shandite Co3Sn2S2 was determined by photoelectron spectroscopy and compared with ab initio band structure calculations. Presented results give evidence that this compound has half-metallic ferromagnetic properties.

Study on structures and properties of ammonia clusters (NH3)n (n=1-5) and liquid ammonia in terms of ab initio method and atom-bond electronegativity equalization method ammonia-8P fluctuating charge potential model.

PubMed

Yu, Ling; Yang, Zhong-Zhi

2010-05-07

Structures, binding energies, and vibrational frequencies of (NH(3))(n) (n=2-5) isomers and dynamical properties of liquid ammonia have been explored using a transferable intermolecular potential eight point model including fluctuating charges and flexible body based on a combination of the atom-bond electronegativity equalization and molecular (ABEEM) mechanics (ABEEM ammonia-8P) in this paper. The important feature of this model is to divide the charge sites of one ammonia molecule into eight points region containing four atoms, three sigma bonds, and a lone pair, and allows the charges in system to fluctuate responding to the ambient environment. Due to the explicit descriptions of charges and special treatment of hydrogen bonds, the results of equilibrium geometries, dipole moments, cluster interaction energies, vibrational frequencies for the gas phase of small ammonia clusters, and radial distribution function for liquid ammonia calculated with the ABEEM ammonia-8P potential model are in good agreement with those measured by available experiments and those obtained from high level ab initio calculations. The properties of ammonia dimer are studied in detail involving the structure and one-dimensional, two-dimensional potential energy surface. As for interaction energies, the root mean square deviation is 0.27 kcal/mol, and the linear correlation coefficient reaches 0.994.

Are polynuclear superhalogens without halogen atoms probable? A high-level ab initio case study on triple-bridged binuclear anions with cyanide ligands

NASA Astrophysics Data System (ADS)

Yin, Bing; Li, Teng; Li, Jin-Feng; Yu, Yang; Li, Jian-Li; Wen, Zhen-Yi; Jiang, Zhen-Yi

2014-03-01

The first theoretical exploration of superhalogen properties of polynuclear structures based on pseudohalogen ligand is reported here via a case study on eight triply-bridged [Mg2(CN)5]- clusters. From our high-level ab initio results, all these clusters are superhalogens due to their high vertical electron detachment energies (VDE), of which the largest value is 8.67 eV at coupled-cluster single double triple (CCSD(T)) level. Although outer valence Green's function results are consistent with CCSD(T) in most cases, it overestimates the VDEs of three anions dramatically by more than 1 eV. Therefore, the combined usage of several theoretical methods is important for the accuracy of purely theoretical prediction of superhalogen properties of new structures. Spatial distribution of the extra electron of high-VDE anions here indicates two features: remarkable aggregation on bridging CN units and non-negligible distribution on every CN unit. These two features lower the potential and kinetic energies of the extra electron respectively and thus lead to high VDE. Besides superhalogen properties, the structures, relative stabilities and thermodynamic stabilities with respect to detachment of CN-1 were also investigated for these anions. The collection of these results indicates that polynuclear structures based on pseudohalogen ligand are promising candidates for new superhalogens with enhanced properties.

Are polynuclear superhalogens without halogen atoms probable? A high-level ab initio case study on triple-bridged binuclear anions with cyanide ligands.

PubMed

Yin, Bing; Li, Teng; Li, Jin-Feng; Yu, Yang; Li, Jian-Li; Wen, Zhen-Yi; Jiang, Zhen-Yi

2014-03-07

The first theoretical exploration of superhalogen properties of polynuclear structures based on pseudohalogen ligand is reported here via a case study on eight triply-bridged [Mg2(CN)5](-) clusters. From our high-level ab initio results, all these clusters are superhalogens due to their high vertical electron detachment energies (VDE), of which the largest value is 8.67 eV at coupled-cluster single double triple (CCSD(T)) level. Although outer valence Green's function results are consistent with CCSD(T) in most cases, it overestimates the VDEs of three anions dramatically by more than 1 eV. Therefore, the combined usage of several theoretical methods is important for the accuracy of purely theoretical prediction of superhalogen properties of new structures. Spatial distribution of the extra electron of high-VDE anions here indicates two features: remarkable aggregation on bridging CN units and non-negligible distribution on every CN unit. These two features lower the potential and kinetic energies of the extra electron respectively and thus lead to high VDE. Besides superhalogen properties, the structures, relative stabilities and thermodynamic stabilities with respect to detachment of CN(-1) were also investigated for these anions. The collection of these results indicates that polynuclear structures based on pseudohalogen ligand are promising candidates for new superhalogens with enhanced properties.

In vitro screening of organotin compounds and sediment extracts for cytotoxicity to fish cells.

PubMed

Giltrap, Michelle; Macken, Ailbhe; McHugh, Brendan; McGovern, Evin; Foley, Barry; Davoren, Maria

2011-01-01

The present study reports an in vitro screening method for contaminants in sediment samples utilizing an RTG-2 cell line. This technique integrates cytotoxicity testing with analytical chemistry with the aim of achieving a toxicity evaluation of the sediment sample. The toxic effect of individual organotin (OT) compounds and their presence in the sediment sample is the focus of the present study; however, other contaminants are also discussed. The following OT compounds: tributyltin (TBT), dibutyltin (DBT), monobutyltin (MBT), triphenyltin (TPT), diphenyltin (DPT), and a sediment solvent extract are exposed to the RTG-2 fish cell line. Both the alamar blue (AB) and neutral red (NR) assays are used to assess cytotoxicity after 24-h and 96-h exposure. Methodology for preparation of a sediment solvent extract suitable for biological testing and analytical determination is also described. With the RTG-2 cells, the AB and NR assays had comparable sensitivity for each individual OT compound exposure after 24 h, with TPT being the most toxic compound tested. The individual OT compound concentrations required to induce a 50% toxic effect on the cells (369 ng ml⁻¹ TBT, 1,905 ng ml⁻¹ DBT) did not equate to the concentrations of these contaminants present in the sediment extract that induced a 50% effect on the cells (294 ng ml⁻¹ TBT, 109 ng ml⁻¹ DBT). The solvent extract therefore exhibited a greater toxicity, and this suggests that the toxic effects observed were not due to OT compounds alone. The presence of other contaminants in the solvent extract is confirmed with chemical analysis, warranting further toxicity testing of contaminant mixtures and exposure to the cell line to further elucidate a complete toxicity evaluation. © 2010 SETAC.

Chemical oxidation of a malodorous compound, indole, using iron entrapped in calcium alginate beads.

PubMed

Ben Hammouda, Samia; Adhoum, Nafaâ; Monser, Lotfi

2016-01-15

Iron-alginate beads (Fe-ABs) were successfully prepared by the ion-gelation method, and applied as heterogeneous Fenton catalysts for the removal of a malodorous compound 'indole'. Similarly, copper-enriched alginate beads (Cu-ABs) were synthesized and tested as like-Fenton catalyst, however, their application proved not to be effective for this purpose. Fe-ABs catalysts were characterized by FTIR, SEM, EDS and AAS spectroscopy. Results pointed out that the parameters affecting Fenton catalysis must be carefully chosen to avoid excessive iron release. Under optimal conditions, complete indole removal and considerably high reduction of TOC, without significant leaching was achieved. Indole decay followed a pseudo-first-order kinetics. The absolute rate constant for indole hydroxylation was 3.59×10(9) M(-1) s(-1), as determined by the competition kinetics method. Four reaction intermediates (Isatin, Dioxindole, Oxindole and Anthralinic acid) were identified by ULC/MS/MS analysis. Short-chain aliphatic carboxylic acids like formic, acetic, oxalic, maleic, oxamic and pyruvic acids were identified by ion exclusion chromatography and as end-products. Based on the identified by-products, a plausible mineralization pathway was proposed. Moreover, the catalyst was recovered quantitatively by simple filtration and reused for several times without significant loss of activity. Copyright © 2015 Elsevier B.V. All rights reserved.

Developability assessment of clinical drug products with maximum absorbable doses.

PubMed

Ding, Xuan; Rose, John P; Van Gelder, Jan

2012-05-10

Maximum absorbable dose refers to the maximum amount of an orally administered drug that can be absorbed in the gastrointestinal tract. Maximum absorbable dose, or D(abs), has proved to be an important parameter for quantifying the absorption potential of drug candidates. The purpose of this work is to validate the use of D(abs) in a developability assessment context, and to establish appropriate protocol and interpretation criteria for this application. Three methods for calculating D(abs) were compared by assessing how well the methods predicted the absorption limit for a set of real clinical candidates. D(abs) was calculated for these clinical candidates by means of a simple equation and two computer simulation programs, GastroPlus and an program developed at Eli Lilly and Company. Results from single dose escalation studies in Phase I clinical trials were analyzed to identify the maximum absorbable doses for these compounds. Compared to the clinical results, the equation and both simulation programs provide conservative estimates of D(abs), but in general D(abs) from the computer simulations are more accurate, which may find obvious advantage for the simulations in developability assessment. Computer simulations also revealed the complex behavior associated with absorption saturation and suggested in most cases that the D(abs) limit is not likely to be achieved in a typical clinical dose range. On the basis of the validation findings, an approach is proposed for assessing absorption potential, and best practices are discussed for the use of D(abs) estimates to inform clinical formulation development strategies. Copyright © 2012 Elsevier B.V. All rights reserved.

Importance of Real-Time Assays To Distinguish Multidrug Efflux Pump-Inhibiting and Outer Membrane-Destabilizing Activities in Escherichia coli.

PubMed

Misra, Rajeev; Morrison, Keith D; Cho, Hyun Jae; Khuu, Thanh

2015-08-01

The constitutively expressed AcrAB multidrug efflux system of Escherichia coli shows a high degree of homology with the normally silent AcrEF system. Exposure of a strain with acrAB deleted to antibiotic selection pressure frequently leads to the insertion sequence-mediated activation of the homologous AcrEF system. In this study, we used strains constitutively expressing either AcrAB or AcrEF from their normal chromosomal locations to resolve a controversy about whether phenylalanylarginine β-naphthylamide (PAβN) inhibits the activities of AcrAB and AcrEF and/or acts synergistically with antibiotics by destabilizing the outer membrane permeability barrier. Real-time efflux assays allowed a clear distinction between the efflux pump-inhibiting activity of PAβN and the outer membrane-destabilizing action of polymyxin B nonapeptide (PMXBN). When added in equal amounts, PAβN, but not PMXBN, strongly inhibited the efflux activities of both AcrAB and AcrEF pumps. In contrast, when outer membrane destabilization was assessed by the nitrocefin hydrolysis assay, PMXBN exerted a much greater damaging effect than PAβN. Strong action of PAβN in inhibiting efflux activity compared to its weak action in destabilizing the outer membrane permeability barrier suggests that PAβN acts mainly by inhibiting efflux pumps. We concluded that at low concentrations, PAβN acts specifically as an inhibitor of both AcrAB and AcrEF efflux pumps; however, at high concentrations, PAβN in the efflux-proficient background not only inhibits efflux pump activity but also destabilizes the membrane. The effects of PAβN on membrane integrity are compounded in cells unable to extrude PAβN. The increase in multidrug-resistant bacterial pathogens at an alarming rate has accelerated the need for implementation of better antimicrobial stewardship, discovery of new antibiotics, and deeper understanding of the mechanism of drug resistance. The work carried out in this study highlights the importance of employing real-time fluorescence-based assays in differentiating multidrug efflux-inhibitory and outer membrane-destabilizing activities of antibacterial compounds. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Generation of a novel monoclonal antibody that recognizes the alpha (α)-amidated isoform of a valine residue.

PubMed

Antón Palma, Benito; Leff Gelman, Philippe; Medecigo Ríos, Mayra; Calva Nieves, Juan Carlos; Acevedo Ortuño, Rodolfo; Matus Ortega, Maura Epifanía; Hernández Calderón, Jorge Alberto; Hernández Miramontes, Ricardo; Flores Zamora, Anabel; Salazar Juárez, Alberto

2015-10-13

Alpha (α)-amidation of peptides is a mechanism required for the conversion of prohormones into functional peptide sequences that display biological activities, receptor recognition and signal transduction on target cells. Alpha (α)-amidation occurs in almost all species and amino acids identified in nature. C-terminal valine amide neuropeptides constitute the smallest group of functional peptide compounds identified in neurosecretory structures in vertebrate and invertebrate species. The α-amidated isoform of valine residue (Val-CONH2) was conjugated to KLH-protein carrier and used to immunize mice. Hyperimmune animals displaying high titers of valine amide antisera were used to generate stable hybridoma-secreting mAbs. Three productive hybridoma (P15A4, P17C11, and P18C5) were tested against peptides antigens containing both the C-terminal α-amidated (-CONH2) and free α-carboxylic acid (-COO(-)) isovariant of the valine residue. P18C5 mAb displayed the highest specificity and selectivity against C-terminal valine amidated peptide antigens in different immunoassays. P18C5 mAb-immunoreactivity exhibited a wide distribution along the neuroaxis of the rat brain, particularly in brain areas that did not cross-match with the neuronal distribution of known valine amide neuropeptides (α-MSH, adrenorphin, secretin, UCN1-2). These brain regions varied in the relative amount of putative novel valine amide peptide immunoreactive material (nmol/μg protein) estimated through a fmol-sensitive solid-phase radioimmunoassay (RIA) raised for P18C5 mAb. Our results demonstrate the versatility of a single mAb able to differentiate between two structural subdomains of a single amino acid. This mAb offers a wide spectrum of potential applications in research and medicine, whose uses may extend from a biological reagent (used to detect valine amidated peptide substances in fluids and tissues) to a detoxifying reagent (used to neutralize exogenous toxic amide peptide compounds) or as a specific immunoreagent in immunotherapy settings (used to reduce tumor growth and tumorigenesis) among many others.

Ab initio study of the diatomic fluorides FeF, CoF, NiF, and CuF.

PubMed

Koukounas, Constantine; Mavridis, Aristides

2008-11-06

The late-3d transition-metal diatomic fluorides MF = FeF, CoF, NiF, and CuF have been studied using variational multireference (MRCI) and coupled-cluster [RCCSD(T)] methods, combined with large to very large basis sets. We examined a total of 35 (2S+1)|Lambda| states, constructing as well 29 full potential energy curves through the MRCI method. All examined states are ionic, diabatically correlating to M(+)+F(-)((1)S). Notwithstanding the "eccentric" character of the 3d transition metals and the difficulties to accurately be described with all-electron ab initio methods, our results are, in general, in very good agreement with available experimental numbers.

Partitioning-Defective 1a/b Depletion Impairs Glomerular and Proximal Tubule Development.

PubMed

Akchurin, Oleh; Du, Zhongfang; Ramkellawan, Nadira; Dalal, Vidhi; Han, Seung Hyeok; Pullman, James; Müsch, Anne; Susztak, Katalin; Reidy, Kimberly J

2016-12-01

The kidney is a highly polarized epithelial organ that develops from undifferentiated mesenchyme, although the mechanisms that regulate the development of renal epithelial polarity are incompletely understood. Partitioning-defective 1 (Par1) proteins have been implicated in cell polarity and epithelial morphogenesis; however, the role of these proteins in the developing kidney has not been established. Therefore, we studied the contribution of Par1a/b to renal epithelial development. We examined the renal phenotype of newborn compound mutant mice carrying only one allele of Par1a or Par1b. Loss of three out of four Par1a/b alleles resulted in severe renal hypoplasia, associated with impaired ureteric bud branching. Compared with kidneys of newborn control littermates, kidneys of newborn mutant mice exhibited dilated proximal tubules and immature glomeruli, and the renal proximal tubular epithelia lacked proper localization of adhesion complexes. Furthermore, Par1a/b mutants expressed low levels of renal Notch ligand Jag1, activated Notch2, and Notch effecter Hes1. Together, these data demonstrate that Par1a/b has a key role in glomerular and proximal tubule development, likely via modulation of Notch signaling. Copyright © 2016 by the American Society of Nephrology.

High-pressure study of the structural and elastic properties of defect-chalcopyrite HgGa2Se4

NASA Astrophysics Data System (ADS)

Gomis, O.; Vilaplana, R.; Manjón, F. J.; Santamaría-Pérez, D.; Errandonea, D.; Pérez-González, E.; López-Solano, J.; Rodríguez-Hernández, P.; Muñoz, A.; Tiginyanu, I. M.; Ursaki, V. V.

2013-02-01

In this work, we focus on the study of the structural and elastic properties of mercury digallium selenide (HgGa2Se4) which belongs to the family of AB2X4 ordered-vacancy compounds with tetragonal defect chalcopyrite structure. We have carried out high-pressure x-ray diffraction measurements up to 13.2 GPa. Our measurements have been complemented and compared with total-energy ab initio calculations. The equation of state and the axial compressibilities for the low-pressure phase of HgGa2Se4 have been experimentally and theoretically determined and compared to other related ordered-vacancy compounds. The theoretical cation-anion and vacancy-anion distances in HgGa2Se4 have been determined. The internal distance compressibility in HgGa2Se4 has been compared with those that occur in binary HgSe and ɛ-GaSe compounds. It has been found that the Hg-Se and Ga-Se bonds behave in a similar way in the three compounds. It has also been found that bulk compressibility of the compounds decreases following the sequence "ɛ-GaSe > HgGa2Se4 > HgSe." Finally, we have studied the pressure dependence of the theoretical elastic constants and elastic moduli of HgGa2Se4. Our calculations report that the low-pressure phase of HgGa2Se4 becomes mechanically unstable above 13.3 GPa.

Perspective: Size selected clusters for catalysis and electrochemistry

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

Halder, Avik; Curtiss, Larry A.; Fortunelli, Alessandro

We report that size-selected clusters containing a handful of atoms may possess noble catalytic properties different from nano-sized or bulk catalysts. Size- and composition-selected clusters can also serve as models of the catalytic active site, where an addition or removal of a single atom can have a dramatic effect on their activity and selectivity. In this Perspective, we provide an overview of studies performed under both ultra-high vacuum and realistic reaction conditions aimed at the interrogation, characterization and understanding of the performance of supported size-selected clusters in heterogeneous and electrochemical reactions, which address the effects of cluster size, cluster composition,more » cluster-support interactions and reaction conditions, the key parameters for the understanding and control of catalyst functionality. Computational modelling based on density functional theory sampling of local minima and energy barriers or ab initio Molecular Dynamics simulations is an integral part of this research by providing fundamental understanding of the catalytic processes at the atomic level, as well as by predicting new materials compositions which can be validated in experiments. Lastly, we discuss approaches which aim at the scale up of the production of well-defined clusters for use in real world applications.« less

Perspective: Size selected clusters for catalysis and electrochemistry

DOE PAGES

Halder, Avik; Curtiss, Larry A.; Fortunelli, Alessandro; ...

2018-03-15

We report that size-selected clusters containing a handful of atoms may possess noble catalytic properties different from nano-sized or bulk catalysts. Size- and composition-selected clusters can also serve as models of the catalytic active site, where an addition or removal of a single atom can have a dramatic effect on their activity and selectivity. In this Perspective, we provide an overview of studies performed under both ultra-high vacuum and realistic reaction conditions aimed at the interrogation, characterization and understanding of the performance of supported size-selected clusters in heterogeneous and electrochemical reactions, which address the effects of cluster size, cluster composition,more » cluster-support interactions and reaction conditions, the key parameters for the understanding and control of catalyst functionality. Computational modelling based on density functional theory sampling of local minima and energy barriers or ab initio Molecular Dynamics simulations is an integral part of this research by providing fundamental understanding of the catalytic processes at the atomic level, as well as by predicting new materials compositions which can be validated in experiments. Lastly, we discuss approaches which aim at the scale up of the production of well-defined clusters for use in real world applications.« less

Perspective: Size selected clusters for catalysis and electrochemistry

NASA Astrophysics Data System (ADS)

Halder, Avik; Curtiss, Larry A.; Fortunelli, Alessandro; Vajda, Stefan

2018-03-01

Size-selected clusters containing a handful of atoms may possess noble catalytic properties different from nano-sized or bulk catalysts. Size- and composition-selected clusters can also serve as models of the catalytic active site, where an addition or removal of a single atom can have a dramatic effect on their activity and selectivity. In this perspective, we provide an overview of studies performed under both ultra-high vacuum and realistic reaction conditions aimed at the interrogation, characterization, and understanding of the performance of supported size-selected clusters in heterogeneous and electrochemical reactions, which address the effects of cluster size, cluster composition, cluster-support interactions, and reaction conditions, the key parameters for the understanding and control of catalyst functionality. Computational modeling based on density functional theory sampling of local minima and energy barriers or ab initio molecular dynamics simulations is an integral part of this research by providing fundamental understanding of the catalytic processes at the atomic level, as well as by predicting new materials compositions which can be validated in experiments. Finally, we discuss approaches which aim at the scale up of the production of well-defined clusters for use in real world applications.

Spin-orbit coupled systems in the atomic limit: rhenates, osmates, iridates

NASA Astrophysics Data System (ADS)

Paramekanti, Arun; Singh, David J.; Yuan, Bo; Casa, Diego; Said, Ayman; Kim, Young-June; Christianson, A. D.

2018-06-01

Motivated by RIXS experiments on a wide range of complex heavy oxides, including rhenates, osmates, and iridates, we discuss the theory of RIXS for site-localized t2 g orbital systems with strong spin-orbit coupling. For such systems, we present exact diagonalization results for the spectrum at different electron fillings, showing that it accesses "single-particle" and "multiparticle" excitations. This leads to a simple picture for the energies and intensities of the RIXS spectra in Mott insulators such as double perovskites which feature highly localized electrons, and yields estimates of the spin-orbit coupling and Hund's coupling in correlated 5 d oxides. We present new higher resolution RIXS data at the Re L3 edge in Ba2YReO6 which finds a previously unresolved peak splitting, providing further confirmation of our theoretical predictions. Using ab initio electronic structure calculations on Ba2M ReO6 (with M =Re , Os, Ir) we show that while the atomic limit yields a reasonable effective Hamiltonian description of the experimental observations, effects such as t2 g-eg interactions and hybridization with oxygen are important. Our ab initio estimate for the strength of the intersite exchange coupling shows that, compared to the d3 systems, the exchange is one or two orders of magnitude weaker in the d2 and d4 materials, which may partly explain the suppression of long-range magnetic order in the latter compounds. As a way to interpolate between the site-localized picture and our electronic structure band calculations, we discuss the spin-orbital levels of the M O6 cluster. This suggests a possible role for intracluster excitons in Ba2YIrO6 which may lead to a weak breakdown of the atomic Jeff=0 picture and to small magnetic moments.

Representation of Ion–Protein Interactions Using the Drude Polarizable Force-Field

PubMed Central

2016-01-01

Small metal ions play critical roles in numerous biological processes. Of particular interest is how metalloenzymes are allosterically regulated by the binding of specific ions. Understanding how ion binding affects these biological processes requires atomic models that accurately treat the microscopic interactions with the protein ligands. Theoretical approaches at different levels of sophistication can contribute to a deeper understanding of these systems, although computational models must strike a balance between accuracy and efficiency in order to enable long molecular dynamics simulations. In this study, we present a systematic effort to optimize the parameters of a polarizable force field based on classical Drude oscillators to accurately represent the interactions between ions (K+, Na+, Ca2+, and Cl–) and coordinating amino-acid residues for a set of 30 biologically important proteins. By combining ab initio calculations and experimental thermodynamic data, we derive a polarizable force field that is consistent with a wide range of properties, including the geometries and interaction energies of gas-phase ion/protein-like model compound clusters, and the experimental solvation free-energies of the cations in liquids. The resulting models display significant improvements relative to the fixed-atomic-charge additive CHARMM C36 force field, particularly in their ability to reproduce the many-body electrostatic nonadditivity effects estimated from ab initio calculations. The analysis clarifies the fundamental limitations of the pairwise additivity assumption inherent in classical fixed-charge force fields, and shows its dramatic failures in the case of Ca2+ binding sites. These optimized polarizable models, amenable to computationally efficient large-scale MD simulations, set a firm foundation and offer a powerful avenue to study the roles of the ions in soluble and membrane transport proteins. PMID:25578354

Structure of Low-Lying Excited States of Guanine in DNA and Solution: Combined Molecular Mechanics and High-Level Coupled Cluster Studies

DOE PAGES

Kowalski, Karol; Valiev, Marat

2007-01-01

High-level ab-initio equation-of-motion coupled-cluster methods with singles, doubles, and noniterative triples are used, in conjunction with the combined quantum mechanical molecular mechanics approach, to investigate the structure of low-lying excited states of the guanine base in DNA and solvated environments. Our results indicate that while the excitation energy of the first excited state is barely changed compared to its gas-phase counterpart, the excitation energy of the second excited state is blue-shifted by 0.24 eV.

Structure of 2,4-Diaminopyrimidine - Theobromine Alternate Base Pairs

NASA Technical Reports Server (NTRS)

Gengeliczki, Zsolt; Callahan, Michael P.; Kabelac, Martin; Rijs, Anouk M.; deVries, Mattanjah S.

2011-01-01

We report the structure of clusters of 2,4-diaminopyrimidine with 3,7-dimethylxanthine (theobromine) in the gas phase determined by IR-UV double resonance spectroscopy in both the near-IR and mid-IR regions in combination with ab initio computations. These clusters represent potential alternate nucleobase pairs, geometrically equivalent to guanine-cytosine. We have found the four lowest energy structures, which include the Watson-Crick base pairing motif. This Watson-Crick structure has not been observed by resonant two-photon ionization (R2PI) in the gas phase for the canonical DNA base pairs.

Cluster perturbation theory for calculation of electronic properties of ensembles of metal nanoclusters

NASA Astrophysics Data System (ADS)

Zhumagulov, Yaroslav V.; Krasavin, Andrey V.; Kashurnikov, Vladimir A.

2018-05-01

The method is developed for calculation of electronic properties of an ensemble of metal nanoclusters with the use of cluster perturbation theory. This method is applied to the system of gold nanoclusters. The Greens function of single nanocluster is obtained by ab initio calculations within the framework of the density functional theory, and then is used in Dyson equation to group nanoclusters together and to compute the Greens function as well as the electron density of states of the whole ensemble. The transition from insulator state of a single nanocluster to metallic state of bulk gold is observed.

Spin-canting magnetization in an unusual Co4 cluster-based layer compound from a 2,3-dihydroxyquinoxaline ligand.

PubMed

Yang, Chen-I; Chuang, Po-Hsiang; Lee, Gene-Hsiang; Peng, Shie-Ming; Lu, Kuang-Lieh

2012-01-16

The self-assembly of Co(O(2)CPh)(2) with a 2,3-dihydroxyquinoxaline (H(2)dhq) linker has revealed a new two-dimensional cluster-based compound, [Co(4)(OMe)(2)(O(2)CPh)(2)(dhq)(2)(MeOH)(2)](n), which shows spin-canted magnetization and a definite magnetic hysteresis loop.

Conformationally averaged vertical detachment energy of finite size NO3(-)·nH2O clusters: a route connecting few to many.

PubMed

Pathak, Arup Kumar; Samanta, Alok Kumar; Maity, Dilip Kumar

2011-04-07

We report conformationally averaged VDEs (VDE(w)(n)) for different sizes of NO(3)(-)·nH(2)O clusters calculated by using uncorrelated HF, correlated hybrid density functional (B3LYP, BHHLYP) and correlated ab intio (MP2 and CCSD(T)) theory. It is observed that the VDE(w)(n) at the B3LYP/6-311++G(d,p), B3LYP/Aug-cc-Pvtz and CCSD(T)/6-311++G(d,p) levels is very close to the experimentally measured VDE. It is shown that the use of calculated results of the conformationally averaged VDE for small-sized solvated negatively-charged clusters and a microscopic theory-based general expression for the same provides a route to obtain the VDE for a wide range of cluster sizes, including bulk.

Direct evidence for radiative charge transfer after inner-shell excitation and ionization of large clusters

NASA Astrophysics Data System (ADS)

Hans, Andreas; Stumpf, Vasili; Holzapfel, Xaver; Wiegandt, Florian; Schmidt, Philipp; Ozga, Christian; Reiß, Philipp; Ben Ltaief, Ltaief; Küstner-Wetekam, Catmarna; Jahnke, Till; Ehresmann, Arno; Demekhin, Philipp V.; Gokhberg, Kirill; Knie, André

2018-01-01

We directly observe radiative charge transfer (RCT) in Ne clusters by dispersed vacuum-ultraviolet photon detection. The doubly ionized Ne2+-{{{N}}{{e}}}n-1 initial states of RCT are populated after resonant 1s-3p photoexcitation or 1s photoionization of Ne n clusters with < n> ≈ 2800. These states relax further producing Ne+-Ne+-{{{N}}{{e}}}n-2 final states, and the RCT photon is emitted. Ab initio calculations assign the observed RCT signal to the{}{{{N}}{{e}}}2+(2{{{p}}}-2{[}1{{D}}]){--}{{{N}}{{e}}}n-1 initial state, while transitions from other possible initial states are proposed to be quenched by competing relaxation processes. The present results are in agreement with the commonly discussed scenario, where the doubly ionized atom in a noble gas cluster forms a dimer which dissipates its vibrational energy on a picosecond timescale. Our study complements the picture of the RCT process in weakly bound clusters, providing information which is inaccessible by charged particle detection techniques.

Puzzle of magnetic moments of Ni clusters revisited using quantum Monte Carlo method.

PubMed

Lee, Hung-Wen; Chang, Chun-Ming; Hsing, Cheng-Rong

2017-02-28

The puzzle of the magnetic moments of small nickel clusters arises from the discrepancy between values predicted using density functional theory (DFT) and experimental measurements. Traditional DFT approaches underestimate the magnetic moments of nickel clusters. Two fundamental problems are associated with this puzzle, namely, calculating the exchange-correlation interaction accurately and determining the global minimum structures of the clusters. Theoretically, the two problems can be solved using quantum Monte Carlo (QMC) calculations and the ab initio random structure searching (AIRSS) method correspondingly. Therefore, we combined the fixed-moment AIRSS and QMC methods to investigate the magnetic properties of Ni n (n = 5-9) clusters. The spin moments of the diffusion Monte Carlo (DMC) ground states are higher than those of the Perdew-Burke-Ernzerhof ground states and, in the case of Ni 8-9 , two new ground-state structures have been discovered using the DMC calculations. The predicted results are closer to the experimental findings, unlike the results predicted in previous standard DFT studies.

A Novel indole compound that inhibits Pseudomonas aeruginosa growth by targeting MreB is a substrate for MexAB-OprM.

PubMed

Robertson, Gregory T; Doyle, Timothy B; Du, Qun; Duncan, Leonard; Mdluli, Khisimuzi E; Lynch, A Simon

2007-10-01

Drug efflux systems contribute to the intrinsic resistance of Pseudomonas aeruginosa to many antibiotics and biocides and hamper research focused on the discovery and development of new antimicrobial agents targeted against this important opportunistic pathogen. Using a P. aeruginosa PAO1 derivative bearing deletions of opmH, encoding an outer membrane channel for efflux substrates, and four efflux pumps belonging to the resistance nodulation/cell division class including mexAB-oprM, we identified a small-molecule indole-class compound (CBR-4830) that is inhibitory to growth of this efflux-compromised strain. Genetic studies established MexAB-OprM as the principal pump for CBR-4830 and revealed MreB, a prokaryotic actin homolog, as the proximal cellular target of CBR-4830. Additional studies establish MreB as an essential protein in P. aeruginosa, and efflux-compromised strains treated with CBR-4830 transition to coccoid shape, consistent with MreB inhibition or depletion. Resistance genetics further suggest that CBR-4830 interacts with the putative ATP-binding pocket in MreB and demonstrate significant cross-resistance with A22, a structurally unrelated compound that has been shown to promote rapid dispersion of MreB filaments in vivo. Interestingly, however, ATP-dependent polymerization of purified recombinant P. aeruginosa MreB is blocked in vitro in a dose-dependent manner by CBR-4830 but not by A22. Neither compound exhibits significant inhibitory activity against mutant forms of MreB protein that bear mutations identified in CBR-4830-resistant strains. Finally, employing the strains and reagents prepared and characterized during the course of these studies, we have begun to investigate the ability of analogues of CBR-4830 to inhibit the growth of both efflux-proficient and efflux-compromised P. aeruginosa through specific inhibition of MreB function.

Novel Piperazine Arylideneimidazolones Inhibit the AcrAB-TolC Pump in Escherichia coli and Simultaneously Act as Fluorescent Membrane Probes in a Combined Real-Time Influx and Efflux Assay.

PubMed

Bohnert, Jürgen A; Schuster, Sabine; Kern, Winfried V; Karcz, Tadeusz; Olejarz, Agnieszka; Kaczor, Aneta; Handzlik, Jadwiga; Kieć-Kononowicz, Katarzyna

2016-04-01

In this study, we tested five compounds belonging to a novel series of piperazine arylideneimidazolones for the ability to inhibit the AcrAB-TolC efflux pump. The biphenylmethylene derivative (BM-19) and the fluorenylmethylene derivative (BM-38) were found to possess the strongest efflux pump inhibitor (EPI) activities in the AcrAB-TolC-overproducingEscherichia colistrain 3-AG100, whereas BM-9, BM-27, and BM-36 had no activity at concentrations of up to 50 μM in a Nile red efflux assay. MIC microdilution assays demonstrated that BM-19 at 1/4 MIC (intrinsic MIC, 200 μM) was able to reduce the MICs of levofloxacin, oxacillin, linezolid, and clarithromycin 8-fold. BM-38 at 1/4 MIC (intrinsic MIC, 100 μM) was able to reduce only the MICs of oxacillin and linezolid (2-fold). Both compounds markedly reduced the MIC of rifampin (BM-19, 32-fold; and BM-38, 4-fold), which is suggestive of permeabilization of the outer membrane as an additional mechanism of action. Nitrocefin hydrolysis assays demonstrated that in addition to their EPI activity, both compounds were in fact weak permeabilizers of the outer membrane. Moreover, it was found that BM-19, BM-27, BM-36, and BM-38 acted as near-infrared-emitting fluorescent membrane probes, which allowed for their use in a combined influx and efflux assay and thus for tracking of the transport of an EPI across the outer membrane by an efflux pump in real time. The EPIs BM-38 and BM-19 displayed the most rapid influx of all compounds, whereas BM-27, which did not act as an EPI, showed the slowest influx. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

EuCo 2P 2: A Model Molecular-Field Helical Heisenberg Antiferromagnet

DOE PAGES

Sangeetha, N. S.; Cuervo-Reyes, Eduardo; Pandey, Abhishek; ...

2016-07-19

The metallic compound EuCo 2P 2 with the body-centered tetragonal ThCr 2Si 2 structure containing Eu spins-7/2 was previously shown from single-crystal neutron diffraction measurements to exhibit a helical antiferromagnetic (AFM) structure below T N=66.5 K with the helix axis along the c axis and with the ordered moments aligned within the ab plane. Here we report crystallography, electrical resistivity, heat capacity, magnetization, and magnetic susceptibility measurements on single crystals of this compound. We demonstrate that EuCo 2P 2 is a model molecular-field helical Heisenberg antiferromagnet from comparisons of the anisotropic magnetic susceptibility χ, high-field magnetization, and magnetic heat capacitymore » of EuCo 2P 2 single crystals at temperature T≤TN with the predictions of our recent formulation of molecular-field theory. Values of the Heisenberg exchange interactions between the Eu spins are derived from the data. The low-T magnetic heat capacity ~T 3 arising from spin-wave excitations with no anisotropy gap is calculated and found to be comparable to the lattice heat capacity. The density of states at the Fermi energy of EuCo 2P 2 and the related compound BaCo 2P 2 are found from the heat capacity data to be large, 10 and 16 states/eV per formula unit for EuCo 2P 2 and BaCo 2P 2, respectively. These values are enhanced by a factor of ~2.5 above those found from DFT electronic structure calculations for the two compounds. Additionally, the calculations also find ferromagnetic Eu–Eu exchange interactions within the ab plane and AFM interactions between Eu spins in nearest- and next-nearest planes, in agreement with the MFT analysis of χ ab(T≤TN).« less

EuCo 2P 2: A Model Molecular-Field Helical Heisenberg Antiferromagnet

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

Sangeetha, N. S.; Cuervo-Reyes, Eduardo; Pandey, Abhishek

The metallic compound EuCo 2P 2 with the body-centered tetragonal ThCr 2Si 2 structure containing Eu spins-7/2 was previously shown from single-crystal neutron diffraction measurements to exhibit a helical antiferromagnetic (AFM) structure below T N=66.5 K with the helix axis along the c axis and with the ordered moments aligned within the ab plane. Here we report crystallography, electrical resistivity, heat capacity, magnetization, and magnetic susceptibility measurements on single crystals of this compound. We demonstrate that EuCo 2P 2 is a model molecular-field helical Heisenberg antiferromagnet from comparisons of the anisotropic magnetic susceptibility χ, high-field magnetization, and magnetic heat capacitymore » of EuCo 2P 2 single crystals at temperature T≤TN with the predictions of our recent formulation of molecular-field theory. Values of the Heisenberg exchange interactions between the Eu spins are derived from the data. The low-T magnetic heat capacity ~T 3 arising from spin-wave excitations with no anisotropy gap is calculated and found to be comparable to the lattice heat capacity. The density of states at the Fermi energy of EuCo 2P 2 and the related compound BaCo 2P 2 are found from the heat capacity data to be large, 10 and 16 states/eV per formula unit for EuCo 2P 2 and BaCo 2P 2, respectively. These values are enhanced by a factor of ~2.5 above those found from DFT electronic structure calculations for the two compounds. Additionally, the calculations also find ferromagnetic Eu–Eu exchange interactions within the ab plane and AFM interactions between Eu spins in nearest- and next-nearest planes, in agreement with the MFT analysis of χ ab(T≤TN).« less

Structural and functional characterization of a novel molluskan ortholog of TRAF and TNF receptor-associated protein from disk abalone (Haliotis discus discus).

PubMed

Lee, Youngdeuk; Elvitigala, Don Anushka Sandaruwan; Whang, Ilson; Lee, Sukkyoung; Kim, Hyowon; Zoysa, Mahanama De; Oh, Chulhong; Kang, Do-Hyung; Lee, Jehee

2014-09-01

Immune signaling cascades have an indispensable role in the host defense of almost all the organisms. Tumor necrosis factor (TNF) signaling is considered as a prominent signaling pathway in vertebrate as well as invertebrate species. Within the signaling cascade, TNF receptor-associated factor (TRAF) and TNF receptor-associated protein (TTRAP) has been shown to have a crucial role in the modulation of immune signaling in animals. Here, we attempted to characterize a novel molluskan ortholog of TTRAP (AbTTRAP) from disk abalone (Haliotis discus discus) and analyzed its expression levels under pathogenic stress. The complete coding sequence of AbTTRAP consisted of 1071 nucleotides, coding for a 357 amino acid peptide, with a predicted molecular mass of 40 kDa. According to our in-silico analysis, AbTTRAP resembled the typical TTRAP domain architecture, including a 5'-tyrosyl DNA phosphodiesterase domain. Moreover, phylogenetic analysis revealed its common ancestral invertebrate origin, where AbTTRAP was clustered with molluskan counterparts. Quantitative real time PCR showed universally distributed expression of AbTTRAP in selected tissues of abalone, from which more prominent expression was detected in hemocytes. Upon stimulation with two pathogen-derived mitogens, lipopolysaccharide (LPS) and polyinosinic:polycytidylic acid (poly I:C), transcript levels of AbTTRAP in hemocytes and gill tissues were differentially modulated with time. In addition, the recombinant protein of AbTTRAP exhibited prominent endonuclease activity against abalone genomic DNA, which was enhanced by the presence of Mg(2+) in the medium. Collectively, these results reinforce the existence of the TNF signaling cascade in mollusks like disk abalone, further implicating the putative regulatory behavior of TTRAP in invertebrate host pathology. Copyright © 2014 Elsevier Ltd. All rights reserved.

Charge-mediated Fab-Fc interactions in an IgG1 antibody induce reversible self-association, cluster formation, and elevated viscosity.

PubMed

Arora, Jayant; Hu, Yue; Esfandiary, Reza; Sathish, Hasige A; Bishop, Steven M; Joshi, Sangeeta B; Middaugh, C Russell; Volkin, David B; Weis, David D

Concentration-dependent reversible self-association (RSA) of monoclonal antibodies (mAbs) poses a challenge to their pharmaceutical development as viable candidates for subcutaneous delivery. While the role of the antigen-binding fragment (Fab) in initiating RSA is well-established, little evidence supports the involvement of the crystallizable fragment (Fc). In this report, a variety of biophysical tools, including hydrogen exchange mass spectrometry, are used to elucidate the protein interface of such non-covalent protein-protein interactions. Using dynamic and static light scattering combined with viscosity measurements, we find that an IgG1 mAb (mAb-J) undergoes RSA primarily through electrostatic interactions and forms a monomer-dimer-tetramer equilibrium. We provide the first direct experimental mapping of the interface formed between the Fab and Fc domains of an antibody at high protein concentrations. Charge distribution heterogeneity between the positively charged interface spanning complementarity-determining regions CDR3H and CDR2L in the Fab and a negatively charged region in C H 3/Fc domain mediates the RSA of mAb-J. When arginine and NaCl are added, they disrupt RSA of mAb-J and decrease the solution viscosity. Fab-Fc domain interactions between mAb monomers may promote the formation of large transient antibody complexes that ultimately cause increases in solution viscosity. Our findings illustrate how limited specific arrangements of amino-acid residues can cause mAbs to undergo RSA at high protein concentrations and how conserved regions in the Fc portion of the antibody can also play an important role in initiating weak and transient protein-protein interactions.

Unlocking Phacelia tanacetifolia Benth. honey characterization through melissopalynological analysis, color determination and volatiles chemical profiling.

PubMed

Kuś, Piotr M; Jerković, Igor; Marijanović, Zvonimir; Kranjac, Marina; Tuberoso, Carlo I G

2018-04-01

Phacelia tanacetifolia Benth. honey (14 samples) collected in Poland was characterized by melissopalynological analysis, color determination (CIE L*a*b*C ab *h ab ° coordinates) and volatiles (VOCs) composition. VOCs were isolated by headspace solid-phase microextraction (HS-SPME, two fibers) and ultrasound-assisted solvent extraction (USE, two solvents) and analyzed by GC-MS. Principal component analysis (PCA) and hierarchical-tree clustering (HTC) were applied to show trends and form groups and to indicate the most representative unifloral samples. Six samples were pointed out with average pollen 74.9% and color parameters (L=85.1; a*=-0.8; b*=27.9; C ab *=27.9; h ab *=91.9) that were significantly correlated. High abundance of trans-linalool oxide (27.3-45.9%) that was significantly correlated with the pollen percentages, hexan-1-ol (4.4-5.7%) and lavender lactone (0.8% - 1.5%) were characteristic for their headspace. C 13 -norisoprenoids, mainly (E)-/(Z)-3-oxo-retro-α-ionol (4.7-5.4%; 6.9-9.4%) and vomifoliol (9.0-13.0%) dominated in their USE extracts. Copyright © 2018 Elsevier Ltd. All rights reserved.

Development of a tier 1 R5 clade C simian-human immunodeficiency virus as a tool to test neutralizing antibody-based immunoprophylaxis.

PubMed

Siddappa, Nagadenahalli B; Hemashettar, Girish; Wong, Yin Ling; Lakhashe, Samir; Rasmussen, Robert A; Watkins, Jennifer D; Novembre, Francis J; Villinger, François; Else, James G; Montefiori, David C; Ruprecht, Ruth M

2011-04-01

While some recently transmitted HIV clade C (HIV-C) strains exhibited tier 1 neutralization phenotypes, most were tier 2 strains (J Virol 2010; 84:1439). Because induction of neutralizing antibodies (nAbs) through vaccination against tier 2 viruses has proven difficult, we have generated a tier 1, clade C simian-human immunodeficiency virus (SHIV-C) to permit efficacy testing of candidate AIDS vaccines against tier 1 viruses. SHIV-1157ipEL was created by swapping env of a late-stage virus with that of a tier 1, early form. After adaptation to rhesus macaques (RM), passaged SHIV-1157ipEL-p replicated vigorously in vitro and in vivo while maintaining R5 tropism. The virus was reproducibly transmissible intrarectally. Phylogenetically, SHIV-1157ipEL-p Env clustered with HIV-C sequences. All RM chronically infected with SHIV-1157ipEL-p developed high nAb titers against autologous as well as heterologous tier 1 strains. SHIV-1157ipEL-p was reproducibly transmitted in RM, induced cross-clade nAbs, and represents a tool to evaluate anti-HIV-C nAb responses in primates. © 2010 John Wiley & Sons A/S.

Multiple valence superatoms.

PubMed

Reveles, J U; Khanna, S N; Roach, P J; Castleman, A W

2006-12-05

We recently demonstrated that, in gas phase clusters containing aluminum and iodine atoms, an Al(13) cluster behaves like a halogen atom, whereas an Al(14) cluster exhibits properties analogous to an alkaline earth atom. These observations, together with our findings that Al(13)(-) is inert like a rare gas atom, have reinforced the idea that chosen clusters can exhibit chemical behaviors reminiscent of atoms in the periodic table, offering the exciting prospect of a new dimension of the periodic table formed by cluster elements, called superatoms. As the behavior of clusters can be controlled by size and composition, the superatoms offer the potential to create unique compounds with tailored properties. In this article, we provide evidence of an additional class of superatoms, namely Al(7)(-), that exhibit multiple valences, like some of the elements in the periodic table, and hence have the potential to form stable compounds when combined with other atoms. These findings support the contention that there should be no limitation in finding clusters, which mimic virtually all members of the periodic table.

Supernova Cosmology Project

Science.gov Websites

Space Telescope Cluster Supernova Survey: II. The Type Ia Supernova Rate in High-Redshift Galaxy /abs/0809.1648 Constraining Dust and Color Variations of High-z SNe Using NICMOS on the Hubble Space /0804.4142 A New Determination of the High-Redshift Type Ia Supernova Rates with the Hubble Space Telescope

Linkage of interactions in sickle hemoglobin fiber assembly: inhibitory effect emanating from mutations in the AB region of the alpha-chain is annulled by a mutation at its EF corner.

PubMed

Sudha, Rajamani; Anantharaman, Lavanya; Sivaram, Mylavarapu V S; Mirsamadi, Neda; Choudhury, Devapriya; Lohiya, Nirmal K; Gupta, Rasik B; Roy, Rajendra P

2004-05-07

The AB and GH regions of the alpha-chain are located in spatial proximity and contain a cluster of intermolecular contact residues of the sickle hemoglobin (HbS) fiber. We have examined the role of dynamics of AB/GH region on HbS polymerization through simultaneous replacement of non-contact Ala(19) and Ala(21) of the AB corner with more flexible Gly or rigid alpha-aminoisobutyric acid (Aib) residues. The polymerization behavior of HbS with Aib substitutions was similar to the native HbS. In contrast, Gly substitutions inhibited HbS polymerization. Molecular dynamics simulation studies of alpha-chains indicated that coordinated motion of AB and GH region residues present in native (Ala) as well as in Aib mutant was disrupted in the Gly mutant. The inhibitory effect due to Gly substitutions was further explored in triple mutants that included mutation of an inter-doublestrand contact (alphaAsn(78) --> His or Gln) at the EF corner. Although the inhibitory effect of Gly substitutions in the triple mutant was unaffected in the presence of alphaGln(78), His at this site almost abrogated its inhibitory potential. The polymerization studies of point mutants (alphaGln(78) --> His) indicated that the inhibitory effect due to Gly substitutions in the triple mutant was synergistically compensated for by the polymerization-enhancing activity of His(78). Similar synergistic coupling, between alphaHis(78) and an intra-double-strand contact point (alpha16) mutation located in the AB region, was also observed. Thus, two conclusions are made: (i) Gly mutations at the AB corner inhibit HbS polymerization by perturbing the dynamics of the AB/GH region, and (ii) perturbations of AB region (through changes in dynamics of the AB/GH region or abolition of a specific fiber contact site) that influence HbS polymerization do so in concert with alpha78 site at the EF corner. The overall results provide insights about the interaction-linkage between distant regions of the HbS tetramer in fiber assembly.

Formation of Exotic Networks of Water Clusters in Helium Droplets Facilitated by the Presence of Neon Atoms

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

Douberly, Gary E.; Miller, Roger E.; Xantheas, Sotiris S.

Water clusters are formed in helium droplets via the sequential capture of monomers. One or two neon atoms are added to each droplet prior to the addition of water. The infrared spectrum of the droplet ensemble reveals several signatures of polar, water tetramer clusters having dipole moments between 2D and 3D. Comparison with ab initio computations supports the assignment of the cluster networks to noncyclic “3+1” clusters, which are ~5.3 kcal/mol less stable than the global minimum nonpolar cyclic tetramer. The (H2O)3Ne + H2O ring insertion barrier is sufficiently large, such that evaporative helium cooling is capable of kinetically quenchingmore » the nonequilibrium tetramer system prior to its rearrangement to the lower energy cyclic species. To this end, the reported process results in the formation of exotic water cluster networks that are either higher in energy than the most stable gas-phase analogs or not even stable in the gas phase.« less

Hydrogen bonding in water clusters and their ionized counterparts.

PubMed

Neela, Y Indra; Mahadevi, A Subha; Sastry, G Narahari

2010-12-30

Ab initio and DFT computations were carried out on four distinct hydrogen-bonded arrangements of water clusters (H(2)O)(n), n = 2-20, represented as W1D, W2D, W2DH, and W3D. The variation in the strength of hydrogen bond as a function of the chain length is studied. In all the four cases, there is a substantial cooperative interaction, albeit in different degrees. The effect of basis set superposition error (BSSE) on the complexation energy of water clusters has been analyzed. Atoms in molecules (AIM) analysis performed to evaluate the nature of the hydrogen bonding shows a high correlation between hydrogen bond strength and the trends in complexation energy. Solvated water clusters exhibit lower complexation energies compared to corresponding gas-phase geometries on PCM (polarized continuum model) optimization. The feasibility of stripping an electron or addition of an electron increases dramatically as the cluster size increases. Although W3D caged structures are stable for neutral clusters, the helical W2DH arrangement appeared to be an optimal choice for its ionized counterparts.

Stability and migration of large oxygen clusters in UO(2+x): density functional theory calculations.

PubMed

Andersson, D A; Espinosa-Faller, F J; Uberuaga, B P; Conradson, S D

2012-06-21

Using ab initio molecular dynamics simulations and nudged elastic band calculations we examine the finite temperature stability, transition pathways, and migration mechanisms of large oxygen clusters in UO(2+x). Here we specifically consider the recently proposed split quad-interstitial and cuboctahedral oxygen clusters. It is shown that isolated cuboctahedral clusters may transform into more stable configurations that are closely linked to the split quad-interstitial. The split quad-interstitial is stable with respect to single interstitials occupying the empty octahedral holes of the UO(2) lattice. In order to better understand discrepancies between theory and experiments, the simulated atomic pair distribution functions for the split quad-interstitial structures are analyzed with respect to the distribution function for U(4)O(9) previously obtained from neutron diffraction data. Our nudged elastic band calculations suggest that the split quad-interstitial may migrate by translating one of its constituent di-interstitial clusters via a barrier that is lower than the corresponding barrier for individual interstitials, but higher than the barrier for the most stable di-interstitial cluster.

HeI photoelectron spectroscopic studies on the electronic structure of alkyl nitrosamines

NASA Astrophysics Data System (ADS)

Jiang, Peng; Qian, Ximei; Li, Chunhui; Qiao, Chunhua; Wang, Dianxun

1997-10-01

HeI photoelectron spectroscopic (PES) studies on the electronic structure of alkyl nitrosamines R 2N 2O (R = CH 3-, CH 3CH 2-, and CH 3CH 2CH 2-) are reported. The assignment of the PES bands for this series of compounds has been made with the aid of the band shapes, the band intensity and ab initio SCF MO calculations based on the 631 ∗ G basis sets. Both PES experiment and the ab initio SCF MO calculations show that the detoxification ability of nitrosamine with longer alkyl chain is stronger.

Optical absorption spectra and g factor of MgO: Mn2+explored by ab initio and semi empirical methods

NASA Astrophysics Data System (ADS)

Andreici Eftimie, E.-L.; Avram, C. N.; Brik, M. G.; Avram, N. M.

2018-02-01

In this paper we present a methodology for calculations of the optical absorption spectra, ligand field parameters and g factor for the Mn2+ (3d5) ions doped in MgO host crystal. The proposed technique combines two methods: the ab initio multireference (MR) and the semi empirical ligand field (LF) in the framework of the exchange charge model (ECM) respectively. Both methods of calculations are applied to the [MnO6]10-cluster embedded in an extended point charge field of host matrix ligands based on Gellé-Lepetit procedure. The first step of such investigations was the full optimization of the cubic structure of perfect MgO crystal, followed by the structural optimization of the doped of MgO:Mn2+ system, using periodic density functional theory (DFT). The ab initio MR wave functions approaches, such as complete active space self-consistent field (CASSCF), N-electron valence second order perturbation theory (NEVPT2) and spectroscopy oriented configuration interaction (SORCI), are used for the calculations. The scalar relativistic effects have also been taken into account through the second order Douglas-Kroll-Hess (DKH2) procedure. Ab initio ligand field theory (AILFT) allows to extract all LF parameters and spin-orbit coupling constant from such calculations. In addition, the ECM of ligand field theory (LFT) has been used for modelling theoptical absorption spectra. The perturbation theory (PT) was employed for the g factor calculation in the semi empirical LFT. The results of each of the aforementioned types of calculations are discussed and the comparisons between the results obtained and the experimental results show a reasonable agreement, which justifies this new methodology based on the simultaneous use of both methods. This study establishes fundamental principles for the further modelling of larger embedded cluster models of doped metal oxides.

State-of-the-art ab initio potential energy curve for the krypton atom pair and thermophysical properties of dilute krypton gas

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

Jäger, Benjamin, E-mail: benjamin.jaeger@uni-rostock.de; Hellmann, Robert, E-mail: robert.hellmann@uni-rostock.de; Bich, Eckard

2016-03-21

A new reference krypton-krypton interatomic potential energy curve was developed by means of quantum-chemical ab initio calculations for 36 interatomic separations. Highly accurate values for the interaction energies at the complete basis set limit were obtained using the coupled-cluster method with single, double, and perturbative triple excitations as well as t-aug-cc-pV5Z and t-aug-cc-pV6Z basis sets including mid-bond functions, with the 6Z basis set being newly constructed for this study. Higher orders of coupled-cluster terms were considered in a successive scheme up to full quadruple excitations. Core-core and core-valence correlation effects were included. Furthermore, relativistic effects were studied not only atmore » a scalar relativistic level using second-order direct perturbation theory, but also utilizing full four-component and Gaunt-effect computations. An analytical pair potential function was fitted to the interaction energies, which is characterized by a depth of 200.88 K with an estimated standard uncertainty of 0.51 K. Thermophysical properties of low-density krypton were calculated for temperatures up to 5000 K. Second and third virial coefficients were obtained from statistical thermodynamics. Viscosity and thermal conductivity as well as the self-diffusion coefficient were computed using the kinetic theory of gases. The theoretical results are compared with experimental data and with results for other pair potential functions from the literature, especially with those calculated from the recently developed ab initio potential of Waldrop et al. [J. Chem. Phys. 142, 204307 (2015)]. Highly accurate experimental viscosity data indicate that both the present ab initio pair potential and the one of Waldrop et al. can be regarded as reference potentials, even though the quantum-chemical methods and basis sets differ. However, the uncertainties of the present potential and of the derived properties are estimated to be considerably lower.« less

Analytic energy gradients for the orbital-optimized third-order Møller-Plesset perturbation theory

NASA Astrophysics Data System (ADS)

Bozkaya, Uǧur

2013-09-01

Analytic energy gradients for the orbital-optimized third-order Møller-Plesset perturbation theory (OMP3) [U. Bozkaya, J. Chem. Phys. 135, 224103 (2011)], 10.1063/1.3665134 are presented. The OMP3 method is applied to problematic chemical systems with challenging electronic structures. The performance of the OMP3 method is compared with those of canonical second-order Møller-Plesset perturbation theory (MP2), third-order Møller-Plesset perturbation theory (MP3), coupled-cluster singles and doubles (CCSD), and coupled-cluster singles and doubles with perturbative triples [CCSD(T)] for investigating equilibrium geometries, vibrational frequencies, and open-shell reaction energies. For bond lengths, the performance of OMP3 is in between those of MP3 and CCSD. For harmonic vibrational frequencies, the OMP3 method significantly eliminates the singularities arising from the abnormal response contributions observed for MP3 in case of symmetry-breaking problems, and provides noticeably improved vibrational frequencies for open-shell molecules. For open-shell reaction energies, OMP3 exhibits a better performance than MP3 and CCSD as in case of barrier heights and radical stabilization energies. As discussed in previous studies, the OMP3 method is several times faster than CCSD in energy computations. Further, in analytic gradient computations for the CCSD method one needs to solve λ-amplitude equations, however for OMP3 one does not since λ _{ab}^{ij(1)} = t_{ij}^{ab(1)} and λ _{ab}^{ij(2)} = t_{ij}^{ab(2)}. Additionally, one needs to solve orbital Z-vector equations for CCSD, but for OMP3 orbital response contributions are zero owing to the stationary property of OMP3. Overall, for analytic gradient computations the OMP3 method is several times less expensive than CCSD (roughly ˜4-6 times). Considering the balance of computational cost and accuracy we conclude that the OMP3 method emerges as a very useful tool for the study of electronically challenging chemical systems.

Analytic energy gradients for the orbital-optimized third-order Møller-Plesset perturbation theory.

PubMed

Bozkaya, Uğur

2013-09-14

Analytic energy gradients for the orbital-optimized third-order Møller-Plesset perturbation theory (OMP3) [U. Bozkaya, J. Chem. Phys. 135, 224103 (2011)] are presented. The OMP3 method is applied to problematic chemical systems with challenging electronic structures. The performance of the OMP3 method is compared with those of canonical second-order Møller-Plesset perturbation theory (MP2), third-order Møller-Plesset perturbation theory (MP3), coupled-cluster singles and doubles (CCSD), and coupled-cluster singles and doubles with perturbative triples [CCSD(T)] for investigating equilibrium geometries, vibrational frequencies, and open-shell reaction energies. For bond lengths, the performance of OMP3 is in between those of MP3 and CCSD. For harmonic vibrational frequencies, the OMP3 method significantly eliminates the singularities arising from the abnormal response contributions observed for MP3 in case of symmetry-breaking problems, and provides noticeably improved vibrational frequencies for open-shell molecules. For open-shell reaction energies, OMP3 exhibits a better performance than MP3 and CCSD as in case of barrier heights and radical stabilization energies. As discussed in previous studies, the OMP3 method is several times faster than CCSD in energy computations. Further, in analytic gradient computations for the CCSD method one needs to solve λ-amplitude equations, however for OMP3 one does not since λ(ab)(ij(1))=t(ij)(ab(1)) and λ(ab)(ij(2))=t(ij)(ab(2)). Additionally, one needs to solve orbital Z-vector equations for CCSD, but for OMP3 orbital response contributions are zero owing to the stationary property of OMP3. Overall, for analytic gradient computations the OMP3 method is several times less expensive than CCSD (roughly ~4-6 times). Considering the balance of computational cost and accuracy we conclude that the OMP3 method emerges as a very useful tool for the study of electronically challenging chemical systems.

In situ formed catalytically active ruthenium nanocatalyst in room temperature dehydrogenation/dehydrocoupling of ammonia-borane from Ru(cod)(cot) precatalyst.

PubMed

Zahmakiran, Mehmet; Ayvalı, Tuğçe; Philippot, Karine

2012-03-20

The development of simply prepared and effective catalytic materials for dehydrocoupling/dehydrogenation of ammonia-borane (AB; NH(3)BH(3)) under mild conditions remains a challenge in the field of hydrogen economy and material science. Reported herein is the discovery of in situ generated ruthenium nanocatalyst as a new catalytic system for this important reaction. They are formed in situ during the dehydrogenation of AB in THF at 25 °C in the absence of any stabilizing agent starting with homogeneous Ru(cod)(cot) precatalyst (cod = 1,5-η(2)-cyclooctadiene; cot = 1,3,5-η(3)-cyclooctatriene). The preliminary characterization of the reaction solutions and the products was done by using ICP-OES, ATR-IR, TEM, XPS, ZC-TEM, GC, EA, and (11)B, (15)N, and (1)H NMR, which reveal that ruthenium nanocatalyst is generated in situ during the dehydrogenation of AB from homogeneous Ru(cod)(cot) precatalyst and B-N polymers formed at the initial stage of the catalytic reaction take part in the stabilization of this ruthenium nanocatalyst. Moreover, following the recently updated approach (Bayram, E.; et al. J. Am. Chem. Soc.2011, 133, 18889) by performing Hg(0), CS(2) poisoning experiments, nanofiltration, time-dependent TEM analyses, and kinetic investigation of active catalyst formation to distinguish single metal or in the present case subnanometer Ru(n) cluster-based catalysis from polymetallic Ru(0)(n) nanoparticle catalysis reveals that in situ formed Ru(n) clusters (not Ru(0)(n) nanoparticles) are kinetically dominant catalytically active species in our catalytic system. The resulting ruthenium catalyst provides 120 total turnovers over 5 h with an initial turnover frequency (TOF) value of 35 h(-1) at room temperature with the generation of more than 1.0 equiv H(2) at the complete conversion of AB to polyaminoborane (PAB; [NH(2)BH(2)](n)) and polyborazylene (PB; [NHBH](n)) units.

State-of-the-art ab initio potential energy curve for the krypton atom pair and thermophysical properties of dilute krypton gas.

PubMed

Jäger, Benjamin; Hellmann, Robert; Bich, Eckard; Vogel, Eckhard

2016-03-21

A new reference krypton-krypton interatomic potential energy curve was developed by means of quantum-chemical ab initio calculations for 36 interatomic separations. Highly accurate values for the interaction energies at the complete basis set limit were obtained using the coupled-cluster method with single, double, and perturbative triple excitations as well as t-aug-cc-pV5Z and t-aug-cc-pV6Z basis sets including mid-bond functions, with the 6Z basis set being newly constructed for this study. Higher orders of coupled-cluster terms were considered in a successive scheme up to full quadruple excitations. Core-core and core-valence correlation effects were included. Furthermore, relativistic effects were studied not only at a scalar relativistic level using second-order direct perturbation theory, but also utilizing full four-component and Gaunt-effect computations. An analytical pair potential function was fitted to the interaction energies, which is characterized by a depth of 200.88 K with an estimated standard uncertainty of 0.51 K. Thermophysical properties of low-density krypton were calculated for temperatures up to 5000 K. Second and third virial coefficients were obtained from statistical thermodynamics. Viscosity and thermal conductivity as well as the self-diffusion coefficient were computed using the kinetic theory of gases. The theoretical results are compared with experimental data and with results for other pair potential functions from the literature, especially with those calculated from the recently developed ab initio potential of Waldrop et al. [J. Chem. Phys. 142, 204307 (2015)]. Highly accurate experimental viscosity data indicate that both the present ab initio pair potential and the one of Waldrop et al. can be regarded as reference potentials, even though the quantum-chemical methods and basis sets differ. However, the uncertainties of the present potential and of the derived properties are estimated to be considerably lower.

The Heat of Formation of HNO

NASA Technical Reports Server (NTRS)

Lee, Timothy J.; Dateo, Christopher E.

1995-01-01

The HNO molecule is of interest in both combustion and atmospheric chemistry. For example, Guadagnini et al. have recently presented ab initio potential energy surfaces for the three lowest lying electronic states of HNO and then used these in examining several chemical reactions that take place in the combustion of nitrogen containing fuels and in the oxidation of atmospheric nitrogen. We have previously studied the ground state potential energy surface (i.e., stationary points along the HNO reversible reaction HON path), vibrational spectrum (using an accurate quartic force field), zero-point energy, and bonding of HNO using coupled-cluster ab initio methods. HNO is also very interesting because of the unique nature of its bonding characteristics. That is, the potential energy surface is very flat along the H-N bonding coordinate thereby giving unusual harmonic and fundamental vibrational frequencies, and the H-N bond energy is rather weak in comparison to other H-N bond energies. In fact, using experimental heats of formation for HNO, H, and NO, the H- bond energy is computed to be only 49.9 kcal/ mol (298 K). However, ab initio calculations of isodesmic reaction energies involving HNO, FNO, ClNO, and several other molecules have shown that there is an inconsistency in the experimental heats of formation of the XNO (X double bond H, F, and Cl) species. Hence the motivation for this study was to determine a very accurate (Delta)H(sub f, sup o) value for HNO using state-of-the-art ab initio methods. Based on many recent studies it is evident that the singles and doubles coupled-cluster method that includes a perturbational estimate of the effects of connected triple excitations, denoted CCSD(T), in conjunction with large one-particle basis sets should be reliable to better than +/- 0.8 kcal/mol for this quantity. The computational methodology is described in the next section followed by our results and discussion. Conclusions are presented in the final section.

The Heat of Formation of HNO

NASA Technical Reports Server (NTRS)

Lee, Timothy J.; Dateo, Christopher E.

1995-01-01

The HNO molecule is of interest in both combustion and atmospheric chemistry. For example, Guadagnini et al. have recently presented ab initio potential energy surfaces for the three lowest lying electronic states of HNO and then used these in examining several chemical reactions that take place in the combustion of nitrogen containing fuels and in the oxidation of atmospheric nitrogen. We have previously studied the ground state potential energy surface (i.e., stationary points along the HNO rev. reaction HON path), vibrational spectrum (using an accurate quartic force field), zero-point energy, and bonding of HNO using coupled-cluster ab initio methods. HNO is also very interesting because of the unique nature of its bonding characteristics. That is, the potential energy surface is very flat along the H-N bonding coordinate thereby giving unusual harmonic and fundamental vibrational frequencies, and the H-N bond energy is rather weak in comparison to other H-N bond energies. In fact, using experimental heats of formation for HO, H, and NO, the H- bond energy is computed to be only 49.9 kcal/ mol (298 K). However, ab initio calculations of isodesmic reaction energies involving HNO, FNO, ClNO, and several other molecules have shown that there is an inconsistency in the experimental heats of formation of the XNO (X=H, F, and Cl) species. Hence the motivation for this study was to determine a very accurate(DELTA)H(sup o)(sub f) value for HNO using state of-the-art ab initio methods. Based on many recent studies it is evident that the singles and doubles coupled-cluster method that includes a perturbational estimate of the effects of connected triple excitations, denoted CCSD(T), in conjunction with large one-particle basis sets should be reliable to better than +0.8 kcal/mol for this quantity. The computational methodology is described in the next section followed by our results and discussion. Conclusions are presented in the final section.

Four-stranded mini microtubules formed by Prosthecobacter BtubAB show dynamic instability.

PubMed

Deng, Xian; Fink, Gero; Bharat, Tanmay A M; He, Shaoda; Kureisaite-Ciziene, Danguole; Löwe, Jan

2017-07-18

Microtubules, the dynamic, yet stiff hollow tubes built from αβ-tubulin protein heterodimers, are thought to be present only in eukaryotic cells. Here, we report a 3.6-Å helical reconstruction electron cryomicroscopy structure of four-stranded mini microtubules formed by bacterial tubulin-like Prosthecobacter dejongeii BtubAB proteins. Despite their much smaller diameter, mini microtubules share many key structural features with eukaryotic microtubules, such as an M-loop, alternating subunits, and a seam that breaks overall helical symmetry. Using in vitro total internal reflection fluorescence microscopy, we show that bacterial mini microtubules treadmill and display dynamic instability, another hallmark of eukaryotic microtubules. The third protein in the btub gene cluster, BtubC, previously known as "bacterial kinesin light chain," binds along protofilaments every 8 nm, inhibits BtubAB mini microtubule catastrophe, and increases rescue. Our work reveals that some bacteria contain regulated and dynamic cytomotive microtubule systems that were once thought to be only useful in much larger and sophisticated eukaryotic cells.

In vitro phase I metabolism of gamabufotalin and arenobufagin: Reveal the effect of substituent group on metabolic stability.

PubMed

Feng, Yujie; Wang, Chao; Tian, Xiangge; Huo, Xiaokui; Feng, Lei; Sun, Chengpeng; Ge, Guangbo; Yang, Ling; Ning, Jing; Ma, Xiaochi

2017-09-01

Bufadienolides are a major class of bioactive compounds derived from amphibian skin secretion. Gamabufotalin (GB) and arenobufagin (AB) are among the top of the intensively investigated natural bufadienolides for their outstanding biological activities. This study aimed to characterize the phase I metabolism of GB and AB with respect to the metabolic profiles, enzymes involved, and catalytic efficacy, thereafter tried to reveal substituent effects on metabolism. Two mono-hydroxylated products of GB and AB were detected in the incubation mixtures, and they were accurately identified as 1- and 5-hydroxylated bufadienolides by NMR and HPLC-MS techniques. Reaction phenotyping studies demonstrated that CYP3A mediated the metabolism of the two bufadienolides with a high specific selectivity. Further kinetic evaluation demonstrated that the metabolism stability of GB and AB were better than other reported bufadienolides. Additionally, the CYP3A5 preference for hydroxylation of AB was observed, which was different to the selectivity of CYP3As for bufadienolides suggested by our previous report. This study can provide important data for elucidating the phase I metabolism of GB and AB and can lead to a better understanding of the bufadienolide-CYP3A interaction which is helpful for preclinical development and rational use of bufadienolides. Copyright © 2017 Elsevier B.V. All rights reserved.

Degradation of phenolic compounds with hydrogen peroxide catalyzed by enzyme from Serratia marcescens AB 90027.

PubMed

Yao, Ri-Sheng; Sun, Min; Wang, Chun-Ling; Deng, Sheng-Song

2006-09-01

In this paper, the degradation of phenolic compounds using hydrogen peroxide as oxidizer and the enzyme extract from Serratia marcescens AB 90027 as catalyst was reported. With such an enzyme/H2O2 combination treatment, a high chemical oxygen demand (COD) removal efficiency was achieved, e.g., degradation of hydroquinone exceeded 96%. From UV-visible and IR spectra, the degradation mechanisms were judged as a process of phenyl ring cleavage. HPLC analysis shows that in the degradation p-benzoquinone, maleic acid and oxalic acid were formed as intermediates and that they were ultimately converted to CO2 and H2O. With the enzyme/H2O2 treatment, vanillin, hydroquinone, catechol, o-aminophenol, p-aminophenol, phloroglucinol and p-hydroxybenzaldehyde were readily degraded, whereas the degradation of phenol, salicylic acid, resorcinol, p-cholorophenol and p-nitrophenol were limited. Their degradability was closely related to the properties and positions of their side chain groups. Electron-donating groups, such as -OH, -NH2 and -OCH3 enhanced the degradation, whereas electron-withdrawing groups, such as -NO2, -Cl and -COOH, had a negative effect on the degradation of these compounds in the presence of enzyme/H2O2. Compounds with -OH at ortho and para positions were more readily degraded than those with -OH at meta positions.

The design and synthesis of 9-phenylcyclohepta[d]pyrimidine-2,4-dione derivatives as potent non-nucleoside inhibitors of HIV reverse transcriptase.

PubMed

Wang, Xiaowei; Lou, Qinghua; Guo, Ying; Xu, Yang; Zhang, Zhili; Liu, Junyi

2006-09-07

Novel compounds, which can be considered as conformationally restricted analogues of MKC-442, have been synthesized and tested as inhibitors of the reverse transcriptase of human immunodeficiency virus type-1 (HIV-1). Reaction of urea with a beta-ketoester furnished 6,7,8,9-tetrahydro-9-phenyl-1H-cyclohepta[d]pyrimidine-2,4-(3H,5H)-dione (6a) and 6,7,8,9-tetrahydro-9-p-tolyl-1H-cyclohepta[d]pyrimidine-2,4-(3H,5H)-dione (6b) which were then alkylated at the N-1 position with chloromethyl ether, allyl bromide and benzyl bromide to afford the target compounds 7a-b, 8a-b, 9 and 10, respectively. The seven-membered, annelated compounds have a relatively rigid structures and can lock the orientation of the aromatic ring. Chemical modification at N-1 of the pyrinidine ring and the 9-phenyl ring was attempted, with the aim of improving the antiretroviral activity. In particular, replacement of the aliphatic group with the phenyl moiety at the terminus of N-1 side chain can enhance the activity. The most active compounds showed activity in the low micromolar range with IC50 values comparable to that of nevirapine. The biological activity results are in accordance with the docking results.

A spatial scan statistic for compound Poisson data.

PubMed

Rosychuk, Rhonda J; Chang, Hsing-Ming

2013-12-20

The topic of spatial cluster detection gained attention in statistics during the late 1980s and early 1990s. Effort has been devoted to the development of methods for detecting spatial clustering of cases and events in the biological sciences, astronomy and epidemiology. More recently, research has examined detecting clusters of correlated count data associated with health conditions of individuals. Such a method allows researchers to examine spatial relationships of disease-related events rather than just incident or prevalent cases. We introduce a spatial scan test that identifies clusters of events in a study region. Because an individual case may have multiple (repeated) events, we base the test on a compound Poisson model. We illustrate our method for cluster detection on emergency department visits, where individuals may make multiple disease-related visits. Copyright © 2013 John Wiley & Sons, Ltd.

How Many-Body Correlations and α Clustering Shape He 6

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

Romero-Redondo, Carolina; Quaglioni, Sofia; Navrátil, Petr

The Borromean 6He nucleus is an exotic system characterized by two halo neutrons orbiting around a compact 4He (or α) core, in which the binary subsystems are unbound. The simultaneous reproduction of its small binding energy and extended matter and point-proton radii has been a challenge for ab initio theoretical calculations based on traditional bound-state methods. Using soft nucleon-nucleon interactions based on chiral effective field theory potentials, we show that supplementing the model space with 4He + n + n cluster degrees of freedom largely solves this issue. Lastly, we analyze the role played by α clustering and many-body correlations,more » and study the dependence of the energy spectrum on the resolution scale of the interaction.« less

How Many-Body Correlations and α Clustering Shape He 6

DOE PAGES

Romero-Redondo, Carolina; Quaglioni, Sofia; Navrátil, Petr; ...

2016-11-23

The Borromean 6He nucleus is an exotic system characterized by two halo neutrons orbiting around a compact 4He (or α) core, in which the binary subsystems are unbound. The simultaneous reproduction of its small binding energy and extended matter and point-proton radii has been a challenge for ab initio theoretical calculations based on traditional bound-state methods. Using soft nucleon-nucleon interactions based on chiral effective field theory potentials, we show that supplementing the model space with 4He + n + n cluster degrees of freedom largely solves this issue. Lastly, we analyze the role played by α clustering and many-body correlations,more » and study the dependence of the energy spectrum on the resolution scale of the interaction.« less

Dark Energy Domination In The Virgocentric Flow

NASA Astrophysics Data System (ADS)

Byrd, Gene; Chernin, A. D.; Karachentsev, I. D.; Teerikorpi, P.; Valtonen, M.; Dolgachev, V. P.; Domozhilova, L. M.

2011-04-01

Dark energy (DE) was first observationally detected at large Gpc distances. If it is a vacuum energy formulated as Einstein's cosmological constant, Λ, DE should also have dynamical effects at much smaller scales. Previously, we found its effects on much smaller Mpc scales in our Local Group (LG) as well as in other nearby groups. We used new HST observations of member 3D distances from the group centers and Doppler shifts. We find each group's gravity dominates a bound central system of galaxies but DE antigravity results in a radial recession increasing with distance from the group center of the outer members. Here we focus on the much larger (but still cosmologically local) Virgo Cluster and systems around it using new observations of velocities and distances. We propose an analytic model whose key parameter is the zero-gravity radius (ZGR) from the cluster center where gravity and DE antigravity balance. DE brings regularity to the Virgocentric flow. Beyond Virgo's 10 Mpc ZGR, the flow curves to approach a linear global Hubble law at larger distances. The Virgo cluster and its outer flow are similar to the Local Group and its local outflow with a scaling factor of about 10; the ZGR for Virgo is 10 times larger than that of the LG. The similarity of the two systems on the scales of 1 to 30 Mpc suggests that a quasi-stationary bound central component and an expanding outflow applies to a wide range of groups and clusters due to small scale action of DE as well as gravity. Chernin, et al 2009 Astronomy and Astrophysics 507, 1271 http://arxiv.org/abs/1006.0066 http://arxiv.org/abs/1006.0555

The Grism Lens-Amplified Survey from Space (GLASS). I. Survey Overview and First Data Release

NASA Astrophysics Data System (ADS)

Treu, T.; Schmidt, K. B.; Brammer, G. B.; Vulcani, B.; Wang, X.; Bradač, M.; Dijkstra, M.; Dressler, A.; Fontana, A.; Gavazzi, R.; Henry, A. L.; Hoag, A.; Huang, K.-H.; Jones, T. A.; Kelly, P. L.; Malkan, M. A.; Mason, C.; Pentericci, L.; Poggianti, B.; Stiavelli, M.; Trenti, M.; von der Linden, A.

2015-10-01

We give an overview of the Grism Lens Amplified Survey from Space (GLASS), a large Hubble Space Telescope program aimed at obtaining grism spectroscopy of the fields of 10 massive clusters of galaxies at redshift z = 0.308-0.686, including the Hubble Frontier Fields (HFF). The Wide Field Camera 3 (WFC3) yields near-infrared spectra of the cluster cores covering the wavelength range 0.81-1.69 μm through grisms G102 and G141, while the Advanced Camera for Surveys in parallel mode provides G800L spectra of the infall regions of the clusters. The WFC3 spectra are taken at two almost orthogonal position angles in order to minimize the effects of confusion. After summarizing the scientific drivers of GLASS, we describe the sample selection as well as the observing strategy and data processing pipeline. We then utilize MACS J0717.5+3745, a HFF cluster and the first one observed by GLASS, to illustrate the data quality and the high-level data products. Each spectrum brighter than {H}{{AB}}=23 is visually inspected by at least two co-authors and a redshift is measured when sufficient information is present in the spectra. Furthermore, we conducted a thorough search for emission lines through all of the GLASS WFC3 spectra with the aim of measuring redshifts for sources with continuum fainter than {H}{{AB}}=23. We provide a catalog of 139 emission-line-based spectroscopic redshifts for extragalactic sources, including three new redshifts of multiple image systems (one probable, two tentative). In addition to the data itself, we also release software tools that are helpful to navigate the data.

A Chandra Survey of Milky Way Globular Clusters. I. Emissivity and Abundance of Weak X-Ray Sources

NASA Astrophysics Data System (ADS)

Cheng, Zhongqun; Li, Zhiyuan; Xu, Xiaojie; Li, Xiangdong

2018-05-01

Based on archival Chandra data, we have carried out an X-ray survey of 69, or nearly half the known population of, Milky Way globular clusters (GCs), focusing on weak X-ray sources, mainly cataclysmic variables (CVs) and coronally active binaries (ABs). Using the cumulative X-ray luminosity per unit stellar mass (i.e., X-ray emissivity) as a proxy of the source abundance, we demonstrate a paucity (lower by 41% ± 27% on average) of weak X-ray sources in most GCs relative to the field, which is represented by the Solar Neighborhood and Local Group dwarf elliptical galaxies. We also revisit the mutual correlations among the cumulative X-ray luminosity (L X), cluster mass (M), and stellar encounter rate (Γ), finding {L}{{X}}\\propto {M}0.74+/- 0.13, {L}{{X}}\\propto {{{Γ }}}0.67+/- 0.07 and {{Γ }}\\propto {M}1.28+/- 0.17. The three quantities can further be expressed as {L}{{X}}\\propto {M}0.64+/- 0.12 {{{Γ }}}0.19+/- 0.07, which indicates that the dynamical formation of CVs and ABs through stellar encounters in GCs is less dominant than previously suggested, and that the primordial formation channel has a substantial contribution. Taking these aspects together, we suggest that a large fraction of primordial, soft binaries have been disrupted in binary–single or binary–binary stellar interactions before they could otherwise evolve into X-ray-emitting close binaries, whereas the same interactions also have led to the formation of new close binaries. No significant correlations between {L}{{X}}/{L}K and cluster properties, including dynamical age, metallicity, and structural parameters, are found.

Pathogenesis of chronic cluster headache and bouts: role of tryptamine, arginine metabolism and α1-agonists.

PubMed

D'Andrea, G; Bussone, G; Di Fiore, P; Perini, F; Gucciardi, A; Bolner, A; Aguggia, M; Saracco, G; Galloni, E; Giordano, G; Leon, A

2017-05-01

The aim of this study was to explore the possible role of tryptamine in the pathogenesis of chronic cluster headache along with that of adrenaline and noradrenaline (α-agonists) together with arginine metabolism in the origin of cluster bouts. Plasma levels of tyramine, tryptamine, serotonin, 5-hydroxyindolacetic acid, noradrenalin, adrenalin and the markers of arginine metabolism such as arginine, homoarginine, citrulline, ADMA and NMMA, were measured in 23 chronic cluster headache patients (10 chronic cluster ab initio and 13 transformed from episodic cluster) and 28 control subjects. The plasma levels of tyramine, tryptamine, noradrenalin and adrenalin were found several times higher in chronic cluster headache patients compared to controls, whereas the plasma levels of arginine, homoarginine and citrulline were significantly lower. No differences were found in the plasma levels of serotonin, 5-hydroxyindolacetic, ADMA and NMMA between chronic cluster headache patients and control subjects. These results provide support for a role of tryptamine in the pathogenesis of chronic cluster headache and, in particular, in the duration of the cluster bouts. In addition, the low levels of the nitric oxide substrates together with the high levels of noradrenalin and adrenalin suggest an activation of endothelial TAAR1 receptors followed by the release of nitric oxide in the circulation that may constitute the final step of the physiopathology of cluster crisis.

Microbial communities related to volatile organic compound emission in automobile air conditioning units.

PubMed

Diekmann, Nina; Burghartz, Melanie; Remus, Lars; Kaufholz, Anna-Lena; Nawrath, Thorben; Rohde, Manfred; Schulz, Stefan; Roselius, Louisa; Schaper, Jörg; Mamber, Oliver; Jahn, Dieter; Jahn, Martina

2013-10-01

During operation of mobile air conditioning (MAC) systems in automobiles, malodours can occur. We studied the microbial communities found on contaminated heat exchanger fins of 45 evaporators from car MAC systems which were operated in seven different regions of the world and identified corresponding volatile organic compounds. Collected biofilms were examined by scanning electron microscopy and fluorescent in situ hybridization. The detected bacteria were loosely attached to the metal surface. Further analyses of the bacteria using PCR-based single-strand conformation polymorphism and sequencing of isolated 16S rRNA gene fragments identified highly divergent microbial communities with multiple members of the Alphaproteobacteriales, Methylobacteria were the prevalent bacteria. In addition, Sphingomonadales, Burkholderiales, Bacillales, Alcanivorax spp. and Stenotrophomonas spp. were found among many others depending on the location the evaporators were operated. Interestingly, typical pathogenic bacteria related to air conditioning systems including Legionella spp. were not found. In order to determine the nature of the chemical compounds produced by the bacteria, the volatile organic compounds were examined by closed loop stripping analysis and identified by combined gas chromatography/mass spectrometry. Sulphur compounds, i.e. di-, tri- and multiple sulphides, acetylthiazole, aromatic compounds and diverse substituted pyrazines were detected. Mathematical clustering of the determined microbial community structures against their origin identified a European/American/Arabic cluster versus two mainly tropical Asian clusters. Interestingly, clustering of the determined volatiles against the origin of the corresponding MAC revealed a highly similar pattern. A close relationship of microbial community structure and resulting malodours to the climate and air quality at the location of MAC operation was concluded.

X-ray attenuation coefficients of high-atomic-number, hexanuclear transition metal cluster compounds: a new paradigm for radiographic contrast agents.

PubMed

Mullan, B F; Madsen, M T; Messerle, L; Kolesnichenko, V; Kruger, J

2000-04-01

The purpose of this study was to examine the radiologic attenuation properties of the parent cluster compounds, particularly attenuation as a function of discrete photon energy, before investigating ligand substitutions, which are necessary to improve cluster biocompatibility and to impart desirable physicochemical properties. The linear attenuation coefficients for solutions of the cluster compounds Ta6Br14, K8Ta6O19, and (H3O)2W6Cl14 were determined at 60, 80, 103, 122, and 140 keV from gamma-ray transmission measurements with americium-241, xenon-133, gadolinium-153, cobalt-57, and technetium-99m radioactive sources. Transmission measurements were obtained for a fixed time interval that ensured a statistically accurate count distribution exceeding 20,000 counts through the sample for each trial. On a strictly mole per liter basis, a 0.075 mol/L aqueous solution of K8Ta6O19 showed 1.08 times the attenuation of 0.063 mol/L aqueous iohexol at 60 keV and 3.30 times the attenuation at 80 keV. Similarly, a 0.05 mol/L methanolic solution of (H3O)2W6Cl4 showed 0.96 times (96%) the attenuation of 0.063 mol/L aqueous iohexol at 60 keV but 3.09 times the attenuation of the iohexol solution at 80 keV. Attenuations of 0.063 mol/L aqueous iohexol and 0.0125 mol/L Ta6Br14 (ie, at approximately one-fifth the iohexol concentration) were comparable at greater than 60 keV. These results confirm the theoretic potential for use of early transition metal cluster compounds as radiographic contrast agents. At higher x-ray energies, cluster compounds demonstrate multiplied x-ray attenuation relative to iodinated contrast agents.

Structural similarities between hematoidin crystals and asteroid bodies: evidence of lipid composition.

PubMed

Brenner, D S; Drachenberg, C B; Papadimitriou, J C

2001-02-01

Hematoidin crystals (HC) are found in tissues where extravasated erythrocytes undergo degradation. Previous studies have determined that hematoidin is composed, in part, of a bilirubin-like pigment. In a previous study (Papadimitriou and Drachenberg, Ultrastruct. Pathol. 16, 413-421, 1992), we demonstrated that giant cell asteroid bodies (AB) are formed by membrane lipid bilayers. We evaluated three cases in which HC developed within splenic infarcts. The crystals were analyzed by light microscopy (LM), electron microscopy (EM), and X-ray microanalysis. A case of sarcoidosis with multiple epithelioid granulomas containing AB was studied for comparison. By LM the HC demonstrated intense, golden-color, fine threads, both intracellularly and extracellularly, in small and large clusters, and in radiating, star-shape patterns ranging in size from 2 to 200 microm. By EM the HC were composed of a core of empty clefts, consistent with dissolved lipids, suggestive of cholesterol crystals, and were surrounded by myelinoid membrane aggregates. The AB showed by LM significant morphological similarities with the intracellular HC. By EM, the AB were composed of a core of dense phospholipid bilayer tubes surrounded by a halo of myelinoid membranes. No accumulation of specific elements was found in either HC or AB by X-ray microanalysis. HC and AB show a similar star-shape morphology by both LM and EM. We postulate that this shape is due to the physicochemical properties of the accumulated lipids which originate from superfluous cell membranes created during cell fusion in the case of AB and after cellular (predominantly red cell) breakdown in the case of HC. The golden color of the HC likely results from adsorption of hydrophobic bilirubin-like pigments left over from erythrocyte breakdown into the accumulated lipids. Thus, this study shows two different (patho)physiological processes that lead to a markedly similar morphological end-product and provides further support to our proposed mechanism for AB formation.

TOUCHSTONE II: a new approach to ab initio protein structure prediction.

PubMed

Zhang, Yang; Kolinski, Andrzej; Skolnick, Jeffrey

2003-08-01

We have developed a new combined approach for ab initio protein structure prediction. The protein conformation is described as a lattice chain connecting C(alpha) atoms, with attached C(beta) atoms and side-chain centers of mass. The model force field includes various short-range and long-range knowledge-based potentials derived from a statistical analysis of the regularities of protein structures. The combination of these energy terms is optimized through the maximization of correlation for 30 x 60,000 decoys between the root mean square deviation (RMSD) to native and energies, as well as the energy gap between native and the decoy ensemble. To accelerate the conformational search, a newly developed parallel hyperbolic sampling algorithm with a composite movement set is used in the Monte Carlo simulation processes. We exploit this strategy to successfully fold 41/100 small proteins (36 approximately 120 residues) with predicted structures having a RMSD from native below 6.5 A in the top five cluster centroids. To fold larger-size proteins as well as to improve the folding yield of small proteins, we incorporate into the basic force field side-chain contact predictions from our threading program PROSPECTOR where homologous proteins were excluded from the data base. With these threading-based restraints, the program can fold 83/125 test proteins (36 approximately 174 residues) with structures having a RMSD to native below 6.5 A in the top five cluster centroids. This shows the significant improvement of folding by using predicted tertiary restraints, especially when the accuracy of side-chain contact prediction is >20%. For native fold selection, we introduce quantities dependent on the cluster density and the combination of energy and free energy, which show a higher discriminative power to select the native structure than the previously used cluster energy or cluster size, and which can be used in native structure identification in blind simulations. These procedures are readily automated and are being implemented on a genomic scale.

Theoretical study of the H2 reaction with a Pt4 (111) cluster

NASA Astrophysics Data System (ADS)

Cruz, A.; Bertin, V.; Poulain, E.; Benitez, J. I.; Castillo, S.

2004-04-01

The Cs symmetry reaction of the H2 molecule on a Pt4 (111) clusters, has been studied using ab initio multiconfiguration self-consistent field plus extensive multireference configuration interaction variational and perturbative calculations. The H2 interaction by the vertex and by the base of a tetrahedral Pt4 cluster were studied in ground and excited triplet and singlet states (closed and open shells), where the reaction curves are obtained through many avoided crossings. The Pt4 cluster captures and activates the hydrogen molecule; it shows a similar behavior compared with other Ptn (n=1,2,3) systems. The Pt4 cluster in their lowest five open and closed shell electronic states: 3B2, 1B2, 1A1 3A1, 1A1, respectively, may capture and dissociate the H2 molecule without activation barriers for the hydrogen molecule vertex approach. For the threefolded site reaction, i.e., by the base, the situation is different, the hydrogen adsorption presents some barriers. The potential energy minima occur outside and inside the cluster, with strong activation of the H-H bond. In all cases studied, the Pt4 cluster does not absorb the hydrogen molecule.

Structural Evolution and Atom Clustering in β-SiAlON: β-Si 6–z Al z O z N 8–z

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

Cozzan, Clayton; Griffith, Kent J.; Laurita, Geneva

2017-02-06

SiAlON ceramics, solid solutions based on the Si 3N 4 structure, are important, lightweight structural materials with intrinsically high strength, high hardness, and high thermal and chemical stability. Described by the chemical formula β-Si 6–zAl zO zN 8–z, from a compositional viewpoint, these materials can be regarded as solid solutions between Si 3N 4 and Al 3O 3N. A key aspect of the structural evolution with increasing Al and O (z in the formula) is to understand how these elements are distributed on the β-Si 3N 4 framework. The average and local structural evolution of highly phase-pure samples of β-Simore » 6–zAl zO zN 8–z with z = 0.050, 0.075, and 0.125 are studied here, using a combination of X-ray diffraction, NMR studies, and density functional theory calculations. Synchrotron X-ray diffraction establishes sample purity and indicates subtle changes in the average structure with increasing Al content in these compounds. Solid-state magic-angle-spinning 27Al NMR experiments, coupled with detailed ab initio calculations of NMR spectra of Al in different AlO qN 4–q tetrahedra (0 ≤ q ≤ 4), reveal a tendency of Al and O to cluster in these materials. Independently, the calculations suggest an energetic preference for Al–O bond formation, instead of a random distribution, in the β-SiAlON system.« less

Ab initio investigation of Ti2Al(C,N) solid solutions

NASA Astrophysics Data System (ADS)

Arróyave, Raymundo; Radovic, Miladin

2011-10-01

Mn+1AXn phases (M: early transition metal, A: IIIA- or IVA-group element, X: carbon or nitrogen) are layered ternary compounds that possess both metal- and ceramic-like properties with numerous potential applications in bulk and thin film forms, particularly under high-temperature conditions. In this work, we use the cluster expansion formalism to investigate the energetics of C-N interactions across the entire Ti2AlC-Ti2AlN composition range. It is shown that there is a definite tendency for ordering in the C,N sublattice. However, the molar volume and bulk modulus of the ordered structures found along the Ti2AlC-Ti2AlN composition range show small deviations from the (linear) rule of mixing, indicating that despite the ordering tendencies, the C-N interactions are not strong and the solution becomes disordered at relatively low temperatures. Random solid solutions of Ti2AlC1-xNx are simulated using special quasirandom structures (SQS) with x=0.25, 0.50, and 0.75. The thermodynamic properties of these structures are compared to those of the structures found to belong to the ground state through the cluster expansion approach. It is found that the structural properties of these approximations to random alloys do not deviate significantly from Vegard's law. The trend in the structural parameters of these SQS are found to agree well with available experimental data and the predictions of the bulk modulus suggest a very weak alloying effect—with respect to Vegard's law—on the elastic properties of Ti2AlC1-xNx.

Anticoagulant Activity of a Unique Sulfated Pyranosic (1→3)-β-l-Arabinan through Direct Interaction with Thrombin*

PubMed Central

Fernández, Paula V.; Quintana, Irene; Cerezo, Alberto S.; Caramelo, Julio J.; Pol-Fachin, Laercio; Verli, Hugo; Estevez, José M.; Ciancia, Marina

2013-01-01

A highly sulfated 3-linked β-arabinan (Ab1) with arabinose in the pyranose form was obtained from green seaweed Codium vermilara (Bryopsidales). It comprised major amounts of units sulfated on C-2 and C-4 and constitutes the first polysaccharide of this type isolated in the pure form and fully characterized. Ab1 showed anticoagulant activity by global coagulation tests. Less sulfated arabinans obtained from the same seaweed have less or no activity. Ab1 exerts its activity through direct and indirect (antithrombin- and heparin cofactor II-mediated) inhibition of thrombin. Direct thrombin inhibition was studied in detail. By native PAGE, it was possible to detect formation of a complex between Ab1 and human thrombin (HT). Ab1 binding to HT was measured by fluorescence spectroscopy. CD spectra of the Ab1 complex suggested that ligand binding induced a small conformational change on HT. Ab1-thrombin interactions were studied by molecular dynamic simulations using the persulfated octasaccharide as model compound. Most carbohydrate-protein contacts would occur by interaction of sulfate groups with basic amino acid residues on the surface of the enzyme, more than 60% of them being performed by the exosite 2-composing residues. In these interactions, the sulfate groups on C-2 were shown to interact more intensely with the thrombin structure. In contrast, the disulfated oligosaccharide does not promote major conformational modifications at the catalytic site when complexed to exosite 1. These results show that this novel pyranosic sulfated arabinan Ab1 exerts its anticoagulant activity by a mechanism different from those found previously for other sulfated polysaccharides and glycosaminoglycans. PMID:23161548

Syntheses, structures and characterizations of three novel vanadium selenites with organically bonded copper/nickel complex

NASA Astrophysics Data System (ADS)

Qian, Cheng; Kong, Fang; Mao, Jiang-Gao

2016-06-01

A series of vanadium selenites covalently bonded with metal-organic complex, namely, Ni(2,2-bipy)2V2O4(SeO3)2 (1), Cu(2,2-bipy)V2O4(SeO3)2·0.5H2O (2) and Cu2(2,2-bipy)2V5O12(SeO3)2 (3) (2,2-bipy=2,2-bipyridine) have been hydrothermally synthesized and structurally characterized. They exhibit three different structural dimensions, from 0D cluster, 1D chain to 2D layer. Compound 1 features a 0D {Ni(2,2-bipy)2V2O4(SeO3)2}2 dimeric cluster composed of two {Ni(2,2-bipy)2}2+ moieties connected by the {V4O8(SeO3)4}4- cluster. Compound 2 shows a 1D {Cu(2,2-bipy)V2O4(SeO3)2}n chain in which the {Cu2(2,2-bipy)2}4+ moieties are bridged by the {V4O8(SeO3)4}4- clusters. Compound 3 displays a 2D structure consisted of mixed valence vanadium selenites layers {VIVVV4SeIV2O18}n4- and {Cu(2,2-bipy)}2+ complex moieties. The adjacent layers are further interconnected via π-π interactions between the 2,2-bipy ligands exhibiting an interesting 3D supramolecular architecture. Both compound 1 and 2 contain a new {V4O8(SeO3)4}4- cluster and compound 3 exhibits the first 2D vanadate polyhedral layer in vanadium selenites/tellurites with organic moieties.

Microhydration of caesium compounds: Cs, CsOH, CsI and Cs₂I₂ complexes with one to three H₂O molecules of nuclear safety interest.

PubMed

Sudolská, Mária; Cantrel, Laurent; Cernušák, Ivan

2014-04-01

Structure and thermodynamic properties (standard enthalpies of formation and Gibbs free energies) of hydrated caesium species of nuclear safety interest, Cs, CsOH, CsI and its dimer Cs₂I₂, with one up to three water molecules, are calculated to assess their possible existence in severe accident occurring to a pressurized water reactor. The calculations were performed using the coupled cluster theory including single, double and non-iterative triple substitutions (CCSD(T)) in conjunction with the basis sets (ANO-RCC) developed for scalar relativistic calculations. The second-order spin-free Douglas-Kroll-Hess Hamiltonian was used to account for the scalar relativistic effects. Thermodynamic properties obtained by these correlated ab initio calculations (entropies and thermal capacities at constant pressure as a function of temperature) are used in nuclear accident simulations using ASTEC/SOPHAEROS software. Interaction energies, standard enthalpies and Gibbs free energies of successive water molecules addition determine the ordering of the complexes. CsOH forms the most hydrated stable complexes followed by CsI, Cs₂I₂, and Cs. CsOH still exists in steam atmosphere even at quite high temperature, up to around 1100 K.

Novel Inhibitors of Cholesterol Degradation in Mycobacterium tuberculosis Reveal How the Bacterium’s Metabolism Is Constrained by the Intracellular Environment

PubMed Central

VanderVen, Brian C.; Fahey, Ruth J.; Lee, Wonsik; Liu, Yancheng; Abramovitch, Robert B.; Memmott, Christine; Crowe, Adam M.; Eltis, Lindsay D.; Perola, Emanuele; Deininger, David D.; Wang, Tiansheng; Locher, Christopher P.; Russell, David G.

2015-01-01

Mycobacterium tuberculosis (Mtb) relies on a specialized set of metabolic pathways to support growth in macrophages. By conducting an extensive, unbiased chemical screen to identify small molecules that inhibit Mtb metabolism within macrophages, we identified a significant number of novel compounds that limit Mtb growth in macrophages and in medium containing cholesterol as the principle carbon source. Based on this observation, we developed a chemical-rescue strategy to identify compounds that target metabolic enzymes involved in cholesterol metabolism. This approach identified two compounds that inhibit the HsaAB enzyme complex, which is required for complete degradation of the cholesterol A/B rings. The strategy also identified an inhibitor of PrpC, the 2-methylcitrate synthase, which is required for assimilation of cholesterol-derived propionyl-CoA into the TCA cycle. These chemical probes represent new classes of inhibitors with novel modes of action, and target metabolic pathways required to support growth of Mtb in its host cell. The screen also revealed a structurally-diverse set of compounds that target additional stage(s) of cholesterol utilization. Mutants resistant to this class of compounds are defective in the bacterial adenylate cyclase Rv1625/Cya. These data implicate cyclic-AMP (cAMP) in regulating cholesterol utilization in Mtb, and are consistent with published reports indicating that propionate metabolism is regulated by cAMP levels. Intriguingly, reversal of the cholesterol-dependent growth inhibition caused by this subset of compounds could be achieved by supplementing the media with acetate, but not with glucose, indicating that Mtb is subject to a unique form of metabolic constraint induced by the presence of cholesterol. PMID:25675247

Basis set and electron correlation effects on the polarizability and second hyperpolarizability of model open-shell π-conjugated systems

NASA Astrophysics Data System (ADS)

Champagne, Benoı̂t; Botek, Edith; Nakano, Masayoshi; Nitta, Tomoshige; Yamaguchi, Kizashi

2005-03-01

The basis set and electron correlation effects on the static polarizability (α) and second hyperpolarizability (γ) are investigated ab initio for two model open-shell π-conjugated systems, the C5H7 radical and the C6H8 radical cation in their doublet state. Basis set investigations evidence that the linear and nonlinear responses of the radical cation necessitate the use of a less extended basis set than its neutral analog. Indeed, double-zeta-type basis sets supplemented by a set of d polarization functions but no diffuse functions already provide accurate (hyper)polarizabilities for C6H8 whereas diffuse functions are compulsory for C5H7, in particular, p diffuse functions. In addition to the 6-31G*+pd basis set, basis sets resulting from removing not necessary diffuse functions from the augmented correlation consistent polarized valence double zeta basis set have been shown to provide (hyper)polarizability values of similar quality as more extended basis sets such as augmented correlation consistent polarized valence triple zeta and doubly augmented correlation consistent polarized valence double zeta. Using the selected atomic basis sets, the (hyper)polarizabilities of these two model compounds are calculated at different levels of approximation in order to assess the impact of including electron correlation. As a function of the method of calculation antiparallel and parallel variations have been demonstrated for α and γ of the two model compounds, respectively. For the polarizability, the unrestricted Hartree-Fock and unrestricted second-order Møller-Plesset methods bracket the reference value obtained at the unrestricted coupled cluster singles and doubles with a perturbative inclusion of the triples level whereas the projected unrestricted second-order Møller-Plesset results are in much closer agreement with the unrestricted coupled cluster singles and doubles with a perturbative inclusion of the triples values than the projected unrestricted Hartree-Fock results. Moreover, the differences between the restricted open-shell Hartree-Fock and restricted open-shell second-order Møller-Plesset methods are small. In what concerns the second hyperpolarizability, the unrestricted Hartree-Fock and unrestricted second-order Møller-Plesset values remain of similar quality while using spin-projected schemes fails for the charged system but performs nicely for the neutral one. The restricted open-shell schemes, and especially the restricted open-shell second-order Møller-Plesset method, provide for both compounds γ values close to the results obtained at the unrestricted coupled cluster level including singles and doubles with a perturbative inclusion of the triples. Thus, to obtain well-converged α and γ values at low-order electron correlation levels, the removal of spin contamination is a necessary but not a sufficient condition. Density-functional theory calculations of α and γ have also been carried out using several exchange-correlation functionals. Those employing hybrid exchange-correlation functionals have been shown to reproduce fairly well the reference coupled cluster polarizability and second hyperpolarizability values. In addition, inclusion of Hartree-Fock exchange is of major importance for determining accurate polarizability whereas for the second hyperpolarizability the gradient corrections are large.

Design of hydrophobic polyoxometalate hybrid assemblies beyond surfactant encapsulation.

PubMed

Song, Yu-Fei; McMillan, Nicola; Long, De-Liang; Thiel, Johannes; Ding, Yulong; Chen, Haisheng; Gadegaard, Nikolaj; Cronin, Leroy

2008-01-01

Grafting of C-6, C-16 and C-18 alkyl chains onto the hydrophilic Mn-Anderson clusters (compounds 2-4) has been achieved. Exchange of the tetrabutyl ammonium (TBA) with dimethyldioctadecyl ammonium (DMDOA) results in the formation of new polyoxometalate (POM) assemblies (compounds 5-6), in which the POM cores are covalently functionalized by hydrophilic alkyl-chains and enclosed by surfactant of DMDOABr. As a result, we have been able to design and synthesize POM-containing hydrophobic materials beyond surfactant encapsulation. In solid state, scanning electron and transmission electron microscopy (SEM and TEM) studies of the TBA salts of compounds 3 and 4 show highly ordered, uniform, reproducible assemblies with unique segmented rodlike morphology. SEM and TEM studies of the DMDOA salts of compounds 5 and 6 show that they form spherical and sea urchin 3D objects in different solvent systems. In solution, the physical properties of compound 5 and 6 (combination of surfactant-encapsulated cluster (SEC) and surface-grafted cluster (SGC)) show a liquid-to-gel phase transition in pure chloroform below 0 degrees C, which are much lower than other reported SECs. By utilizing light scattering measurements, the nanoparticle size for compounds 5 and 6 were measured at 5 degrees C and 30 degrees C, respectively. Other physical properties including differential scanning calorimetry have been reported.

Characterization of anticancer agents by their growth inhibitory activity and relationships to mechanism of action and structure.

PubMed

Keskin, O; Bahar, I; Jernigan, R L; Beutler, J A; Shoemaker, R H; Sausville, E A; Covell, D G

2000-04-01

An analysis of the growth inhibitory potency of 122 anticancer agents available from the National Cancer Institute anticancer drug screen is presented. Methods of singular value decomposition (SVD) were applied to determine the matrix of distances between all compounds. These SVD-derived dissimilarity distances were used to cluster compounds that exhibit similar tumor growth inhibitory activity patterns against 60 human cancer cell lines. Cluster analysis divides the 122 standard agents into 25 statistically distinct groups. The first eight groups include structurally diverse compounds with reactive functionalities that act as DNA-damaging agents while the remaining 17 groups include compounds that inhibit nucleic acid biosynthesis and mitosis. Examination of the average activity patterns across the 60 tumor cell lines reveals unique 'fingerprints' associated with each group. A diverse set of structural features are observed for compounds within these groups, with frequent occurrences of strong within-group structural similarities. Clustering of cell types by their response to the 122 anticancer agents divides the 60 cell types into 21 groups. The strongest within-panel groupings were found for the renal, leukemia and ovarian cell panels. These results contribute to the basis for comparisons between log(GI(50)) screening patterns of the 122 anticancer agents and additional tested compounds.

A bronze matryoshka: the discrete intermetalloid cluster [Sn@Cu12@Sn20](12-) in the ternary phases A12Cu12Sn21 (A = Na, K).

PubMed

Stegmaier, Saskia; Fässler, Thomas F

2011-12-14

The synthesis and crystal structure of the first ternary A-Cu-Sn intermetallic phases for the heavier alkali metals A = Na to Cs is reported. The title compounds A(12)Cu(12)Sn(21) show discrete 33-atom intermetalloid Cu-Sn clusters {Sn@Cu(12)@Sn(20)}, which are composed of {Sn(20)} pentagonal dodecahedra surrounding {Cu(12)} icosahedra with single Sn atoms at the center. Na(12)Cu(12)Sn(21) and K(12)Cu(12)Sn(21) were characterized by single-crystal XRD studies, and the successful synthesis of analogous A-Cu-Sn compounds with A = Rb and Cs is deduced from powder XRD data. The isotypic A(12)Cu(12)Sn(21) phases crystallize in the cubic space group Pn ̅3m (No. 224), with the Cu-Sn clusters adopting a face centered cubic arrangement. A formal charge of 12- can be assigned to the {Sn@Cu(12)@Sn(20)} cluster unit, and the interpretation of the title compounds as salt-like intermetallic phases featuring discrete anionic intermetalloid [Sn@Cu(12)@Sn(20)](12-) clusters separated by alkali metal cations is supported by electronic structure calculations. For both Na(12)Cu(12)Sn(21) and K(12)Cu(12)Sn(21), DFT band structure calculations (TB-LMTO-ASA) reveal a band gap. The discrete [Sn@Cu(12)@Sn(20)](12-) cluster is analyzed in consideration of the molecular orbitals obtained from hybrid DFT calculations (Gaussian 09) for the cluster anion. The [Sn@Cu(12)@Sn(20)](12-) cluster MOs can be classified with labels indicating the numbers of radial and angular nodes, in the style of spherical shell models of cluster bonding. © 2011 American Chemical Society

Assessment of types of synthetic cannabinoids in narcotic cases assessed by the Council of Forensic Medicine between 2011-2015, Ankara, Turkey.

PubMed

Göl, Ersin; Çok, İsmet

2017-11-01

Synthetic cannabinoids mimic the effects of cannabis and are the largest and fastest growing class of newly appearing designer drugs. Reports have revealed that various types of synthetic cannabinoids are mixed with herbal substances. The present study investigated the herbal substance cases involving synthetic cannabinoids in Ankara and nearby cities in Turkey. Data were collected from the reports of synthetic cannabinoids that were analyzed between January 01, 2011 and December 31, 2015 in the Ankara Narcotic Department of the Council of Forensic Medicine at the request of the judicial authorities. In all, 4610 narcotic reports were obtained and reviewed. Among these narcotic reports during the period, 370 reports (8%) were related to synthetic cannabinoids. 28 synthetic cannabinoid compounds could be identified in herbals: 5-F-AB-PINACA, 5-F-AKB-48, 5-F-NNEI, 5-F-PB-22, AB-CHMINACA, AB-FUBINACA, AB-PINACA, ADB-CHMINACA, ADB-FUBINACA, AKB-48, AM-2201, EAM-2201, JWH-018, JWH-022, JWH-031, JWH-122, JWH-201, JWH-210, JWH-250, JWH-251, JWH-307, MAM-2201, NM-2201, PB-22, RCS-4, THJ-2201, UR-144, XLR-11. The amount of herbals was 30.72g, 329.22g, 665.89g, 4844.7g, and 5684.3g in 2011, 2012, 2013, 2014, and 2015, respectively. Generally, herbals contained more than one synthetic cannabinoids. ADB-FUBINACA was the most common synthetic cannabinoid among the herbals determined in this study, which was 3132.43g, excepting multi-synthetic cannabinoid herbals. The amount and diversity of synthetic cannabinoid compounds have increased dramatically between 2011 and 2015. Copyright © 2017 Elsevier B.V. All rights reserved.

Sources, composition and absorption Ångström exponent of light-absorbing organic components in aerosol extracts from the Los Angeles Basin.

PubMed

Zhang, Xiaolu; Lin, Ying-Hsuan; Surratt, Jason D; Weber, Rodney J

2013-04-16

We investigate the sources, chemical composition, and spectral properties of light-absorbing organic aerosol extracts (i.e., brown carbon, or BrC) in the Los Angeles (LA) Basin during the CalNex-2010 field campaign. Light absorption of PM2.5 water-soluble components at 365 nm (Abs365), used as a proxy for water-soluble BrC, was well correlated with water-soluble organic carbon (WSOC) (r(2) = 0.55-0.65), indicating secondary organic aerosol (SOA) formation from anthropogenic emissions was the major source of water-soluble BrC in this region. Normalizing Abs365 to WSOC mass yielded an average solution mass absorption efficiency (MAE365) of 0.71 m(2) g(-1) C. Detailed chemical speciation of filter extracts identified eight nitro-aromatic compounds that were correlated with Abs365. These compounds accounted for ∼4% of the overall water-soluble BrC absorption. Methanol-extracted BrC in LA was approximately 3 and 21 times higher than water-soluble BrC at 365 and 532 nm, respectively, and had a MAE365 of 1.58 m(2) g(-1) C (Abs365 normalized to organic carbon mass). The water-insoluble BrC was strongly correlated with ambient elemental carbon concentration, suggesting similar sources. Absorption Ångström exponent (Å(a)) (fitted between 300 and 600 nm wavelengths) was 3.2 (±1.2) for the PILS water-soluble BrC measurement, compared to 4.8 (±0.5) and 7.6 (±0.5) for methanol- and water-soluble BrC from filter extracts, respectively. These results show that fine particle BrC was prevalent in the LA basin during CalNex, yet many of its properties and potential impacts remain unknown.

Filaments Production and Fused Deposition Modelling of ABS/Carbon Nanotubes Composites

PubMed Central

Fambri, Luca

2018-01-01

Composite acrylonitrile–butadiene–styrene (ABS)/carbon nanotubes (CNT) filaments at 1, 2, 4, 6 and 8 wt %, suitable for fused deposition modelling (FDM) were obtained by using a completely solvent-free process based on direct melt compounding and extrusion. The optimal CNT content in the filaments for FDM was found to be 6 wt %; for this composite, a detailed investigation of the thermal, mechanical and electrical properties was performed. Presence of CNT in ABS filaments and 3D-printed parts resulted in a significant enhancement of the tensile modulus and strength, accompanied by a reduction of the elongation at break. As documented by dynamic mechanical thermal analysis, the stiffening effect of CNTs in ABS is particularly pronounced at high temperatures. Besides, the presence of CNT in 3D-printed parts accounts for better creep and thermal dimensional stabilities of 3D-printed parts, accompanied by a reduction of the coefficient of thermal expansion). 3D-printed nanocomposite samples with 6 wt % of CNT exhibited a good electrical conductivity, even if lower than pristine composite filaments. PMID:29346291

{sup 75}As NMR study of the oriented pnictide superconducting compound NdFeAsO{sub 0.83}F{sub 0.17}

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

Pahari, Bholanath

Magnetization and {sup 75}As nuclear magnetic resonance (NMR) measurements in the superconductor NdFeAsO{sub 0.83}F{sub 0.17} (T{sub C}~46 K) are performed in order to investigate the effect of the Nd 4f electrons in the superconducting property. The magnetization curve displays a Nd 4f moments generated Curie-Weiss signal in the field of 7 T. {sup 75}As NMR spectra in the oriented sample (H{sub 0}‖ab) are recorded at 7 T in the temperature range 10–300 K and temperature dependent {sup 75}As NMR shift, K{sub ab} has been obtained. The K{sub ab} curve shows a Curie-Weiss type contribution. The magnitude of hyperfine field, H{submore » hf} (4.4 kOe/μ{sub B}) estimated from the K{sub ab} vs χ plot indicates a non-negligible RKKY-type interaction between localized Nd 4f moments mediated by itinerant Fe 3d electrons.« less

Probing the stereoselective interaction of ofloxacin enantiomers with corresponding monoclonal antibodies by multiple spectrometry

NASA Astrophysics Data System (ADS)

Mu, Hongtao; Xu, Zhenlin; Liu, Yingju; Sun, Yuanming; Wang, Baoling; Sun, Xiulan; Wang, Zhanhui; Eremin, Sergei; Zherdev, Anatoly V.; Dzantiev, Boris B.; Lei, Hongtao

2018-04-01

Although stereoselective antibody has immense potential in chiral compounds detection and separation, the interaction traits between stereoselective antibody and the corresponding antigenic enantiomers are not yet fully exploited. In this study, the stereospecific interactions between ofloxacin isomers and corresponding monoclonal antibodies (McAb-WR1 and McAb-MS1) were investigated using time-resolved fluorescence, steady-state fluorescence, and circular dichroism (CD) spectroscopic methods. The chiral recognition discrepancies of antibodies with ofloxacin isomers were reflected through binding constant, number of binding sites, driving forces and conformational changes. The major interacting forces of McAb-WR1 and McAb-MS1 chiral interaction systems were hydrophobic force and van der Waals forces joined up with hydrogen bonds, respectively. Synchronous fluorescence spectra and CD spectra results showed that the disturbing of tyrosine and tryptophan micro-environments were so slightly that no obvious secondary structure changes were found during the chiral hapten binding. Clarification of stereospecific interaction of antibody will facilitate the application of immunoassay to analyze chiral contaminants in food and other areas.

Filaments Production and Fused Deposition Modelling of ABS/Carbon Nanotubes Composites.

PubMed

Dul, Sithiprumnea; Fambri, Luca; Pegoretti, Alessandro

2018-01-18

Composite acrylonitrile-butadiene-styrene (ABS)/carbon nanotubes (CNT) filaments at 1, 2, 4, 6 and 8 wt %, suitable for fused deposition modelling (FDM) were obtained by using a completely solvent-free process based on direct melt compounding and extrusion. The optimal CNT content in the filaments for FDM was found to be 6 wt %; for this composite, a detailed investigation of the thermal, mechanical and electrical properties was performed. Presence of CNT in ABS filaments and 3D-printed parts resulted in a significant enhancement of the tensile modulus and strength, accompanied by a reduction of the elongation at break. As documented by dynamic mechanical thermal analysis, the stiffening effect of CNTs in ABS is particularly pronounced at high temperatures. Besides, the presence of CNT in 3D-printed parts accounts for better creep and thermal dimensional stabilities of 3D-printed parts, accompanied by a reduction of the coefficient of thermal expansion). 3D-printed nanocomposite samples with 6 wt % of CNT exhibited a good electrical conductivity, even if lower than pristine composite filaments.

Associative Asymmetry of Compound Words

ERIC Educational Resources Information Center

Caplan, Jeremy B.; Boulton, Kathy L.; Gagné, Christina L.

2014-01-01

Early verbal-memory researchers assumed participants represent memory of a pair of unrelated items with 2 independent, separately modifiable, directional associations. However, memory for pairs of unrelated words (A-B) exhibits associative symmetry: a near-perfect correlation between accuracy on forward (A??) and backward (??B) cued recall. This…

Machine learning of molecular electronic properties in chemical compound space

NASA Astrophysics Data System (ADS)

Montavon, Grégoire; Rupp, Matthias; Gobre, Vivekanand; Vazquez-Mayagoitia, Alvaro; Hansen, Katja; Tkatchenko, Alexandre; Müller, Klaus-Robert; Anatole von Lilienfeld, O.

2013-09-01

The combination of modern scientific computing with electronic structure theory can lead to an unprecedented amount of data amenable to intelligent data analysis for the identification of meaningful, novel and predictive structure-property relationships. Such relationships enable high-throughput screening for relevant properties in an exponentially growing pool of virtual compounds that are synthetically accessible. Here, we present a machine learning model, trained on a database of ab initio calculation results for thousands of organic molecules, that simultaneously predicts multiple electronic ground- and excited-state properties. The properties include atomization energy, polarizability, frontier orbital eigenvalues, ionization potential, electron affinity and excitation energies. The machine learning model is based on a deep multi-task artificial neural network, exploiting the underlying correlations between various molecular properties. The input is identical to ab initio methods, i.e. nuclear charges and Cartesian coordinates of all atoms. For small organic molecules, the accuracy of such a ‘quantum machine’ is similar, and sometimes superior, to modern quantum-chemical methods—at negligible computational cost.

Polymorphic improvement of Stillinger-Weber potential for InGaN

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

Zhou, Xiaowang W.; Jones, Reese E.; Chu, Kevin

A Stillinger-Weber potential is computationally very efficient for molecular dynamics simulations. Despite its simple mathematical form, the Stillinger-Weber potential can be easily parameterized to ensure that crystal structures with tetrahedral bond angles (e.g., diamond-cubic, zinc-blende, and wurtzite) are stable and have the lowest energy. As a result, the Stillinger-Weber potential has been widely used to study a variety of semiconductor elements and alloys. When studying an A-B binary system, however, the Stillinger-Weber potential is associated with two major drawbacks. First, it significantly overestimates the elastic constants of elements A and B, limiting its use for systems involving both compounds andmore » elements (e.g., an A/AB multilayer). Second, it prescribes equal energy for zinc-blende and wurtzite crystals, limiting its use for compounds with large stacking fault energies. Here in this paper, we utilize the polymorphic potential style recently implemented in LAMMPS to develop a modified Stillinger-Weber potential for InGaN that overcomes these two problems.« less

Polymorphic improvement of Stillinger-Weber potential for InGaN

NASA Astrophysics Data System (ADS)

Zhou, X. W.; Jones, R. E.; Chu, K.

2017-12-01

A Stillinger-Weber potential is computationally very efficient for molecular dynamics simulations. Despite its simple mathematical form, the Stillinger-Weber potential can be easily parameterized to ensure that crystal structures with tetrahedral bond angles (e.g., diamond-cubic, zinc-blende, and wurtzite) are stable and have the lowest energy. As a result, the Stillinger-Weber potential has been widely used to study a variety of semiconductor elements and alloys. When studying an A-B binary system, however, the Stillinger-Weber potential is associated with two major drawbacks. First, it significantly overestimates the elastic constants of elements A and B, limiting its use for systems involving both compounds and elements (e.g., an A/AB multilayer). Second, it prescribes equal energy for zinc-blende and wurtzite crystals, limiting its use for compounds with large stacking fault energies. Here, we utilize the polymorphic potential style recently implemented in LAMMPS to develop a modified Stillinger-Weber potential for InGaN that overcomes these two problems.

Observation of ferroelastic domains in layered magnetic compounds using birefringence imaging

NASA Astrophysics Data System (ADS)

Miura, Yoko; Okumura, Kazuya; Manaka, Hirotaka

2018-03-01

The two-dimensional Heisenberg antiferromagnet (C2H5NH3)2CuCl4 is a candidate compound for the coexistence of ferroelectricity and ferroelasticity; however, the microscopic observations of multiferroic domains may still be unclear. In-plane birefringence imaging measurements were performed to observe the manner in which the ferroelectric and the ferroelastic domains change during phase transitions between 15 K and 300 K. It was found that 90° ferroelastic domains appeared in the ab-plane at 300 K. As the temperature decreased toward 15 K, each domain inverted at a certain temperature (T a) without structural or magnetic phase transitions. The value of T a was found to be significantly influenced by external stresses; therefore, birefringence imaging techniques are useful for investigating variations in ferroelastic domains with temperature. Furthermore, a structural phase transition from orthorhombic to monoclinic or triclinic occurred at 230 ~ 240 K; however, no spontaneous polarization appeared in the ab-plane over the entire investigated range.

Ab initio and density functional force field studies on the IR spectra and structure of diazonium dicyanomethylide (diazodicyanomethane)

NASA Astrophysics Data System (ADS)

Georgieva, Miglena K.

2004-03-01

The structure of diazonium dicyanomethylide (diazodicyanomethane) +N 2-C(CN) 2-↔N 2C(CN) 2 has been studied on the basis of ab initio HF, MP2 and DFT BLYP force field calculations, as well as of literature IR spectra and X-ray diffraction structural data. The results have been compared with those obtained for a series of chemical relatives of the title compound, i.e. molecules, push-pull molecules, anions and zwitterions, containing α-dicyano or diazo fragments, and especially substituted ammonium dicyanomethylides and diazomethane +N 2-CH 2-↔N 2CH 2. It has been found on the basis of spectral, bond length, bond order and electric charge analyses that the diazonium (or carbanionic, left) canonical form is much more important for the title zwitterion, than the corresponding one for diazomethane. So, the title compound can be named (and considered as) both diazonium dicyanomethylide and dicyanodiazomethane.

Polymorphic improvement of Stillinger-Weber potential for InGaN

DOE PAGES

Zhou, Xiaowang W.; Jones, Reese E.; Chu, Kevin

2017-12-21

A Stillinger-Weber potential is computationally very efficient for molecular dynamics simulations. Despite its simple mathematical form, the Stillinger-Weber potential can be easily parameterized to ensure that crystal structures with tetrahedral bond angles (e.g., diamond-cubic, zinc-blende, and wurtzite) are stable and have the lowest energy. As a result, the Stillinger-Weber potential has been widely used to study a variety of semiconductor elements and alloys. When studying an A-B binary system, however, the Stillinger-Weber potential is associated with two major drawbacks. First, it significantly overestimates the elastic constants of elements A and B, limiting its use for systems involving both compounds andmore » elements (e.g., an A/AB multilayer). Second, it prescribes equal energy for zinc-blende and wurtzite crystals, limiting its use for compounds with large stacking fault energies. Here in this paper, we utilize the polymorphic potential style recently implemented in LAMMPS to develop a modified Stillinger-Weber potential for InGaN that overcomes these two problems.« less