Correction: Assembly and relaxation behaviours of phosphatidylethanolamine monolayers investigated by polarization and frequency resolved SFG-VS.

PubMed

Wei, Feng; Xiong, Wei; Li, Wenhui; Lu, Wangting; Allen, Heather C; Zheng, Wanquan

2016-06-14

Correction for 'Assembly and relaxation behaviours of phosphatidylethanolamine monolayers investigated by polarization and frequency resolved SFG-VS' by Feng Wei et al., Phys. Chem. Chem. Phys., 2015, 17, 25114-25122.

Correction: Influence of particle size and dielectric environment on the dispersion behaviour and surface plasmon in nickel nanoparticles.

PubMed

Sharma, Vikash; Chotia, Chanderbhan; Tarachand; Ganesan, Vedachalaiyer; Okram, Gunadhor S

2017-07-21

Correction for 'Influence of particle size and dielectric environment on the dispersion behaviour and surface plasmon in nickel nanoparticles' by Vikash Sharma et al., Phys. Chem. Chem. Phys., 2017, 19, 14096-14106.

Correction: Spectroscopic characteristics of the OSIRIS near-backscattering crystal analyser spectrometer on the ISIS pulsed neutron source.

PubMed

Telling, Mark T F; Campbell, Stuart I; Engberg, Dennis; Martín Y Marero, David; Andersen, Ken H

2016-03-21

Correction for 'Spectroscopic characteristics of the OSIRIS near-backscattering crystal analyser spectrometer on the ISIS pulsed neutron source' by Mark T. F. Telling et al., Phys. Chem. Chem. Phys., 2005, 7, 1255-1261.

Correction: The effect of recombination under short-circuit conditions on the determination of charge transport properties in nanostructured photoelectrodes.

PubMed

Villanueva-Cab, J; Anta, J A; Oskam, G

2016-05-28

Correction for 'The effect of recombination under short-circuit conditions on the determination of charge transport properties in nanostructured photoelectrodes' by J. Villanueva-Cab et al., Phys. Chem. Chem. Phys., 2016, 18, 2303-2308.

Correction: Conceptual design of tetraazaporphyrin- and subtetraazaporphyrin-based functional nanocarbon materials: electronic structures, topologies, optical properties, and methane storage capacities.

PubMed

Belosludov, Rodion V; Rhoda, Hannah M; Zhdanov, Ravil K; Belosludov, Vladimir R; Kawazoe, Yoshiyuki; Nemykin, Victor N

2017-08-02

Correction for 'Conceptual design of tetraazaporphyrin- and subtetraazaporphyrin-based functional nanocarbon materials: electronic structures, topologies, optical properties, and methane storage capacities' by Rodion V. Belosludov et al., Phys. Chem. Chem. Phys., 2016, 18, 13503-13518.

NMR parameters in column 13 metal fluoride compounds (AlF₃, GaF₃, InF₃ and TlF) from first principle calculations.

PubMed

Sadoc, Aymeric; Biswal, Mamata; Body, Monique; Legein, Christophe; Boucher, Florent; Massiot, Dominique; Fayon, Franck

2014-01-01

The relationship between the experimental (19)F isotropic chemical shift and the (19)F isotropic shielding calculated using the gauge including projector augmented-wave (GIPAW) method with PBE functional is investigated in the case of GaF3, InF3, TlF and several AlF3 polymorphs. It is shown that the linear correlation between experimental and DFT-PBE calculated values previously established on alkali, alkaline earth and rare earth of column 3 basic fluorides (Sadoc et al., Phys. Chem. Chem. Phys. 13 (2011) 18539-18550) remains valid in the case of column 13 metal fluorides, indicating that it allows predicting (19)F solid state NMR spectra of a broad range of crystalline fluorides with a relatively good accuracy. For the isostructural α-AlF3, GaF3 and InF3 phases, PBE-DFT geometry optimization leads to noticeably overbended M-F-M bond angles and underestimated (27)Al, (71)Ga and (115)In calculated quadrupolar coupling constants. For the studied compounds, whose structures are built of corner shared MF6 octahedra, it is shown that the electric field gradient (EFG) tensor at the cationic sites is not related to distortions of the octahedral units, in contrast to what previously observed for isolated AlF6 octahedra in fluoroaluminates. Copyright © 2014 Elsevier Inc. All rights reserved.

Comment on "Density functional theory analysis of structural and electronic properties of orthorhombic perovskite CH3NH3PbI3" by Y. Wang et al., Phys. Chem. Chem. Phys., 2014, 16, 1424-1429.

PubMed

Even, J; Pedesseau, L; Katan, C

2014-05-14

Yun Wang et al. used density functional theory (DFT) to investigate the orthorhombic phase of CH3NH3PbI3, which has recently shown outstanding properties for photovoltaic applications. Whereas their analysis of ground state properties may represent a valuable contribution to understanding this class of materials, effects of spin-orbit coupling (SOC) cannot be overlooked as was shown in earlier studies. Moreover, their discussion on optical properties may be misleading for non-DFT-experts, and the nice agreement between experimental and calculated band gap is fortuitous, stemming from error cancellations between SOC and many-body effects. Lastly, Bader charges suggest potential problems during crystal structure optimization.

Comment on ``Nonlinear gyrokinetic theory with polarization drift'' [Phys. Plasmas 17, 082304 (2010)

NASA Astrophysics Data System (ADS)

Leerink, S.; Parra, F. I.; Heikkinen, J. A.

2010-12-01

In this comment, we show that by using the discrete particle distribution function the changes of the phase-space volume of gyrocenter coordinates due to the fluctuating E ×B velocity do not explicitly appear in the Poisson equation and the [Sosenko et al., Phys. Scr. 64, 264 (2001)] result is recovered. It is demonstrated that there is no contradiction between the work presented by Sosenko et al. and the work presented by [Wang et al., Phys. Plasmas 17, 082304 (2010)].

Correction: Towards the rationalization of catalytic activity values by means of local hyper-softness on the catalytic site: a criticism about the use of net electric charges.

PubMed

Martínez-Araya, Jorge Ignacio; Grand, André; Glossman-Mitnik, Daniel

2016-01-28

Correction for 'Towards the rationalization of catalytic activity values by means of local hyper-softness on the catalytic site: a criticism about the use of net electric charges' by Jorge Ignacio Martínez-Araya et al., Phys. Chem. Chem. Phys., 2015, DOI: 10.1039/c5cp03822g.

Communication: The absolute shielding scales of oxygen and sulfur revisited

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

Komorovsky, Stanislav; Repisky, Michal; Malkin, Elena

2015-03-07

We present an updated semi-experimental absolute shielding scale for the {sup 17}O and {sup 33}S nuclei. These new shielding scales are based on accurate rotational microwave data for the spin–rotation constants of H{sub 2}{sup 17}O [Puzzarini et al., J. Chem. Phys. 131, 234304 (2009)], C{sup 17}O [Cazzoli et al., Phys. Chem. Chem. Phys. 4, 3575 (2002)], and H{sub 2}{sup 33}S [Helgaker et al., J. Chem. Phys. 139, 244308 (2013)] corrected both for vibrational and temperature effects estimated at the CCSD(T) level of theory as well as for the relativistic corrections to the relation between the spin–rotation constant and the absolutemore » shielding constant. Our best estimate for the oxygen shielding constants of H{sub 2}{sup 17}O is 328.4(3) ppm and for C{sup 17}O −59.05(59) ppm. The relativistic correction for the sulfur shielding of H{sub 2}{sup 33}S amounts to 3.3%, and the new sulfur shielding constant for this molecule is 742.9(4.6) ppm.« less

Revealing electronic structure changes in Chevrel phase cathodes upon Mg insertion using X-ray absorption spectroscopy

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

Wan, Liwen F.; Wright, Joshua; Perdue, Brian R.

Following previous work predicting the electronic response of the Chevrel phase Mo6S8 upon Mg insertion (Thole et al., Phys. Chem. Chem. Phys., 2015, 17, 22548), we provide the experimental proof, evident in X-ray absorption spectroscopy, to illustrate the charge compensation mechanism of the Chevrel phase compound during Mg insertion and de-insertion processes.

On the equivalence of LIST and DIIS methods for convergence acceleration

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

Garza, Alejandro J.; Scuseria, Gustavo E.

2015-04-28

Self-consistent field extrapolation methods play a pivotal role in quantum chemistry and electronic structure theory. We, here, demonstrate the mathematical equivalence between the recently proposed family of LIST methods [Wang et al., J. Chem. Phys. 134, 241103 (2011); Y. K. Chen and Y. A. Wang, J. Chem. Theory Comput. 7, 3045 (2011)] and the general form of Pulay’s DIIS [Chem. Phys. Lett. 73, 393 (1980); J. Comput. Chem. 3, 556 (1982)] with specific error vectors. Our results also explain the differences in performance among the various LIST methods.

Comment on “Theoretical analysis of high-field transport in graphene on a substrate” [J. Appl. Phys. 116, 034507 (2014)

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

Tan, Michael L. P.; Arora, Vijay K., E-mail: vijay.arora@wilkes.edu; Department of Electrical Engineering and Physics, Wilkes University, Wilkes-Barre, Pennsylvania 18766

2014-12-21

In a recent article, Serov et al. [J. Appl. Phys. 116, 034507 (2014)] claim: “This study represents the first time that the high-field behavior in graphene on a substrate was investigated taking into account intrinsic graphene properties,” ignoring the most recent anisotropic distribution function [V. K. Arora et al., J. Appl. Phys. 112, 114330 (2012)] also published in J. Appl. Phys., targeting the same experimental data [V. E. Dorgan et al., Appl. Phys. Lett. 97, 082112 (2010)]. The claim of Serov et al. of being first is refuted and many shortcomings of the hydrodynamic model for a highly quantum andmore » degenerate graphene nanolayer are pointed out.« less

New “Tau-Leap” Strategy for Accelerated Stochastic Simulation

PubMed Central

2015-01-01

The “Tau-Leap” strategy for stochastic simulations of chemical reaction systems due to Gillespie and co-workers has had considerable impact on various applications. This strategy is reexamined with Chebyshev’s inequality for random variables as it provides a rigorous probabilistic basis for a measured τ-leap thus adding significantly to simulation efficiency. It is also shown that existing strategies for simulation times have no probabilistic assurance that they satisfy the τ-leap criterion while the use of Chebyshev’s inequality leads to a specified degree of certainty with which the τ-leap criterion is satisfied. This reduces the loss of sample paths which do not comply with the τ-leap criterion. The performance of the present algorithm is assessed, with respect to one discussed by Cao et al. (J. Chem. Phys.2006, 124, 044109), a second pertaining to binomial leap (Tian and Burrage J. Chem. Phys.2004, 121, 10356; Chatterjee et al. J. Chem. Phys.2005, 122, 024112; Peng et al. J. Chem. Phys.2007, 126, 224109), and a third regarding the midpoint Poisson leap (Peng et al., 2007; Gillespie J. Chem. Phys.2001, 115, 1716). The performance assessment is made by estimating the error in the histogram measured against that obtained with the so-called stochastic simulation algorithm. It is shown that the current algorithm displays notably less histogram error than its predecessor for a fixed computation time and, conversely, less computation time for a fixed accuracy. This computational advantage is an asset in repetitive calculations essential for modeling stochastic systems. The importance of stochastic simulations is derived from diverse areas of application in physical and biological sciences, process systems, and economics, etc. Computational improvements such as those reported herein are therefore of considerable significance. PMID:25620846

New "Tau-Leap" Strategy for Accelerated Stochastic Simulation.

PubMed

Ramkrishna, Doraiswami; Shu, Che-Chi; Tran, Vu

2014-12-10

The "Tau-Leap" strategy for stochastic simulations of chemical reaction systems due to Gillespie and co-workers has had considerable impact on various applications. This strategy is reexamined with Chebyshev's inequality for random variables as it provides a rigorous probabilistic basis for a measured τ-leap thus adding significantly to simulation efficiency. It is also shown that existing strategies for simulation times have no probabilistic assurance that they satisfy the τ-leap criterion while the use of Chebyshev's inequality leads to a specified degree of certainty with which the τ-leap criterion is satisfied. This reduces the loss of sample paths which do not comply with the τ-leap criterion. The performance of the present algorithm is assessed, with respect to one discussed by Cao et al. ( J. Chem. Phys. 2006 , 124 , 044109), a second pertaining to binomial leap (Tian and Burrage J. Chem. Phys. 2004 , 121 , 10356; Chatterjee et al. J. Chem. Phys. 2005 , 122 , 024112; Peng et al. J. Chem. Phys. 2007 , 126 , 224109), and a third regarding the midpoint Poisson leap (Peng et al., 2007; Gillespie J. Chem. Phys. 2001 , 115 , 1716). The performance assessment is made by estimating the error in the histogram measured against that obtained with the so-called stochastic simulation algorithm. It is shown that the current algorithm displays notably less histogram error than its predecessor for a fixed computation time and, conversely, less computation time for a fixed accuracy. This computational advantage is an asset in repetitive calculations essential for modeling stochastic systems. The importance of stochastic simulations is derived from diverse areas of application in physical and biological sciences, process systems, and economics, etc. Computational improvements such as those reported herein are therefore of considerable significance.

Ir Spectroscopic Studies on Microsolvation of HCl by Water

NASA Astrophysics Data System (ADS)

Mani, Devendra; Schwan, Raffael; Fischer, Theo; Dey, Arghya; Kaufmann, Matin; Redlich, Britta; van der Meer, Lex; Schwaab, Gerhard; Havenith, Martina

2016-06-01

Acid dissociation reactions are at the heart of chemistry. These reactions are well understood at the macroscopic level. However, a microscopic level understanding is still in the early stages of development. Questions such as 'how many H_2O molecules are needed to dissociate one HCl molecule?' have been posed and explored both theoretically and experimentally.1-5 Most of the theoretical calculations predict that four H_2O molecules are sufficient to dissociate one HCl molecule, resulting in the formation of a solvent separated H_3O+(H_2O)3Cl- cluster.1-3 IR spectroscopy in helium nanodroplets has earlier been used to study this dissociation process.3-5 However, these studies were carried out in the region of O-H and H-Cl stretch, which is dominated by the spectral features of undissociated (HCl)m-(H_2O)n clusters. This contributed to the ambiguity in assigning the spectral features arising from the dissociated cluster.4,5 Recent predictions from Bowman's group, suggest the presence of a broad spectral feature (1300-1360 wn) for the H_3O+(H_2O)3Cl- cluster, corresponding to the umbrella motion of H_3O+ moiety.6 This region is expected to be free from the spectral features due to the undissociated clusters. In conjunction with the FELIX laboratory, we have performed experiments on the (HCl)m(H_2O)n (m=1-2, n≥4) clusters, aggregated in helium nanodroplets, in the 900-1700 wn region. Mass selective measurements on these clusters revealed the presence of a weak-broad feature which spans between 1000-1450 wn and depends on both HCl as well as H_2O concentration. Measurements are in progress for the different deuterated species. The details will be presented in the talk. References: 1) C.T. Lee et al., J. Chem. Phys., 104, 7081 (1996). 2) H. Forbert et al., J. Am. Chem. Soc., 133, 4062 (2011). 3) A. Gutberlet et al., Science, 324, 1545 (2009). 4) S. D. Flynn et al., J. Phys. Chem. Lett., 1, 2233 (2010). 5) M. Letzner et al., J. Chem. Phys., 139, 154304 (2013). 6) J. M

Sulfur Geochemical Analysis and Interpretation with ChemCam on the Curiosity Rover

NASA Astrophysics Data System (ADS)

Clegg, S. M.; Anderson, R. B.; Frydenvang, J.; Forni, O.; Newsom, H. E.; Blaney, D. L.; Maurice, S.; Wiens, R. C.

2017-12-01

The Curiosity rover has encountered many forms of sulfur including calcium sulfate veins [1], hydrated Mg sulfates, and Fe sulfates along the traverse through Gale crater. A new SO3 calibration model for the remote Laser-Induced Breakdown Spectroscopy (LIBS) technique used by the ChemCam instrument enables improved quantitative analysis of SO3, which has not been previously reported by ChemCam on a routine or quantitative basis. In this paper, the details of this new LIBS calibration model will be described and applied to many disparate Mars targets. Among them, Mavor contains a calcium sulfate vein surrounded by bedrock. In contrast, Jake M. is a float rock, Wernecke is a bedrock, Cumberland and Windjana are drill targets. In 2015 the ChemCam instrument team completed a re-calibration of major elements based on a significantly expanded set of >500 geochemical standards using the ChemCam testbed at Los Alamos National Laboratory [2]. In addition to these standards, the SO3 compositional range was recently extended with a series of doped samples containing various mixtures of Ca- and Mg-sulfate with basalt BHVO2. Spectra from these standards were processed per [4]. Calibration and Mars spectra were converted to peak-area-summed LIBS spectra that enables the SO3 calibration. These peak-area spectra were used to generate three overlapping partial least squares (PLS1) calibration sub-models as described by Anderson et al. [3, 5]. ChemCam analysis of Mavor involved a 3x3 raster in which locations 5 and 6 primarily probed Ca-sulfate material. The new ChemCam SO3 compositions for Mavor 5 and Mavor 6 are 48.6±1.2 and 50.3±1.2 wt% SO3, respectively. The LIBS spectra also recorded the presence of other elements that are likely responsible for the departure from pure Ca-sulfate chemistry. On the low-abundance side, the remaining 7 Mavor locations, Jake M., Cumberland, Windjana, and Wernecke all contain much lower SO3, between 1.4±0.5 wt% and 2.3±0.3 wt% SO3. [1] Nachon et

Elucidating the Complex Lineshapes Resulting from the Highly Sensitive, Ion Selective, Technique Nice-Ohvms

NASA Astrophysics Data System (ADS)

Hodges, James N.; Siller, Brian; McCall, Benjamin J.

2015-06-01

The technique Noise Immune Cavity Enhanced Optical Heterodyne Velocity Modulation Spectroscopy, or NICE-OHVMS, has been used to great effect to precisely and accurately measure a variety of molecular ion transitions from species such as H_3^+, CH_5^+, HeH^+, and HCO^+, achieving MHz or in some cases sub-MHz uncertainty. It is a powerful technique, but a complete theoretical understanding of the complex NICE-OHVMS lineshape is needed to fully unlock its potential. NICE-OHVMS is the direct result of the combination of the highly sensitive spectroscopic technique Noise Immune Cavity Enhanced Optical Heterodyne Molecular Spectroscopy(NICE-OHMS) with Velocity Modulation Spectroscopy(VMS), applying the most sensitive optical detection method with ion species selectivity. The theoretical underpinnings of NICE-OHMS lineshapes are well established, as are those of VMS. This presentation is the logical extension of those two preceding bodies of work. Simulations of NICE-OHVMS lineshapes under a variety of conditions and fits of experimental data to the model are presented. The significance and accuracy of the various inferred parameters, along with the prospect of using them to extract additional information from observed transitions, are discussed. J.~N. Hodges, et al. J. Chem. Phys. (2013), 139, 164201. A.~J. Perry, et al. J. Chem. Phys. (2014), 141, 101101. K.~N. Crabtree, et al. Chem. Phys. Lett. (2012), 551, 1-6. F.~M. Schmidt, et al. J. Opt. Soc. Amer. A (2008), 24, 1392--1405. J.~W. Farley, J. Chem. Phys. (1991), 95, 5590--5602.

A practical method to avoid zero-point leak in molecular dynamics calculations: application to the water dimer.

PubMed

Czakó, Gábor; Kaledin, Alexey L; Bowman, Joel M

2010-04-28

We report the implementation of a previously suggested method to constrain a molecular system to have mode-specific vibrational energy greater than or equal to the zero-point energy in quasiclassical trajectory calculations [J. M. Bowman et al., J. Chem. Phys. 91, 2859 (1989); W. H. Miller et al., J. Chem. Phys. 91, 2863 (1989)]. The implementation is made practical by using a technique described recently [G. Czako and J. M. Bowman, J. Chem. Phys. 131, 244302 (2009)], where a normal-mode analysis is performed during the course of a trajectory and which gives only real-valued frequencies. The method is applied to the water dimer, where its effectiveness is shown by computing mode energies as a function of integration time. Radial distribution functions are also calculated using constrained quasiclassical and standard classical molecular dynamics at low temperature and at 300 K and compared to rigorous quantum path integral calculations.

A Systematic Evaluation of the Extent of Photochemical Processing in Different Types of Secondary Organic Aerosols in the Aqueous Phase

NASA Astrophysics Data System (ADS)

Romonosky, D.; Lee, H.; Epstein, S. A.; Nizkorodov, S.; Laskin, J.; Laskin, A.

2013-12-01

al. Photolytic processing of secondary organic aerosols dissolved in cloud droplets. Phys. Chem. Chem. Phys. 2011, 13, 12199. Nguyen et al. Direct aqueous photochemistry of isoprene high-NOx secondary organic aerosol. Phys. Chem. Chem. Phys. 2012, 14, 9702. Walser et al. Photochemical aging of secondary organic aerosol particles generated from the oxidation of d-limonene. J. Phys. Chem. A 2007, 111, 1907.

PubChemSR: A search and retrieval tool for PubChem

PubMed Central

Hur, Junguk; Wild, David J

2008-01-01

Background Recent years have seen an explosion in the amount of publicly available chemical and related biological information. A significant step has been the emergence of PubChem, which contains property information for millions of chemical structures, and acts as a repository of compounds and bioassay screening data for the NIH Roadmap. There is a strong need for tools designed for scientists that permit easy download and use of these data. We present one such tool, PubChemSR. Implementation PubChemSR (Search and Retrieve) is a freely available desktop application written for Windows using Microsoft .NET that is designed to assist scientists in search, retrieval and organization of chemical and biological data from the PubChem database. It employs SOAP web services made available by NCBI for extraction of information from PubChem. Results and Discussion The program supports a wide range of searching techniques, including queries based on assay or compound keywords and chemical substructures. Results can be examined individually or downloaded and exported in batch for use in other programs such as Microsoft Excel. We believe that PubChemSR makes it straightforward for researchers to utilize the chemical, biological and screening data available in PubChem. We present several examples of how it can be used. PMID:18482452

ChemCam Science Objectives for the Mars Science Laboratory (MSL) Rover

NASA Technical Reports Server (NTRS)

Wiens, R.; Maurice, S.; Bridges, N.; Clark, B.; Cremers, D.; Herkenhoff, K.; Kirkland, L.; Mangold, N.; Manhes, G.; Mauchien, P.

2005-01-01

ChemCam consists of two remote sensing instruments. One, a Laser-Induced Breakdown Spectroscopy (LIBS) instrument provides rapid elemental composition data on rocks and soils within 13 m of the rover. By using laser pulses, it can remove dust or profile through weathering layers remotely. The other instrument, the Remote Micro-Imager (RMI), provides the highest resolution images between 2 m and infinity. At approximately 80 Rad field of view, its resolution exceeds that of MER Pancam by at least a factor of four. The ChemCam instruments are described in a companion paper by Maurice et al. [1]. Here we present the science objectives for the ChemCam instrument package.

ChemCam Science Objectives for the Mars Science Laboratory (MSL) Rover

NASA Technical Reports Server (NTRS)

Wiens, R.; Maurice, S.; Bridges, N.; Clark, B.; Cremers, D.; Herkenhoff, K.; Kirkland, L.; Mangold, N.; Manhes, G.; Mauchien, P.

2005-01-01

ChemCam consists of two remote sensing instruments. One, a Laser-Induced Breakdown Spectroscopy (LIBS) instrument provides rapid elemental composition data on rocks and soils within 13 m of the rover. By using laser pulses, it can remove dust or profile through weathering layers remotely. The other instrument, the Remote Micro-Imager (RMI), provides the highest resolution images between 2 m and infinity. At approximately 80 Rad field of view, its resolution exceeds that of MER Pancam by at least a factor of four. The ChemCam instruments are described in a companion paper by Maurice et al. Here we present the science objectives for the ChemCam instrument package.

The new insight into dynamic crossover in glass forming liquids from the apparent enthalpy analysis

NASA Astrophysics Data System (ADS)

Martinez-Garcia, Julio Cesar; Martinez-Garcia, Jorge; Rzoska, Sylwester J.; Hulliger, Jürg

2012-08-01

One of the most intriguing phenomena in glass forming systems is the dynamic crossover (TB), occurring well above the glass temperature (Tg). So far, it was estimated mainly from the linearized derivative analysis of the primary relaxation time τ(T) or viscosity η(T) experimental data, originally proposed by Stickel et al. [J. Chem. Phys. 104, 2043 (1996), 10.1063/1.470961; Stickel et al. J. Chem. Phys. 107, 1086 (1997)], 10.1063/1.474456. However, this formal procedure is based on the general validity of the Vogel-Fulcher-Tammann equation, which has been strongly questioned recently [T. Hecksher et al. Nature Phys. 4, 737 (2008), 10.1038/nphys1033; P. Lunkenheimer et al. Phys. Rev. E 81, 051504 (2010), 10.1103/PhysRevE.81.051504; J. C. Martinez-Garcia et al. J. Chem. Phys. 134, 024512 (2011)], 10.1063/1.3514589. We present a qualitatively new way to identify the dynamic crossover based on the apparent enthalpy space (H_a^' = {{dln τ }/{d({1/T})}}) analysis via a new plot ln H_a^' vs. 1/T supported by the Savitzky-Golay filtering procedure for getting an insight into the noise-distorted high order derivatives. It is shown that depending on the ratio between the "virtual" fragility in the high temperature dynamic domain (mhigh) and the "real" fragility at Tg (the low temperature dynamic domain, m = mlow) glass formers can be splitted into two groups related to f < 1 and f > 1, (f = mhigh/mlow). The link of this phenomenon to the ratio between the apparent enthalpy and activation energy as well as the behavior of the configurational entropy is indicated.

Impact of a new wavelength-dependent representation of methane photolysis branching ratios on the modeling of Titan’s atmospheric photochemistry

NASA Astrophysics Data System (ADS)

Gans, B.; Peng, Z.; Carrasco, N.; Gauyacq, D.; Lebonnois, S.; Pernot, P.

2013-03-01

A new wavelength-dependent model for CH4 photolysis branching ratios is proposed, based on the values measured recently by Gans et al. (Gans, B. et al. [2011]. Phys. Chem. Chem. Phys. 13, 8140-8152). We quantify the impact of this representation on the predictions of a photochemical model of Titan’s atmosphere, on their precision, and compare to earlier representations. Although the observed effects on the mole fraction of the species are small (never larger than 50%), it is possible to draw some recommendations for further studies: (i) the Ly-α branching ratios of Wang et al. (Wang, J.H. et al. [2000]. J. Chem. Phys. 113, 4146-4152) used in recent models overestimate the CH2:CH3 ratio, a factor to which a lot of species are sensitive; (ii) the description of out-of-Ly-α branching ratios by the “100% CH3” scenario has to be avoided, as it can bias significantly the mole fractions of some important species (C3H8); and (iii) complementary experimental data in the 130-140 nm range would be useful to constrain the models in the Ly-α deprived 500-700 km altitude range.

Theoretical description of the mixed-field orientation of asymmetric-top molecules: A time-dependent study

NASA Astrophysics Data System (ADS)

Omiste, Juan J.; González-Férez, Rosario

2016-12-01

We present a theoretical study of the mixed-field-orientation of asymmetric-top molecules in tilted static electric field and nonresonant linearly polarized laser pulse by solving the time-dependent Schrödinger equation. Within this framework, we compute the mixed-field orientation of a state-selected molecular beam of benzonitrile (C7H5N ) and compare with the experimental observations [J. L. Hansen et al., Phys. Rev. A 83, 023406 (2011), 10.1103/PhysRevA.83.023406] and with our previous time-independent descriptions [J. J. Omiste et al., Phys. Chem. Chem. Phys. 13, 18815 (2011), 10.1039/c1cp21195a]. For an excited rotational state, we investigate the field-dressed dynamics for several field configurations as those used in the mixed-field experiments. The nonadiabatic phenomena and their consequences on the rotational dynamics are analyzed in detail.

Visible Photodissociation Spectra of the 1-METHYL and 2-METHYLNAPHTHALENE Cations: Laser Spectroscopy and Theoretical Simulations

NASA Astrophysics Data System (ADS)

Friha, Hela; Feraud, Geraldine; Falvo, Cyril; Parneix, Pascal; Pino, Thomas; Brechignac, Philippe; Troy, Tyler; Schmidt, Timothy; Dhaouadi, Zoubeida

2014-06-01

Naphthalene (Np) and its methylated derivatives (1-Me-Np and 2-Me-Np) are prototype molecules for spectroscopists as first members of the polycyclic aromatic hydrocarbons (PAHs) family. High resolution studies are capable to explore the details of the internal rotation of the methyl group. Although this was achieved in neutral PAHs, the task is not the same in cations. Me-Np cations have been probed by resonance-enhanced multiphoton dissociation, showing only very broad and unresolved spectra, while absorption in argon matrix revealed more resolved vibronic bands. The electronic absorption gas phase spectra of 1-Me-Np^+ and 2-Me-Np^+ were measured using an Ar-tagging technique. In both cases, a band system was observed in the visible range and assigned to the D_2← D_0 transition. The 1-Me-Np^+ absorption bands revealed a red shift of 808 cm-1, relative to Np^+ (14 906 cm-1), while for 2-Me-Np^+ a blue shift of 226 cm-1 was found. A short vibrational progression was also observed. Moreover, insights into the internal rotation motion of the CH_3 were inferred, although intrinsic broadening due to intramolecular relaxation was present. These measurements were supported by detailed quantum chemical calculations that allowed exploration of the potential energy curves, along with a complete simulation of the harmonic FC factors using the cumulant Gaussian fluctuations formalism, extended to include the internal rotation. see for instance Baba et al, J.Phys.Chem.A, 2009, 113, 2366 Dunbar et al, J. Am. Chem. Soc. 1976, 98, 7994-7999; J.Phys.Chem. 1985, 89, 3617 Andrews et al, J.Phys.Chem. 1982, 86, 2916 Pino et al, J. Chem. Phys. 1999, 111, 7337-7347

Literature information in PubChem: associations between PubChem records and scientific articles.

PubMed

Kim, Sunghwan; Thiessen, Paul A; Cheng, Tiejun; Yu, Bo; Shoemaker, Benjamin A; Wang, Jiyao; Bolton, Evan E; Wang, Yanli; Bryant, Stephen H

2016-01-01

PubChem is an open archive consisting of a set of three primary public databases (BioAssay, Compound, and Substance). It contains information on a broad range of chemical entities, including small molecules, lipids, carbohydrates, and (chemically modified) amino acid and nucleic acid sequences (including siRNA and miRNA). Currently (as of Nov. 2015), PubChem contains more than 150 million depositor-provided chemical substance descriptions, 60 million unique chemical structures, and 225 million biological activity test results provided from over 1 million biological assay records. Many PubChem records (substances, compounds, and assays) include depositor-provided cross-references to scientific articles in PubMed. Some PubChem contributors provide bioactivity data extracted from scientific articles. Literature-derived bioactivity data complement high-throughput screening (HTS) data from the concluded NIH Molecular Libraries Program and other HTS projects. Some journals provide PubChem with information on chemicals that appear in their newly published articles, enabling concurrent publication of scientific articles in journals and associated data in public databases. In addition, PubChem links records to PubMed articles indexed with the Medical Subject Heading (MeSH) controlled vocabulary thesaurus. Literature information, both provided by depositors and derived from MeSH annotations, can be accessed using PubChem's web interfaces, enabling users to explore information available in literature related to PubChem records beyond typical web search results. Graphical abstractLiterature information for PubChem records is derived from various sources.

Response to "Comment on `Solitonic and chaotic behaviors for the nonlinear dust-acoustic waves in a magnetized dusty plasma'" [Phys. Plasmas 24, 094701 (2017)

NASA Astrophysics Data System (ADS)

Zhen, Hui-Ling; Tian, Bo; Xie, Xi-Yang; Wu, Xiao-Yu; Wen, Xiao-Yong

2018-02-01

On our previous construction [H. L. Zhen et al., Phys. Plasmas 23, 052301 (2016)] of the soliton solutions of a model describing the dynamics of the dust particles in a weakly ionized, collisional dusty plasma comprised of the negatively charged cold dust particles, hot ions, hot electrons, and stationary neutrals in the presence of an external static magnetic field, Ali et al. [Phys. Plasmas 24, 094701 (2017)] have commented that there exists a different form of Eq. (4) from that shown in Zhen et al. [Phys. Plasmas 23, 052301 (2016)] and that certain interesting phenomena with the dust neutral collision frequency ν0>0 are ignored in Zhen et al. [Phys. Plasmas 23, 052301 (2016)]. In this Reply, according to the transformation given by the Ali et al. [Phys. Plasmas 24, 094701 (2017)] comment, we present some one-, two-, and N-soliton solutions which have not been obtained in the Ali et al. [Phys. Plasmas 24, 094701 (2017)] comment. We point out that our previous solutions in Zhen et al. [Phys. Plasmas 23, 052301 (2016)] are still valid because of the similarity between the two dispersion relations of previous solutions in Zhen et al. [Phys. Plasmas 23, 052301 (2016)] and the solutions presented in this Reply. Based on our soliton solutions in this Reply, it is found that the soliton amplitude is inversely related to Zd and B0, but positively related to md and α, where α refers to the coefficient of the nonlinear term, Zd and md are the charge number and mass of a dust particle, respectively, B0 represents the strength of the external static magnetic field. We also find that the two solitons are always in parallel during the propagation.

Fixed node diffusion Monte Carlo using a genetic algorithm: a study of the CO-(4)He(N) complex, N = 1…10.

PubMed

Ramilowski, Jordan A; Farrelly, David

2012-06-14

The diffusion Monte Carlo (DMC) method is a widely used algorithm for computing both ground and excited states of many-particle systems; for states without nodes the algorithm is numerically exact. In the presence of nodes approximations must be introduced, for example, the fixed-node approximation. Recently we have developed a genetic algorithm (GA) based approach which allows the computation of nodal surfaces on-the-fly [Ramilowski and Farrelly, Phys. Chem. Chem. Phys., 2010, 12, 12450]. Here GA-DMC is applied to the computation of rovibrational states of CO-(4)He(N) complexes with N≤ 10. These complexes have been the subject of recent high resolution microwave and millimeter-wave studies which traced the onset of microscopic superfluidity in a doped (4)He droplet, one atom at a time, up to N = 10 [Surin et al., Phys. Rev. Lett., 2008, 101, 233401; Raston et al., Phys. Chem. Chem. Phys., 2010, 12, 8260]. The frequencies of the a-type (microwave) series, which correlate with end-over-end rotation in the CO-(4)He dimer, decrease from N = 1 to 3 and then smoothly increase. This signifies the transition from a molecular complex to a quantum solvated system. The frequencies of the b-type (millimeter-wave) series, which evolves from free rotation of the rigid CO molecule, initially increase from N = 0 to N∼ 6 before starting to decrease with increasing N. An interesting feature of the b-type series, originally observed in the high resolution infra-red (IR) experiments of Tang and McKellar [J. Chem. Phys., 2003, 119, 754] is that, for N = 7, two lines are observed. The GA-DMC algorithm is found to be in good agreement with experimental results and possibly detects the small (∼0.7 cm(-1)) splitting in the b-series line at N = 7. Advantages and disadvantages of GA-DMC are discussed.

Advanced Chemical Measurements of Smoke from DoD-prescribed Burns

DTIC Science & Technology

2014-04-01

and in the Yucatan Peninsula of Mexico. Keene et al. [2006] 72 observed ΔHONO/ΔNOx ratios (50th percentile) for African samples of grass (0.048...h from a plume in the Yucatan . In context, O3 formation is probably ubiquitous in tropical biomass burning plumes, but O3 destruction, as well as...via two dimensional heteronuclear NMR spectroscopy,” Phys. Chem. Chem. Phys., 11, 7810–7818, (2009). Marschner, H. 1986. Mineral Nutrition of

Comment on ``Turbulent equipartition theory of toroidal momentum pinch'' [Phys. Plasmas 15, 055902 (2008)

NASA Astrophysics Data System (ADS)

Peeters, A. G.; Angioni, C.; Strintzi, D.

2009-03-01

The comment addresses questions raised on the derivation of the momentum pinch velocity due to the Coriolis drift effect [A. G. Peeters et al., Phys. Rev. Lett. 98, 265003 (2007)]. These concern the definition of the gradient, and the scaling with the density gradient length. It will be shown that the turbulent equipartition mechanism is included within the derivation using the Coriolis drift, with the density gradient scaling being the consequence of drift terms not considered in [T. S. Hahm et al., Phys. Plasmas 15, 055902 (2008)]. Finally the accuracy of the analytic models is assessed through a comparison with the full gyrokinetic solution.

Analysis of photon count data from single-molecule fluorescence experiments

NASA Astrophysics Data System (ADS)

Burzykowski, T.; Szubiakowski, J.; Rydén, T.

2003-03-01

We consider single-molecule fluorescence experiments with data in the form of counts of photons registered over multiple time-intervals. Based on the observation schemes, linking back to works by Dehmelt [Bull. Am. Phys. Soc. 20 (1975) 60] and Cook and Kimble [Phys. Rev. Lett. 54 (1985) 1023], we propose an analytical approach to the data based on the theory of Markov-modulated Poisson processes (MMPP). In particular, we consider maximum-likelihood estimation. The method is illustrated using a real-life dataset. Additionally, the properties of the proposed method are investigated through simulations and compared to two other approaches developed by Yip et al. [J. Phys. Chem. A 102 (1998) 7564] and Molski [Chem. Phys. Lett. 324 (2000) 301].

Summary of PhysPAG Activity

NASA Astrophysics Data System (ADS)

Nousek, John A.

2014-01-01

The Physics of the Cosmos Program Analysis Group (PhysPAG) is responsible for solicitiing and coordinating community input for the development and execution of NASA's Physics of the Cosmos (PCOS) program. In this session I will report on the activity of the PhysPAG, and solicit community involvement in the process of defining PCOS objectives, planning SMD architecture, and prioritizing PCOS activities. I will also report on the activities of the PhysPAG Executive Committee, which include the chairs of the Science Analysis Groups/ Science Interest Groups which fall under the PhysPAG sphere of interest. Time at the end of the presentation willl be reserved for questions and discussion from the community.

Rapid Analysis of Energetic and Geo-Materials Using Laser Induced Breakdown Spectroscopy

DTIC Science & Technology

2013-04-01

et al ., Anal Bioanal Chem ( 2006 ) 385, 316. 5. Mohamed, W. T. Y., Prog Phys (2007) 2, 42. 6. Elhassan, A., et al ., Spectrochim Acta B (2008) 63...Anal (2005) 5, 21. 20. Anzano, J. M., et al ., Anal Chim Acta ( 2006 ) 575, 230. 21. Rusak, D. A., et al ., TrAC Trend Anal Chem (1998) 17, 453. 22. Martin...Spectrosc Reviews (2004) 39, 27. 25. Winefordner, J. D., et al ., J Anal Atom Spectrom (2004) 19, 1061. 26. Cremers , D. A., and Radziemski, L. J.,

A molecular theory of cartilage viscoelasticity.

PubMed

Kovach, I S

1996-03-07

Recent work on the subject of cartilage mechanics has begun to focus on the relationship between the microscopic structure of cartilage and its macroscopic mechanical properties (Bader et al., Biochem. Biophys. Acta, 1116 (1992) 147-154; Buschmann, PhD Thesis, Massachusetts Institute of Technology, 1992; Kovach, Biophys. Chem., 53 (1995) 181-187; Lai et al., J. Biochem. Eng., 113 (1991) 245-248; Armstrong and Mow, J. Bone Jt. Surg., 64A (1982) 88; Jackson and James, Biorheology, 19 (1982) 317-330). This paper reviews recent theoretical developments and presents a comprehensive explanation of the viscoelastic properties of cartilage in terms of molecular structure. In doing this, a closed form hybrid solution to the non-linear, cylindrical Poisson-Boltzmann equation is developed to describe the charge-dependent component of the equilibrium elasticity arising from polysaccharide charge (Benham, J. Chem. Phys., 79 (4) (1983) 1969-1973; Einevoll and Hemmer, J. Phys. Chem., 89 (1) (1988) 474-484; Fixman, J. Chem. Phys., 70 (11) (1979) 4995-5001; Ramanathan and Woodburg, J. Chem. Phys., 82 (3) (1985) 1482-1491; Wennerstrom et al., J. Chem. Phys., 76 (9) (1982) 4665-4670). This solution agrees with numerical solutions found in the literature (Buschmann, PhD Thesis, Massachusetts Institute of Technology, 1992). The charge-independent, entropic contribution to the equilibrium elasticity is explained in a manner similar to that recently presented for concentrated proteoglycan solution (Kovach, Biophys. Chem., 53 (1995) 181-187). This approach exploits a lattice model of the solution, subject to a Bragg-Williams type approximation to derive the volume dependence of polysaccharide configuration entropy (Flory, Principles of Polymer Chemistry, Cornell University Press, Ithaca, NY, 1953; Huggins, Some properties of Solutions of Long-chain Compounds, 1941, pp. 151-157; Stanley, Introduction to Phase Transitions and Critical Phenomena, Oxford University Press, Oxford, 1971

betaFIT: A computer program to fit pointwise potentials to selected analytic functions

NASA Astrophysics Data System (ADS)

Le Roy, Robert J.; Pashov, Asen

2017-01-01

This paper describes program betaFIT, which performs least-squares fits of sets of one-dimensional (or radial) potential function values to four different types of sophisticated analytic potential energy functional forms. These families of potential energy functions are: the Expanded Morse Oscillator (EMO) potential [J Mol Spectrosc 1999;194:197], the Morse/Long-Range (MLR) potential [Mol Phys 2007;105:663], the Double Exponential/Long-Range (DELR) potential [J Chem Phys 2003;119:7398], and the "Generalized Potential Energy Function (GPEF)" form introduced by Šurkus et al. [Chem Phys Lett 1984;105:291], which includes a wide variety of polynomial potentials, such as the Dunham [Phys Rev 1932;41:713], Simons-Parr-Finlan [J Chem Phys 1973;59:3229], and Ogilvie-Tipping [Proc R Soc A 1991;378:287] polynomials, as special cases. This code will be useful for providing the realistic sets of potential function shape parameters that are required to initiate direct fits of selected analytic potential functions to experimental data, and for providing better analytical representations of sets of ab initio results.

Influence of the Renner-Teller Coupling in CO+H Collision Dynamics

NASA Astrophysics Data System (ADS)

Ndengue, Steve Alexandre; Dawes, Richard

2017-06-01

Carbon monoxide is after molecular hydrogen the second most abundant molecule in the universe and an important molecule for processes occurring in the atmosphere, hydrocarbon combustion and the interstellar medium. The rate coefficients of CO in collision with dominant species like H, H_2, He, etc are necessary to understand the CO emission spectrum or to model combustion chemistry processes. The inelastic scattering of CO with H has been intensively studied theoretically in the past decades,^1 mostly using the so-called WKS PES^6 developed by Werner et al. or recently a modified version by Song et al.^2 Though the spectroscopic agreement of the WKS surface with experiment is quite good, so far the studies of scattering dynamics have neglected coupling to an electronic excited state. We present new results on a set of HCO surfaces of the ground and the excited Renner-Teller coupled electronic states^3 with the principal objective of studying the influence of the Renner-Teller coupling on the inelastic scattering of CO+H. Our calculations done using the MCTDH^4 algorithm in the 0-2 eV energy range allow evaluation of the contribution of the Renner-Teller coupling on the rovibrationally inelastic scattering and discuss the relevance and reliability of the calculations. References:} 1. N. Balakrishnan, M. Yan and A. Dalgarno, Astrophys. J. 568, 443 (2002); B.C. Shepler et al, Astron. & Astroph. 475, L15 (2007); L. Song et al, J. Chem. Phys. 142, 204303 (2015); K.M. Walker et al, Astroph. J. 811, 27 (2015). 2. L. Song et al, Astrophys. J. 813, 96 (2015). 3. H.-M. Keller et al, J. Chem. Phys. 105, 4983 (1996). 4. S. Ndengue, R. Dawes and H. Guo, J. Chem. Phys. 144, 244301 (2016). 5. M.H. Beck et al., Phys. Rep. 324, 1 (2000).

Highly Regioregular Polythiophenes for Magneto-Optical Applications

DTIC Science & Technology

2010-07-01

Macromolecules, 2007, 40, 8142-8150 Lieven De Cremer et.al., Macromolecules, 2008, 41, 568-578 Lieven De Cremer et.al., Macromolecules, 2008, 41, 591-598 Marnix...Vangheluwe et.al., Macromolecules, 2008, 41, 1041-1044 David Cornelis et.al., Chem. Mater. 2008, 20, 2133-2143 Palash Gangopadhyay et.al., J. Phys

Inverse modelling of radionuclide release rates using gamma dose rate observations

NASA Astrophysics Data System (ADS)

Hamburger, Thomas; Evangeliou, Nikolaos; Stohl, Andreas; von Haustein, Christoph; Thummerer, Severin; Wallner, Christian

2015-04-01

inversion method uses a Bayesian formulation considering uncertainties for the a priori source term and the observations (Eckhardt et al., 2008, Stohl et al., 2012). The a priori information on the source term is a first guess. The gamma dose rate observations are used to improve the first guess and to retrieve a reliable source term. The details of this method will be presented at the conference. This work is funded by the Bundesamt für Strahlenschutz BfS, Forschungsvorhaben 3612S60026. References Davoine, X. and Bocquet, M., Atmos. Chem. Phys., 7, 1549-1564, 2007. Devell, L., et al., OCDE/GD(96)12, 1995. Eckhardt, S., et al., Atmos. Chem. Phys., 8, 3881-3897, 2008. Saunier, O., et al., Atmos. Chem. Phys., 13, 11403-11421, 2013. Stohl, A., et al., Atmos. Environ., 32, 4245-4264, 1998. Stohl, A., et al., Atmos. Chem. Phys., 5, 2461-2474, 2005. Stohl, A., et al., Atmos. Chem. Phys., 12, 2313-2343, 2012.

Comment on 'Three-dimensional numerical investigation of electron transport with rotating spoke in a cylindrical anode layer Hall plasma accelerator'[Phys. Plasmas 19, 073519 (2012)

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

Ellison, C. L.; Parker, J. B.; Raitses, Y.

The oscillation behavior described by Tang et al.[Phys. Plasmas 19, 073519 (2012)] differs too greatly from previous experimental and numerical studies to claim observation of the same phenomenon. Most significantly, the rotation velocity by Tang et al.[Phys. Plasmas 19, 073519 (2012)] is three orders of magnitude larger than that of typical 'rotating spoke' phenomena. Several physical and numerical considerations are presented to more accurately understand the numerical results of Tang et al.[Phys. Plasmas 19, 073519 (2012)] in light of previous studies.

Summary of PhysPAG Activities

NASA Astrophysics Data System (ADS)

Ritz, Steven M.

2013-01-01

The Physics of the Cosmos (PCOS) Program Analysis Group (PhysPAG) provides an important interface between the scientific community and NASA in matters related to PCOS objectives, and also provides opportunities for community discussions. An Executive Committee facilitates the work of several subgroups, including an Inflation Probe Science Analysis Group (IPSAG), an X-ray group (XRSAG) , a gamma-ray,group (GRSAG), a gravitational wave group (GWSAG), and a cosmic-ray group (CRSAG). In addition to identifying opportunities and issues, these groups also help articulate technology needs. Membership in all the SAGs is completely open, with information and newsletter signups available on the PhysPAG pages at the PCOS program website. The PhysPAG reports to the Astrophysics Subcommittee of the NASA Advisory Council. A summary of PhysPAG activities will be given, along with time for questions and discussion.

High-pressure phase transitions of strontianite

NASA Astrophysics Data System (ADS)

Speziale, S.; Biedermann, N.; Reichmann, H. J.; Koch-Mueller, M.; Heide, G.

2015-12-01

Strontianite (SrCO3) is isostructural to aragonite, a major high-pressure polymorph of calcite. Thus it is a material of interest to investigate the high-pressure phase behavior of aragonite-group minerals. SrCO3 is a common component of natural carbonates and knowing its physical properties at high pressures is necessary to properly model the thermodynamic properties of complex carbonates, which are major crustal minerals but are also present in the deep Earth [Brenker et al., 2007] and control carbon cycling in the Earth's mantle. The few available high-pressure studies of SrCO3 disagree regarding both pressure stability and structure of the post-aragonite phase [Lin & Liu, 1997; Ono et al., 2005; Wang et al. 2015]. To clarify such controversies we investigated the high-pressure behavior of synthetic SrCO3 by Raman spectroscopy. Using a diamond anvil cell we compressed single-crystals or powder of strontianite (synthesized at 4 GPa and 1273 K for 24h in a multi anvil apparatus), and measured Raman scattering up to 78 GPa. SrCO3 presents a complex high-pressure behavior. We observe mode softening above 20 GPa and a phase transition at 25 - 26.9 GPa, which we interpret due to the CO3 groups rotation, in agreement with Lin & Liu [1997]. The lattice modes in the high-pressure phase show dramatic changes which may indicate a change from 9-fold coordinated Sr to a 12-fold-coordination [Ono, 2007]. Our results confirm that the high-pressure phase of strontianite is compatible with Pmmn symmetry. References Brenker, F.E. et al. (2007) Earth and Planet. Sci. Lett., 260, 1; Lin, C.-C. & Liu, L.-G. (1997) J. Phys. Chem. Solids, 58, 977; Ono, S. et al. (2005) Phys. Chem. Minerals, 32, 8; Ono, S. (2007) Phys. Chem. Minerals, 34, 215; Wang, M. et al. (2015) Phys Chem Minerals 42, 517.

Communication: Unraveling the 4He droplet-mediated soft-landing from ab initio-assisted and time-resolved density functional simulations: Au@4He300/TiO2(110)

NASA Astrophysics Data System (ADS)

de Lara-Castells, María Pilar; Aguirre, Néstor F.; Stoll, Hermann; Mitrushchenkov, Alexander O.; Mateo, David; Pi, Martí

2015-04-01

An ab-initio-based methodological scheme for He-surface interactions and zero-temperature time-dependent density functional theory for superfluid 4He droplets motion are combined to follow the short-time collision dynamics of the Au@4He300 system with the TiO2(110) surface. This composite approach demonstrates the 4He droplet-assisted sticking of the metal species to the surface at low landing energy (below 0.15 eV/atom), thus providing the first theoretical evidence of the experimentally observed 4He droplet-mediated soft-landing deposition of metal nanoparticles on solid surfaces [Mozhayskiy et al., J. Chem. Phys. 127, 094701 (2007) and Loginov et al., J. Phys. Chem. A 115, 7199 (2011)].

Study of hydrogen-molecule guests in type II clathrate hydrates using a force-matched potential model parameterised from ab initio molecular dynamics

NASA Astrophysics Data System (ADS)

Burnham, Christian J.; Futera, Zdenek; English, Niall J.

2018-03-01

The force-matching method has been applied to parameterise an empirical potential model for water-water and water-hydrogen intermolecular interactions for use in clathrate-hydrate simulations containing hydrogen guest molecules. The underlying reference simulations constituted ab initio molecular dynamics (AIMD) of clathrate hydrates with various occupations of hydrogen-molecule guests. It is shown that the resultant model is able to reproduce AIMD-derived free-energy curves for the movement of a tagged hydrogen molecule between the water cages that make up the clathrate, thus giving us confidence in the model. Furthermore, with the aid of an umbrella-sampling algorithm, we calculate barrier heights for the force-matched model, yielding the free-energy barrier for a tagged molecule to move between cages. The barrier heights are reasonably large, being on the order of 30 kJ/mol, and are consistent with our previous studies with empirical models [C. J. Burnham and N. J. English, J. Phys. Chem. C 120, 16561 (2016) and C. J. Burnham et al., Phys. Chem. Chem. Phys. 19, 717 (2017)]. Our results are in opposition to the literature, which claims that this system may have very low barrier heights. We also compare results to that using the more ad hoc empirical model of Alavi et al. [J. Chem. Phys. 123, 024507 (2005)] and find that this model does very well when judged against the force-matched and ab initio simulation data.

Preface to Special Issue of ChemSusChem on Perovskite Optoelectronics.

PubMed

Bolink, Henk J; Mhaisalkar, Subodh G

2017-10-09

This Editorial introduces one of two companion Special Issues on "Halide Perovskites for Optoelectronics Applications" in ChemSusChem and Energy Technology following the ICMAT 2017 Conference in Singapore. More information on the other Special Issue can be found in the Editorial published in Energy Technology. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Retrieval of tropospheric HCHO in El Salvador using ground based DOAS

NASA Astrophysics Data System (ADS)

Abarca, W.; Gamez, K.; Rudamas, C.

2017-12-01

Formaldehyde (HCHO) is the most abundant carbonyl in the atmosphere, being an intermediate product in the oxidation of most volatile organic compounds (VOCs). HCHO is carcinogenic, and highly water soluble [1]. HCHO can originate from biomass burning and fossil fuel combustion and has been observed from satellite and ground-based sensors by using the Differential Optical Absorption Spectroscopy (DOAS) technique [2].DOAS products can be used for air quality monitoring, validation of chemical transport models, validation of satellite tropospheric column density retrievals, among others [3]. In this study, we report on column density levels of HCHO measured by ground based Multi-Axis -DOAS in different locations of El Salvador in March, 2015. We have not observed large differences of the HCHO column density values at different viewing directions. This result points out a reasonably polluted and hazy atmosphere in the measuring sites, as reported by other authors [4]. Average values ranging from 1016 to 1017 molecules / cm2 has been obtained. The contribution of vehicular traffic and biomass burning to the column density levels in these sites of El Salvador will be discussed. [1] A. R. Garcia et al., Atmos. Chem. Phys. 6, 4545 (2006) [2] E. Peters et al., Atmos. Chem. Phys. 12, 11179 (2012) [3] T. Vlemmix, et al. Atmos. Meas. Tech., 8, 941-963, 2015 [4] A. Heckel et al., Atmos. Chem. Phys. 5, (2005)

Application of Symmetry-Broken H2-H2 Potential Energy Surface to Low Energy o-/p-H2+HD Collisions of Astrophysical Interest

NASA Astrophysics Data System (ADS)

Sultanov, R. A.; Guster, D.; Adhukari, S. K.

2011-05-01

A possibility of correct description of non-symmetrical HD+H2 collision at low temperatures (T≤300 K) is considered by applying symmetrical H2-H2 potential energy surface (PES) [Diep, P. & Johnson, K. 2000, J. Chem. Phys. 113, 3480 (DJ PES)]. With the use of a special mathematical transformation technique, which was applied to this surface, and a quantum dynamical method we obtained a quite satisfactory agreement with previous results when another H2-H2 PES was used [Boothroyd, A.I. et al. 2002, J. Chem. Phys. 116, 666 (BMKP PES)].

Halogenation effects on electron collisions with CF3Cl, CF2Cl2, and CFCl3

NASA Astrophysics Data System (ADS)

Freitas, T. C.; Lopes, A. R.; Azeredo, A. D.; Bettega, M. H. F.

2016-04-01

We report differential and integral elastic cross sections for low-energy electron collisions with CF3Cl, CF2Cl2, and CFCl3 molecules for energies ranging from 0.1 eV to 30 eV. The calculations were performed using the Schwinger multichannel method with pseudopotentials in the static-exchange and static-exchange plus polarization approximations. The influence of the permanent electric dipole moment on the cross sections was included using the Born closure scheme. A very good agreement between our calculations and the experimental results of Jones [J. Chem. Phys. 84, 813 (1986)], Mann and Linder [J. Phys. B 25, 1621 (1992); 25, 1633 (1992)] and Hoshino et al. [J. Chem. Phys. 138, 214305 (2013)] was found. We also compare our results with the calculations of Beyer et al. [Chem. Phys. 255, 1 (2000)] using the R-matrix method, where we find good agreement with respect to the location of the resonances, and with the calculations of Hoshino et al. using the independent atom method with screening corrected additivity rule, where we find qualitative agreement at energies above 20 eV. Additional electronic structure calculations were carried out in order to help in the interpretation of the scattering results. The stabilization the lowest σ∗ resonance due to the exchange of fluorine by chlorine atoms (halogenation effect) follows a simple linear relation with the energy of the lowest unoccupied molecular orbitals and can be considered as a signature of the halogenation effect.

Trace Gases and Aerosols Simulated Over the Indian Domain: Evaluation of the Model Wrf-Chem

NASA Astrophysics Data System (ADS)

Michael, M.; Yadav, A.; Tripathi, S. N.; Venkataraman, C.; Kanawade, V. P.

2012-12-01

As the anthropogenic emissions from the Asian countries contribute substantially to the global aerosol loading, the study of the distribution of trace gases and aerosols over this region has received increasing attention in recent years. In the present work, the aerosol properties over the Indian domain during the pre-monsoon season has been addressed. The "online" meteorological and chemical transport Weather Research and Forecasting-Chemistry (WRF-Chem) model has been implemented over Indian subcontinent for three consecutive summers in 2008, 2009 and 2010.The initial and boundary conditions are obtained from NCAR reanalysis data. The global emission inventories (REanalysis of the TROpospheric chemical composition (RETRO) and Emissions Database for Global Atmospheric Research (EDGAR)) have been used and are projected for the period of study using the method provided in Ohara et al. (2007). The emission rates of sulfur dioxide, black carbon, organic carbon and PM2.5 available in the global inventory are replaced with the high resolution emission inventory developed over India for the present study. The model simulates meteorological parameters, trace gases and particulate matter. Simulated mixing ratios of trace gases (Ozone, carbon monoxide, nitrogen oxides, and SO2) are compared with ground based as well as satellite observations over India with specific focus on Indo-Gangetic Plain. Simulated aerosol optical depth are in good agreement with those observed by Aerosol Robotic Network (AERONET). The vertical profiles of extinction coefficient have been compared with the Micro Pulse Lidar Network (MPLnet) data. The simulated mass concentration of BC shows very good agreement with those observed at a few ground stations. The vertical profiles of BC have also been compared with aircraft observations carried out during summer of 2008 and 2009, resulting in good agreement. This study shows that WRF-Chem model captures many important features of the observations and

Comment on "Comment on 'Constant temperature molecular dynamics simulations by means of a stochastic collision model. II. The harmonic oscillator' [J. Chem. Phys. 104, 3732 (1996)]" [J. Chem. Phys. 106, 1646 (1997)].

PubMed

Kast, Stefan M

2004-03-08

An argument brought forward by Sholl and Fichthorn against the stochastic collision-based constant temperature algorithm for molecular dynamics simulations developed by Kast et al. is refuted. It is demonstrated that the large temperature fluctuations noted by Sholl and Fichthorn are due to improperly chosen initial conditions within their formulation of the algorithm. With the original form or by suitable initialization of their variant no deficient behavior is observed.

Coupled cluster calculations for static and dynamic polarizabilities of C60

NASA Astrophysics Data System (ADS)

Kowalski, Karol; Hammond, Jeff R.; de Jong, Wibe A.; Sadlej, Andrzej J.

2008-12-01

New theoretical predictions for the static and frequency dependent polarizabilities of C60 are reported. Using the linear response coupled cluster approach with singles and doubles and a basis set especially designed to treat the molecular properties in external electric field, we obtained 82.20 and 83.62 Å3 for static and dynamic (λ =1064 nm) polarizabilities. These numbers are in a good agreement with experimentally inferred data of 76.5±8 and 79±4 Å3 [R. Antoine et al., J. Chem. Phys.110, 9771 (1999); A. Ballard et al., J. Chem. Phys.113, 5732 (2000)]. The reported results were obtained with the highest wave function-based level of theory ever applied to the C60 system.

Investigation of ZPE and temperature effects on the Eley-Rideal recombination of hydrogen atoms on graphene using a multidimensional graphene-H-H potential

NASA Astrophysics Data System (ADS)

Sizun, M.; Bachellerie, D.; Aguillon, F.; Sidis, V.

2010-09-01

We study the Eley-Rideal recombination of H atoms on graphene under the physical conditions of the interstellar medium. Effects of the ZPE motions of the chemisorbed H atom and of the graphene thermal motions are investigated. Classical molecular dynamics calculations undertaken with the multidimensional potential of Bachellerie et al. [Phys. Chem. Chem. Phys. 11 (2009) 2715] are reported. The ZPE effects are the strongest. The closer the collision energy is to the classical reaction threshold the more sizeable the effects. The quantum reaction cross section is also estimated below and above the classical threshold using a capture model.

Exploiting PubChem for Virtual Screening

PubMed Central

Xie, Xiang-Qun

2011-01-01

Importance of the field PubChem is a public molecular information repository, a scientific showcase of the NIH Roadmap Initiative. The PubChem database holds over 27 million records of unique chemical structures of compounds (CID) derived from nearly 70 million substance depositions (SID), and contains more than 449,000 bioassay records with over thousands of in vitro biochemical and cell-based screening bioassays established, with targeting more than 7000 proteins and genes linking to over 1.8 million of substances. Areas covered in this review This review builds on recent PubChem-related computational chemistry research reported by other authors while providing readers with an overview of the PubChem database, focusing on its increasing role in cheminformatics, virtual screening and toxicity prediction modeling. What the reader will gain These publicly available datasets in PubChem provide great opportunities for scientists to perform cheminformatics and virtual screening research for computer-aided drug design. However, the high volume and complexity of the datasets, in particular the bioassay-associated false positives/negatives and highly imbalanced datasets in PubChem, also creates major challenges. Several approaches regarding the modeling of PubChem datasets and development of virtual screening models for bioactivity and toxicity predictions are also reviewed. Take home message Novel data-mining cheminformatics tools and virtual screening algorithms are being developed and used to retrieve, annotate and analyze the large-scale and highly complex PubChem biological screening data for drug design. PMID:21691435

Isotherm-Based Thermodynamic Model for Solute Activities of Asymmetric Electrolyte Aqueous Solutions.

PubMed

Nandy, Lucy; Dutcher, Cari S

2017-09-21

Adsorption isotherm-based statistical thermodynamic models can be used to determine solute concentration and solute and solvent activities in aqueous solutions. Recently, the number of adjustable parameters in the isotherm model of Dutcher et al. J. Phys. Chem. A/C 2011, 2012, 2013 were reduced for neutral solutes as well as symmetric 1:1 electrolytes by using a Coulombic model to describe the solute-solvent energy interactions (Ohm et al. J. Phys. Chem. A 2015, Nandy et al. J. Phys. Chem. A 2016). Here, the Coulombic treatment for symmetric electrolytes is extended to establish improved isotherm model equations for asymmetric 1-2 and 1-3 electrolyte systems. The Coulombic model developed here results in prediction of activities and other thermodynamic properties in multicomponent systems containing ions of arbitrary charge. The model is found to accurately calculate the osmotic coefficient over the entire solute concentration range with two model parameters, related to intermolecular solute-solute and solute-solvent spacing. The inorganic salts and acids treated here are generally considered to be fully dissociated. However, there are certain weak acids that do not dissociate completely, such as the bisulfate ion. In this work, partial dissociation of the bisulfate ion from sulfuric acid is treated as a mixture, with an additional model parameter that accounts for the dissociation ratio of the dissociated ions to nondissociated ions.

A theoretical study on hot charge-transfer states and dimensional effects of organic photocells based on an ideal diode model.

PubMed

Shimazaki, Tomomi; Nakajima, Takahito

2017-05-21

This paper discusses an ideal diode model with hot charge-transfer (CT) states to analyze the power conversion efficiency of an organic photocell. A free carrier generation mechanism via sunlight in an organic photocell consists of four microscopic processes: photon absorption, exciton dissociation, CT, and charge separation. The hot CT state effect has been actively investigated to understand the charge separation process. We previously reported a theoretical method to calculate the efficiency of the charge separation process via a hot CT state (T. Shimazaki et al., Phys. Chem. Chem. Phys., 2015, 17, 12538 and J. Chem. Phys., 2016, 144, 234906). In this paper, we integrate the simulation method into the ideal photocell diode model and calculate several properties such as short circuit current, open circuit voltage, and power conversion efficiency. Our results highlight that utilizing the dimensional (entropy) effect together with the hot CT state can play an essential role in developing more efficient organic photocell devices.

A comment on "The interaction of X2 (X = F, Cl, and Br) with active sites of graphite" [Xu et al., Chem. Phys. Lett., 418, 413 (2006)

NASA Astrophysics Data System (ADS)

Lechner, Christoph; Baranek, Philippe; Vach, Holger

2018-04-01

In their article, Xu et al. (2006) present the adsorption energies for the chemisorption of the three halogens F2 , Cl2 , and Br2 on the active sites of graphite. The three investigated systems are the three most stable surfaces, (0 0 1), (1 0 0), and (1 1 0); the latter two are also called zigzag and armchair surface, respectively. Due to some inconsistencies in their article, we re-evaluated the results of Xu et al. in order to investigate the impact on the adsorption energies of the halogens. For the (0 0 1) surface, our results agree with Xu et al. However, for the other two surfaces we find major differences. Contrary to Xu et al., we find that the halogens adsorb the strongest on the zigzag surface. The second strongest adsorption is found on the armchair surface for the symmetric configurations, the third strongest for the asymmetric configurations. Several reasons are given which explain this discrepancy. The most striking source of error in the work of Xu et al. is due to the fact that they did not choose the correct spin multiplicities for the model systems which means that they performed the calculations in excited states. This leads to errors between 50 and 600% for the zigzag surface and 3-42% for the armchair surface.

X-ray computed microtomography of sea ice - comment on "A review of air-ice chemical and physical interactions (AICI): liquids, quasi-liquids, and solids in snow" by Bartels-Rausch et al. (2014)

NASA Astrophysics Data System (ADS)

Obbard, R. W.

2015-07-01

This comment addresses a statement made in "A review of air-ice chemical and physical interactions (AICI): liquids, quasi-liquids, and solids in snow" by Bartels-Rausch et al. (Atmos. Chem. Phys., 14, 1587-1633, doi:10.5194/acp-14-1587-2014, 2014). Here we rebut the assertion that X-ray computed microtomography of sea ice fails to reveal liquid brine inclusions by discussing the phases present at the analysis temperature.

Hyperbolic metamaterial nanostructures to tune charge-transfer dynamics (Conference Presentation)

NASA Astrophysics Data System (ADS)

Lee, Kwang Jin; Xiao, Yiming; Woo, Jae Heun; Kim, Eun Sun; Kreher, David; Attias, André-Jean; Mathevet, Fabrice; Ribierre, Jean-Charles; Wu, Jeong Weon; André, Pascal

2016-09-01

Charge transfer (CT) is an essential phenomenon relevant to numerous fields including biology, physics and chemistry.1-5 Here, we demonstrate that multi-layered hyperbolic metamaterial (HMM) substrates alter organic semiconductor CT dynamics.6 With triphenylene:perylene diimide dyad supramolecular self-assemblies prepared on HMM substrates, we show that both charge separation (CS) and charge recombination (CR) characteristic times are increased by factors of 2.5 and 1.6, respectively, resulting in longer-lived CT states. We successfully rationalize the experimental data by extending Marcus theory framework with dipole image interactions tuning the driving force. The number of metal-dielectric pairs alters the HMM interfacial effective dielectric constant and becomes a solid analogue to solvent polarizability. Based on the experimental results and extended Marcus theory framework, we find that CS and CR processes are located in normal and inverted regions on Marcus parabola diagram, respectively. The model and further PH3T:PCBM data show that the phenomenon is general and that molecular and substrate engineering offer a wide range of kinetic tailoring opportunities. This work opens the path toward novel artificial substrates designed to control CT dynamics with potential applications in fields including optoelectronics, organic solar cells and chemistry. 1. Marcus, Rev. Mod. Phys., 1993, 65, 599. 2. Marcus, Phys. Chem. Chem. Phys., 2012, 14, 13729. 3. Lambert, et al., Nat. Phys., 2012, 9, 10. 4. C. Clavero, Nat. Photon., 2014, 8, 95. 5. A. Canaguier-Durand, et al., Angew. Chem. Int. Ed., 2013, 52, 10533. 6. K. J. Lee, et al., Submitted, 2015, arxiv.org/abs/1510.08574.

Halogenation effects on electron collisions with CF{sub 3}Cl, CF{sub 2}Cl{sub 2}, and CFCl{sub 3}

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

Freitas, T. C., E-mail: tcf03@fisica.ufpr.br; Lopes, A. R.; Bettega, M. H. F.

2016-04-28

We report differential and integral elastic cross sections for low-energy electron collisions with CF{sub 3}Cl, CF{sub 2}Cl{sub 2}, and CFCl{sub 3} molecules for energies ranging from 0.1 eV to 30 eV. The calculations were performed using the Schwinger multichannel method with pseudopotentials in the static-exchange and static-exchange plus polarization approximations. The influence of the permanent electric dipole moment on the cross sections was included using the Born closure scheme. A very good agreement between our calculations and the experimental results of Jones [J. Chem. Phys. 84, 813 (1986)], Mann and Linder [J. Phys. B 25, 1621 (1992); 25, 1633 (1992)]more » and Hoshino et al. [J. Chem. Phys. 138, 214305 (2013)] was found. We also compare our results with the calculations of Beyer et al. [Chem. Phys. 255, 1 (2000)] using the R-matrix method, where we find good agreement with respect to the location of the resonances, and with the calculations of Hoshino et al. using the independent atom method with screening corrected additivity rule, where we find qualitative agreement at energies above 20 eV. Additional electronic structure calculations were carried out in order to help in the interpretation of the scattering results. The stabilization the lowest σ{sup ∗} resonance due to the exchange of fluorine by chlorine atoms (halogenation effect) follows a simple linear relation with the energy of the lowest unoccupied molecular orbitals and can be considered as a signature of the halogenation effect.« less

Multichannel-quantum-defect-theory treatment of preionized and predissociated triplet gerade levels of H2

NASA Astrophysics Data System (ADS)

Matzkin, A.; Jungen, Ch.; Ross, S. C.

2000-12-01

Multichannel quantum defect theory (MQDT) is used to calculate highly excited predissociated and preionized triplet gerade states of H2. The treatment is ab initio and is based on the clamped-nuclei quantum-defect matrices and dipole transition moments derived from quantum-chemical potential energy curves by Ross et al. [Can. J. Phys. (to be published)]. Level positions, predissociation or preionization widths and relative intensities are found to be in good agreement with those observed by Lembo et al. [Phys. Rev. A 38, 3447 (1988); J. Chem. Phys. 92, 2219 (1990)] by an optical-optical double resonance photoionization or depletion technique.

Improved Analytical Potentials for the a ^3Σu+ and X ^1Σg+ States of {Cs_2}

NASA Astrophysics Data System (ADS)

Baldwin, Jesse; Le Roy, Robert J.

2012-06-01

Recent studies of the collisional properties of ultracold Cs atoms have led to a renewed interest in the singlet and triplet ground-state potential energy functions of Cs_2. Coxon and Hajigeorgiou recently determined an analytic potential function for the X ^1Σ_g^+ state that accurately reproduces a large body of spectroscopic data that spanned 99.45% of the potential well. However, their potential explicitly incorporates only the three leading inverse-power terms in the long-range potential, and does not distinguish between the three asymptotes associated with the different Cs atom spin states. Similarly, Xie et al. have reported two versions of an analytic potential energy function for the a ^3Σ_u^+ state that they determined from direct potential fits to emission data that spanned 93 % of its potential energy well. However, the tail of their potential function model was not constrained to have the inverse-power-sum form required by theory. Moreover, a physically correct description of cold atom collision phenomena requires the long-range inverse-power tails of these two potentials to be identical, and they are not. Thus, these functions cannot be expected to describe cold atom collision properties correctly. The present paper describes our efforts to determine improved analytic potential energy functions for these states that have identical long-range tails, and fully represent all of the spectroscopic data used in the earlier worka,b,c as well as photoassociation data that was not considered there and experimental values of the collisional scattering lengths for the two states. J. A. Coxon and P. Hajigeorgiou, J. Chem. Phys. 132, 09105 (2010). F. Xie et al. J. Chem. Phys. 130 051102 (2009). F. Xie et al. J. Chem. Phys. 135, 024303 (2011) J. G. Danzl et al., Science, 321, 1062 (2008). C. Chin, et al., Phys. Rev. Lett. 85, 2717 (2000) P. J. Leo, C. J. Williams, and P. S. Julienne, Phys. Rev. Lett. 85, 2721 (2000)

PubChem promiscuity: a web resource for gathering compound promiscuity data from PubChem.

PubMed

Canny, Stephanie A; Cruz, Yasel; Southern, Mark R; Griffin, Patrick R

2012-01-01

Promiscuity counts allow for a better understanding of a compound's assay activity profile and drug potential. Although PubChem contains a vast amount of compound and assay data, it currently does not have a convenient or efficient method to obtain in-depth promiscuity counts for compounds. PubChem promiscuity fills this gap. It is a Java servlet that uses NCBI Entrez (eUtils) web services to interact with PubChem and provide promiscuity counts in a variety of categories along with compound descriptors, including PAINS-based functional group detection. http://chemutils.florida.scripps.edu/pcpromiscuity southern@scripps.edu

PubChem promiscuity: a web resource for gathering compound promiscuity data from PubChem

PubMed Central

Canny, Stephanie A.; Cruz, Yasel; Southern, Mark R.; Griffin, Patrick R.

2012-01-01

Summary: Promiscuity counts allow for a better understanding of a compound's assay activity profile and drug potential. Although PubChem contains a vast amount of compound and assay data, it currently does not have a convenient or efficient method to obtain in-depth promiscuity counts for compounds. PubChem promiscuity fills this gap. It is a Java servlet that uses NCBI Entrez (eUtils) web services to interact with PubChem and provide promiscuity counts in a variety of categories along with compound descriptors, including PAINS-based functional group detection. Availability: http://chemutils.florida.scripps.edu/pcpromiscuity Contact: southern@scripps.edu PMID:22084255

Dynamics of an excess hole in the 1-methyl-1-butyl-pyrrolidinium dicyanamide ionic-liquid

NASA Astrophysics Data System (ADS)

Wu, Fei; Xu, Changhui; Margulis, Claudio J.

2018-05-01

In a set of recent publications [C. J. Margulis et al., J. Am. Chem. Soc. 133, 20186 (2011); C. H. Xu et al., J. Am. Chem. Soc. 135, 17528 (2013); C. H. Xu and C. J. Margulis, J. Phys. Chem. B 119, 532 (2015); and K. B. Dhungana et al., J. Phys. Chem. B 121, 8809 (2017)], we explored for selected ionic liquids the early stages of excess charge localization and reactivity relevant both to electrochemical and radiation chemistry processes. In particular, Xu and Margulis [J. Phys. Chem. B 119, 532 (2015)] explored the dynamics of an excess electron in 1-methyl-1-butyl-pyrrolidinium dicyanamide. When electrons are produced from an ionic liquid, the more elusive hole species are also generated. Depending on the nature of cations and anions and the relative alignment of their electronic states in the condensed phase, the very early hole species can nominally be neutral radicals—if the electron is generated from anions—or doubly charged radical cations if their origin is from cations. However, in reality early excess charge localization is more complex and often involves more than one ion. The dynamics and the transient spectroscopy of the hole are the main objects of this study. We find that in the case of 1-methyl-1-butyl-pyrrolidinium dicyanamide, it is the anions that can most easily lose an electron becoming radical species, and that hole localization is mostly on anionic nitrogen. We also find that the driving force for localization of an excess hole appears to be smaller than that for an excess electron in 1-methyl-1-butyl-pyrrolidinium dicyanamide. The early transient hole species can absorb light in the visible, ultraviolet, and near infrared regions, and we are able to identify the type of states being connected by these transitions.

PubChem BioAssay: 2017 update

PubMed Central

Wang, Yanli; Bryant, Stephen H.; Cheng, Tiejun; Wang, Jiyao; Gindulyte, Asta; Shoemaker, Benjamin A.; Thiessen, Paul A.; He, Siqian; Zhang, Jian

2017-01-01

PubChem's BioAssay database (https://pubchem.ncbi.nlm.nih.gov) has served as a public repository for small-molecule and RNAi screening data since 2004 providing open access of its data content to the community. PubChem accepts data submission from worldwide researchers at academia, industry and government agencies. PubChem also collaborates with other chemical biology database stakeholders with data exchange. With over a decade's development effort, it becomes an important information resource supporting drug discovery and chemical biology research. To facilitate data discovery, PubChem is integrated with all other databases at NCBI. In this work, we provide an update for the PubChem BioAssay database describing several recent development including added sources of research data, redesigned BioAssay record page, new BioAssay classification browser and new features in the Upload system facilitating data sharing. PMID:27899599

AdapChem

NASA Technical Reports Server (NTRS)

Oluwole, Oluwayemisi O.; Wong, Hsi-Wu; Green, William

2012-01-01

AdapChem software enables high efficiency, low computational cost, and enhanced accuracy on computational fluid dynamics (CFD) numerical simulations used for combustion studies. The software dynamically allocates smaller, reduced chemical models instead of the larger, full chemistry models to evolve the calculation while ensuring the same accuracy to be obtained for steady-state CFD reacting flow simulations. The software enables detailed chemical kinetic modeling in combustion CFD simulations. AdapChem adapts the reaction mechanism used in the CFD to the local reaction conditions. Instead of a single, comprehensive reaction mechanism throughout the computation, a dynamic distribution of smaller, reduced models is used to capture accurately the chemical kinetics at a fraction of the cost of the traditional single-mechanism approach.

ChemCam Targeted Science at Gale Crater

NASA Astrophysics Data System (ADS)

Wiens, R. C.; Blaney, D. L.; Clark, B. C.; Bridges, N. T.; Clegg, S. M.; Maurice, S.; Newsom, H. E.; Vaniman, D. T.; Herkenhoff, K. E.; Ollila, A. M.; Gasnault, O.; Pinet, P. C.; Dromart, G.; Barraclough, B. L.; Lasue, J.

2011-12-01

The MSL rover, Curiosity, uses a novel remote-sensing instrument, ChemCam, which combines laser-induced breakdown spectroscopy (LIBS) with a high resolution remote micro-imager (RMI). ChemCam uses a focused, pulsed laser beam at targets up to 7 m away to excite a light-emitting plasma. Spectral analysis identifies elements present and provides rapid semi-quantitative analyses. Repeated laser pulses remove dust and weathering coatings from rock samples to depths >0.5 mm and ~0.4 mm in diameter. The RMI, with ~20x20 mrad field of view, provides a broad-band image with 100 μm resolution. LIBS yields abundances of H, Li, Be, B, C, N, O, F, Na, Mg, Al, Si, P, Cl, K, Ca, Ti, V, Cr, Fe, Ni, Zr, Rb, Sr, As, Ba, and Pb. Interference from atmospheric constituents raises the detection limits of C, N, and O (e.g., >2% wt for C). LIBS is very sensitive to alkali and alkali earth elements, with some detection limits to ~1 ppm at close range. Conversely, LIBS is insensitive to F, Cl, S, P, and N, with detection limits of several wt. %. Pointing accuracy is ~3 mrad, however relative pointing accuracy is better, so line scans and rasters will enable analyses of targeted features to ~1 mm. At Gale Crater, determination of elements not previously analyzed in-situ, i.e., H, Li, Rb, Sr, and Ba, along with other elements will constrain aqueous, hydrothermal and vapor geochemical transport processes. Initial analyses after landing will characterize air fall dust and weathering coatings on local rocks, and profile the soil and surfacial materials including bedforms to investigate compositional differences in near-surface layers. Targets within the landing ellipse include fan and inverted channel deposits derived from the crater rim, which may contain alteration minerals produced by impact hydrothermal processes. Enigmatic deposits with bright fracture fill could represent lake sediments modified by injection of deposits from groundwater. During the drive to the Gale mound, ChemCam will

Chem-2-Chem: A One-to-One Supportive Learning Environment for Chemistry

NASA Astrophysics Data System (ADS)

Báez-Galib, Rosita; Colón-Cruz, Héctor; Resto, Wilfredo; Rubin, Michael R.

2005-12-01

The Chem-2-Chem (C2C) tutoring mentoring program was developed at the University of Puerto Rico at Cayey, an undergraduate institution serving Hispanic students, to increase student retention and help students achieve successful general chemistry course outcomes. This program provides a supportive learning environment designed to address students' academic and emotional needs in a holistic way. Advanced chemistry students offered peer-led, personalized, and individualized learning experiences through tutoring and mentoring to approximately 21% of students enrolled in the general chemistry course. Final grades from official class lists of all general chemistry course sections were analyzed using Student's t -test, paired t -test, and χ 2 analysis. Results during the seven semesters studied show an increase of 29% in successful course outcomes defined as final letter grades of A, B, and C obtained by Chem-2-Chem participants. For each final grade, highly statistically significant differences between participants and nonparticipants were detected. There were also statistically significant differences between successful course outcomes obtained by participants and nonparticipants for each of the semesters studied. This research supports recent trends in chemical education to provide a social context for learning experiences. This peer-led learning strategy can serve as an effective model to achieve excellence in science courses at a wide range of educational institutions.

Checking out ChemCam View

NASA Image and Video Library

2012-08-17

This mosaic shows the calibration target for the Chemistry and Camera ChemCam instrument on NASA Curiosity rover, as seen by the ChemCam remote micro-imager. The 10 images incorporated in this mosaic were taken on Aug. 15.

Research-based resources on PhysPort

NASA Astrophysics Data System (ADS)

Sayre, Eleanor

2017-01-01

PhysPort (http://physport.org) is a website that supports physics faculty in implementing research-based teaching practices in their classrooms. We provide expert recommendations and practical information about teaching methods and assessment. The PhysPort Data Explorer is an intuitive online tool for physics faculty to analyze their assessment data. Faculty upload their students' responses using our secure interface. The Data Explorer matches their pre/post data, scores it, compares it to national data, and graphs it in an interactive and intuitive manner. The Periscope collection on Physport brings together classroom video of students working groups with professional development materials for faculty, pre-service teachers, and learning assistants. To support PhysPort's development efforts, we conduct research on faculty needs around teaching and assessment, secondary analysis of published PER studies, and primary analysis of assessment data. In this talk, I'll introduce some of PhysPort's research-based resources and the research results which support them.

Air Quality Modeling and Forecasting over the United States Using WRF-Chem

NASA Astrophysics Data System (ADS)

Boxe, C.; Hafsa, U.; Blue, S.; Emmanuel, S.; Griffith, E.; Moore, J.; Tam, J.; Khan, I.; Cai, Z.; Bocolod, B.; Zhao, J.; Ahsan, S.; Gurung, D.; Tang, N.; Bartholomew, J.; Rafi, R.; Caltenco, K.; Rivas, M.; Ditta, H.; Alawlaqi, H.; Rowley, N.; Khatim, F.; Ketema, N.; Strothers, J.; Diallo, I.; Owens, C.; Radosavljevic, J.; Austin, S. A.; Johnson, L. P.; Zavala-Gutierrez, R.; Breary, N.; Saint-Hilaire, D.; Skeete, D.; Stock, J.; Salako, O.

2016-12-01

WRF-Chem is the Weather Research and Forecasting (WRF) model coupled with Chemistry. The model simulates the emission, transport, mixing, and chemical transformation of trace gases and aerosols simultaneously with the meteorology. The model is used for investigation of regional-scale air quality, field program analysis, and cloud-scale interactions between clouds and chemistry. The development of WRF-Chem is a collaborative effort among the community led by NOAA/ESRL scientists. The Official WRF-Chem web page is located at the NOAA web site. Our model development is closely linked with both NOAA/ESRL and DOE/PNNL efforts. Description of PNNL WRF-Chem model development is located at the PNNL web site as well as the PNNL Aerosol Modeling Testbed. High school and undergraduate students, representative of academic institutions throughout USA's Tri-State Area (New York, New Jersey, Connecticut), set up WRF-Chem on CUNY CSI's High Performance Computing Center. Students learned the back-end coding that governs WRF-Chems structure and the front-end coding that displays visually specified weather simulations and forecasts. Students also investigated the impact, to select baseline simulations/forecasts, due to the reaction, NO2 + OH + M → HOONO + M (k = 9.2 × 10-12 cm3 molecule-1 s-1, Mollner et al. 2010). The reaction of OH and NO2 to form gaseous nitric acid (HONO2) is among the most influential and in atmospheric chemistry. Till a few years prior, its rate coefficient remained poorly determined under tropospheric conditions because of difficulties in making laboratory measurements at 760 torr. These activities fosters student coding competencies and deep insights into weather forecast and air quality.

Communication: Unraveling the {sup 4}He droplet-mediated soft-landing from ab initio-assisted and time-resolved density functional simulations: Au@{sup 4}He{sub 300}/TiO{sub 2}(110)

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

Lara-Castells, María Pilar de, E-mail: Pilar.deLara.Castells@csic.es; Aguirre, Néstor F.; Stoll, Hermann

2015-04-07

An ab-initio-based methodological scheme for He-surface interactions and zero-temperature time-dependent density functional theory for superfluid {sup 4}He droplets motion are combined to follow the short-time collision dynamics of the Au@{sup 4}He{sub 300} system with the TiO{sub 2}(110) surface. This composite approach demonstrates the {sup 4}He droplet-assisted sticking of the metal species to the surface at low landing energy (below 0.15 eV/atom), thus providing the first theoretical evidence of the experimentally observed {sup 4}He droplet-mediated soft-landing deposition of metal nanoparticles on solid surfaces [Mozhayskiy et al., J. Chem. Phys. 127, 094701 (2007) and Loginov et al., J. Phys. Chem. A 115,more » 7199 (2011)].« less

Response to "Comment on `Magnetic geometry and physics of advanced divertors: The X-divertor and the snowflake' " [Phys. Plasmas 21, 054701 (2014)

NASA Astrophysics Data System (ADS)

Kotschenreuther, Mike; Valanju, Prashant; Covele, Brent; Mahajan, Swadesh

2014-05-01

Relying on coil positions relative to the plasma, the "Comment on `Magnetic geometry and physics of advanced divertors: The X-divertor and the snowflake' " [Phys. Plasmas 21, 054701 (2014)], emphasizes a criterion for divertor characterization that was critiqued to be ill posed [M. Kotschenreuther et al., Phys. Plasmas 20, 102507 (2013)]. We find that no substantive physical differences flow from this criteria. However, using these criteria, the successful NSTX experiment by Ryutov et al. [Phys. Plasmas 21, 054701 (2014)] has the coil configuration of an X-divertor (XD), rather than a snowflake (SF). On completing the divertor index (DI) versus distance graph for this NSTX shot (which had an inexplicably missing region), we find that the DI is like an XD for most of the outboard wetted divertor plate. Further, the "proximity condition," used to define an SF [M. Kotschenreuther et al., Phys. Plasmas 20, 102507 (2013)], does not have a substantive physics basis to override metrics based on flux expansion and line length. Finally, if the criteria of the comment are important, then the results of NSTX-like experiments could have questionable applicability to reactors.

Electronic Structure in Thin Film Organic Semiconductors

DTIC Science & Technology

2009-06-27

Peltekis, C. McGuinness, and A. Matsuura, J. Chem. Phys. 129, 224705, (2008) c) "The Local Electronic Structure of Tin Phthalocyanine studied by...interfaces in a Cu(100)-benzenethiolate- pentacene heterostructure", Phys. Rev. Lett. 100, 027601 (2008). 21. O.V. Molodtsova, M. Grobosch, M. Knupfer...1999). 37. N.J. Watkins, S. Zorba, and Y. Gao, "Interface formation of pentacene on Al2O3", J. Appl. Phys. 96, 425 (2004). 38. K.V. Chauhan, I

One decade of space-based isoprene emission estimates: Interannual variations and emission trends between 2005 and 2014

NASA Astrophysics Data System (ADS)

Bauwens, Maite; Stavrakou, Trissevgeni; Müller, Jean-François; De Smedt, Isabelle; Van Roozendael, Michel

2016-04-01

rainforests of Equatorial Africa and South America. The top-down isoprene fluxes are available at a resolution of 0.5°x0.5° between 2005 and 2014 at the GlobEmission website (http://www.globemission.eu). References: Arneth, A., et al.: Process-based estimates of terrestrial ecosystem isoprene emissions: incorporating the effects of a direct CO 2-isoprene interaction, Atmos. Chem. Phys., 7(1), 31-53, 2007. Arneth, A., et al.: Global terrestrial isoprene emission models: sensitivity to variability in climate and vegetation, Atmos. Chem. Phys., 11(15), 8037-8052, 2011. Bauwens, M., et al.: Satellite-based isoprene emission estimates (2007-2012) from the GlobEmission project, in ACCENT-Plus Symposium 2013 Proceedings., 2014. Stavrakou, T., et al.: Isoprene emissions over Asia 1979 - 2012: impact of climate and land-use changes, Atmos. Chem. Phys., 14(9), 4587-4605, doi:10.5194/acp-14-4587-2014, 2014. Stavrakou, T., et al.: How consistent are top-down hydrocarbon emissions based on formaldehyde observations from GOME-2 and OMI?, Atmos. Chem. Phys., 15(20), 11861-11884, doi:10.5194/acp-15-11861-2015, 2015. Stavrakou, T., et al.: Evaluating the performance of pyrogenic and biogenic emission inventories against one decade of space-based formaldehyde columns, Atmos. Chem. Phys., 9(3), 1037-1060, doi:10.5194/acp-9-1037-2009, 2009.

Heats of Vaporization of Room Temperature Ionic Liquids by Tunable Vacuum Ultraviolet Photoionization

DTIC Science & Technology

2009-12-07

18) Emel’yanenko, V. N.; Verevkin, S. P.; Heintz, A.; Corfield, J.-A.; deyko, A.; Lovelock , K. R. J.; Licence, P.; Jones, R. G. J. Phys. Chem. B 2008...112, 11734. (19) Armstrong, J. P.; Hurst, C.; Jones, R. G.; Licence, P.; Lovelock , K. R. J.; Satterly, C. J.; Villar-Garcia, I. J. Phys. Chem. Chem...Phys. 2007, 9, 982. (20) Lovelock , K. R. J.; Deyko, A.; Corfield, J.-A.; Gooden, P. N.; Licence, P.; Jones, R. G. ChemPhysChem 2009, 10, 337. (21

Laboratory studies of key gas-phase HOx-NOx coupling reactions.

NASA Astrophysics Data System (ADS)

Dillon, Terry J.; Dulitz, Katrin; Crowley, John N.

2013-04-01

The HOx (OH & HO2) and NOx (NO & NO2) families of atmospheric radicals are coupled via a number of gas-phase reactions. These reactions have a substantial impact by controlling radical propagation / termination in catalytic cycles, so modifying the oxidation power of the atmosphere and its rate of O3 production. However, field measurements {1-3} have demonstrated that our understanding of HOx - NOx chemistry is incomplete. We have identified four reactions (R1-R4) where the database is particularly unsatisfactory, leading to large uncertainties in atmospheric models {4-5}. HO2 + NO -> OH + NO2 (R1a) HO2 + NO (+ M) -> HNO3 (+ M) (R1b) NO2* + H2O -> NO2 + H2O (R2a) NO2* + H2O -> OH + HONO (R2b) NO3* + H2O -> NO3 + H2O (R3a) NO3* + H2O -> OH + HNO3 (R3b) OH + HNO3 -> H2O + NO3 (R4) In this experimental work, laser-based kinetic and spectroscopic tools were used to investigate recent observations {6-7} of HNO3 formation from the (otherwise radical propagating) HO2 + NO (R1), and OH formation following absorption of abundant, long wavelength photons by NO2 {8} and NO3 in the presence of water vapour (R2, R3). Uncertainties {9} associated with a classical HOx-NOx coupling reaction (R4) were also addressed. Critical photochemical parameters so derived have included absolute rate coefficients for (R1) and (R4) and product yields (R1b, R2b, R3b). The atmospheric implications of these results will be discussed. References: {1} Faloona, I. et al. J. Geophys. Res., 105, 3771-3783, 2000.; {2} Thakur, A.N. et al., Atmos. Environ., 33, 1403-1422, 1999.; {3} Wennberg, P.O. et al., Geophys. Res. Lett., 26, 1373-1376, 1999.; {4} Cariolle, D. et al., Atmos. Chem. Phys., 8, 4061-4068, 2008.; {5} Wennberg P.O. and Dabdub, D. Science, 319, 2008. ; {6} Butkovskaya, N. et al., J. Phys. Chem. A, 111, 9047-9053, 2007.; {7} Butkovskaya, N. et al., J. Phys. Chem. A, 109, 6509-6520, 2005.; {8} Li, S.P. et al., Science, 319, 1657-1660, 2008. {9} Brown, S.S. et al., J. Phys. Chem., 103, 3031

First principles study of hydrogen bond symmetrization in δ-AlOOH

NASA Astrophysics Data System (ADS)

Pillai, Sharad Babu; Jha, Prafulla K.; Padmalal, Akash; Maurya, D. M.; Chamyal, L. S.

2018-03-01

The high pressure behaviour of the hydrous mineral δ-AlOOH has been investigated by many experimental and theoretical studies, but the discrepancy in predicting the value of hydrogen symmetrization pressure was not resolved. Here, we investigated the high pressure behaviour of δ-AlOOH using first principles calculations and found that with proper optimization using pressure routine control, local density approximation (LDA) predicts the hydrogen symmetrization pressure as 15 GPa which is in good agreement with the experimentally predicted value which resolves the existing discrepancy and hence proving the validity of LDA in predicting the hydrogen symmetrization pressure. We further studied the compressibility behaviour of δ-AlOOH at low pressures and confirmed the P21nm to Pnnm transition of δ-AlOOH shown by the experimental work [Kuribayashi et al., Phys. Chem. Miner. 41, 303-312 (2014)]. We have also analysed the dependence of elastic constants, elastic moduli, sound velocities, and Raman spectrum of δ-AlOOH with pressure and found that a subtle change in the position of the hydrogen atom at hydrogen symmetrization pressure results into drastic changes in elastic and vibrational properties. Further, this study has been used to discuss the seismic anomalies observed in the upper mantle beneath the Deccan Volcanic Province in India and the Java subduction zone in the eastern flank of the Indian Ocean.

The Rovibronic Spectra of the Cyclopentadienyl Radical

NASA Astrophysics Data System (ADS)

Sharma, Ketan; Miller, Terry A.; Stanton, John F.; Nesbitt, David

2017-06-01

Cyclopentadienyl (Cp) radical has been subject to numerous studies for the greater part of half a century. Experimental work has involved photo-electron spectroscopy, laser induced fluorescence excitation and emission, infrared absorption spectroscopy, and recently rotationally resolved spectra in the CH stretch region taken at JILA. Even more theoretical works appear in the literature, but substantial advances in computation have occurred since their completion. Cp's highly symmetric (D_{5h}) structure and doubly degenerate electronic ground (˜{X}^2E_1^{''}), which is subject to linear Jahn-Teller distortion, have been a great motivation for work on it. We have commenced new computational work to obtain a broad understanding of the electronic, vibrational, and rotational, i.e. rovibronic, structure of the Cp radical as revealed by its spectra, with particular emphasis on the new infrared spectra. The goal is to guide experiments and their analyses and reconcile results from spectroscopy and quantum chemistry calculations. T. Ichino, et al. J. Chem. Phys. 129, 084310 (2008) L. Yu, S. C. Foster, J. M. Williamson, M. C. Heaven and T. A. Miller J. Phys. Chem. 92, 4263 (1988) B. E. Applegate, A. J. Bezant and T. A. Miller J. Chem. Phys 114, 4869 (2001) D. Leicht, M. Kaufmann, G. Schwaab, and M. Havenith J. Chem. Phys. 145, 7 (2016), 074304.

Comment on ``Equation of state of aluminum nitride and its shock response'' [J. Appl. Phys. 76, 4077 (1994)

NASA Astrophysics Data System (ADS)

Rosenberg, Z.; Brar, N. S.

1995-11-01

A recent article by Dandekar, Abbate, and Frankel [J. Appl. Phys. 76, 4077 (1994)] reviews existing data on high-pressure properties of aluminum nitride (AlN) in an effort to build an equation of state for this material. A rather large portion of that article is devoted to the shear strength of AlN and, in particular, to our data of 1991 with longitudinal and lateral stress gauges [Z. Rosenberg, N. S. Brar, and S. J. Bless, J. Appl. Phys. 70, 167 (1991)]. Since our highest data point has an error of 1 GPa, much of the discussion and conclusions of Dandekar and co-workers are not relevant once this error in data reduction is corrected. We also discuss the relevance of our shear strength data for various issues, such as the phase transformation of AlN at 20 GPa and the general shape of Hugoniot curves for brittle solids.

Summary of PhysPAG Activities

NASA Astrophysics Data System (ADS)

Ritz, Steven M.

2012-01-01

The Physics of the Cosmos (PCOS) Program Analysis Group (PhysPAG) provides an important interface between the scientific community and NASA in matters related to PCOS objectives. An Executive Committee facilitates the work of several subgroups, including a Technology Science Analysis Group and an Inflation Probe Science Analysis Group. Work is also starting in areas of X-ray, gamma-ray, and gravitational wave astrophysics. The PAG reports to the Astrophysics Subcommittee of the NASA Advisory Council. A summary of PhysPAG activities will be given, along with time for questions and discussion.

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

Umino, Satoru; Takahashi, Hideaki, E-mail: hideaki@m.tohoku.ac.jp; Morita, Akihiro

In a recent work, we developed a method [H. Takahashi et al., J. Chem. Phys. 143, 084104 (2015)] referred to as exchange-core function (ECF) approach, to compute exchange repulsion E{sub ex} between solute and solvent in the framework of the quantum mechanical (QM)/molecular mechanical (MM) method. The ECF, represented with a Slater function, plays an essential role in determining E{sub ex} on the basis of the overlap model. In the work of Takahashi et al. [J. Chem. Phys. 143, 084104 (2015)], it was demonstrated that our approach is successful in computing the hydrogen bond energies of minimal QM/MM systems includingmore » a cationic QM solute. We provide in this paper the extension of the ECF approach to the free energy calculation in condensed phase QM/MM systems by combining the ECF and the QM/MM-ER approach [H. Takahashi et al., J. Chem. Phys. 121, 3989 (2004)]. By virtue of the theory of solutions in energy representation, the free energy contribution δμ{sub ex} from the exchange repulsion was naturally formulated. We found that the ECF approach in combination with QM/MM-ER gives a substantial improvement on the calculation of the hydration free energy of a hydronium ion. This can be attributed to the fact that the ECF reasonably realizes the contraction of the electron density of the cation due to the deficit of an electron.« less

Using Nice-Ohvms Lineshapes to Study Relaxation Rates and Transition Dipole Moments

NASA Astrophysics Data System (ADS)

Hodges, James N.; McCall, Benjamin J.

2016-06-01

Noise Immune Cavity Enhanced Optical Heterodyne Velocity Modulation Spectroscopy (NICE-OHVMS) is a successful technique that we have developed to sensitively, precisely, and accurately record transitions of molecular ions. It has been used exclusively as a method for precise transition frequency measurement via saturation and fitting of the resultant Lamb dips. NICE-OHVMS has been employed to improve the uncertainties on H_3^+, CH_5^+, HeH^+, and OH^+, reducing the transition frequency uncertainties by two orders of magnitude. Because NICE-OHVMS is a saturation technique, this provides a unique opportunity to access information about the ratio of the transition dipole moment to the relaxation rate of the transition. This can be done in two ways, either through comparison of Lamb dip depth to the transition profile or comparison of the absorption intensity and dispersion intensity. Due to the complexity of the modulation scheme, there are many parameters that affect the apparent intensity of the recorded lineshape. A complete understanding of the lineshape is required to make the measurements of interest. Here we present a model that accounts for the heterodyne modulation and velocity modulation, assuming that the fundamental lineshape is represented by a Voigt profile. Fits to data are made and interpreted in order to extract the saturation parameter. K.N. Crabtree et al., Chem. Phys. Lett. 551, 1 (2012). J.N. Hodges et al., J. Chem. Phys. 139, 164201 (2013). A.J. Perry et al., J. Mol. Spectrosc. 317, 71 (2015). A.J. Perry et al., J. Chem. Phys. 141, 101101 (2014). C.R. Marcus et al., Astrophys. J. 817, 138 (2016).

Path integral molecular dynamics for exact quantum statistics of multi-electronic-state systems.

PubMed

Liu, Xinzijian; Liu, Jian

2018-03-14

An exact approach to compute physical properties for general multi-electronic-state (MES) systems in thermal equilibrium is presented. The approach is extended from our recent progress on path integral molecular dynamics (PIMD), Liu et al. [J. Chem. Phys. 145, 024103 (2016)] and Zhang et al. [J. Chem. Phys. 147, 034109 (2017)], for quantum statistical mechanics when a single potential energy surface is involved. We first define an effective potential function that is numerically favorable for MES-PIMD and then derive corresponding estimators in MES-PIMD for evaluating various physical properties. Its application to several representative one-dimensional and multi-dimensional models demonstrates that MES-PIMD in principle offers a practical tool in either of the diabatic and adiabatic representations for studying exact quantum statistics of complex/large MES systems when the Born-Oppenheimer approximation, Condon approximation, and harmonic bath approximation are broken.

Path integral molecular dynamics for exact quantum statistics of multi-electronic-state systems

NASA Astrophysics Data System (ADS)

Liu, Xinzijian; Liu, Jian

2018-03-01

An exact approach to compute physical properties for general multi-electronic-state (MES) systems in thermal equilibrium is presented. The approach is extended from our recent progress on path integral molecular dynamics (PIMD), Liu et al. [J. Chem. Phys. 145, 024103 (2016)] and Zhang et al. [J. Chem. Phys. 147, 034109 (2017)], for quantum statistical mechanics when a single potential energy surface is involved. We first define an effective potential function that is numerically favorable for MES-PIMD and then derive corresponding estimators in MES-PIMD for evaluating various physical properties. Its application to several representative one-dimensional and multi-dimensional models demonstrates that MES-PIMD in principle offers a practical tool in either of the diabatic and adiabatic representations for studying exact quantum statistics of complex/large MES systems when the Born-Oppenheimer approximation, Condon approximation, and harmonic bath approximation are broken.

Comment on 'Effects of magnetic field gradient on ion beam current in cylindrical Hall ion source' [J. Appl. Phys. 102, 123305 (2007)

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

Raitses, Y.; Smirnov, A.; Fisch, N. J.

It is argued that the key difference in the cylindrical Hall thruster (CHT) as compared to the end-Hall ion source cannot be exclusively attributed to the magnetic field topology [Tang et al., J. Appl. Phys. 102, 123305 (2007)]. With a similar mirror-type topology, the CHT configuration provides the electric field with nearly equipotential magnetic field surfaces and a better suppression of the electron cross-field transport, as compared to both the end-Hall ion source and the cylindrical Hall ion source of [Tang et al., J. Appl. Phys. 102, 123305 (2007)].

Semiclassical Wigner theory of photodissociation in three dimensions: Shedding light on its basis

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

Arbelo-González, W.; CNRS, Institut des Sciences Moléculaires, UMR 5255, 33405 Talence; Université Bordeaux, Institut des Sciences Moléculaires, UMR 5255, 33405 Talence

2015-04-07

The semiclassical Wigner theory (SCWT) of photodissociation dynamics, initially proposed by Brown and Heller [J. Chem. Phys. 75, 186 (1981)] in order to describe state distributions in the products of direct collinear photodissociations, was recently extended to realistic three-dimensional triatomic processes of the same type [Arbelo-González et al., Phys. Chem. Chem. Phys. 15, 9994 (2013)]. The resulting approach, which takes into account rotational motions in addition to vibrational and translational ones, was applied to a triatomic-like model of methyl iodide photodissociation and its predictions were found to be in nearly quantitative agreement with rigorous quantum results, but at a muchmore » lower computational cost, making thereby SCWT a potential tool for the study of polyatomic reaction dynamics. Here, we analyse the main reasons for this agreement by means of an elementary model of fragmentation explicitly dealing with the rotational motion only. We show that our formulation of SCWT makes it a semiclassical approximation to an approximate planar quantum treatment of the dynamics, both of sufficient quality for the whole treatment to be satisfying.« less

Simulation of vibrational dephasing of I(2) in solid Kr using the semiclassical Liouville method.

PubMed

Riga, Jeanne M; Fredj, Erick; Martens, Craig C

2006-02-14

In this paper, we present simulations of the decay of quantum coherence between vibrational states of I(2) in its ground (X) electronic state embedded in a cryogenic Kr matrix. We employ a numerical method based on the semiclassical limit of the quantum Liouville equation, which allows the simulation of the evolution and decay of quantum vibrational coherence using classical trajectories and ensemble averaging. The vibrational level-dependent interaction of the I(2)(X) oscillator with the rare-gas environment is modeled using a recently developed method for constructing state-dependent many-body potentials for quantum vibrations in a many-body classical environment [J. M. Riga, E. Fredj, and C. C. Martens, J. Chem. Phys. 122, 174107 (2005)]. The vibrational dephasing rates gamma(0n) for coherences prepared between the ground vibrational state mid R:0 and excited vibrational state mid R:n are calculated as a function of n and lattice temperature T. Excellent agreement with recent experiments performed by Karavitis et al. [Phys. Chem. Chem. Phys. 7, 791 (2005)] is obtained.

Symmetry of extremely floppy molecules: Molecular states beyond rotation-vibration separation

NASA Astrophysics Data System (ADS)

Schmiedt, Hanno; Schlemmer, Stephan; Jensen, Per

2015-10-01

Traditionally, molecules are theoretically described as near-static structures rotating in space. Vibrational motion causing small structural deformations induces a perturbative treatment of the rotation-vibration interaction, which fails in highly fluxional molecules, where all vibrational motions have amplitudes comparable in size to the linear dimensions of the molecule. An example is protonated methane (CH 5+ ) [P. Kumar and D. Marx, Phys. Chem. Chem. Phys. 8, 573 (2006); Z. Jin et al., J. Phys. Chem. A 110, 1569 (2006); and A. S. Petit et al., J. Phys. Chem. A 118, 7206 (2014)]. For these molecules, customary theory fails to simulate reliably even the low-energy spectrum [T. Oka, Science 347, 1313-1314 (2015) and O. Asvany et al., Science 347, 1346-1349 (2015)]. Within the traditional view of rotation and vibration being near-separable, rotational and vibrational wavefunctions can be symmetry classified separately in the molecular symmetry (MS) group [P. Bunker and P. Jensen, Molecular Symmetry and Spectroscopy, NRC Monograph Publishing Program (NRC Research Press, 2006)]. In this article, we discuss a fundamental group theoretical approach to the problem of determining the symmetries of molecular rotation-vibration states. We will show that all MS groups discussed so far are isomorphic to subgroups of the special orthogonal group in three dimensions SO(3). This leads to a group theoretical foundation of the technique of equivalent rotations [H. Longuet-Higgins, Mol. Phys. 6, 445 (1963)]. The group G240 (the MS group of protonated methane) represents, to the best of our knowledge, the first example of a MS group which is not isomorphic to a subgroup of SO(3) (nor of O(3) or of SU(2)). Because of this, a separate symmetry classification of vibrational and rotational wavefunctions becomes impossible in this MS group, consistent with the fact that a decoupling of vibrational and rotational motion is impossible. We discuss here the consequences of this. In

LANL Researcher Roger Wiens Discusses ChemCam

ScienceCinema

Wiens, Roger

2018-01-16

Discussion of the ChemCam instrument on the Curiosity Rover that occurred during the NASA press conference prior to launch of the Mars Science Laboratory. The ChemCam instrument was developed by Los Alamos National Laboratory and the French Space Institute. Los Alamos National Laboratory researcher Roger Wiens discusses the instrument on this video. ChemCam uses a laser to "zap" features of the Martian landscape and then uses a spectrometer to gather information about the composition of the sample. ChemCam will help the Curiosity Rover determine whether Mars is or was habitable. The Rover is expected to touch down on the Red Planet on August 5, 2012.

Progress Towards a High-Precision Infrared Spectroscopic Survey of the H_3^+ Ion

NASA Astrophysics Data System (ADS)

Perry, Adam J.; Hodges, James N.; Markus, Charles R.; Kocheril, G. Stephen; Jenkins, Paul A., II; McCall, Benjamin J.

2015-06-01

The trihydrogen cation, H_3^+, represents one of the most important and fundamental molecular systems. Having only two electrons and three nuclei, H_3^+ is the simplest polyatomic system and is a key testing ground for the development of new techniques for calculating potential energy surfaces and predicting molecular spectra. Corrections that go beyond the Born-Oppenheimer approximation, including adiabatic, non-adiabatic, relativistic, and quantum electrodynamic corrections are becoming more feasible to calculate. As a result, experimental measurements performed on the H_3^+ ion serve as important benchmarks which are used to test the predictive power of new computational methods. By measuring many infrared transitions with precision at the sub-MHz level it is possible to construct a list of the most highly precise experimental rovibrational energy levels for this molecule. Until recently, only a select handful of infrared transitions of this molecule have been measured with high precision (˜ 1 MHz). Using the technique of Noise Immune Cavity Enhanced Optical Heterodyne Velocity Modulation Spectroscopy, we are aiming to produce the largest high-precision spectroscopic dataset for this molecule to date. Presented here are the current results from our survey along with a discussion of the combination differences analysis used to extract the experimentally determined rovibrational energy levels. O. Polyansky, et al., Phil. Trans. R. Soc. A (2012), 370, 5014. M. Pavanello, et al., J. Chem. Phys. (2012), 136, 184303. L. Diniz, et al., Phys. Rev. A (2013), 88, 032506. L. Lodi, et al., Phys. Rev. A (2014), 89, 032505. J. Hodges, et al., J. Chem. Phys (2013), 139, 164201.

Chem-Braze Abradable Seal Attachment

DTIC Science & Technology

1980-05-01

bonding system for attaching sintered abradable seals such as FELTMETAL® to titanium -, steel- and nickel-base compressor blade tip-shrouds has been... blade tip-shrouds was developed. The improved Chem-Braze system incorporates glycerin as an inhibitor to prevent premature evaporation which prolongs...compressor blade tip-shrouds using the improved Chem-Braze system compared to attachment with gold-nickel braze. p. p. FORM . . yn

Fermi orbital self-interaction corrected electronic structure of molecules beyond local density approximation

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

Hahn, T., E-mail: torsten.hahn@physik.tu-freiberg.de; Liebing, S.; Kortus, J.

2015-12-14

The correction of the self-interaction error that is inherent to all standard density functional theory calculations is an object of increasing interest. In this article, we apply the very recently developed Fermi-orbital based approach for the self-interaction correction [M. R. Pederson et al., J. Chem. Phys. 140, 121103 (2014) and M. R. Pederson, J. Chem. Phys. 142, 064112 (2015)] to a set of different molecular systems. Our study covers systems ranging from simple diatomic to large organic molecules. We focus our analysis on the direct estimation of the ionization potential from orbital eigenvalues. Further, we show that the Fermi orbitalmore » positions in structurally similar molecules appear to be transferable.« less

Hydrogen-bond memory and water-skin supersolidity resolving the Mpemba paradox.

PubMed

Zhang, Xi; Huang, Yongli; Ma, Zengsheng; Zhou, Yichun; Zhou, Ji; Zheng, Weitao; Jiang, Qing; Sun, Chang Q

2014-11-14

The Mpemba paradox, that is, hotter water freezes faster than colder water, has baffled thinkers like Francis Bacon, René Descartes, and Aristotle since B.C. 350. However, a commonly accepted understanding or theoretical reproduction of this effect remains challenging. Numerical reproduction of observations, shown herewith, confirms that water skin supersolidity [Zhang et al., Phys. Chem. Chem. Phys., DOI: ] enhances the local thermal diffusivity favoring heat flowing outwardly in the liquid path. Analysis of experimental database reveals that the hydrogen bond (O:H-O) possesses memory to emit energy at a rate depending on its initial storage. Unlike other usual materials that lengthen and soften all bonds when they absorb thermal energy, water performs abnormally under heating to lengthen the O:H nonbond and shorten the H-O covalent bond through inter-oxygen Coulomb coupling [Sun et al., J. Phys. Chem. Lett., 2013, 4, 3238]. Cooling does the opposite to release energy, like releasing a coupled pair of bungees, at a rate of history dependence. Being sensitive to the source volume, skin radiation, and the drain temperature, the Mpemba effect proceeds only in the strictly non-adiabatic 'source-path-drain' cycling system for the heat "emission-conduction-dissipation" dynamics with a relaxation time that drops exponentially with the rise of the initial temperature of the liquid source.

Utilizing the Power of Nanostructures to Their Fullest Capability in Energetic Formulations

DTIC Science & Technology

2016-02-01

aluminum-cyclopentadienyl clusters. J Phys Chem A. 2011;115(48):14100– 14109. Zeng Q, Jiang X, Yu A, Lu G. Growth mechanisms of silver nanoparticles : a...assemblies of gas generators containing nanoscale Al (conventional Al nanoparticles and Al nanoclusters) to overcome the sintering and/or oxide-formation...issues. Experimentally, a previously published hypothesis for the mechanism leading to enhanced energy release from Al nanoparticles in the presence of

Pulsed Photolytic Density Scaling Experiment for BiF

DTIC Science & Technology

1989-05-01

on Lasers 86, ed. W. B. Lacina, Soc. for Opt. and Quantum Electronics, STS Press. 281 (1987). 9a. R. F. Heidner, H . Helvajian , J. S. Holloway, and J. B...Koffend, J. Chem. Phys. 84, 2137 (1986). 9b. H . Helvajian , J. S. Holloway, and J. B. Koffend, J. Chem. Phys. (in press). 10. J. B. Koffend and R. F...C. E. Gardner, and R. F. Heidner, J. Chem. Phys. 83, 2904 (1985). 13. R. F. Heidner, H . Helvajian , and J. B. Koffend, J. Chem. Phys. 87, 520 (1987

Reactive Removal of BiF Ground State

DTIC Science & Technology

1990-09-28

1978). 3. W E. Jones and T D. McLean, J. Mol. Spectrosc. 90, 481 (1981). 4. R. E Heidner, H . Helvajian , J. S. Holloway, and J. B. Koffend, J. Chem...Phys. 84, 2137 (1986). 5. C. R. Jones and H . P. Broida, J. Chem. Phys. 60, 4369 (1974). 6. H . Helvajian , J. S. Holloway, and J. B. Koffend, J. Chem...Phys. Rev. A6, 631 (1972). 27. H . Hotop and W C. Lineberger, J. Phys. Chem. Ref. Data 4, 539 (1985). 28. J.M. Herbelin, Conf. Proc., Intl. Gonf. on

LANL Researcher Roger Wiens Discusses ChemCam

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

Wiens, Roger

2012-02-15

Discussion of the ChemCam instrument on the Curiosity Rover that occurred during the NASA press conference prior to launch of the Mars Science Laboratory. The ChemCam instrument was developed by Los Alamos National Laboratory and the French Space Institute. Los Alamos National Laboratory researcher Roger Wiens discusses the instrument on this video. ChemCam uses a laser to "zap" features of the Martian landscape and then uses a spectrometer to gather information about the composition of the sample. ChemCam will help the Curiosity Rover determine whether Mars is or was habitable. The Rover is expected to touch down on the Redmore » Planet on August 5, 2012.« less

Direct Methanol Fuel Cell Battery Replacement Program

DTIC Science & Technology

2011-04-11

Matthey PtRu in operating direct methanol fuel cells” Phys. Chem. Chem. Phys., 10, 6430-6437 (2008) 2. Harry Rivera, Jamie S. Lawton , David E. Budil and...Phys. Chem. B, 112, (29) 8542-8548 (2008) 3. Jamie S. Lawton , Eugene S. Smotkin and David E. Budil, “ESR Investigation of Microviscosity, Microscopic

Rovibrational Quantum Dynamics of the Methane-Water Dimer

NASA Astrophysics Data System (ADS)

Sarka, János; Császár, Attila; Mátyus, Edit

2017-06-01

The challenging quantum dynamical description of the CH_4.H_2O complex has been solved variationally to provide theoretical explanation and assignment to the high-resolution spectroscopic measurements of the methane-water dimer carried out some twenty years ago. The computational results are in excellent agreement with the reported experimental transitions and the experimentally observed reversed rovibrational sequences, i.e., formally negative rotational excitation energies, are also obtained in the computations. In order to better understand the origin of these peculiar features in the energy-level spectrum, we studied all four possible combinations of the light and heavy isotopologues of methane and water and analyzed their rovibrational states using two limiting model systems: the rigidly rotating (RR) molecule and the coupled rotor (CR) system corresponding to the coupling of the two rotating monomers. All rovibrational quantum dynamical computations^{a,c} were carried out with rigid monomers and J = 0,1,2 total angular momentum quantum numbers using the fourth-age quantum chemical code GENIUSH and two different methane-water potential energy surfaces (PES). The numerical and formal analysis of the wave functions give insight into a fascinating complex world worth for further theoretical and experimental inquiries. J. Sarka, A. G. Császár, S. C. Althorpe, D. J. Wales and E. Mátyus, Phys. Chem. Chem. Phys. 18, 22816 (2016). L. Dore, R. C. Cohen, C. A. Schmuttenmaer, K. L. Busarow, M. J. Elrod, J. G. Loeser and R. J. Saykally, J. Chem. Phys. 100, 863 (1994). J. Sarka, A. G. Császár and E. Mátyus, Phys. Chem. Chem. Phys. accepted for publication (2017).} E. Mátyus, G. Czakó and A. G. Császár, J. Chem. Phys. 130, 134112 (2009). C. Fábri, E. Mátyus and A. G. Császár, J. Chem. Phys. 134, 074105 (2011). O. Akin-Ojo and K. Szalewicz, J. Chem. Phys. 123, 134311 (2005). C. Qu, R. Conte, P. L. Houston and J. M. Bowman, Phys. Chem. Chem. Phys. 17, 8172 (2015).

Calculation of the Gibbs Free Energy of Solvation and Dissociation of HCl in Water via Monte Carlo Simulations and Continuum Solvation Models

DTIC Science & Technology

2013-01-01

Narten, J. Chem. Phys., 1975, 63, 3624–3631. 10 A. Botti, F. Bruni, S. Imberti, M. A. Ricci and A. K. Soper , J. Chem. Phys., 2004, 121, 7840–7848. 11 D...10478. 48 I. Harsányi and L. Pusztai, J. Phys.: Condens. Matter, 2005, 17, S59–S65. 49 A. Botti, F. Bruni, M. A. Ricci and A. K. Soper , J. Chem. Phys

Exploring the free energy surface using ab initio molecular dynamics

NASA Astrophysics Data System (ADS)

Samanta, Amit; Morales, Miguel A.; Schwegler, Eric

2016-04-01

Efficient exploration of configuration space and identification of metastable structures in condensed phase systems are challenging from both computational and algorithmic perspectives. In this regard, schemes that utilize a set of pre-defined order parameters to sample the relevant parts of the configuration space [L. Maragliano and E. Vanden-Eijnden, Chem. Phys. Lett. 426, 168 (2006); J. B. Abrams and M. E. Tuckerman, J. Phys. Chem. B 112, 15742 (2008)] have proved useful. Here, we demonstrate how these order-parameter aided temperature accelerated sampling schemes can be used within the Born-Oppenheimer and the Car-Parrinello frameworks of ab initio molecular dynamics to efficiently and systematically explore free energy surfaces, and search for metastable states and reaction pathways. We have used these methods to identify the metastable structures and reaction pathways in SiO2 and Ti. In addition, we have used the string method [W. E, W. Ren, and E. Vanden-Eijnden, Phys. Rev. B 66, 052301 (2002); L. Maragliano et al., J. Chem. Phys. 125, 024106 (2006)] within the density functional theory to study the melting pathways in the high pressure cotunnite phase of SiO2 and the hexagonal closed packed to face centered cubic phase transition in Ti.

Dielectric spectra broadening as a signature for dipole-matrix interaction. III. Water in adenosine monophosphate/adenosine-5'-triphosphate solutions.

PubMed

Puzenko, Alexander; Levy, Evgeniya; Shendrik, Andrey; Talary, Mark S; Caduff, Andreas; Feldman, Yuri

2012-11-21

In this, the third part of our series on the dielectric spectrum symmetrical broadening of water, we consider the nucleotide aqueous solutions. Where in Parts I [E. Levy et al., J. Chem. Phys. 136, 114502 (2012)] and II [E. Levy et al., J. Chem. Phys. 136, 114503 (2012)], the dipole-dipole or ion-dipole interaction had a dominant feature, now the interplay between these two types of dipole-matrix interactions will be considered. We present the results of high frequency dielectric measurements of different concentrations of adenosine monophosphate/adenosine-5'-triphosphate aqueous solutions. We observed the Cole-Cole broadening of the main relaxation peak of the solvent in the solutions. Moreover, depending on the nucleotide concentration, we observed both types of dipole-matrix interaction. The 3D trajectory approach (described in detail in Part I) is applied in order to highlight the differences between the two types of interaction.

PERSPECTIVE: Snow matters in the polar regions

NASA Astrophysics Data System (ADS)

Sodeau, John

2010-03-01

relatively long history of this topic was surveyed extensively in 2007 and the answer is probably not related to the photolysis of the halogeno-carbons although the transformation processes are still not completely understood (Simpson et al 2007). This topic along with the potential involvement of both iodine and chlorine species is decidedly 'hot' in the intriguing world of polar cryochemistry. The Antony et al (2010) paper is actually entitled 'Is cloud seeding in coastal Antarctica linked to bromine and nitrate variability in snow?'. Although the nitrate ions were discussed in terms of being a simple nutrient in the study, the photochemistry of nitrate ions in snow has actually become an important focus of research in the laboratory. A further review by Grannas et al (2007) is recommended in this respect. But important questions remain regarding the fate of the NO and NO2 molecules produced in the primary photolytic channels, especially if concentrated into ice 'micropockets' (Hellebust et al 2007). Furthermore the impacts of newly discovered reactions such as HO2/NO to directly produce nitric acid, at the expense of NOx, have not yet been quantified in the polar ABL context (Cariolle et al 2008). Then there is peroxyacetylnitrate (PAN; Mills et al 2007) and other organo-nitrates and their possible interactions with mercury and the halides . . . Clearly, Antarctica is not chemically pristine and snow-ice interfaces in both the laboratory and the field have become a very challenging medium for exploring new and unexpected chemistry relevant to our atmosphere. References Abbatt J P D 1994 Heterogeneous reaction of HOBr with HBr and HCl on ice surfaces at 228 K Geophys. Res. Lett. 21 665-8 Antony R et al 2010 Is cloud seeding in coastal Antarctica linked to bromine and nitrate variability in snow? Environ. Res. Lett. 5 014009 Cariolle D et al 2008 Impact of the new HNO3-forming channel of the HO2 + NO reaction on tropospheric HNO3, NOx, HOx and ozone Atmos. Chem. Phys. 8

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

Reppert, Mike; Kell, Adam; Pruitt, Thomas

The vibrational spectral density is an important physical parameter needed to describe both linear and non-linear spectra of multi-chromophore systems such as photosynthetic complexes. Low-temperature techniques such as hole burning (HB) and fluorescence line narrowing are commonly used to extract the spectral density for a given electronic transition from experimental data. We report here that the lineshape function formula reported by Hayes et al. [J. Phys. Chem. 98, 7337 (1994)] in the mean-phonon approximation and frequently applied to analyzing HB data contains inconsistencies in notation, leading to essentially incorrect expressions in cases of moderate and strong electron-phonon (el-ph) coupling strengths.more » A corrected lineshape function L(ω) is given that retains the computational and intuitive advantages of the expression of Hayes et al. [J. Phys. Chem. 98, 7337 (1994)]. Although the corrected lineshape function could be used in modeling studies of various optical spectra, we suggest that it is better to calculate the lineshape function numerically, without introducing the mean-phonon approximation. New theoretical fits of the P870 and P960 absorption bands and frequency-dependent resonant HB spectra of Rb. sphaeroides and Rps. viridis reaction centers are provided as examples to demonstrate the importance of correct lineshape expressions. Comparison with the previously determined el-ph coupling parameters [Johnson et al., J. Phys. Chem. 94, 5849 (1990); Lyle et al., ibid. 97, 6924 (1993); Reddy et al., ibid. 97, 6934 (1993)] is also provided. The new fits lead to modified el-ph coupling strengths and different frequencies of the special pair marker mode, ω{sub sp}, for Rb. sphaeroides that could be used in the future for more advanced calculations of absorption and HB spectra obtained for various bacterial reaction centers.« less

Addition of NH{sub 3} to Al{sub 3}O{sub 3}{sup -}

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

Wyrwas, Richard B.; Jarrold, Caroline Chick; Das, Ujjal

2006-05-28

Recent computational studies on the addition of ammonia (NH{sub 3}) to the Al{sub 3}O{sub 3}{sup -} cluster anion [A. Guevara-Garcia, A. Martinez, and J. V. Ortiz, J. Chem. Phys. 122, 214309 (2005)] have motivated experimental and additional computational studies, reported here. Al{sub 3}O{sub 3}{sup -} is observed to react with a single NH{sub 3} molecule to form the Al{sub 3}O{sub 3}NH{sub 3}{sup -} ion in mass spectrometric studies. This is in contrast to similarly performed studies with water, in which the Al{sub 3}O{sub 5}H{sub 4}{sup -} product was highly favored. However, the anion PE spectrum of the ammoniated species ismore » very similar to that of Al{sub 3}O{sub 4}H{sub 2}{sup -}. The adiabatic electron affinity of Al{sub 3}O{sub 3}NH{sub 3} is determined to be 2.35(5) eV. Based on comparison between the spectra and calculated electron affinities, it appears that NH{sub 3} adds dissociatively to Al{sub 3}O{sub 3}{sup -}, suggesting that the time for the Al{sub 3}O{sub 3}{sup -}{center_dot}NH{sub 3} complex to either overcome or tunnel through the barrier to proton transfer (which is higher for NH{sub 3} than for water) is short relative to the time for collisional cooling in the experiment.« less

Response to 'Comment on 'Continuum modes in rotating plasmas: General equations and continuous spectra for large aspect ratio tokamaks' '[Phys. Plasmas 19, 064701 (2012)

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

Lakhin, V. P.; Ilgisonis, V. I.; Peoples' Friendship University, 3 Ordzhonikidze St., Moscow 117198

2012-06-15

The equations for the continuous spectra derived in our paper [V. P. Lakhin and V. I. Ilgisonis, Phys. Plasmas 18, 092103 (2011)] can be reduced to the matrix form used by Goedbloed et al.[Phys. Plasmas 11, 28 (2004)]. It is shown that the assumptions made in our paper provide the elliptic flow regime and guarantee the existence of plasma equilibrium with nested magnetic surfaces of circular cross-section. The new results on magnetohydrodynamic instabilities of such tokamak equilibria obtained in our paper but absent in the paper by Goedbloed et al. are emphasized.

Precision Measurement of the Rovibrational Energy-Level Structure of ^{4}He^{+}_{2}

NASA Astrophysics Data System (ADS)

Semeria, Luca; Jansen, Paul; Agner, Josef A.; Schmutz, Hansjürg; Merkt, Frederic

2017-06-01

He_{2}^{+} is a three-electron system for which highly accurate ab initio calculations are possible. The latest calculations of the rovibrational energies of He_{2}^{+} by Tung et al. have a reported accuracy of 120 MHz, although they do not include relativistic and quantum electrodynamics (QED) effects. We determined the rovibrational structure of ^{4}He^{+}_{2} from measurements of the Rydberg spectrum of metastable a ^3Σ_u^+ He_{2} (He^{*}_{2} hereafter) and Rydberg-series extrapolation using multichannel quantum-defect-theory. He^{*}_{2} molecules are produced in supersonic beams with velocities tunable down to about 100 m/s by combining a cryogenic supersonic-beam source with a multistage Zeeman decelerator. They are then excited to high-np Rydberg states by single-photon excitation. In the experiments, we use a pulsed uv laser system, with a near Fourier-transform-limited bandwidth of 150 MHz. The Zeeman deceleration reduces the systematic uncertainty arising from a possible Doppler shift and greatly simplifies the spectral assignment because of its spin-rotational state selectivity. Results will be presented on the rotational structure of the lowest three vibrational levels of He^{+}_{2}. The unprecedented accuracy that we have obtained for the v^{+}=0 rotational intervals of He_{2}^{+} enables the quantification of the relativistic and QED corrections by comparison with the results of Tung et al.^a W.-C. Tung, M. Pavanello and L. Adamowicz, J. Chem. Phys., 136, 104309, 2012. C. Jungen, Elements of Quantum Defect Theory, in : Handbook of High-resolution Spectroscopy, 2001. D. Sprecher, J. Liu, T. Krähenmann, M. Schäfer, and F. Merkt, J. Chem. Phys., 140, 064304, 2014. A. W. Wiederkehr, S. D. Hogan, M. Andrist, H. Schmutz, B. Lambillotte, J. A. Agner, and F. Merkt., J. Chem. Phys., 135, 214202, 2011. M. Motsch, P. Jansen, J. A. Agner, H. Schmutz, and F. Merkt, Phys. Rev. A, 89, 043420, 2014. P. Jansen, L. Semeria, L. E. Hofer, S. Scheidegger, J. A. Agner

Charging and Discharging of Amorphous Solid Water Ice: Effects of Porosity

NASA Astrophysics Data System (ADS)

Bu, Caixia; Baragiola, Raul A.

2015-11-01

(2008); [3] U. Raut et al., J. Chem. Phys. 127, 204713 (2007); [4] C. Bu and R. B. Baragiola, J. Chem. Phys. 143, 074702 (2015); [5] C. Bu et al., J. Chem. Phys. 142, 134702 (2015); [6] M. J. Iedema et al., J. Phys. Chem. B 102, 9203 (1998).

A Java API for working with PubChem datasets.

PubMed

Southern, Mark R; Griffin, Patrick R

2011-03-01

PubChem is a public repository of chemical structures and associated biological activities. The PubChem BioAssay database contains assay descriptions, conditions and readouts and biological screening results that have been submitted by the biomedical research community. The PubChem web site and Power User Gateway (PUG) web service allow users to interact with the data and raw files are available via FTP. These resources are helpful to many but there can also be great benefit by using a software API to manipulate the data. Here, we describe a Java API with entity objects mapped to the PubChem Schema and with wrapper functions for calling the NCBI eUtilities and PubChem PUG web services. PubChem BioAssays and associated chemical compounds can then be queried and manipulated in a local relational database. Features include chemical structure searching and generation and display of curve fits from stored dose-response experiments, something that is not yet available within PubChem itself. The aim is to provide researchers with a fast, consistent, queryable local resource from which to manipulate PubChem BioAssays in a database agnostic manner. It is not intended as an end user tool but to provide a platform for further automation and tools development. http://code.google.com/p/pubchemdb.

Readying ChemCam

NASA Image and Video Library

2012-08-17

This image shows the calibration target for the Chemistry and Camera ChemCam instrument on NASA Curiosity rover. The calibration target is one square and a group of nine circles that look dark in the black-and-white image.

Ultraviolet Photoionization Efficiency of the Vaporized Ionic Liquid 1-Butyl-3-Methylimidazolium Tricyanomethanide: Direct Detection of the Intact Ion Pair (Post Print)

DTIC Science & Technology

2012-09-21

Lovelock , K. R. J.; Satterly, C. J.; Villar-Garcia, I. J. Phys. Chem. Chem. Phys. 2007, 9, 982−990. (11) Strasser, D.; Goulay, F.; Kelkar, M. S.; Maginn, E...J.; Leone, S. R. J. Phys. Chem. A 2007, 111, 3191−3915. (12) Lovelock , K. R. J.; Deyko, A.; Corfield, J.-A.; Gooden, P. N.; Licence, P.; Jones, R. G

Work cost of thermal operations in quantum thermodynamics

NASA Astrophysics Data System (ADS)

Renes, Joseph M.

2014-07-01

Adopting a resource theory framework of thermodynamics for quantum and nano systems pioneered by Janzing et al. (Int. J. Th. Phys. 39, 2717 (2000)), we formulate the cost in the useful work of transforming one resource state into another as a linear program of convex optimization. This approach is based on the characterization of thermal quasiorder given by Janzing et al. and later by Horodecki and Oppenheim (Nat. Comm. 4, 2059 (2013)). Both characterizations are related to an extended version of majorization studied by Ruch, Schranner and Seligman under the name mixing distance (J. Chem. Phys. 69, 386 (1978)).

Combining density functional and incremental post-Hartree-Fock approaches for van der Waals dominated adsorbate-surface interactions: Ag{sub 2}/graphene

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

Lara-Castells, María Pilar de, E-mail: Pilar.deLara.Castells@csic.es; Mitrushchenkov, Alexander O.; Stoll, Hermann

2015-09-14

A combined density functional (DFT) and incremental post-Hartree-Fock (post-HF) approach, proven earlier to calculate He-surface potential energy surfaces [de Lara-Castells et al., J. Chem. Phys. 141, 151102 (2014)], is applied to describe the van der Waals dominated Ag{sub 2}/graphene interaction. It extends the dispersionless density functional theory developed by Pernal et al. [Phys. Rev. Lett. 103, 263201 (2009)] by including periodic boundary conditions while the dispersion is parametrized via the method of increments [H. Stoll, J. Chem. Phys. 97, 8449 (1992)]. Starting with the elementary cluster unit of the target surface (benzene), continuing through the realistic cluster model (coronene), andmore » ending with the periodic model of the extended system, modern ab initio methodologies for intermolecular interactions as well as state-of-the-art van der Waals-corrected density functional-based approaches are put together both to assess the accuracy of the composite scheme and to better characterize the Ag{sub 2}/graphene interaction. The present work illustrates how the combination of DFT and post-HF perspectives may be efficient to design simple and reliable ab initio-based schemes in extended systems for surface science applications.« less

Conceptual DFT analysis of the fragility spectra of atoms along the minimum energy reaction coordinate.

PubMed

Ordon, Piotr; Komorowski, Ludwik; Jedrzejewski, Mateusz

2017-10-07

Theoretical justification has been provided to the method for monitoring the sequence of chemical bonds' rearrangement along a reaction path, by tracing the evolution of the diagonal elements of the Hessian matrix. Relations between the divergences of Hellman-Feynman forces and the energy and electron density derivatives have been demonstrated. By the proof presented on the grounds of the conceptual density functional theory formalism, the spectral amplitude observed on the atomic fragility spectra [L. Komorowski et al., Phys. Chem. Chem. Phys. 18, 32658 (2016)] reflects selectively the electron density modifications in bonds of an atom. In fact the spectral peaks for an atom reveal changes of the electron density occurring with bonds creation, breaking, or varying with the reaction progress.

Conceptual DFT analysis of the fragility spectra of atoms along the minimum energy reaction coordinate

NASA Astrophysics Data System (ADS)

Ordon, Piotr; Komorowski, Ludwik; Jedrzejewski, Mateusz

2017-10-01

Theoretical justification has been provided to the method for monitoring the sequence of chemical bonds' rearrangement along a reaction path, by tracing the evolution of the diagonal elements of the Hessian matrix. Relations between the divergences of Hellman-Feynman forces and the energy and electron density derivatives have been demonstrated. By the proof presented on the grounds of the conceptual density functional theory formalism, the spectral amplitude observed on the atomic fragility spectra [L. Komorowski et al., Phys. Chem. Chem. Phys. 18, 32658 (2016)] reflects selectively the electron density modifications in bonds of an atom. In fact the spectral peaks for an atom reveal changes of the electron density occurring with bonds creation, breaking, or varying with the reaction progress.

Mirjana Dimitrievska | NREL

Science.gov Websites

understanding the structure-dependent vibrational properties and reorientational behavior of different alkali Sad, Serbia Featured Publications M. Dimitrievska et al., "Structure-dependent vibrational : Structure and luminescence," J. Phys. Chem. C 120(33), 18887-18894 (2016). DOI: http://dx.doi.org

A Java API for working with PubChem datasets

PubMed Central

Southern, Mark R.; Griffin, Patrick R.

2011-01-01

Summary: PubChem is a public repository of chemical structures and associated biological activities. The PubChem BioAssay database contains assay descriptions, conditions and readouts and biological screening results that have been submitted by the biomedical research community. The PubChem web site and Power User Gateway (PUG) web service allow users to interact with the data and raw files are available via FTP. These resources are helpful to many but there can also be great benefit by using a software API to manipulate the data. Here, we describe a Java API with entity objects mapped to the PubChem Schema and with wrapper functions for calling the NCBI eUtilities and PubChem PUG web services. PubChem BioAssays and associated chemical compounds can then be queried and manipulated in a local relational database. Features include chemical structure searching and generation and display of curve fits from stored dose–response experiments, something that is not yet available within PubChem itself. The aim is to provide researchers with a fast, consistent, queryable local resource from which to manipulate PubChem BioAssays in a database agnostic manner. It is not intended as an end user tool but to provide a platform for further automation and tools development. Availability: http://code.google.com/p/pubchemdb Contact: southern@scripps.edu PMID:21216779

Communication: Stiff and soft nano-environments and the "Octopus Effect" are the crux of ionic liquid structural and dynamical heterogeneity

NASA Astrophysics Data System (ADS)

Daly, Ryan P.; Araque, Juan C.; Margulis, Claudio J.

2017-08-01

In a recent set of articles [J. C. Araque et al., J. Phys. Chem. B 119(23), 7015-7029 (2015) and J. C. Araque et al., J. Chem. Phys. 144, 204504 (2016)], we proposed the idea that for small neutral and charged solutes dissolved in ionic liquids, deviation from simple hydrodynamic predictions in translational and rotational dynamics can be explained in terms of diffusion through nano-environments that are stiff (high electrostriction, charge density, and number density) and others that are soft (charge depleted). The current article takes a purely solvent-centric approach in trying to provide molecular detail and intuitive visual understanding of time-dependent local mobility focusing on the most common case of an ionic liquid with well defined polar and apolar nano-domains. We find that at intermediate time scales, apolar regions are fluid, whereas the charge network is much less mobile. Because apolar domains and cationic heads must diffuse as single species, at long time the difference in mobility also necessarily dissipates.

Ice nucleation rates near ˜225 K

NASA Astrophysics Data System (ADS)

Amaya, Andrew J.; Wyslouzil, Barbara E.

2018-02-01

We have measured the ice nucleation rates, Jice, in supercooled nano-droplets with radii ranging from 6.6 nm to 10 nm and droplet temperatures, Td, ranging from 225 K to 204 K. The initial temperature of the 10 nm water droplets is ˜250 K, i.e., well above the homogeneous nucleation temperature for micron sized water droplets, TH ˜235 K. The nucleation rates increase systematically from ˜1021 cm-3 s-1 to ˜1022 cm-3 s-1 in this temperature range, overlap with the nucleation rates of Manka et al. [Phys. Chem. Chem. Phys. 14, 4505 (2012)], and suggest that experiments with larger droplets would extrapolate smoothly the rates of Hagen et al. [J. Atmos. Sci. 38, 1236 (1981)]. The sharp corner in the rate data as temperature drops is, however, difficult to match with available theory even if we correct classical nucleation theory and the physical properties of water for the high internal pressure of the nanodroplets.

Ab initio prediction of the vibration-rotation-tunneling spectrum of HCl-(H2O)2

NASA Astrophysics Data System (ADS)

Wormer, P. E. S.; Groenenboom, G. C.; van der Avoird, A.

2001-08-01

Quantum calculations of the vibration-rotation-tunneling (VRT) levels of the trimer HCl-(H2O)2 are presented. Two internal degrees of freedom are considered—the rotation angles of the two nonhydrogen-bonded (flipping) hydrogens in the complex—together with the overall rotation of the trimer in space. The kinetic energy expression of van der Avoird et al. [J. Chem. Phys. 105, 8034 (1996)] is used in a slightly modified form. The experimental microwave geometry of Kisiel et al. [J. Chem. Phys. 112, 5767 (2000)] served as input in the generation of a planar reference structure. The two-dimensional potential energy surface is generated ab initio by the iterative coupled-cluster method based on singly and doubly excited states with triply excited states included noniteratively [CCSD(T)]. Frequencies of vibrations and tunnel splittings are predicted for two isotopomers. The effect of the nonadditive three-body forces is considered and found to be important.

Relativistic corrections to the ground state of H2 calculated without using the Born-Oppenheimer approximation

NASA Astrophysics Data System (ADS)

Wang, L. M.; Yan, Z.-C.

2018-06-01

The Schrödinger equation for the ground state of the hydrogen molecule H2 is solved by applying the Rayleigh-Ritz variational method in Hylleraas coordinates without using the Born-Oppenheimer approximation. The nonrelativistic energy eigenvalue is converged to -1.164 025 030 880 (7 ) atomic units. The leading-order relativistic corrections, including the mass-velocity, Darwin, orbit-orbit, spin-spin, and relativistic recoil terms, are evaluated perturbatively. Together with the higher-order relativistic and quantum electrodynamic corrections obtained by Puchalski et al. [Phys. Rev. Lett. 117, 263002 (2016), 10.1103/PhysRevLett.117.263002], we determine the dissociation energy of the hydrogen molecule, D0=36 118.069 71 (33 ) cm-1 , which agrees with the two recent experimental results of Liu et al. [J. Chem. Phys. 130, 174306 (2009), 10.1063/1.3120443], 36 118.069 62 (37 ) cm-1 , and Altmann et al. [Phys. Rev. Lett. 120, 043204 (2018), 10.1103/PhysRevLett.120.043204], 36 118.069 45 (31 ) cm-1 .

The NH3Cl+ Cation

DTIC Science & Technology

2004-05-21

Chem. 1966, 5, 1791; (c) H. W. Roesky, O. Glemser, D. Bormann, Chem. Ber. 1966, 99, 1589; (d) A. V. Pankratov , N. I. Savenkova, Russ. J. Inorg. Chem...J. Am. Chem. Soc. 1991 , 113, 3795. [6] (a) J. K. Ruff, J. Am. Chem. Soc. 1965, 87, 1140; J. K. Ruff, Inorg. Chem. 1966, 5, 1791; (c) A. R. Young, D...unlimited 9 [12] (a) M. Brumm, G. Frenking, W. Koch, Chem. Phys. Lett. 1991 , 182, 310; (b) M. Brumm, G. Frenking, J. Breidung, W. Thiel, Chem. Phys

Using WRF-Chem to investigate the impact of night time nitrate radical chemistry and N2O5 heterogeneous chemistry on the chemical composition of the UK troposphere.

NASA Astrophysics Data System (ADS)

Archer-Nicholls, S.; Lowe, D.; Utembe, S.; McFiggans, G.

2012-04-01

of two flight periods: one during July 2010; the other during January 2011. We have run five model scenarios for both these periods: a base case, with standard emissions and chemistry; two scenarios with standard chemistry, but with halved and doubled NOx transport emissions respectively; and two scenarios with standard emissions, but one without N2O5 heterogeneous chemistry, and the other with the Cl- reaction pathway disabled. We will present results from the application of WRF-Chem to model the regional chemical composition of the atmosphere about the UK. Sensitivities to changing emission profiles and the impact of N2O5 heterogeneous chemistry will be discussed. Preliminary comparisons between model results and aircraft data will be shown. The strengths and weaknesses of our modelling approach, in particular the gains and drawbacks of using a fully coupled online model for use in this campaign, will be highlighted. The wider impacts of the processes investigated on the regional climate and air quality will be further discussed. Allan, B., et. al. (2000); J. Geophys. Res., 105, doi: 10.1046/j.1365-2370.2000.00208. Bertram, T. H., Thornton, J. A. (2009); Atmos. Chem. Phys., 9, 8351-8363, doi: 10.5194/acp-9-8351-2009 Grell, G., et. al. (2005); Atmos. Environ., 39, 6957- 6975. doi: 10.1016/j.atmosenv.2005.04.027 Topping, D., Lowe, D. & McFiggans, G. (2012); Geosci. Model Dev., 5, 1-13. doi:10.5194/gmd-5-1-2012 Watson, L., et. al. (2008); Atmos. Environ., 42, 7196- 7204, doi: 10.1016/j.atmosenv.2008.07.034 Zaveri, R. A., et. al. (2008); J. Geophys. Res., 113, doi:10.1029/2007JD008782

Getting the Most out of PubChem for Virtual Screening

PubMed Central

Kim, Sunghwan

2016-01-01

Introduction With the emergence of the “big data” era, the biomedical research community has great interest in exploiting publicly available chemical information for drug discovery. PubChem is an example of public databases that provide a large amount of chemical information free of charge. Areas covered This article provides an overview of how PubChem’s data, tools, and services can be used for virtual screening and reviews recent publications that discuss important aspects of exploiting PubChem for drug discovery. Expert opinion PubChem offers comprehensive chemical information useful for drug discovery. It also provides multiple programmatic access routes, which are essential to build automated virtual screening pipelines that exploit PubChem data. In addition, PubChemRDF allows users to download PubChem data and load them into a local computing facility, facilitating data integration between PubChem and other resources. PubChem resources have been used in many studies for developing bioactivity and toxicity prediction models, discovering polypharmacologic (multi-target) ligands, and identifying new macromolecule targets of compounds (for drug-repurposing or off-target side effect prediction). These studies demonstrate the usefulness of PubChem as a key resource for computer-aided drug discovery and related area. PMID:27454129

Comment on “Surface electromagnetic wave equations in a warm magnetized quantum plasma” [Phys. Plasmas 21, 072114 (2014)

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

Moradi, Afshin, E-mail: a.moradi@kut.ac.ir

2016-07-15

In a recent article [C. Li et al., Phys. Plasmas 21, 072114 (2014)], Li et al. studied the propagation of surface waves on a magnetized quantum plasma half-space in the Voigt configuration (in this case, the magnetic field is parallel to the surface but is perpendicular to the direction of propagation). Here, we present a fresh look at the problem and obtain a new form of dispersion relation of surface waves of the system. We find that our new dispersion relation does not agree with the result obtained by Li et al.

PubChem applications in drug discovery: a bibliometric analysis

PubMed Central

Cheng, Tiejun; Pan, Yongmei; Hao, Ming; Wang, Yanli; Bryant, Stephen H.

2014-01-01

A bibliometric analysis of PubChem applications is presented by reviewing 1132 research articles. The massive volume of chemical structure and bioactivity data in PubChem and its online services has been used globally in various fields including chemical biology, medicinal chemistry and informatics research. PubChem supports drug discovery in many aspects such as lead identification and optimization, compound–target profiling, polypharmacology studies and unknown chemical identity elucidation. PubChem has also become a valuable resource for developing secondary databases, informatics tools and web services. The growing PubChem resource with its public availability offers support and great opportunities for the interrogation of pharmacological mechanisms and the genetic basis of diseases, which are vital for drug innovation and repurposing. PMID:25168772

A general method for constructing multidimensional molecular potential energy surfaces from {ital ab} {ital initio} calculations

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

Ho, T.; Rabitz, H.

1996-02-01

A general interpolation method for constructing smooth molecular potential energy surfaces (PES{close_quote}s) from {ital ab} {ital initio} data are proposed within the framework of the reproducing kernel Hilbert space and the inverse problem theory. The general expression for an {ital a} {ital posteriori} error bound of the constructed PES is derived. It is shown that the method yields globally smooth potential energy surfaces that are continuous and possess derivatives up to second order or higher. Moreover, the method is amenable to correct symmetry properties and asymptotic behavior of the molecular system. Finally, the method is generic and can be easilymore » extended from low dimensional problems involving two and three atoms to high dimensional problems involving four or more atoms. Basic properties of the method are illustrated by the construction of a one-dimensional potential energy curve of the He{endash}He van der Waals dimer using the exact quantum Monte Carlo calculations of Anderson {ital et} {ital al}. [J. Chem. Phys. {bold 99}, 345 (1993)], a two-dimensional potential energy surface of the HeCO van der Waals molecule using recent {ital ab} {ital initio} calculations by Tao {ital et} {ital al}. [J. Chem. Phys. {bold 101}, 8680 (1994)], and a three-dimensional potential energy surface of the H{sup +}{sub 3} molecular ion using highly accurate {ital ab} {ital initio} calculations of R{umlt o}hse {ital et} {ital al}. [J. Chem. Phys. {bold 101}, 2231 (1994)]. In the first two cases the constructed potentials clearly exhibit the correct asymptotic forms, while in the last case the constructed potential energy surface is in excellent agreement with that constructed by R{umlt o}hse {ital et} {ital al}. using a low order polynomial fitting procedure. {copyright} {ital 1996 American Institute of Physics.}« less

Collisional Quenching of Highly-Excited H2 due to H2 Collisions

NASA Astrophysics Data System (ADS)

Wan, Yier; Yang, Benhui H.; Stancil, Phillip C.; Naduvalath, Balakrishnan; Forrey, Robert C.; This work was partially support by Hubble grant HST-AT-13899. We thank Kyle Walkerassistance with vrrmm.

2017-06-01

Collision-induced energy transfer involving H2 molecules are of significant interest, since H2 is the most abundant molecular species in the universe. Collisional de-excitation rate coefficients of the H2-H2 system are necessary to produce accurate models of astrophysical environments. However, accurate calculations of collisional energy transfer are still a challenging problem, especially for highly-excited H2 because a large number of levels must be included in the calculation.Currently, most data are limited to initial rotational levels j up to 8 or initial vibrational levels up to 3. The vast majority of these results involve some form of a reduced-dimensional approach which may be of questionable accuracy. A reliable and accurate four-dimensional PES computed by Patkowski et al. is used in this work along with two quantum scattering programs (MOLSCAT and vrrmm). Another accurate full-dimensional PES has been reported for the H2-H2 system by Hinde.Not all transitions will be explicitly calculated. A zero-energy scaling technique (ZEST) is used to estimate some intermediate transitions from calculated rate coefficients. New inelastic quenching cross section for para-H2+para-H2 collisions with initial level j= 10, 12, 14, 18, 24 are calculated. Calculations for other de-excitation transitions from higher initial levels and collisions involving other spin isomer of hydrogen, ortho-H2+para-H2, ortho-H2+ortho-H2 and para-H2+ortho-H2 are in progress. The coupled- states approximation is also applied to obtain cross sections at high energy.K. Patkowski, et al., J. Chem. Phys. 129, 094304 (2008).J. M. Hutson and S. Green, MOLSCAT Computer code, v14 (1994).K. Walker, 2013, VRRMM: Vibrational/Rotational Rich Man’s MOLSCAT v3.1.K. Walker, Song, L., Yang, B. H.,et al. 2015, ApJ, \\811,27.S. Green, J. Chem. Phys. 62, 2271 (1975).Flower, D. R., Roueff, E. 1998, J. Phys. B, 31, 2935.T. -G. Lee, N. Balakrishnan, R. C. Forrey, P. C. Stancil, G. Shaw, D. R. Schultz, and G. J

Synthesis and Characterization of Silyldichloramines, Their Reactions with F- Ions, Stability of N2CI2 and NCI2(-), and Formation of NCI3 (Postprint)

DTIC Science & Technology

2007-01-01

S. Can. J. Chem. 1987, 65, 88. (23) Werner, H. J.; Knowles, P. J.; Amos, R. D.; Bernhardsson, A.; Berning, A.; Celani, P.; Cooper, D. L.; Deegan , M. J...Phys. Chem. 1988, 92, 3033. (25) Knowles, P. J.; Hampel, C.; Werner, H. J. J. Chem. Phys. 1994, 99, 5219. (26) Deegan , M. J. O.; Knowles, P. J. Chem

Entropic Elastic Processes in Protein Mechanisms. Part 2. Simple (Passive) and Coupled (Active) Development of Elastic Forces,

DTIC Science & Technology

1986-01-01

al., 1985; Pethig, 1979; Zana and Tondre, 1972; Schneider, et al., 1969; Cho, et al., 1985). Interestingly an increase in ultrasonic absorption has...Health Hazards of Microwave Radiation (Czerski, P., ed.), Polish Medical Publishers, Warsaw, Poland, pp. 152-159. Senior, R. M., Griffin, G. L., Mecham...and Oosawa, F. (1985). Nature 316, 366-369. Zana , R. and Tondre, C. (1972). J. Phys. Chem. 76, 1737-1743. Figure Legends: Figure Primary structure of

Electron Energy Deposition in Atomic Oxygen

DTIC Science & Technology

1986-12-31

the parametric fits developed by Jackman et al^ where the cross section is expressed as ij -14 6.5x10 Cf ij ( 1 -¥~ n 4L ^ ’ij (7) and the...Res. 72, 3967 (1967). 4. H.S. Porter, C.H. Jackman and A.E.S. Green, J. Chem. Phys. 65, 154 (1976) and references therein. 5. P.M. Banks, C.R...1966). 28. S.P. Roundtree and R.J.W. Henry, Phys. Rev. A6, 2106 (1972). 29. T. Sawada and P.S. Ganas, Phys. Rev. A7, 617 (1973). 30. C.H. Jackman

Revision of 'Cumulative effect of the filamentation and Weibel instabilities in counterstreaming thermal plasmas' [Phys. Plasmas 13, 102107 (2006)

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

Stockem, A.; Lazar, M.; Department of Physics and Engineering Physics, University of Saskatchewan, Saskatoon

2008-01-15

Dispersion formalism reported in Lazar et al. [Phys. Plasmas 13, 102107 (2006)] is affected by errors due to the misfitting of the distribution function (1) used to interpret the counterstreaming plasmas, with the general dispersion relations (4) and (5), where distribution function (1) has been inserted to find the unstable solutions. The analytical approach is reviewed here, providing a correct analytical and numerical description for the cumulative effect of filamentation and Weibel instabilities arising in initially counterstreaming plasmas with temperature anisotropies. The growth rates are plotted again, and for the cumulative mode, they are orders of magnitude larger than thosemore » obtained in Lazar et al. [Phys. Plasmas 13, 102107 (2006)]. Physically, this can be understood as an increasing of the efficiency of magnetic field generation, and rather enhances the potential role of magnetic instabilities for the fast magnetization scenario in astrophysical applications.« less

Photoinduced Electron Transfer in the Strong Coupling Regime: Waveguide-Plasmon Polaritons.

PubMed

Zeng, Peng; Cadusch, Jasper; Chakraborty, Debadi; Smith, Trevor A; Roberts, Ann; Sader, John E; Davis, Timothy J; Gómez, Daniel E

2016-04-13

Reversible exchange of photons between a material and an optical cavity can lead to the formation of hybrid light-matter states where material properties such as the work function [ Hutchison et al. Adv. Mater. 2013 , 25 , 2481 - 2485 ], chemical reactivity [ Hutchison et al. Angew. Chem., Int. Ed. 2012 , 51 , 1592 - 1596 ], ultrafast energy relaxation [ Salomon et al. Angew. Chem., Int. Ed. 2009 , 48 , 8748 - 8751 ; Gomez et al. J. Phys. Chem. B 2013 , 117 , 4340 - 4346 ], and electrical conductivity [ Orgiu et al. Nat. Mater. 2015 , 14 , 1123 - 1129 ] of matter differ significantly to those of the same material in the absence of strong interactions with the electromagnetic fields. Here we show that strong light-matter coupling between confined photons on a semiconductor waveguide and localized plasmon resonances on metal nanowires modifies the efficiency of the photoinduced charge-transfer rate of plasmonic derived (hot) electrons into accepting states in the semiconductor material. Ultrafast spectroscopy measurements reveal a strong correlation between the amplitude of the transient signals, attributed to electrons residing in the semiconductor and the hybridization of waveguide and plasmon excitations.

Controlled Neutralization of Anions in Cryogenic Matrices by Near-Threshold Photodetachment

NASA Astrophysics Data System (ADS)

Ludwig, Ryan M.; Moore, David T.

2014-06-01

Using matrix isolation FTIR, we have observed the formation of anionic copper carbonyl complexes [Cu(CO)n]- (n=1-3) following co-deposition of Cu- and counter-cations (Ar+ or Kr+) into argon matrices doped with CO. The infrared bands have been previously assigned in argon matrix studies employing laser ablation, however they were quite weak compared to the bands for the corresponding neutral species. In the current study, when the deposition is carried out in fully darkened conditions at 10 K with high CO concentrations (1-2%), only the bands for the anionic complexes are observed initially via FTIR. However, upon mild irradiation with broadband visible light, the anionic bands are rapidly depleted, with concomitant appearance of bands corresponding to neutral copper carbonyl complexes. This photo-triggered neutralization is attributed to photodetachment of electrons from the anions, which then "flow" through the solid argon matrix to recombine in the matrix with non-adjacent trapping sites. This mechanism is supported by the appearance of a new band near 1515 wn, assigned to the (CO)2- species in argon. The wavelength dependence of the photodetachment will be discussed in detail, although preliminary indications are that the thresholds for the copper carbonyls, which are normally in the infrared, are shifted into the visible region of the spectrum in argon matrices. This likely occurs because the conduction band of solid argon is known to lie about 1 eV above the vacuum level, and thus the electron must have at least this much energy in order to escape into the matrix and find a trapping site. Funding support from NSF CAREER Award CHE-0955637 is gratefully acknowledged Ryan M. Ludwig and David T. Moore, J. Chem. Phys. 139, 244202 (2013) Zhou, M.; Andrews, L., J. Chem. Phys. 111, 4548 (1999). Thompson, W.E.; Jacox, M.E.; J. Chem. Phys. 91, 735 (1991). Stanzel, J. et al.; Collect. Czech. Chem. Comm. 72, 1 (2007). Harbich, W. et al.; Phys. Rev. B. 76, 104306 (2007).

Developing a new parameterization framework for the heterogeneous ice nucleation of atmospheric aerosol particles

NASA Astrophysics Data System (ADS)

Ullrich, Romy; Hiranuma, Naruki; Hoose, Corinna; Möhler, Ottmar; Niemand, Monika; Steinke, Isabelle; Wagner, Robert

2014-05-01

. Chem. Phys. 12, 9817-9854 Niemand, M., Möhler, O., Vogel, B., Hoose, C., Connolly, P., Klein, H., Bingemer, H., DeMott, P.J., Skrotzki, J. and Leisner, T. (2012) J. Atmos. Sci. 69, 3077-3092 Steinke, I., Möhler, O., Kiselev, A., Niemand, M., Saathoff, H., Schnaiter, M., Skrotzki, J., Hoose, C. and Leisner, T. (2011) Atmos. Chem. Phys. 11, 12945-12958 Wagner, R., Möhler, O., Saathoff, H., Schnaiter, M. and Leisner, T. (2010) Atmos. Chem. Phys. 10, 7617-7641 Wagner, R., Möhler, O., Saathoff, H., Schnaiter, M. and Leisner, T. (2011) Atmos. Chem. Phys. 11, 2083-2110

Chemical Demilitarization Assembled Chemical Weapons Alternatives (Chem Demil-ACWA)

DTIC Science & Technology

2015-12-01

Weapons Alternatives (Chem Demil-ACWA) is performing a portion of the chemical warfare materiel elimination mission. In 1996, Congress and the...Selected Acquisition Report (SAR) RCS: DD-A&T(Q&A)823-243 Chemical Demilitarization-Assembled Chemical Weapons Alternatives (Chem Demil-ACWA) As...Date Assigned: December 19, 2010 Program Information Program Name Chemical Demilitarization-Assembled Chemical Weapons Alternatives (Chem Demil

Automated Discovery of New Chemical Reactions and Accurate Calculation of Their Rates

DTIC Science & Technology

2015-06-02

formation of organic acids in reactions of the Criegee intermediate with aldehydes and ketones . Phys. Chem. Chem. Phys. 2013, 15, 16841-16852. [39...dioxolan-3-ol – our second case study - we confirmed that fragmentation of the cyclic peroxide leads to two possible pairs of acid and aldehyde products...Rate Prediction via Group Additivity, Part 2: H-Abstraction from Alkenes, Alkynes, Alcohols, Aldehydes , and Acids by H Atoms. J. Phys. Chem. A 2001, 105

Terahertz vibration-rotation-tunneling (VRT) spectroscopy of the d6-water trimer: Complete characterization of the 2.94 THz torsional band ( kn = ±2 1 ← 0 0)

NASA Astrophysics Data System (ADS)

Han, Jia-xiang; Takahashi, Lynelle K.; Lin, Wei; Lee, Eddy; Keutsch, Frank N.; Saykally, Richard J.

2006-06-01

We report the measurement and analysis of the complete perpendicular kn = ±2 1 ← 0 0 (D 2O) 3 torsional band (origin 2940.9376(3) GHz), the upper state of which is the highest-energy (98.09912 cm -1) torsional state yet observed. All known torsional transitions were included in a new global analysis of the six observed torsional bands, using the effective Hamiltonians derived by van der Avoird et al. [M. R. Viant, M. G. Brown, J. D. Cruzan, R. J. Saykally, M. Geleijns, A. van der Avoird, J. Chem. Phys. 110 (1999) 4369; A. van der Avoird, E. H. T. Olthof, P. E. S. Wormer, J. Chem. Phys. 105 (1996) 8034]. The experimental results will facilitate the descriptions of three-body interactions in water intermolecular potential energy surfaces (IPSs).

What the multiline signal (MLS) simulation data with average of weighted computations reveal about the Mn hyperfine interactions and oxidation states of the manganese cluster in OEC?

NASA Astrophysics Data System (ADS)

Baituti, Bernard

2017-11-01

al. (Phys. Chem. Chem. Phys. (PCCP) 16(17), 7799-812 2014), but the present results clearly indicate that heterogeneity in hyperfine couplings exist in samples as typically prepared.

PubChem3D: conformer ensemble accuracy

PubMed Central

2013-01-01

Background PubChem is a free and publicly available resource containing substance descriptions and their associated biological activity information. PubChem3D is an extension to PubChem containing computationally-derived three-dimensional (3-D) structures of small molecules. All the tools and services that are a part of PubChem3D rely upon the quality of the 3-D conformer models. Construction of the conformer models currently available in PubChem3D involves a clustering stage to sample the conformational space spanned by the molecule. While this stage allows one to downsize the conformer models to more manageable size, it may result in a loss of the ability to reproduce experimentally determined “bioactive” conformations, for example, found for PDB ligands. This study examines the extent of this accuracy loss and considers its effect on the 3-D similarity analysis of molecules. Results The conformer models consisting of up to 100,000 conformers per compound were generated for 47,123 small molecules whose structures were experimentally determined, and the conformers in each conformer model were clustered to reduce the size of the conformer model to a maximum of 500 conformers per molecule. The accuracy of the conformer models before and after clustering was evaluated using five different measures: root-mean-square distance (RMSD), shape-optimized shape-Tanimoto (STST-opt) and combo-Tanimoto (ComboTST-opt), and color-optimized color-Tanimoto (CTCT-opt) and combo-Tanimoto (ComboTCT-opt). On average, the effect of clustering decreased the conformer model accuracy, increasing the conformer ensemble’s RMSD to the bioactive conformer (by 0.18 ± 0.12 Å), and decreasing the STST-opt, ComboTST-opt, CTCT-opt, and ComboTCT-opt scores (by 0.04 ± 0.03, 0.16 ± 0.09, 0.09 ± 0.05, and 0.15 ± 0.09, respectively). Conclusion This study shows the RMSD accuracy performance of the PubChem3D conformer models is operating as designed. In addition, the effect of PubChem3D

Physics of the Cosmos Program Analysis Group (PhysPAG) Report

NASA Astrophysics Data System (ADS)

Nousek, John A.

2015-01-01

The Physics of the Cosmos Program Analysis Group (PhysPAG) serves as a forum for soliciting and coordinating input and analysis from the scientific community in support of the PCOS program objectives. I will outline the activities of the PhysPAG over the past year, since the last meeting during the AAS meeting in National Harbor, and mention the activities of the PhysPAG related Scientific Interest Groups.

ChemOkey: A Game to Reinforce Nomenclature

ERIC Educational Resources Information Center

Kavak, Nusret

2012-01-01

Learning the symbolic language of chemistry is a difficult task that can be frustrating for students. This article introduces a game, ChemOkey, that can help students learn the names and symbols of common ions and their compounds in a fun environment. ChemOkey, a game similar to Rummikub, is played with a set of 106 plastic or wooden tiles. The…

Using a Nondirect Product Basis to Compute J > 0 Rovibrational States of H3+

NASA Astrophysics Data System (ADS)

Jaquet, Ralph; Carrington, Tucker

2013-10-01

We have used a Lanczos algorithm with a nondirect product basis to compute energy levels of H3+ with J values as large as 46. Energy levels computed on the potential surface of M. Pavanello, et al. (J. Chem. Phys. 2012, 136, 184303) agree well with previous calculations for low J values.

Negative Differential Resistance in Insulating Systems: From Molecules to Polymers

NASA Astrophysics Data System (ADS)

Pati, Swapan

2007-03-01

We have developed a microscopic theory to explain the negative differential resistance behavior in molecular bridges. This feature has been observed in many molecules with different on/off ratios, sharpness of the current peak and the critical bias. Our theory, based on simple dimer model (both Peierls and donor/acceptor) together with bias driven conformational/ electronic change, covers almost all the experimental characteristics for a large number of real molecular systems and encompasses all the theory that has been known till date. Similar argument is also extended to Mott insulator, where we find a large number of insulator/quasi-metal transitions in finite size chains and a thermodynamic insulator/metal transition in polymers due to the application of static electric field between two ends of the chain. The interplay between charge inhomogenities and electric field induced polarization will be discussed in a number of cases. We will also show that none of these transitions follow Landau-Zener mechanism. I shall also discuss our theoretical proposal for the experimental strategies to stabilize highly unstable and reactive metal clusters like Al4Li4 and their analogs. Reference: 1. S. Lakshmi and Swapan K. Pati, Phys. Rev. B 72, 193410 (2005). 2. S. Lakshmi, Ayan Datta and Swapan K. Pati, Phys. Rev. B 72, 045131 (2005). 3. S. Lakshmi and Swapan K. Pati, Spl on Nanosc and Tech, Pramana, 65, 593. (2005). 4. S. Sengupta, S. Lakshmi and Swapan K Pati, J. Phys. Cond. Mat. 18, 9189 (2006). 5. Swapan K. Pati and S. Ramasesha, J. Phys. Condens. Matter 16, 989 (2004). 6. S.Lakshmi and Swapan K. Pati, J. Chem. Phys. 121, 11998 (2004). 7. S. Dutta, S. Lakshmi and Swapan K Pati, Submitted (2006). 8. A. Datta and Swapan K. Pati, J. Am. Chem. Soc. 127, 3496 (2005). 9. Sairam S. M., A. Datta and Swapan K. Pati, J. Phys. Chem. B 110, 20098 (2006). 10. A. Datta, Sairam S. M. and Swapan K. Pati, Acc. Chem. Res. (to appear)

Inverse modelling of radionuclide release rates using gamma dose rate observations

NASA Astrophysics Data System (ADS)

Hamburger, Thomas; Stohl, Andreas; von Haustein, Christoph; Thummerer, Severin; Wallner, Christian

2014-05-01

relatively sparse grid and the temporal resolution of available data may be low within the order of hours or a day. Gamma dose rates on the other hand are observed routinely on a much denser grid and higher temporal resolution. Gamma dose rate measurements contain no explicit information on the observed spectrum of radionuclides and have to be interpreted carefully. Nevertheless, they provide valuable information for the inverse evaluation of the source term due to their availability (Saunier et al., 2013). We present a new inversion approach combining an atmospheric dispersion model and observations of radionuclide activity concentrations and gamma dose rates to obtain the source term of radionuclides. We use the Lagrangian particle dispersion model FLEXPART (Stohl et al., 1998; Stohl et al., 2005) to model the atmospheric transport of the released radionuclides. The gamma dose rates are calculated from the modelled activity concentrations. The inversion method uses a Bayesian formulation considering uncertainties for the a priori source term and the observations (Eckhardt et al., 2008). The a priori information on the source term is a first guess. The gamma dose rate observations will be used with inverse modelling to improve this first guess and to retrieve a reliable source term. The details of this method will be presented at the conference. This work is funded by the Bundesamt für Strahlenschutz BfS, Forschungsvorhaben 3612S60026. References Davoine, X. and Bocquet, M., Atmos. Chem. Phys., 7, 1549-1564, 2007. Devell, L., et al., OCDE/GD(96)12, 1995. Eckhardt, S., et al., Atmos. Chem. Phys., 8, 3881-3897, 2008. Saunier, O., et al., Atmos. Chem. Phys., 13, 11403-11421, 2013. Stohl, A., et al., Atmos. Environ., 32, 4245-4264, 1998. Stohl, A., et al., Atmos. Chem. Phys., 5, 2461-2474, 2005. Stohl, A., et al., Atmos. Chem. Phys., 12, 2313-2343, 2012.

Prediction of water-rock interaction to 50 kb and 1,000 °C with equations of state for aqueous species

NASA Astrophysics Data System (ADS)

Sverjensky, D. A.; Harrison, B. W.; Azzolini, D.

2012-12-01

out by computing standard Gibbs free energies of aqueous species using the new values of ɛH2O and ρH2O in the revised HKF equations to predict equilibrium constants which in turn enabled prediction of the solubility of calcite for comparison with experimental measurements to 16 kb at 700 °C [12]. The results were almost identical with solubility predictions made with the density model up to 30 kb and high temperatures. These preliminary results strongly suggest that geochemically useful predictions can now be made that will facilitate analysis of water-rock interactions in the Earth at depths much greater than previously possible. [1] Shock, E. L. et al., GCA 61, 907 (1997). [2] Johnson, J. W. et al., Comp. & Geosci. 18, 899 (1992). [3] Manning, C. E., Earth Planet. Sci. Lett. 223, 1 (2004). [4] Franck, E. U. et al., Ber. Bun. Ges.-Phys.Chem. Chem. Phys. 94, 199 (1990). [5] Heger, K. et al., Ber. Bun. Ges.-Phys.Chem. Chem. Phys. 84, 758 (1980). [6] Fernandez, D. P., J. Phys.Chem. Ref. Data 26, 1125 (1997). [7] Zhang, Z. and Duan, Z., Phys. Earth Planet. Ints. 149, 335 (2005). [8] Burnham, C. W. et al., Amer. J. Sci. 267, 70 (1969). [9] Withers, A. C. et al., GCA 64, 1051 (2000). [10] Wasserman, E. et al., GCA 59, 1 (1995). [11] Pan, D. et al., http://meetings.aps.org/link/BAPS.2012.MAR.P25.8 [12] Caciagli, N.C. and Manning, C.E., Contribs. Min. & Petrol. 146, 275 (2003).

Jet-Cooled Spectroscopy on the Ailes Infrared Beamline of the Synchrotron Radiation Facility Soleil

NASA Astrophysics Data System (ADS)

Georges, Robert

2015-06-01

. Vervloet, Phys. Chem. Chem. Phys. 15, 10141-10150 (2013) The cyclic ground state structure of the HF trimer revealed by far-infrared jet-cooled Fourier transform spectroscopy. P. Asselin, P. Soulard, B. Madebène, M. Goubet, T. R. Huet, R. Georges, O. Pirali and P. Roy, Phys. Chem. Chem. Phys. 16(10), 4797-806 (2014) Standard free energy of the equilibrium between the trans-monomer and the cyclic-dimer of acetic acid in the gas phase from infrared spectroscopy. M. Goubet, P. Soulard, O. Pirali, P. Asselin, F. Réal, S. Gruet, T. R. Huet, P. Roy and R. Georges, Phys. Chem. Chem. Phys. DOI: 10.1039/c4cp05684a

Formation Conditions of Basalts at Gale Crater, Mars from ChemCam Analyses

NASA Astrophysics Data System (ADS)

Filiberto, J.; Bridges, J.; Dasgupta, R.; Edwards, P.; Schwenzer, S. P.; Wiens, R. C.

2015-12-01

Surface igneous rocks shed light onto the chemistry, tectonic, and thermal state of planetary interiors. For the purpose of comparative planetology, therefore, it is critical to fully utilize the compositional diversity of igneous rocks for different terrestrial planets. For Mars, igneous float rocks and conglomerate clasts at Gale Crater, as analyzed by ChemCam [1] using a new calibration [2], have a larger range in chemistry than have been analyzed at any other landing site or within the Martian meteorite collection [3, 4]. These rocks may reflect different conditions of melting within the Martian interior than any previously analyzed basalts. Here we present new formation conditions for basaltic and trachybasalt/dioritic rocks at Gale Crater from ChemCam analyses following previous procedures [5, 6]. We then compare these estimates of basalt formation with previous estimates for rocks from the Noachian (Gusev Crater, Meridiani Planum, and a clast in the NWA 7034 meteorite [5, 6]), Hesperian (surface volcanics [7]), and Amazonian (surface volcanics and shergottites [7-8]), to calculate an average mantle potential temperature for different Martian epochs and investigate how the interior of Mars has changed through time. Finally, we will compare Martian mantle potential temperatures with petrologic estimate of cooling for the Earth. Our calculated estimate for the mantle potential temperature (TP) of rocks at Gale Crater is 1450 ± 45 °C which is within error of previous estimates for Noachian aged rocks [5, 6]. The TP estimates for the Hesperian and Amazonian, based on orbital analyses of the crust [7], are lower in temperature than the estimates for the Noachian. Our results are consistent with simple convective cooling of the Martian interior. [1] Wiens R. et al. (2012) Space Sci Rev 170. 167-227. [2] Anderson R. et al. (2015) LPSC. Abstract #7031. [3] Schmidt M.E. et al. (2014) JGRP 2013JE004481. [4] Sautter V. et al. (2014) JGRP 2013JE004472. [5] Filiberto J

Positron scattering from carbon dioxide

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

Zecca, Antonio; Perazzolli, Chiara; Moser, Norberto

2006-07-15

We report total cross section measurements for positron scattering from carbon dioxide (CO{sub 2}). The energy range of the present measurements is 0.1-20.0 eV. The present study is undertaken to both try and resolve a discrepancy in the literature between the earlier low-energy works of Hoffman et al. [Phys. Rev. A 25, 1393 (1982)] and Kimura et al. [J. Chem. Phys. 107, 6616 (1997)], and to extend the available data to lower energies. We find generally good agreement with the data of Hoffman et al. over the common experimental energy range. A comparison of the present data with available calculationsmore » is also made, as is a comparison with corresponding electron total cross section data.« less

Broadband Microwave Spectroscopy as a Tool to Study Dispersion Interactions in Camphor-Alcohol Systems

NASA Astrophysics Data System (ADS)

Fatima, Mariyam; Perez, Cristobal; Schnell, Melanie

2016-06-01

Many biological processes such as chemical recognition and protein folding are mainly controlled by the interplay between hydrogen bonds and dispersive forces. Broadband rotational spectroscopy studies of weakly bound complexes are able to accurately reveal the structures and internal dynamics of molecular clusters isolated in the gas phase. To investigate the influence of the interplay between different types of weak intermolecular interactions and how it controls the preferred active sites of an amphiphilic molecule, we are using camphor (C10H16O, 1,7,7-trimethylbicyclo[2.2.1]hepta-2-one) with different aliphatic alcohol systems. Camphor is a conformationally rigid bicyclic molecule endowed with considerable steric hindrance and has a single polar group (-C=O). The rotational spectrum of camphor and its structure has been previously reported [1] as well as multiple clusters with water [2]. In order to determine the structure of the camphor-alcohol complexes, we targeted low energy rotational transitions in the 2-8 GHz range under the isolated conditions of a molecular jet in the gas phase. The data obtained suggests that camphor forms one complex with methanol and two with ethanol, with differences in the intermolecular interaction in both complexes. With these results, we aim to study the shift in intermolecular interaction from hydrogen bonding to dispersion with the increase in the size of the aliphatic alcohol. [1] Z. Kisiel, et al., Phys. Chem. Chem. Phys., 5 (2003), 820-826. [2] C. Pérez, et al, J. Phys. Chem. Lett., 7 (2016), 154-160.

A Neutron and X-Ray Diffraction Study of Ca-Mg-Cu Metallic Glasses (Postprint)

DTIC Science & Technology

2014-04-01

North DM. Phys Chem Liq 1968;1:1. [25] Wright AC. J Non-Cryst Solids 1989;112:33. [26] Patterson AL. Z Kristallogr 1935;90:517. [27] Soper AK. J Phys...PJ, Cundall JA. Acta Cryst 1965;19:807. [31] Hannon AC. Nucl Instrum Meth A 2005;551:88. [32] Soper AK. Gudrun software, http://www.isis.stfc.ac.uk...instruments/sandals/ data-analysis/gudrun8864.html. [33] Hannon AC, Howells WS, Soper AK. IOP Conf Ser 1990;107:193. [34] Soper AK. GudrunX software

Handbook of Phase Transition Sulfides, Selenides and Tellurides,

DTIC Science & Technology

1984-07-01

guidance and control. The Contracting Officer is Mrs. S. Williams, DESC, Dayton, Ohio. The Contracting Officers Technical Representative is Mr. H . C...higher temperature phase change where AgGaS2 becomes metallic. REFERENCES (AgGaS2 ) 1. H . Hahn, et.al., Z. Anorg. Chem., 271, 153 (1953). 2. M.V. Hobden...Phys. Soc. Japan, Vol. 23, 37 (1967). 10. H.H. Dorner, H.P. Geserich, and H . Rickert, Phys. Stat. Sol. (a), Vol. 37, K85 (1970). 11. P. Bruesch and J

Physics and chemistry-driven artificial neural network for predicting bioactivity of peptides and proteins and their design.

PubMed

Huang, Ri-Bo; Du, Qi-Shi; Wei, Yu-Tuo; Pang, Zong-Wen; Wei, Hang; Chou, Kuo-Chen

2009-02-07

Predicting the bioactivity of peptides and proteins is an important challenge in drug development and protein engineering. In this study we introduce a novel approach, the so-called "physics and chemistry-driven artificial neural network (Phys-Chem ANN)", to deal with such a problem. Unlike the existing ANN approaches, which were designed under the inspiration of biological neural system, the Phys-Chem ANN approach is based on the physical and chemical principles, as well as the structural features of proteins. In the Phys-Chem ANN model the "hidden layers" are no longer virtual "neurons", but real structural units of proteins and peptides. It is a hybridization approach, which combines the linear free energy concept of quantitative structure-activity relationship (QSAR) with the advanced mathematical technique of ANN. The Phys-Chem ANN approach has adopted an iterative and feedback procedure, incorporating both machine-learning and artificial intelligence capabilities. In addition to making more accurate predictions for the bioactivities of proteins and peptides than is possible with the traditional QSAR approach, the Phys-Chem ANN approach can also provide more insights about the relationship between bioactivities and the structures involved than the ANN approach does. As an example of the application of the Phys-Chem ANN approach, a predictive model for the conformational stability of human lysozyme is presented.

ChemPreview: an augmented reality-based molecular interface.

PubMed

Zheng, Min; Waller, Mark P

2017-05-01

Human computer interfaces make computational science more comprehensible and impactful. Complex 3D structures such as proteins or DNA are magnified by digital representations and displayed on two-dimensional monitors. Augmented reality has recently opened another door to access the virtual three-dimensional world. Herein, we present an augmented reality application called ChemPreview with the potential to manipulate bio-molecular structures at an atomistic level. ChemPreview is available at https://github.com/wallerlab/chem-preview/releases, and is built on top of the Meta 1 platform https://www.metavision.com/. ChemPreview can be used to interact with a protein in an intuitive way using natural hand gestures, thereby making it appealing to computational chemists or structural biologists. The ability to manipulate atoms in real world could eventually provide new and more efficient ways of extracting structural knowledge, or designing new molecules in silico. Copyright © 2017 Elsevier Inc. All rights reserved.

radEq Add-On Module for CFD Solver Loci-CHEM

NASA Technical Reports Server (NTRS)

McCloud, Peter

2013-01-01

Loci-CHEM to be applied to flow velocities where surface radiation due to heating from compression and friction becomes significant. The module adds a radiation equilibrium boundary condition to the computational fluid dynamics (CFD) code to produce accurate results. The module expanded the upper limit for accurate CFD solutions of Loci-CHEM from Mach 4 to Mach 10 based on Space Shuttle Orbiter Re-Entry trajectories. Loci-CHEM already has a very promising architecture and performance, but absence of radiation equilibrium boundary condition limited the application of Loci-CHEM to below Mach 4. The immediate advantage of the add-on module is that it allows Loci-CHEM to work with supersonic flows up to Mach 10. This transformed Loci-CHEM from a rocket engine- heritage CFD code with general subsonic and low-supersonic applications, to an aeroheating code with hypersonic applications. The follow-on advantage of the module is that it is a building block for additional add-on modules that will solve for the heating generated at Mach numbers higher than 10.

Engaging Organic Chemistry Students Using ChemDraw for iPad

ERIC Educational Resources Information Center

Morsch, Layne A.; Lewis, Michael

2015-01-01

Drawing structures, mechanisms, and syntheses is a vital part of success in organic chemistry courses. ChemDraw for iPad has been used to increase classroom experiences in the preparation of high quality chemical drawings. The embedded Flick-to-Share allows for simple, real-time exchange of ChemDraw documents. ChemDraw for iPad also allows…

Chem-E-Car Downunder.

ERIC Educational Resources Information Center

Rhodes, Martin

2002-01-01

Presents the Chem-E-Car competition in which students build a small car powered by a chemical reaction. Focuses on a controlled chemical reaction in which the car travels a required specific distance and stops. Requires participants to prepare poster presentations. (YDS)

Controlling Self-Assembly in Al(110) Homoepitaxy

NASA Astrophysics Data System (ADS)

Tiwary, Yogesh; Fichthorn, Kristen

2010-03-01

Homoepitaxial growth on Al(110) exhibits nanoscale self-assembly into huts with well-defined (100) and (111) facets [1]. Although some of the diffusion mechanisms underlying this kinetic self-assembly were identified and incorporated into a two-dimensional model [2], we used density-functional theory (DFT) to identify many other mechanisms that are needed to describe the three-dimensional assembly seen experimentally [3]. We developed a three-dimensional kinetic Monte Carlo (KMC) model of Al(110) homoepitaxy. The inputs to the model were obtained from DFT [3,4]. Our model is in agreement with experimentally observed trends for this system. We used KMC to predict self-assembly under various growth conditions. To achieve precise placement of Al nanohuts, we simulated thermal-field-directed assembly [5]. Our results indicate that this technique can be used to create uniform arrays of nanostructures. [1] F. Buatier de Mongeot, W. Zhu, A. Molle, R. Buzio, C. Boragno, U. Valbusa, E. Wang, and Z. Zhang, Phys. Rev. Lett. 91, 016102 (2003). [2] W. Zhu, F. Buatier de Mongeot, U. Valbusa, E. G. Wang, and Z. Y. Zhang, Phys. Rev. Lett. 92, 106102 (2004). [3] Y. Tiwary and K. A. Fichthorn, submitted to Phys. Rev. B. [4] Y. Tiwary and K. A. Fichthorn, Phys. Rev. B 78, 205418 (2008). [5] C. Zhang and R. Kalyanaraman, Appl. Phys. Lett. 83, 4827 (2003).

Aging and Rejuvenation with Fractional Derivatives

DTIC Science & Technology

2004-09-10

Chechkin , J. Klafter, V . Yu . Gonchar , R. Metzler, and L. V . Tanatarov, Phys. Rev. E 67, 010102(R) (2003). [12] I. M. Sokolov and R. Metzler, Phys. Rev. E 67...051106 (2001). [7] A . V . Chechkin , R. Gorenflo, and I. M. Sokolov, Phys. Rev. E 66, 046129 (2002). [8] J. Bisquert, Phys. Rev. Lett. 91, 010602 (2003...9] R. Metzler and J. Klafter, J. Phys. Chem. B 104 3851 (2000). [10] E. Barkai and R. J. Silbey, J. Phys. Chem. B 104 3866 (2000).

Quantum Mechanical Studies of Molecular Hyperpolarizabilities.

DTIC Science & Technology

1980-04-30

exponent , reflects the screening of an electron in a given orbital by the interior electrons in the atom or molecule. In practice, when studying...Basis sets have evolved over the years in molecular quantum mechanics until sets of orbital exponents for the different atoms composing the molecule have...and R. P. Hurst , J. Chem. Phys. 46, 2356 (1967); S. P. LickmannI and J. W. Moskowitz, J. Chem. Phys. 54, 3622 7T971). 26. T. H. Dunning, J. Chem. Phys

Franck-Condon simulation of the single-vibronic-level emission spectra of HPCl/DPCl and the chemiluminescence spectrum of HPCl, including anharmonicity.

PubMed

Chau, Foo-Tim; Mok, Daniel K W; Lee, Edmond P F; Dyke, John M

2004-07-22

Restricted-spin coupled-cluster single-double plus perturbative triple excitation [RCCSD(T)] potential energy functions (PEFs) were calculated for the X (2)A" and A (2)A' states of HPCl employing the augmented correlation-consistent polarized-valence-quadruple-zeta (aug-cc-pVQZ) basis set. Further geometry optimization calculations were carried out on both electronic states of HPCl at the RCCSD(T) level with all electron and quasirelativistic effective core potential basis sets of better than the aug-cc-pVQZ quality, and also including some core electrons, in order to obtain more reliable geometrical parameters and relative electronic energy of the two states. Anharmonic vibrational wave functions of the two states of HPCl and DPCl, and Franck-Condon (FC) factors of the A (2)A'-X (2)A" transition were computed employing the RCCSD(T)/aug-cc-pVQZ PEFs. Calculated FC factors with allowance for Duschinsky rotation and anharmonicity were used to simulate the single-vibronic-level (SVL) emission spectra of HPCl and DPCl reported by Brandon et al. [J. Chem. Phys. 119, 2037 (2003)] and the chemiluminescence spectrum reported by Bramwell et al. [Chem. Phys. Lett. 331, 483 (2000)]. Comparison between simulated and observed SVL emission spectra gives the experimentally derived equilibrium geometry of the A (2)A' state of HPCl of r(e)(PCl) = 2.0035 +/- 0.0015 A, theta(e) = 116.08 +/- 0.60 degrees, and r(e)(HP) = 1.4063+/-0.0015 A via the iterative Franck-Condon analysis procedure. Comparison between simulated and observed chemiluminescence spectra confirms that the vibrational population distribution of the A (2)A' state of HPCl is non-Boltzmann, as proposed by Baraille et al. [Chem. Phys. 289, 263 (2003)].

On the density scaling of pVT data and transport properties for molecular and ionic liquids.

PubMed

López, Enriqueta R; Pensado, Alfonso S; Fernández, Josefa; Harris, Kenneth R

2012-06-07

In this work, a general equation of state (EOS) recently derived by Grzybowski et al. [Phys. Rev. E 83, 041505 (2011)] is applied to 51 molecular and ionic liquids in order to perform density scaling of pVT data employing the scaling exponent γ(EOS). It is found that the scaling is excellent in most cases examined. γ(EOS) values range from 6.1 for ammonia to 13.3 for the ionic liquid [C(4)C(1)im][BF(4)]. These γ(EOS) values are compared with results recently reported by us [E. R. López, A. S. Pensado, M. J. P. Comuñas, A. A. H. Pádua, J. Fernández, and K. R. Harris, J. Chem. Phys. 134, 144507 (2011)] for the scaling exponent γ obtained for several different transport properties, namely, the viscosity, self-diffusion coefficient, and electrical conductivity. For the majority of the compounds examined, γ(EOS) > γ, but for hexane, heptane, octane, cyclopentane, cyclohexane, CCl(4), dimethyl carbonate, m-xylene, and decalin, γ(EOS) < γ. In addition, we find that the γ(EOS) values are very much higher than those of γ for alcohols, pentaerythritol esters, and ionic liquids. For viscosities and the self-diffusion coefficient-temperature ratio, we have tested the relation linking EOS and dynamic scaling parameters, proposed by Paluch et al. [J. Phys. Chem. Lett. 1, 987-992 (2010)] and Grzybowski et al. [J. Chem. Phys. 133, 161101 (2010); Phys. Rev. E 82, 013501 (2010)], that is, γ = (γ(EOS)/φ) + γ(G), where φ is the stretching parameter of the modified Avramov relation for the density scaling of a transport property, and γ(G) is the Grüneisen constant. This relationship is based on data for structural relaxation times near the glass transition temperature for seven molecular liquids, including glass formers, and a single ionic liquid. For all the compounds examined in our much larger database the ratio (γ(EOS)/φ) is actually higher than γ, with the only exceptions of propylene carbonate and 1-methylnaphthalene. Therefore, it seems the relation

Searching Online Chemical Data Repositories via the ChemAgora Portal.

PubMed

Zanzi, Antonella; Wittwehr, Clemens

2017-12-26

ChemAgora, a web application designed and developed in the context of the "Data Infrastructure for Chemical Safety Assessment" (diXa) project, provides search capabilities to chemical data from resources available online, enabling users to cross-reference their search results with both regulatory chemical information and public chemical databases. ChemAgora, through an on-the-fly search, informs whether a chemical is known or not in each of the external data sources and provides clikable links leading to the third-party web site pages containing the information. The original purpose of the ChemAgora application was to correlate studies stored in the diXa data warehouse with available chemical data. Since the end of the diXa project, ChemAgora has evolved into an independent portal, currently accessible directly through the ChemAgora home page, with improved search capabilities of online data sources.

Application of a New Ensemble Conserving Quantum Dynamics Simulation Algorithm to Liquid para-Hydrogen and ortho-Deuterium

DOE PAGES

Smith, Kyle K.G.; Poulsen, Jens Aage; Nyman, Gunnar; ...

2015-06-30

Here, we apply the Feynman-Kleinert Quasi-Classical Wigner (FK-QCW) method developed in our previous work [Smith et al., J. Chem. Phys. 142, 244112 (2015)] for the determination of the dynamic structure factor of liquid para-hydrogen and ortho-deuterium at state points of (T = 20.0 K, n = 21.24 nm -3) and (T = 23.0 K, n = 24.61 nm -3), respectively. When applied to this challenging system, it is shown that this new FK-QCW method consistently reproduces the experimental dynamic structure factor reported by Smith et al. [J. Chem. Phys. 140, 034501 (2014)] for all momentum transfers considered. Moreover, this showsmore » that FK-QCW provides a substantial improvement over the Feynman-Kleinert linearized path-integral method, in which purely classical dynamics are used. Furthermore, for small momentum transfers, it is shown that FK-QCW provides nearly the same results as ring-polymer molecular dynamics (RPMD), thus suggesting that FK-QCW provides a potentially more appealing algorithm than RPMD since it is not formally limited to correlation functions involving linear operators.« less

Global potential energy surface of ground state singlet spin O4

NASA Astrophysics Data System (ADS)

Mankodi, Tapan K.; Bhandarkar, Upendra V.; Puranik, Bhalchandra P.

2018-02-01

A new global potential energy for the singlet spin state O4 system is reported using CASPT2/aug-cc-pVTZ ab initio calculations. The geometries for the six-dimensional surface are constructed using a novel point generation scheme that employs randomly generated configurations based on the beta distribution. The advantage of this scheme is apparent in the reduction of the number of required geometries for a reasonably accurate potential energy surface (PES) and the consequent decrease in the overall computational effort. The reported surface matches well with the recently published singlet surface by Paukku et al. [J. Chem. Phys. 147, 034301 (2017)]. In addition to the O4 PES, the ground state N4 PES is also constructed using the point generation scheme and compared with the existing PES [Y. Paukku et al., J. Chem. Phys. 139, 044309 (2013)]. The singlet surface is constructed with the aim of studying high energy O2-O2 collisions and predicting collision induced dissociation cross section to be used in simulating non-equilibrium aerothermodynamic flows.

Application of a new ensemble conserving quantum dynamics simulation algorithm to liquid para-hydrogen and ortho-deuterium.

PubMed

Smith, Kyle K G; Poulsen, Jens Aage; Nyman, Gunnar; Cunsolo, Alessandro; Rossky, Peter J

2015-06-28

We apply the Feynman-Kleinert Quasi-Classical Wigner (FK-QCW) method developed in our previous work [Smith et al., J. Chem. Phys. 142, 244112 (2015)] for the determination of the dynamic structure factor of liquid para-hydrogen and ortho-deuterium at state points of (T = 20.0 K, n = 21.24 nm(-3)) and (T = 23.0 K, n = 24.61 nm(-3)), respectively. When applied to this challenging system, it is shown that this new FK-QCW method consistently reproduces the experimental dynamic structure factor reported by Smith et al. [J. Chem. Phys. 140, 034501 (2014)] for all momentum transfers considered. This shows that FK-QCW provides a substantial improvement over the Feynman-Kleinert linearized path-integral method, in which purely classical dynamics are used. Furthermore, for small momentum transfers, it is shown that FK-QCW provides nearly the same results as ring-polymer molecular dynamics (RPMD), thus suggesting that FK-QCW provides a potentially more appealing algorithm than RPMD since it is not formally limited to correlation functions involving linear operators.

Application of a New Ensemble Conserving Quantum Dynamics Simulation Algorithm to Liquid para-Hydrogen and ortho-Deuterium

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

Smith, Kyle K.G.; Poulsen, Jens Aage; Nyman, Gunnar

Here, we apply the Feynman-Kleinert Quasi-Classical Wigner (FK-QCW) method developed in our previous work [Smith et al., J. Chem. Phys. 142, 244112 (2015)] for the determination of the dynamic structure factor of liquid para-hydrogen and ortho-deuterium at state points of (T = 20.0 K, n = 21.24 nm -3) and (T = 23.0 K, n = 24.61 nm -3), respectively. When applied to this challenging system, it is shown that this new FK-QCW method consistently reproduces the experimental dynamic structure factor reported by Smith et al. [J. Chem. Phys. 140, 034501 (2014)] for all momentum transfers considered. Moreover, this showsmore » that FK-QCW provides a substantial improvement over the Feynman-Kleinert linearized path-integral method, in which purely classical dynamics are used. Furthermore, for small momentum transfers, it is shown that FK-QCW provides nearly the same results as ring-polymer molecular dynamics (RPMD), thus suggesting that FK-QCW provides a potentially more appealing algorithm than RPMD since it is not formally limited to correlation functions involving linear operators.« less

Application of a new ensemble conserving quantum dynamics simulation algorithm to liquid para-hydrogen and ortho-deuterium

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

Smith, Kyle K. G., E-mail: kylesmith@utexas.edu; Poulsen, Jens Aage, E-mail: jens72@chem.gu.se; Nyman, Gunnar, E-mail: nyman@chem.gu.se

We apply the Feynman-Kleinert Quasi-Classical Wigner (FK-QCW) method developed in our previous work [Smith et al., J. Chem. Phys. 142, 244112 (2015)] for the determination of the dynamic structure factor of liquid para-hydrogen and ortho-deuterium at state points of (T = 20.0 K, n = 21.24 nm{sup −3}) and (T = 23.0 K, n = 24.61 nm{sup −3}), respectively. When applied to this challenging system, it is shown that this new FK-QCW method consistently reproduces the experimental dynamic structure factor reported by Smith et al. [J. Chem. Phys. 140, 034501 (2014)] for all momentum transfers considered. This shows that FK-QCWmore » provides a substantial improvement over the Feynman-Kleinert linearized path-integral method, in which purely classical dynamics are used. Furthermore, for small momentum transfers, it is shown that FK-QCW provides nearly the same results as ring-polymer molecular dynamics (RPMD), thus suggesting that FK-QCW provides a potentially more appealing algorithm than RPMD since it is not formally limited to correlation functions involving linear operators.« less

AEGIS Automated Targeting for the MSL ChemCam Instrument

NASA Astrophysics Data System (ADS)

Estlin, T.; Anderson, R. C.; Blaney, D. L.; Bornstein, B.; Burl, M. C.; Castano, R.; Gaines, D.; Judd, M.; Thompson, D. R.; Wiens, R. C.

2013-12-01

The Autonomous Exploration for Gathering Increased Science (AEGIS) system enables automated science data collection by a planetary rover. AEGIS has been in use on the Mars Exploration Rover (MER) mission Opportunity rover since 2010 to provide onboard targeting of the MER Panoramic Camera based on scientist-specified objectives. AEGIS is now being applied for use with the Mars Science Laboratory (MSL) mission ChemCam spectrometer. ChemCam uses a Laser Induced Breakdown Spectrometer (LIBS) to analyze the elemental composition of rocks and soil from up to seven meters away. ChemCam's tightly-focused laser beam (350-550 um) enables targeting of very fine-scale terrain features. AEGIS is being applied in two ways to help ChemCam collect valuable science data. The first application is to enable automated targeting of ChemCam during or after or in the middle of long drives. The majority of ChemCam measurements are collected by allowing the science team to select specific targets in rover images. However this requires the rover to stay in the same area while images are downlinked, analyzed for targets, and new commands uplinked. The only data that can be acquired without this communication cycle is via blind targeting, where measurements are often of soil patches vs. instead of more valuable targets such as rocks with specific properties. AEGIS is being applied to automatically analyze images onboard and select targets for ChemCam analysis. This approach allows the rover to autonomously select and sequence targeted measurements in an opportunistic fashion at different points along the rover's drive path. Rock targets can be prioritized for measurement based on various geologically relevant features, including size, shape and albedo. A second application is to enable intelligent pointing refinement of ChemCam when acquiring data of small targets, such as veins or concretions that are only a few millimeters wide. Due to backlash and other pointing challenges, it can often

An experimental/theoretical method to measure the capacitive compactness of an aqueous electrolyte surrounding a spherical charged colloid

NASA Astrophysics Data System (ADS)

Moraila-Martínez, Carmen Lucía; Guerrero-García, Guillermo Iván; Chávez-Páez, Martín; González-Tovar, Enrique

2018-04-01

The capacitive compactness has been introduced very recently [G. I. Guerrero-García et al., Phys. Chem. Chem. Phys. 20, 262-275 (2018)] as a robust and accurate measure to quantify the thickness, or spatial extension, of the electrical double layer next to either an infinite charged electrode or a spherical macroion. We propose here an experimental/theoretical scheme to determine the capacitive compactness of a spherical electrical double layer that relies on the calculation of the electrokinetic charge and the associated mean electrostatic potential at the macroparticle's surface. This is achieved by numerically solving the non-linear Poisson-Boltzmann equation of point ions around a colloidal sphere and matching the corresponding theoretical mobility, predicted by the O'Brien and White theory [J. Chem. Soc., Faraday Trans. 2 74, 1607-1626 (1978)], with experimental measurements of the electrophoretic mobility under the same conditions. This novel method is used to calculate the capacitive compactness of NaCl and CaCl2 electrolytes surrounding a negatively charged polystyrene particle as a function of the salt concentration.

Immersion freezing by SnomaxTM particles: Comparison of results from different instruments

NASA Astrophysics Data System (ADS)

Wex, Heike; Stratmann, Frank; Rösch, Michael; Niedermeier, Dennis; Nilius, Björn; Möhler, Ottmar; Mitra, Subir K.; Koop, Thomas; Jantsch, Evelyn; Hiranuma, Naruki; Diehl, Karoline; Curtius, Joachim; Budke, Carsten; Boose, Yvonne; Augustin, Stefanie

2014-05-01

to work equally well, hence freezing by SnomaxTM can be considered to show no time dependence. Particularly data from LACIS and BINARY, i.e. from the "fastest" and "slowest" measurements, were found to agree very well. Acknowledgement: This work was done within the framework of the DFG funded Ice Nucleation research UnIT (INUIT, FOR 1525). Literature Budke et al. (2013), Investigation of Heterogeneous Ice Nucleation Using a Novel Optical Freezing Array, AIP Conference Proceedings, 1527, 949-951, doi: 10.1064/1.4803429. Bundke et al. (2008), The fast Ice Nucleus chamber FINCH, Atmos. Res. 90, 180-186. Chou et al. (2011), Ice nuclei properties within a Saharan dust event at the Jungfraujoch in the Swiss Alps, Atmos. Chem. Phys., 11, 4725-4738. Connolly, et al. (2009), Studies of heterogeneous freezing by three different desert dust samples, Atmos. Chem. Phys., 9, 2805-2824. Diehl et al. (2011), The Mainz vertical wind tunnel facility: A review of 25 years of laboratory experiments on cloud physics and chemistry. In: J.D. Pereira (Ed.), Wind tunnels: Aerodynamics, models, and experiments. Nova Science Publishers, Inc., Chapter 2. Diehl et al. (2009), Homogeneous freezing of single sulfuric and nitric acid solution drops levitated in an acoustic trap, Atm. Res., 94, 356-361, doi:10.1016/j.atmosres.2009.06.001. Hartmann et al. (2011), Homogeneous and heterogeneous ice nucleation at LACIS: Operating principle and theoretical studies, Atmos. Chem. Phys., 11, 1753-1767. Hartmann et al. (2013), Immersion freezing of ice nucleating active protein complexes, Atmos. Chem. Phys., 13, 5751-5766. Murray et al. (2012), Ice nucleation by particles immersed in supercooled cloud droplets, Chem. Soc. Rev., 41, 6519-6554. Niedermeier et al. (2014), A computationally-efficient description of heterogeneous freezing: A simplified version of the Soccer ball model, Geophys. Res. Lett., 10.1002/2013GL058684. Vali, G. (1971), Quantitative evaluation of experimental results on heterogeneous

Engineering Analysis in the Chem-E-Car Competition

ERIC Educational Resources Information Center

Lewis, Randy S.; Moshfeghian, Aliakbar; Madihally, Sundararajan V.

2006-01-01

The AIChE Chem-E-Car competition provides students an opportunity to demonstrate their design and teamwork skills. Engineering analysis is not required at the national competition and is often not applied. This work describes an engineering analysis of a Chem-E-Car to predict the distance traveled by the car. Engineering analysis is advantageous…

Proceedings of the High Energy Density Matter (HEDM) Conference Held in New Orleans, Louisiana on 12-15 March 1989

DTIC Science & Technology

1989-07-01

distance in a planar arrangement of ArH3 , with the argon directly above the apical hydrogen. Matcha and 3, Milleur’ confined their calculations for...Phys. .11, 27 (1976). 7. W. J. Stevens, H-. Basch, and M. Krauss, J. Chem. Phys. il 6026 (1984). 8. R. L. Matcha , and Mac B. Milleur, J. Chem. Phys. f2

An Examination of Models of Relaxation in Complex Systems. I. Continuous Time Random Walk (CTRW) Models.

DTIC Science & Technology

1986-02-04

Laberge , Phys. Chem. Glasses 14, 122 (1973); F.S. Howell, R. Bose, P.B. Macedo and C.T. Moynihan, J. Phys. Chem. 78, 639 (1974). 30. K.L. Ngai, R.W...J.R. Stevens , J. Polym. Sci.: Polym. Phys. Ed. 17, 1547 (1979); 21, 605 (1983). 41. For Polyethyl acrylate (PEA) see G. Williams and D.C. Watts in

Fitting the High-Resolution Spectroscopic Data for Ncncs

NASA Astrophysics Data System (ADS)

Kisiel, Zbigniew; Winnewisser, Brenda P.; Winnewisser, Manfred; De Lucia, Frank C.; Tokaryk, Dennis; Ross, Stephen Cary; Billinghurst, Brant E.

2014-06-01

NCNCS is a quasi-linear molecule that displays plentiful spectroscopic signatures of transition from the asymmetric top to the linear rotor regime. The transition takes place on successive excitation of the ν_7 bending mode at ca 80 cm-1. The unusual spectroscopic manifestations on crossing the barrier to linearity are explained by quantum monodromy and described quantitatively by the generalised semi-rigid bender Hamiltonian. Nevertheless, analysis to experimental accuracy of the extensive mm-wave spectrum of NCNCS recorded with the FASSST technique has only so far been achieved with the use of separate J(J+1) expansions for each (v_7, K_a) transition sequence.^c In addition, several selective perturbations identified between transition sequences in different vibrational levels^c are still unfitted. Presently we seek effective approximations to the vibration-rotation Hamiltonian that would allow combining multiple sequences into a fit, would allow a perturbation analysis, and could use mm-wave data together with high-resolution infrared measurements of NCNCS made at the Canadian Light Source. The understanding of effective fits to low-K_a subsets of rotational transitions in the FASSST spectrum has already allowed confident assignment of the 34S and both 13C isotopic species of NCNCS in natural abundance, as will be described. B.P.Winnewisser, et al., Phys. Rev. Lett. 95 243002 (2005). M.Winnewisser, et al., J. Mol. Struct. 798, 1 (2006). B.P.Winnewisser, et al., Phys. Chem. Chem. Phys. 12, 8158 (2010).

Nonlocal and nonlinear electrostatics of a dipolar Coulomb fluid.

PubMed

Sahin, Buyukdagli; Ralf, Blossey

2014-07-16

We study a model Coulomb fluid consisting of dipolar solvent molecules of finite extent which generalizes the point-like dipolar Poisson-Boltzmann model (DPB) previously introduced by Coalson and Duncan (1996 J. Phys. Chem. 100 2612) and Abrashkin et al (2007 Phys. Rev. Lett. 99 077801). We formulate a nonlocal Poisson-Boltzmann equation (NLPB) and study both linear and nonlinear dielectric response in this model for the case of a single plane geometry. Our results shed light on the relevance of nonlocal versus nonlinear effects in continuum models of material electrostatics.

A Neutron and X-ray Diffraction Study of Ca-Mg-Cu Metallic Glasses (Preprint)

DTIC Science & Technology

2011-07-01

A.L. Patterson, Z Kristallogr 90(1935)517. 29. A.K. Soper , J. Phys.: Condens. Matter 19(2007)335206. 30. P.G. Mikolaj and C.J. Pings, Phys. Chem...Liq. 1(1968)93. 31. P.J. Black and J.A. Cundall, Acta Cryst. 19(1965)807. 32. A.C. Hannon, Nucl. Instrum. Meth. A 551(2005)88. 33. A.K. Soper ...Gudrun software: http://www.isis.stfc.ac.uk/instruments/sandals/data- analysis/gudrun8864.html. 34. A.C. Hannon, W.S. Howells and A.K. Soper , IOP Conf

Comparison of Photon Stimulated Dissociation of Gas Phase, Solid, and Chemisorbed Water.

DTIC Science & Technology

1983-09-01

C.C. [25] T. Shibaguchi. H . Onuki and R. Onaka 1. Phys. Soc. Parks. G. Loubriel and ,. H . Stulen, Chem. Phys. Letter Japan 42 (1977) 152. 80 (1981) 48...reduces the effectiveness of th& Ŗa " I " excitation for H desorption. The lbT24a1 and ib’T13a𔃾a two bole-one electron states are sufficiently long...peristent for H ’ desorption from the HO phases studied. The core level PSD specutm from solid DO is also Jnterpreted. Al of the results are found to be

Numerical simulation of transmission coefficient using c-number Langevin equation

NASA Astrophysics Data System (ADS)

Barik, Debashis; Bag, Bidhan Chandra; Ray, Deb Shankar

2003-12-01

We numerically implement the reactive flux formalism on the basis of a recently proposed c-number Langevin equation [Barik et al., J. Chem. Phys. 119, 680 (2003); Banerjee et al., Phys. Rev. E 65, 021109 (2002)] to calculate transmission coefficient. The Kramers' turnover, the T2 enhancement of the rate at low temperatures and other related features of temporal behavior of the transmission coefficient over a range of temperature down to absolute zero, noise correlation, and friction are examined for a double well potential and compared with other known results. This simple method is based on canonical quantization and Wigner quasiclassical phase space function and takes care of quantum effects due to the system order by order.

Kinetic Monte Carlo simulations of fluorine and vacancies concentration at the CeO2(111) surface

NASA Astrophysics Data System (ADS)

Mattiello, S.; Kolling, S.; Heiliger, C.

2017-09-01

Recently, a new identification of the experimental depressions of scanning tunnelling microscopy images on the {{CeO}}2(111) surface as fluorine impurities has been proposed in Kullgren et al (2014 Phys. Rev. Lett. 112 156102). In particular, the high immobility of the depressions seems to be in contradiction with the low diffusion barrier for the oxygen vacancies. Consequently, the oxygen vacancies concentration has to disappear. The first aim of this paper is to confirm dynamically the recent interpretation of the experimental finding. For this purpose, we investigate the competition between fluorine and oxygen vacancies using two dimensional kinetic Monte Carlo simulations (kMC) as compared to an appropriate Langmuir model. We calculate the concentration of the vacancies and of the fluorine for the surface (111) of {{CeO}}2 for a UHV condition as a function of the fluorine-oxygen mixture in the gas phase as well as of the binding energies of fluorine and oxygen. We found that at a temperature of T=573 {{K}}, at which the experimental measurements were conducted, vacancies cannot exist. This confirms the possibility of fluorine impurities in Kullgren et al (2014 Phys. Rev. Lett. 112 156102). The second aim of the present paper is to perform a first dynamical estimation of the fluorine binding energy value {E}{Fl} that allows one to describe the experimental data in Pieper et al (2012 Phys. Chem. Chem. Phys. 14 15361). Using 2D-kMC simulations, we found {E}{Fl}\\in [-5.53,-5.27] {eV} which can be used for comparison to density functional theory calculations in further works.

Alkali trace elements in Gale crater, Mars, with ChemCam: Calibration update and geological implications

NASA Astrophysics Data System (ADS)

Payré, V.; Fabre, C.; Cousin, A.; Sautter, V.; Wiens, R. C.; Forni, O.; Gasnault, O.; Mangold, N.; Meslin, P.-Y.; Lasue, J.; Ollila, A.; Rapin, W.; Maurice, S.; Nachon, M.; Le Deit, L.; Lanza, N.; Clegg, S.

2017-03-01

The Chemistry Camera (ChemCam) instrument onboard Curiosity can detect minor and trace elements such as lithium, strontium, rubidium, and barium. Their abundances can provide some insights about Mars' magmatic history and sedimentary processes. We focus on developing new quantitative models for these elements by using a new laboratory database (more than 400 samples) that displays diverse compositions that are more relevant for Gale crater than the previous ChemCam database. These models are based on univariate calibration curves. For each element, the best model is selected depending on the results obtained by using the ChemCam calibration targets onboard Curiosity. New quantifications of Li, Sr, Rb, and Ba in Gale samples have been obtained for the first 1000 Martian days. Comparing these data in alkaline and magnesian rocks with the felsic and mafic clasts from the Martian meteorite NWA7533—from approximately the same geologic period—we observe a similar behavior: Sr, Rb, and Ba are more concentrated in soluble- and incompatible-element-rich mineral phases (Si, Al, and alkali-rich). Correlations between these trace elements and potassium in materials analyzed by ChemCam reveal a strong affinity with K-bearing phases such as feldspars, K-phyllosilicates, and potentially micas in igneous and sedimentary rocks. However, lithium is found in comparable abundances in alkali-rich and magnesium-rich Gale rocks. This very soluble element can be associated with both alkali and Mg-Fe phases such as pyroxene and feldspar. These observations of Li, Sr, Rb, and Ba mineralogical associations highlight their substitution with potassium and their incompatibility in magmatic melts.

The CHEM Study Story.

ERIC Educational Resources Information Center

Merrill, Richard J.; Ridgway, David W.

The history of the planning, funding, preparation of preliminary materials, teacher preparation, trial teaching, evaluation, revision and final publication of the CHEM Study materials is presented. The anecdotal account points out the difficulties encountered, the solutions found and the pitfalls avoided so that the experience gained may be useful…

The Another Assimilation System for WRF-Chem (AAS4WRF): a new mass-conserving emissions pre-processor for WRF-Chem regional modelling

NASA Astrophysics Data System (ADS)

Vara Vela, A. L.; Muñoz, A.; Lomas, A., Sr.; González, C. M.; Calderon, M. G.; Andrade, M. D. F.

2017-12-01

The Weather Research and Forecasting with Chemistry (WRF-Chem) community model have been widely used for the study of pollutants transport, formation of secondary pollutants, as well as for the assessment of air quality policies implementation. A key factor to improve the WRF-Chem air quality simulations over urban areas is the representation of anthropogenic emission sources. There are several tools that are available to assist users in creating their own emissions based on global emissions information (e.g. anthro_emiss, prep_chem_src); however, there is no single tool that will construct local emissions input datasets for any particular domain at this time. Because the official emissions pre-processor (emiss_v03) is designed to work with domains located over North America, this work presents the Another Assimilation System for WRF-Chem (AAS4WRF), a ncl based mass-conserving emissions pre-processor designed to create WRF-Chem ready emissions files from local inventories on a lat/lon projection. AAS4WRF is appropriate to scale emission rates from both surface and elevated sources, providing the users an alternative way to assimilate their emissions to WRF-Chem. Since it was successfully tested for the first time for the city of Lima, Peru in 2014 (managed by SENAMHI, the National Weather Service of the country), several studies on air quality modelling have applied this utility to convert their emissions to those required for WRF-Chem. Two case studies performed in the metropolitan areas of Sao Paulo and Manizales in Brazil and Colombia, respectively, are here presented in order to analyse the influence of using local or global emission inventories in the representation of regulated air pollutants such as O3 and PM2.5. Although AAS4WRF works with local emissions information at the moment, further work is being conducted to make it compatible with global/regional emissions data file format. The tool is freely available upon request to the corresponding author.

A study of the turn-up effect in the electron momentum spectroscopy

NASA Astrophysics Data System (ADS)

Dal Cappello, C.; Menas, F.; Houamer, S.; Popov, Yu V.; Roy, A. C.

2015-10-01

Recently, a number of electron momentum spectroscopy measurements for the ionization of atoms and molecules have shown that the triple differential cross section (TDCS) has an unexpected higher intensity in a low momentum regime (Brunger M J, Braidwood S W, Mc Carthy I E and Weigold E 1994 J. Phys. B: At. Mol. Opt. Phys. 27 L597, Hollebone B P, Neville J J, Zheng Y, Brion C E, Wang Y and Davidson E R 1995 Chem. Phys. 196 13, Brion C E, Zheng Y, Rolke J, Neville J J, McCarthy I E and Wang J 1998 J. Phys. B: At. Mol. Opt. Phys. 31 L223, Ren X G, Ning C G, Deng J K, Zhang S F, Su G L, Huang F and Li G Q 2005 Phys. Rev. Lett. 94 163201, Deng J K, et al 2001 J. Chem. Phys. 114 882, Ning C G, Ren X G, Deng J K, Su G L, Zhang S F and Li G Q 2006 Phys. Rev. A 73 022704). This surprising result is now called the turn-up effect. Our aim is to investigate such an effect by studying the case of the ionization of atomic hydrogen in an excited state using the 3C model (Brauner M, Briggs J S and Klar H 1989 J. Phys. B: At. Mol. Opt. Phys. 22 2265) which is able to describe all the measured results of the single ionization of atomic hydrogen in its ground state for an incident energy beyond 200 eV. A comparison is also made of the findings of the present method with those of the plane wave impulse approximation and distorted wave models.

BiF/NF2 Kinetics Studies: Mechanism and Conversion Efficiency

DTIC Science & Technology

1990-08-31

68A, 61 (1964) 9. R. F Heidner III, H . Helvajian , J. S. Holloway, and J. B. Koffend, J. Chem. Phys. 84, 2137 (1986). 10. R. J. Malins and D. W Setser, J...Heidner III, H . Helvajian , J. S. Holloway, and J. B. Koffend, J. Chem. Phys. 93, 7818 (1989). 15. C. H . Corliss and W R. Bozman, Experimental Transition...MS Informal Report, UC-34a, UC-LASL (July 1980). 18. R. F Heidner III, H . Helvajian , J. S. Holloway, and J. B. Koffend, J. Chem. Phys. 93, 7813 (1989

Application of distance correction to ChemCam laser-induced breakdown spectroscopy measurements

DOE PAGES

Mezzacappa, A.; Melikechi, N.; Cousin, A.; ...

2016-04-04

Laser-induced breakdown spectroscopy (LIBS) provides chemical information from atomic, ionic, and molecular emissions from which geochemical composition can be deciphered. Analysis of LIBS spectra in cases where targets are observed at different distances, as is the case for the ChemCam instrument on the Mars rover Curiosity, which performs analyses at distances between 2 and 7.4 m is not a simple task. Previously, we showed that spectral distance correction based on a proxy spectroscopic standard created from first-shot dust observations on Mars targets ameliorates the distance bias in multivariate-based elemental-composition predictions of laboratory data. In this work, we correct an expandedmore » set of neutral and ionic spectral emissions for distance bias in the ChemCam data set. By using and testing different selection criteria to generate multiple proxy standards, we find a correction that minimizes the difference in spectral intensity measured at two different distances and increases spectral reproducibility. When the quantitative performance of distance correction is assessed, there is improvement for SiO 2, Al 2O 3, CaO, FeOT, Na 2O, K 2O, that is, for most of the major rock forming elements, and for the total major-element weight percent predicted. But, for MgO the method does not provide improvements while for TiO 2, it yields inconsistent results. Additionally, we observed that many emission lines do not behave consistently with distance, evidenced from laboratory analogue measurements and ChemCam data. This limits the effectiveness of the method.« less

ChemRad Sample Form Instructions

EPA Pesticide Factsheets

These instructons are intended to assist registered users of the EPA Region 8 Drinking Water Watch website who would like to create ChemRad Sample Forms for monitoring that is required during the current year.

Comment on “Maxwell's equations and electromagnetic Lagrangian density in fractional form” [J. Math. Phys. 53, 033505 (2012)

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

Rabei, Eqab M.; Al-Jamel, A.; Widyan, H.

In a recent paper, Jaradat et al. [J. Math. Phys. 53, 033505 (2012)] have presented the fractional form of the electromagnetic Lagrangian density within the Riemann-Liouville fractional derivative. They claimed that the Agrawal procedure [O. P. Agrawal, J. Math. Anal. Appl. 272, 368 (2002)] is used to obtain Maxwell's equations in the fractional form, and the Hamilton's equations of motion together with the conserved quantities obtained from fractional Noether's theorem are reported. In this comment, we draw the attention that there are some serious steps of the procedure used in their work are not applicable even though their final resultsmore » are correct. Their work should have been done based on a formulation as reported by Baleanu and Muslih [Phys. Scr. 72, 119 (2005)].« less

Cavity Ringdown Spectroscopy and Kinetics of HO_2+HCHO: Detection of the ν_1 and {A}- {X} Bands of HOCH_2OOCAVITY Ringdown Spectroscopy and Kinetics of HO_2+HCHO: Detection of the ν_1 and {A}- {X} Bands of HOCH_2OO

NASA Astrophysics Data System (ADS)

Sprague, Matthew K.; Okumura, Mitchio; Sander, Stanley P.

2011-06-01

The reactions of HO_2 with carbonyl compounds are believed to be a sink for carbonyl compounds in the upper troposphere and lower stratosphere. These reactions proceed through a hydrogen bound intermediate before isomerizing. The reaction of HO_2 + formaldehyde (HCHO) serves as a prototype for this class of reactions, forming the isomerization product hydroxymethylperoxy (HOCH_2OO, HMP). Previous studies measured the spectrum and kinetics of HMP using either FTIR detection of the end products or direct detection of HMP by the unstructured tilde{B}-tilde{X} transition. Despite these studies, considerable uncertainty exists in the rate constant of HMP formation (±80%, 2σ). In this talk, we report the first detection of the ν_1 (OH stretch) and tilde{A}-tilde{X} electronic spectra of the HMP radical. The OH stretch spectrum is broad and featureless, while the tilde{A}(0)-tilde{X}(0) origin and combination band with the OOCO torsion tilde{A}(NOOCO=1)-tilde{X}(0) are rotationally resolved. Quantum chemistry calculations have been performed on both the tilde{A} and tilde{X} states as a function of the OOCO and HOCO dihedral angles to estimate the tilde{A}-tilde{X} transition frequency and to assess the coupling between the two torsional modes. We also present kinetics data showing the rates of production and destruction of HMP. I. Hermans, J. F. Muller, T. L. Nguyen, P. A. Jacobs, and J. Peeters. J. Phys. Chem. A 2005, 109, 4303. F. Su, J. G. Calvert, and J. H. Shaw J. Phys. Chem. 1979, 83, 3185. B. Veyret, R. Lesclaux, M. T. Rayez, J. C. Rayez, R. A. Cox, and G. K. Moortgat J. Phys. Chem. 1989, 93, 2368. J. P. Burrows, G. K. Moortgat, G. S. Tyndall, R. A. Cox, M. E. Jenkin, G. D. Hayman, and B. Veyret J. Phys. Chem. 1989, 93, 2375 S. P. Sander, B. J. Finlayson-Pitts, D. M. Golden, R. E. Huie, C. E. Kolb, M. J. Kurylo, M. J. Molina, et al. Chemical Kinetics and Photochemical Data for Use in Atmospheric Studies, Evaluation Number 16, Jet Propulsion Laboratory, 2009 I

Mars Rock Rocknest 3 Imaged by Curiosity ChemCam

NASA Image and Video Library

2012-11-26

This view of a rock called Rocknest 3 combines two images taken by the Chemistry and Camera ChemCam instrument on the NASA Mars rover Curiosity and indicates five spots where ChemCam had hit the rock with laser pulses to check its composition.

Pressure Effects on the Relaxation of an Excited Nitromethane Molecule in an Argon Bath

DTIC Science & Technology

2015-01-05

pressure. The Schwarzer et al. measurements of the relaxation of azulene in a variety of supercritical fluids including CO2 show that a change in...J. Chem. Phys. 142, 014303 (2015) experimental studies8(b),8(c),14,15 that have used supercritical fluids for which the density can be conveniently...work of Heidelbach et al.20 for azulene/ CO2 and of Paul et al.23 for the C6F6/N2 system. While it is impossible to briefly summarize the vast body of

Fit Point-Wise AB Initio Calculation Potential Energies to a Multi-Dimension Long-Range Model

NASA Astrophysics Data System (ADS)

Zhai, Yu; Li, Hui; Le Roy, Robert J.

2016-06-01

A potential energy surface (PES) is a fundamental tool and source of understanding for theoretical spectroscopy and for dynamical simulations. Making correct assignments for high-resolution rovibrational spectra of floppy polyatomic and van der Waals molecules often relies heavily on predictions generated from a high quality ab initio potential energy surface. Moreover, having an effective analytic model to represent such surfaces can be as important as the ab initio results themselves. For the one-dimensional potentials of diatomic molecules, the most successful such model to date is arguably the ``Morse/Long-Range'' (MLR) function developed by R. J. Le Roy and coworkers. It is very flexible, is everywhere differentiable to all orders. It incorporates correct predicted long-range behaviour, extrapolates sensibly at both large and small distances, and two of its defining parameters are always the physically meaningful well depth {D}_e and equilibrium distance r_e. Extensions of this model, called the Multi-Dimension Morse/Long-Range (MD-MLR) function, linear molecule-linear molecule systems and atom-non-linear molecule system. have been applied successfully to atom-plus-linear molecule, linear molecule-linear molecule and atom-non-linear molecule systems. However, there are several technical challenges faced in modelling the interactions of general molecule-molecule systems, such as the absence of radial minima for some relative alignments, difficulties in fitting short-range potential energies, and challenges in determining relative-orientation dependent long-range coefficients. This talk will illustrate some of these challenges and describe our ongoing work in addressing them. Mol. Phys. 105, 663 (2007); J. Chem. Phys. 131, 204309 (2009); Mol. Phys. 109, 435 (2011). Phys. Chem. Chem. Phys. 10, 4128 (2008); J. Chem. Phys. 130, 144305 (2009) J. Chem. Phys. 132, 214309 (2010) J. Chem. Phys. 140, 214309 (2010)

Assessment of TD-DFT methods and of various spin scaled CIS(D) and CC2 versions for the treatment of low-lying valence excitations of large organic dyes

NASA Astrophysics Data System (ADS)

Goerigk, Lars; Grimme, Stefan

2010-05-01

We present an extension of our previously published benchmark set for low-lying valence transitions of large organic dyes [L. Goerigk et al., Phys. Chem. Chem. Phys. 11, 4611 (2009)]. The new set comprises in total 12 molecules, including two charged species and one with a clear charge-transfer transition. Our previous study on TD-DFT methods is repeated for the new test set with a larger basis set. Additionally, we want to shed light on different spin-scaled variants of the configuration interaction singles with perturbative doubles correction [CIS(D)] and the approximate coupled cluster singles and doubles method (CC2). Particularly for CIS(D) we want to clarify, which of the proposed versions can be recommended. Our results indicate that an unpublished SCS-CIS(D) variant, which is implemented into the TURBOMOLE program package, shows worse results than the original CIS(D) method, while other modified versions perform better. An SCS-CIS(D) version with a parameterization, that has already been used in an application by us recently [L. Goerigk and S. Grimme, ChemPhysChem 9, 2467 (2008)], yields the best results. Another SCS-CIS(D) version and the SOS-CIS(D) method [Y. M. Rhee and M. Head-Gordon, J. Phys. Chem. A 111, 5314 (2007)] perform very similar, though. For the electronic transitions considered herein, there is no improvement observed when going from the original CC2 to the SCS-CC2 method but further adjustment of the latter seems to be beneficial. Double-hybrid density functionals belong to best methods tested here. Particularly B2GP-PLYP provides uniformly good results for the complete set and is considered to be close to chemical accuracy within an ab initio theory of color. For conventional hybrid functionals, a Fock-exchange mixing parameter of about 0.4 seems to be optimum in TD-DFT treatments of large chromophores. A range-separated functional such as, e.g., CAM-B3LYP seems also to be promising.

Research Investigation Directed Toward Extending the Useful Range of the Electromagnetic Spectrum

DTIC Science & Technology

1988-12-31

W. Holber, D. Gaines, C. F. Yu, R. M. Osgood, "Laser Desorption of Polymer in a Plasma Reactor," Appl. Phys. Lett. 52, 11 (1988). vii G. V. Treyz, R...and C. Wittig, Chem. Phys. Lett. 67, 48 (1979). 5 P.B. Beeken , E.A. Hanson, and G.W. Flynn, J. Chem. Phys. 78, 5892 (1983). 6 M.C. Heaven, AFOSR Report

EPR study of chromium-doped forsterite crystals: Cr3+( M1) with associated trivalent ions Al3+ and Sc3+

NASA Astrophysics Data System (ADS)

Ryabov, I. D.

2012-10-01

Electron paramagnetic resonance (EPR) study of single crystals of forsterite co-doped with chromium and scandium has revealed, apart from the known paramagnetic centers Cr3+( M1) and Cr3+( M1)- V_{{{{Mg}}^{2 + } }} ( M2) (Ryabov in Phys Chem Miner 38:177-184, 2011), a new center Cr3+( M1)- V_{{{{Mg}}^{2 + } }} ( M2)-Sc3+ formed by a Cr3+ ion substituting for Mg2+ at the M1 structural position with a nearest-neighbor Mg2+ vacancy at the M2 position and a Sc3+ ion presumably at the nearest-neighbor M1 position. For this center, the conventional zero-field splitting parameters D and E and the principal g values have been determined as follows: D = 33,172(29) MHz, E = 8,482(13) MHz, g = [1.9808(2), 1.9778(2), 1.9739(2)]. The center has been compared with the known ion pair Cr3+( M1)-Al3+ (Bershov et al. in Phys Chem Miner 9:95-101, 1983), for which the refined EPR data have been obtained. Based on these data, the known sharp M1″ line at 13,967 cm-1 (with the splitting of 1.8 cm-1), observed in low-temperature luminescence spectra of chromium-doped forsterite crystals (Glynn et al. in J Lumin 48, 49:541-544, 1991), has been ascribed to the Cr3+( M1)-Al3+ center. It has been found that the concentration of the new center increases from 0 up to 4.4 × 1015 mg-1, whereas that of the Cr3+( M1) and Cr3+( M1)- V_{{{{Mg}}^{2 + } }} ( M2) centers quickly decreases from 7.4 × 1015 mg-1 down to 3 × 1015 mg-1 and from 2.7 × 1015 mg-1 down to 0.5 × 1015 mg-1, i.e., by a factor of 2.5 and 5.4, respectively, with an increase of the Sc content from 0 up to 0.22 wt % (at the same Cr content 0.25 wt %) in the melt. When the Sc content exceeds that of Cr, the concentration of the new center decreases most likely due to the formation of the Sc3+( M1)- V_{{{{Mg}}^{2 + } }} ( M2)-Sc3+ complex instead of the Cr3+( M1)- V_{{{{Mg}}^{2 + } }} ( M2)-Sc3+ center. The formation of such ordered neutral complex is in agreement with the experimental results, concerning the incorporation of Sc

Investigating the heterogeneous freezing behavior of supercooled droplets containing different amounts of SNOMAX

NASA Astrophysics Data System (ADS)

Niedermeier, D.; Budke, C.; Koop, T.; Hartmann, S.; Augustin, S.; Stratmann, F.; Wex, H.

2013-12-01

bacteria, initiate the freezing process (Wolber et al. 1986). The Soccer ball model (Niedermeier et al., 2011) was used to parameterize the ice nucleation behavior of these INA macromolecules. One parameter set (mean contact angle and its standard deviation) could be derived that matches the experimental results of both devices. This parameterization can be used to describe the ice nucleation behavior of the INA bacteria in atmospheric models for a given number concentration being present in the atmosphere. Acknowledgement This work is funded by the German Research Foundation (DFG projects WE 4722/1-1 and KO 2944/2-1, both part of the research unit INUIT). References Budke et al., Proc.19th ICNAA, Fort Collins, CO, USA, 949-951, 2013. Hartmann et al., Atmos. Chem. Phys., 11, 1753-1767, 2011. Hartmann et al., Atmos. Chem. Phys., 13, 5751-5766, 2013. Hoose et al., Environ. Res. Lett. 5, 024009, 2010. Kanitz et al., Geophys. Res. Lett., 38, L17802, 2011. Niedermeier et al., Atmos. Chem. Phys., 11, 8767-8775, 2011. Murray et al., Chem. Soc. Rev., 41, 6519-6554, 2012. Wolber et al., P. Natl. A. Sci., 83, 7256-7260, 1986.

Weak Hydrogen Bonds from Aliphatic and Fluorinated Alocohols to Molecular Nitrogen Detected by Supersonic Jet FTIR Spectroscopy

NASA Astrophysics Data System (ADS)

Oswald, Soenke; Suhm, Martin A.

2017-06-01

Complexes of organic molecules with the main component of earth's atmosphere are of interest, also for a stepwise understanding of the phenomenon of matrix isolation. Via its large quadrupole moment, nitrogen binds strongly to polarized OH groups in hydrogen-bonded dimers. Further complexation leads to a smooth spectral transition from free to embedded molecules which we probe in supersonic jets. Results for 1,1,1,3,3,3-hexafluoro-2-propanol, methanol, t-butyl alcohol, and the conformationally more complex ethanol are presented and assigned with the help of quantum chemical calculations. Kuma, S., Slipchenko, M. N., Kuyanov, K. E., Momose, T., Vilesov, A. F., Infrared Spectra and Intensities of the H_2O and N_2 Complexes in the Range of the ν_1- and ν_3-Bands of Water, J. Phys. Chem. A, 2006, 110, 10046-10052. Coussan, S., Bouteiller, Y., Perchard, J. P., Zheng, W. Q., Rotational Isomerism of Ethanol and Matrix Isolation Infrared Spectroscopy, J. Phys. Chem. A, 1998, 102, 5789-5793. Suhm, M. A., Kollipost, F., Femtisecond single-mole infrared spectroscopy of molecular clusters, Phys. Chem. Chem. Phys., 2013, 15, 10702-10721. Larsen, R. W., Zielke, P., Suhm, M. A., Hydrogen bonded OH stretching modes of methanol clusters: a combined IR and Raman isotopomer study, J. Chem. Phys., 2007, 126, 194307. Zimmermann, D., Häber, T., Schaal, H., Suhm, M. A., Hydrogen bonded rings, chains and lassos: The case of t-butyl alcohol clusters, Mol. Phys., 2001, 99, 413-425. Wassermann, T. N., Suhm, M. A., Ethanol Monomers and Dimers Revisited: A Raman Study of Conformational Preferences and Argon Nanocoating Effects, J. Phys. Chem. A, 2010, 114, 8223-8233.

Dinitrogen Difluoride Chemistry. Improved Synthesis of cis- and trans-N2F2, Synthesis and Characterization of N2F+Sn2F9 High-Level Electronic Structure Calculations of cis-N2F2, trans-N2F2, F2N=N, and N2F+, and Mechanism of the trans-cis Isomerization of N2F2 (Preprint)

DTIC Science & Technology

2010-05-01

measurements of Pankratov and Sokolov who found that within experimental error this value was close to zero.48 We note that the current calculations are...Z. Chem. Phys. Lett. 1977, 50, 418. 9. Christe, K. O.; Wilson, R. D.; Wilson, W. W.; Bau, R.; Sukumar, S.; Dixon, D. A. J. Am. Chem. Soc. 1991 , 113...Phys. Chem. Ref. Data, Mono. 9, Suppl. 1 (1998). 48. Pankratov , A. V.; Sokolov, O. M. Russ. J. Inorg. Chem. 1966, 11, 943. 49. Christe, K. O

A molecular dynamics study of water nucleation using the TIP4P/2005 model

NASA Astrophysics Data System (ADS)

Pérez, Alejandro; Rubio, Angel

2011-12-01

Extensive molecular dynamics simulations were conducted using the TIP4P/2005 water model of Abascal and Vega [J. Chem. Phys. 123, 234505 (2005)] to investigate its condensation from supersaturated vapor to liquid at 330 K. The mean first passage time method [J. Wedekind, R. Strey, and D. Reguera, J. Chem. Phys. 126, 134103 (2007); L. S. Bartell and D. T. Wu, 125, 194503 (2006)] was used to analyze the influence of finite size effects, thermostats, and charged species on the nucleation dynamics. We find that the Nosé-Hoover thermostat and the one proposed by Bussi et al. [J. Chem. Phys. 126, 014101 (2007)] give essentially the same averages. We identify the maximum thermostat coupling time to guarantee proper thermostating for these simulations. The presence of charged species has a dramatic impact on the dynamics, inducing a marked change towards a pure growth regime, which highlights the importance of ions in the formation of liquid droplets in the atmosphere. It was found a small but noticeable sign preference at intermediate cluster sizes (between 5 and 30 water molecules) corresponding mostly to the formation of the second solvation shell around the ion. The TIP4P/2005 water model predicts that anions induce faster formation of water clusters than cations of the same magnitude of charge.

The effect of zero-point energy differences on the isotope dependence of the formation of ozone: a classical trajectory study.

PubMed

Schinke, Reinhard; Fleurat-Lessard, Paul

2005-03-01

The effect of zero-point energy differences (DeltaZPE) between the possible fragmentation channels of highly excited O(3) complexes on the isotope dependence of the formation of ozone is investigated by means of classical trajectory calculations and a strong-collision model. DeltaZPE is incorporated in the calculations in a phenomenological way by adjusting the potential energy surface in the product channels so that the correct exothermicities and endothermicities are matched. The model contains two parameters, the frequency of stabilizing collisions omega and an energy dependent parameter Delta(damp), which favors the lower energies in the Maxwell-Boltzmann distribution. The stabilization frequency is used to adjust the pressure dependence of the absolute formation rate while Delta(damp) is utilized to control its isotope dependence. The calculations for several isotope combinations of oxygen atoms show a clear dependence of relative formation rates on DeltaZPE. The results are similar to those of Gao and Marcus [J. Chem. Phys. 116, 137 (2002)] obtained within a statistical model. In particular, like in the statistical approach an ad hoc parameter eta approximately 1.14, which effectively reduces the formation rates of the symmetric ABA ozone molecules, has to be introduced in order to obtain good agreement with the measured relative rates of Janssen et al. [Phys. Chem. Chem. Phys. 3, 4718 (2001)]. The temperature dependence of the recombination rate is also addressed.

ChemCam Passive Sky Spectroscopy at Gale Crater, Mars: Interannual Variability in Dust Aerosol Particle Size, Missing Water Vapor, and the Molecular Oxygen Problem

NASA Astrophysics Data System (ADS)

McConnochie, T. H.; Smith, M. D.; Wolff, M. J.; Bender, S. C.; Lemmon, M. T.; Wiens, R. C.; Maurice, S.; Gasnault, O.; Lasue, J.; Meslin, P. Y.; Harri, A. M.; Genzer, M.; Kemppinen, O.; Martinez, G.; DeFlores, L. P.; Blaney, D. L.; Johnson, J. R.; Bell, J. F., III; Trainer, M. G.; Lefèvre, F.; Atreya, S. K.; Mahaffy, P. R.; Wong, M. H.; Franz, H. B.; Guzewich, S.; Villanueva, G. L.; Khayat, A. S.

2017-12-01

The Mars Science Laboratory's (MSL) ChemCam spectrometer measures atmospheric aerosol properties and gas abundances by operating in passive mode and observing scattered sky light at two different elevation angles. We have previously [e. g. 1, 2] presented the methodology and results of these ChemCam Passive Sky observations. Here we will focus on three of the more surprising results that we have obtained: (1) depletion of the column water vapor at Gale Crater relative to that of the surrounding region combined with a strong enhancement of the local column water vapor relative to pre-dawn in-situ measurements, (2) an interannual change in the effective particle size of dust aerosol during the aphelion season, and (3) apparent seasonal and interannual variability in molecular oxygen that differs significantly from the expected behavior of a non-condensable trace gas and differs significantly from global climate model expectations. The ChemCam passive sky water vapor measurements are quite robust but their interpretation depends on the details of measurements as well as on the types of water vapor vertical distributions that can be produced by climate models. We have a high degree of confidence in the dust particle size changes but since aerosol results in general are subject to a variety of potential systematic effects our particle size results would benefit from confirmation by other techniques [c.f. 3]. For the ChemCam passive sky molecular oxygen results we are still working to constrain the uncertainties well enough to confirm the observed surprising behavior, motivated by similarly surprising atmospheric molecular oxygen variability observed by MSL's Sample Analysis at Mars (SAM) instrument [4]. REFERENCES: [1] McConnochie, et al. (2017), Icarus (submitted). [2] McConnochie, et al. (2017), abstract # 3201, The 6th International Workshop on the Mars Atmosphere: Granada, Spain. [3] Vicente-Retortillo et al. (2017), GRL, 44. [4] Trainer et al. (2017), 2017 AGU Fall

AutoClickChem: click chemistry in silico.

PubMed

Durrant, Jacob D; McCammon, J Andrew

2012-01-01

Academic researchers and many in industry often lack the financial resources available to scientists working in "big pharma." High costs include those associated with high-throughput screening and chemical synthesis. In order to address these challenges, many researchers have in part turned to alternate methodologies. Virtual screening, for example, often substitutes for high-throughput screening, and click chemistry ensures that chemical synthesis is fast, cheap, and comparatively easy. Though both in silico screening and click chemistry seek to make drug discovery more feasible, it is not yet routine to couple these two methodologies. We here present a novel computer algorithm, called AutoClickChem, capable of performing many click-chemistry reactions in silico. AutoClickChem can be used to produce large combinatorial libraries of compound models for use in virtual screens. As the compounds of these libraries are constructed according to the reactions of click chemistry, they can be easily synthesized for subsequent testing in biochemical assays. Additionally, in silico modeling of click-chemistry products may prove useful in rational drug design and drug optimization. AutoClickChem is based on the pymolecule toolbox, a framework that may facilitate the development of future python-based programs that require the manipulation of molecular models. Both the pymolecule toolbox and AutoClickChem are released under the GNU General Public License version 3 and are available for download from http://autoclickchem.ucsd.edu.

AutoClickChem: Click Chemistry in Silico

PubMed Central

Durrant, Jacob D.; McCammon, J. Andrew

2012-01-01

Academic researchers and many in industry often lack the financial resources available to scientists working in “big pharma.” High costs include those associated with high-throughput screening and chemical synthesis. In order to address these challenges, many researchers have in part turned to alternate methodologies. Virtual screening, for example, often substitutes for high-throughput screening, and click chemistry ensures that chemical synthesis is fast, cheap, and comparatively easy. Though both in silico screening and click chemistry seek to make drug discovery more feasible, it is not yet routine to couple these two methodologies. We here present a novel computer algorithm, called AutoClickChem, capable of performing many click-chemistry reactions in silico. AutoClickChem can be used to produce large combinatorial libraries of compound models for use in virtual screens. As the compounds of these libraries are constructed according to the reactions of click chemistry, they can be easily synthesized for subsequent testing in biochemical assays. Additionally, in silico modeling of click-chemistry products may prove useful in rational drug design and drug optimization. AutoClickChem is based on the pymolecule toolbox, a framework that may facilitate the development of future python-based programs that require the manipulation of molecular models. Both the pymolecule toolbox and AutoClickChem are released under the GNU General Public License version 3 and are available for download from http://autoclickchem.ucsd.edu. PMID:22438795

Alkali trace elements in Gale crater, Mars, with ChemCam: Calibration update and geological implications

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

Payre, Valerie; Fabre, Cecile; Cousin, Agnes

The Chemistry Camera (ChemCam) instrument onboard Curiosity can detect minor and trace elements such as lithium, strontium, rubidium, and barium. Their abundances can provide some insights about Mars' magmatic history and sedimentary processes. We focus on developing new quantitative models for these elements by using a new laboratory database (more than 400 samples) that displays diverse compositions that are more relevant for Gale crater than the previous ChemCam database. These models are based on univariate calibration curves. For each element, the best model is selected depending on the results obtained by using the ChemCam calibration targets onboard Curiosity. New quantificationsmore » of Li, Sr, Rb, and Ba in Gale samples have been obtained for the first 1000 Martian days. Comparing these data in alkaline and magnesian rocks with the felsic and mafic clasts from the Martian meteorite NWA7533—from approximately the same geologic period—we observe a similar behavior: Sr, Rb, and Ba are more concentrated in soluble- and incompatible-element-rich mineral phases (Si, Al, and alkali-rich). Correlations between these trace elements and potassium in materials analyzed by ChemCam reveal a strong affinity with K-bearing phases such as feldspars, K-phyllosilicates, and potentially micas in igneous and sedimentary rocks. However, lithium is found in comparable abundances in alkali-rich and magnesium-rich Gale rocks. This very soluble element can be associated with both alkali and Mg-Fe phases such as pyroxene and feldspar. Here, these observations of Li, Sr, Rb, and Ba mineralogical associations highlight their substitution with potassium and their incompatibility in magmatic melts.« less

Alkali trace elements in Gale crater, Mars, with ChemCam: Calibration update and geological implications

DOE PAGES

Payre, Valerie; Fabre, Cecile; Cousin, Agnes; ...

2017-03-20

The Chemistry Camera (ChemCam) instrument onboard Curiosity can detect minor and trace elements such as lithium, strontium, rubidium, and barium. Their abundances can provide some insights about Mars' magmatic history and sedimentary processes. We focus on developing new quantitative models for these elements by using a new laboratory database (more than 400 samples) that displays diverse compositions that are more relevant for Gale crater than the previous ChemCam database. These models are based on univariate calibration curves. For each element, the best model is selected depending on the results obtained by using the ChemCam calibration targets onboard Curiosity. New quantificationsmore » of Li, Sr, Rb, and Ba in Gale samples have been obtained for the first 1000 Martian days. Comparing these data in alkaline and magnesian rocks with the felsic and mafic clasts from the Martian meteorite NWA7533—from approximately the same geologic period—we observe a similar behavior: Sr, Rb, and Ba are more concentrated in soluble- and incompatible-element-rich mineral phases (Si, Al, and alkali-rich). Correlations between these trace elements and potassium in materials analyzed by ChemCam reveal a strong affinity with K-bearing phases such as feldspars, K-phyllosilicates, and potentially micas in igneous and sedimentary rocks. However, lithium is found in comparable abundances in alkali-rich and magnesium-rich Gale rocks. This very soluble element can be associated with both alkali and Mg-Fe phases such as pyroxene and feldspar. Here, these observations of Li, Sr, Rb, and Ba mineralogical associations highlight their substitution with potassium and their incompatibility in magmatic melts.« less

ConfChem Conference on Flipped Classroom: Spring 2014 ConfChem Virtual Poster Session

ERIC Educational Resources Information Center

Belford, Robert E.; Stoltzfus, Matthew; Houseknecht, Justin B.

2015-01-01

This communication describes the virtual poster session of the Flipped Classroom online ConfChem conference that was hosted by the ACS CHED Committee on Computers in Chemical Education (CCCE) from May 9 to June 12, 2014. During the conference's online discussions, it became evident that multiple participants who were not presenting papers had been…

Symmetrical windowing for quantum states in quasi-classical trajectory simulations: Application to electron transfer

NASA Astrophysics Data System (ADS)

Cotton, Stephen J.; Igumenshchev, Kirill; Miller, William H.

2014-08-01

It has recently been shown [S. J. Cotton and W. H. Miller, J. Chem. Phys. 139, 234112 (2013)] that a symmetrical windowing quasi-classical (SQC) approach [S. J. Cotton and W. H. Miller, J. Phys. Chem. A 117, 7190 (2013)] applied to the Meyer-Miller model [H.-D. Meyer and W. H. Miller, J. Chem. Phys. 70, 3214 (1979)] for the electronic degrees of freedom in electronically non-adiabatic dynamics is capable of quantitatively reproducing quantum mechanical results for a variety of test applications, including cases where "quantum" coherence effects are significant. Here we apply this same SQC methodology, within a flux-side correlation function framework, to calculate thermal rate constants corresponding to several proposed models of electron transfer processes [P. Huo, T. F. Miller III, and D. F. Coker, J. Chem. Phys. 139, 151103 (2013); A. R. Menzeleev, N. Ananth, and T. F. Miller III, J. Chem. Phys. 135, 074106 (2011)]. Good quantitative agreement with Marcus Theory is obtained over several orders of magnitude variation in non-adiabatic coupling. Moreover, the "inverted regime" in thermal rate constants (with increasing bias) known from Marcus Theory is also reproduced with good accuracy by this very simple classical approach. The SQC treatment is also applied to a recent model of photoinduced proton coupled electron transfer [C. Venkataraman, A. V. Soudackov, and S. Hammes-Schiffer, J. Chem. Phys. 131, 154502 (2009)] and population decay of the photoexcited donor state is found to be in reasonable agreement with results calculated via reduced density matrix theory.

Symmetrical windowing for quantum states in quasi-classical trajectory simulations: Application to electron transfer

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

Cotton, Stephen J.; Igumenshchev, Kirill; Miller, William H., E-mail: millerwh@berkeley.edu

It has recently been shown [S. J. Cotton and W. H. Miller, J. Chem. Phys. 139, 234112 (2013)] that a symmetrical windowing quasi-classical (SQC) approach [S. J. Cotton and W. H. Miller, J. Phys. Chem. A 117, 7190 (2013)] applied to the Meyer-Miller model [H.-D. Meyer and W. H. Miller, J. Chem. Phys. 70, 3214 (1979)] for the electronic degrees of freedom in electronically non-adiabatic dynamics is capable of quantitatively reproducing quantum mechanical results for a variety of test applications, including cases where “quantum” coherence effects are significant. Here we apply this same SQC methodology, within a flux-side correlation functionmore » framework, to calculate thermal rate constants corresponding to several proposed models of electron transfer processes [P. Huo, T. F. Miller III, and D. F. Coker, J. Chem. Phys. 139, 151103 (2013); A. R. Menzeleev, N. Ananth, and T. F. Miller III, J. Chem. Phys. 135, 074106 (2011)]. Good quantitative agreement with Marcus Theory is obtained over several orders of magnitude variation in non-adiabatic coupling. Moreover, the “inverted regime” in thermal rate constants (with increasing bias) known from Marcus Theory is also reproduced with good accuracy by this very simple classical approach. The SQC treatment is also applied to a recent model of photoinduced proton coupled electron transfer [C. Venkataraman, A. V. Soudackov, and S. Hammes-Schiffer, J. Chem. Phys. 131, 154502 (2009)] and population decay of the photoexcited donor state is found to be in reasonable agreement with results calculated via reduced density matrix theory.« less

Symmetry in the Generalized Rotor Model for Extremely Floppy Molecules

NASA Astrophysics Data System (ADS)

Schmiedt, Hanno; Jensen, Per; Schlemmer, Stephan

2016-06-01

Protonated methane CH_5^+ is unique: It is an extremely fluxional molecule. All attempts to assign quantum numbers to the high-resolution transitions obtained over the last 20 years have failed because molecular rotation and vibration cannot be separated in the conventional way. The first step towards a theoretical description is to include internal rotational degrees of freedom into the overall ones, which can be used to formulate a fundamentally new zero order approximation for the (now) generalized rotational states and energies. Predictions from this simple five-dimensional rotor model compare very favorably with the combination differences of protonated methane found in recent low temperature experiments. This talk will focus on symmetry aspects and implications of permutation symmetry for the generalized rotational states. Furthermore, refinements of the theory will be discussed, ranging from the generalization to even higher-dimensional rotors to explicit symmetry breaking and corresponding energy splittings. The latter includes the link to well-known theories of internal rotation dynamics and will show the general validity of the presented theory. Schmiedt, H., et al.; J. Chem. Phys. 143 (15), 154302 (2015) Wodraszka, R. et al.; J. Phys. Chem. Lett. 6, 4229-4232 (2015) Asvany, O. et al.; Science, 347, (6228), 1346-1349 (2015)

Curiosity's ChemCam Checks 'Christmas Cove' Colors

NASA Image and Video Library

2017-11-01

The Chemistry and Camera (ChemCam) instrument on NASA's Curiosity Mars rover examined a freshly brushed area on target rock "Christmas Cove" and found spectral evidence of hematite, an iron-oxide mineral. ChemCam sometimes zaps rocks with a laser, but can also be used, as in this case, in a "passive" mode. In this type of investigation, the instrument's telescope delivers to spectrometers the sunlight reflected from a small target point. The upper-left inset of this graphic is an image from ChemCam's Remote Micro-Imager with five labeled points that the instrument analyzed. The image covers an area about 2 inches (5 centimeters) wide, and the bright lines are fractures in the rock filled with calcium sulfate minerals. The five charted lines of the graphic correspond to those five points and show the spectrometer measurements of brightness at thousands of different wavelengths, from 400 nanometers (at the violet end of the visible-light spectrum) to 840 nanometers (in near-infrared). Sections of the spectrum measurements that are helpful for identifying hematite are annotated. These include a dip around 535 nanometers, the green-light portion of the spectrum at which fine-grained hematite tends to absorb more light and reflect less compared to other parts of the spectrum. That same green-absorbing characteristic of the hematite makes it appear purplish when imaged through special filters of Curiosity's Mast Camera and even in usual color images. The spectra also show maximum reflectance values near 750 nanometers, followed by a steep decrease in the spectral slope toward 840 nanometers, both of which are consistent with hematite. This ChemCam examination of Christmas Cove was part of an experiment to determine whether the rock had evidence of hematite under a tan coating of dust. The target area was brushed with Curiosity's Dust Removal Tool prior to these ChemCam passive observations on Sept. 17, 2017, during the 1,819th Martian day, or sol, of Curiosity's work on

A self-consistent density based embedding scheme applied to the adsorption of CO on Pd(111)

NASA Astrophysics Data System (ADS)

Lahav, D.; Klüner, T.

2007-06-01

We derive a variant of a density based embedded cluster approach as an improvement to a recently proposed embedding theory for metallic substrates (Govind et al 1999 J. Chem. Phys. 110 7677; Klüner et al 2001 Phys. Rev. Lett. 86 5954). In this scheme, a local region in space is represented by a small cluster which is treated by accurate quantum chemical methodology. The interaction of the cluster with the infinite solid is taken into account by an effective one-electron embedding operator representing the surrounding region. We propose a self-consistent embedding scheme which resolves intrinsic problems of the former theory, in particular a violation of strict density conservation. The proposed scheme is applied to the well-known benchmark system CO/Pd(111).

NARSTO EPA SS NEW YORK AIR CHEM PM MET DATA

Atmospheric Science Data Center

2018-04-09

NARSTO EPA SS NEW YORK AIR CHEM PM MET DATA Project Title:  NARSTO ... Nitrogen Oxides Ozone Surface Winds Air Temperature Humidity Solar Irradiance Particulate Matter ... Data Guide Documents:  New York Air Chem Guide CPM Summary Report  (PDF) Nitrate ...

Hazardous Waste Cleanup: Cycle Chem Incorporated in Elizabeth, New Jersey

EPA Pesticide Factsheets

Cycle Chem is located at 217 South First Street in Elizabeth, New Jersey. Cycle Chem recovers spent solvents and treats both hazardous and non-hazardous wastes in containers and tanks. The site comprises two acres in an industrial area, surrounded by

Comment on ``Scalings for radiation from plasma bubbles'' [Phys. Plasmas 17, 056708 (2010)

NASA Astrophysics Data System (ADS)

Corde, S.; Stordeur, A.; Malka, V.

2011-03-01

Thomas has recently derived scaling laws for x-ray radiation from electrons accelerated in plasma bubbles, as well as a threshold for the self-injection of background electrons into the bubble [A. G. R. Thomas, Phys. Plasmas 17, 056708 (2010)]. To obtain this threshold, the equations of motion for a test electron are studied within the frame of the bubble model, where the bubble is described by prescribed electromagnetic fields and has a perfectly spherical shape. The author affirms that any elliptical trajectory of the form x'2/γp2+y'2=R2 is solution of the equations of motion (in the bubble frame), within the approximation py'2/px'2≪1. In addition, he highlights that his result is different from the work of Kostyukov et al. [Phys. Rev. Lett. 103, 175003 (2009)], and explains the error committed by Kostyukov-Nerush-Pukhov-Seredov (KNPS). In this comment, we show that numerically integrated trajectories, based on the same equations than the analytical work of Thomas, lead to a completely different result for the self-injection threshold, the result published by KNPS [Phys. Rev. Lett. 103, 175003 (2009)]. We explain why the analytical analysis of Thomas fails and we provide a discussion based on numerical simulations which show exactly where the difference arises. We also show that the arguments of Thomas concerning the error of KNPS do not hold, and that their analysis is mathematically correct. Finally, we emphasize that if the KNPS threshold is found not to be verified in PIC (Particle In Cell) simulations or experiments, it is due to a deficiency of the model itself, and not to an error in the mathematical derivation.

Curiosity ChemCam Removes Dust

NASA Image and Video Library

2013-04-08

This pair of images taken a few minutes apart show how laser firing by NASA Mars rover Curiosity removes dust from the surface of a rock. The images were taken by the remote micro-imager camera in the laser-firing Chemistry and Camera ChemCam.

EarthChem: International Collaboration for Solid Earth Geochemistry in Geoinformatics

NASA Astrophysics Data System (ADS)

Walker, J. D.; Lehnert, K. A.; Hofmann, A. W.; Sarbas, B.; Carlson, R. W.

2005-12-01

The current on-line information systems for igneous rock geochemistry - PetDB, GEOROC, and NAVDAT - convincingly demonstrate the value of rigorous scientific data management of geochemical data for research and education. The next generation of hypothesis formulation and testing can be vastly facilitated by enhancing these electronic resources through integration of available datasets, expansion of data coverage in location, time, and tectonic setting, timely updates with new data, and through intuitive and efficient access and data analysis tools for the broader geosciences community. PetDB, GEOROC, and NAVDAT have therefore formed the EarthChem consortium (www.earthchem.org) as a international collaborative effort to address these needs and serve the larger earth science community by facilitating the compilation, communication, serving, and visualization of geochemical data, and their integration with other geological, geochronological, geophysical, and geodetic information to maximize their scientific application. We report on the status of and future plans for EarthChem activities. EarthChem's development plan includes: (1) expanding the functionality of the web portal to become a `one-stop shop for geochemical data' with search capability across databases, standardized and integrated data output, generally applicable tools for data quality assessment, and data analysis/visualization including plotting methods and an information-rich map interface; and (2) expanding data holdings by generating new datasets as identified and prioritized through community outreach, and facilitating data contributions from the community by offering web-based data submission capability and technical assistance for design, implementation, and population of new databases and their integration with all EarthChem data holdings. Such federated databases and datasets will retain their identity within the EarthChem system. We also plan on working with publishers to ease the assimilation

Aerosols increase upper tropospheric humidity over the North Western Pacific

NASA Astrophysics Data System (ADS)

Riuttanen, Laura; Bister, Marja; John, Viju; Sundström, Anu-Maija; Dal Maso, Miikka; Räisänen, Jouni; de Leeuw, Gerrit; Kulmala, Markku

2014-05-01

Water vapour in the upper troposphere is highly important for the global radiative transfer. The source of upper tropospheric humidity is deep convection, and aerosol effects on them have got attention only recently. E.g., aerosol effects on deep convective clouds have been missing in general circulation models (Quaas et al., 2009). In deep convection, aerosol effect on cloud microphysics may lead to more ice precipitation and less warm rain (Khain et al., 2005), and thus more water vapour in upper troposphere (Bister & Kulmala, 2011). China outflow region over the Pacific Ocean was chosen as a region for a more detailed study, with latitudes 25-45 N and three longitude slots: 120-149 E, 150-179 E and 150-179 W. In this study, we used satellite measurements of aerosol optical depth (AOD) and upper tropospheric humidity (UTH). AOD was obtained from the MODIS instrument onboard Terra satellite, that crosses the equator southward at 10:30 AM local solar time (Remer et al., 2005). UTH was obtained from a microwave humidity sounder (MHS) onboard MetOp-A satellite, with passing time at 9:30 PM local solar time. It measures relative humidity of a layer extending approximately from 500 to 200 hPa. We binned the AOD and UTH data according to daily rainfall product 3B42 from Tropical Rainfall Measuring Mission (TRMM) satellite. Binning the data according to the amount of precipitation gives us a new way to account for the possible aerosol invigoration effect on convection and to alleviate the contamination and causality problems in aerosol indirect effect studies. In this study, we show for the first time, based on satellite data, that there is a connection between upper tropospheric humidity and aerosols. Anthropogenic aerosols from China increase upper tropospheric humidity, which causes a significant positive local radiative forcing in libRadtran radiative transfer model (Mayer & Kylling, 2005). References: Bister, M. & Kulmala, M. (2011). Atmos. Chem. Phys., 11, 4577

Chem-Braze Abradable Seal Attachment to Aircraft Gas Turbine Compressor Components.

DTIC Science & Technology

1982-01-01

seals to compressor blade tip-shrouds using the im- proved Chem-Braze system compared to attachment with gold-nickel braze. The Chem-Braze system has been...used successfully to bond abradable seals to titanium ’ cobalt, nickel and iron base alloys; however, attempts to use Chem-Braze to bond seals to...attaching FELTMETALO seals to steel, titanium , and nickel-based alloys, and ICB bonding procedures were investigated for attaching seals to selected

Immersion freezing induced by different kinds of coal fly ash: Comparing particle generation methods and measurement techniques

NASA Astrophysics Data System (ADS)

Grawe, Sarah; Augustin-Bauditz, Stefanie; Clemen, Hans-Christian; Eriksen-Hammer, Stine; Lubitz, Jasmin; Schneider, Johannes; Stratmann, Frank; Wex, Heike

2017-04-01

factor of 5 at most) when particles are generated via dry dispersion. Furthermore, we found that the ice nucleation ability of all samples is lowered significantly when changing from dry to wet particle generation. The aim of the study is to identify possible reasons for these observations. References: S. Grawe, S. Augustin-Bauditz, S. Hartmann, L. Hellner, J. B. C. Pettersson, A. Prager, F. Stratmann, and H. Wex, Atmos. Chem. Phys., 16, 13911-13928, 2016 S. Hartmann, D. Niedermeier, J. Voigtländer, T. Clauß, R. A. Shaw, H. Wex, A. Kiselev, and F. Stratmann, Atmos. Chem. Phys., 11, 1753-1767, 2011 C. Hoose and O. Möhler, Atmos. Chem. Phys., 12, 9817-9854, 2012 B. J. Murray, D. O'Sullivan, J. D. Atkinson, and M. E. Webb, Chem. Soc. Rev., 41, 6519-6554, 2012 N. S. Umo, B. J. Murray, M. T. Baeza-Romero, J. M. Jones, A. R. Lea-Langton, T. L. Malkin, D. O'Sullivan, L. Neve, J. M. C. Plane, and A. Williams, Atmos. Chem. Phys., 15, 5195-5210, 2015

Photoelectronic Properties of Ternary Niobium Oxides.

DTIC Science & Technology

1980-09-01

K . /Dwi ght ,. 1 d N0,OO0l4-77-C-0387 B . PERFORMING ORGAbi)ATi0N NAME AND ADZRESS 10. PROGRAM ELEMENT. PROIECT. TASK00 Po soArn odAREA a WORK UNIT...Kershaw, R.; Dwight, K .; Wold, A. J. Solid State Chem., 1979, 27, 307. 6. Salmon, 0. N.*J. Phys. Chem., 1961, 65, 550. 7. Koenitzer, J.; Khazai, B ...Ann. Rev. Phys. Chem., 197F, 29, 189. 10. Hormadaly, J.; Subbarao , S. N.; Kershaw, R.; Dwight, K .; Wold, A. J. Solid State Chem., to be published. 1.1

Resonance Fluorescence of a Two-Level Atom Near a Metal Surface. II. Case of a Strong Driving Field,

DTIC Science & Technology

1984-02-01

XYH thanks Prof. M. G. Raymer for a useful discussion. REFERENCES 1. X. Y. Huang, J. Lin and T. F. George, J. Chem. Phys., 80, 893 (1984). 2. X. Y...Mollow, Phys. Rev. A, 15, 1023 (1977). 12. J. L. Carlsten, A. Sz6ke and M. G. Raymer , Phys. Rev. A, 15, 1029 (1977). 13. H. Kuhn, J. Chem. Phys. 53, 101...Evanston, Illinois 60201 Austin, Texas 78712 Dr. Robert M. Hexter Dr. R. P. Van Duyne Department of Chemistry Chemistry Department University of Minnesota

Accurate virial coefficients of gaseous krypton from state-of-the-art ab initio potential and polarizability of the krypton dimer

NASA Astrophysics Data System (ADS)

Song, Bo; Waldrop, Jonathan M.; Wang, Xiaopo; Patkowski, Konrad

2018-01-01

We have developed a new krypton-krypton interaction-induced isotropic dipole polarizability curve based on high-level ab initio methods. The determination was carried out using the coupled-cluster singles and doubles plus perturbative triples method with very large basis sets up to augmented correlation-consistent sextuple zeta as well as the corrections for core-core and core-valence correlation and relativistic effects. The analytical function of polarizability and our recently constructed reference interatomic potential [J. M. Waldrop et al., J. Chem. Phys. 142, 204307 (2015)] were used to predict the thermophysical and electromagnetic properties of krypton gas. The second pressure, acoustic, and dielectric virial coefficients were computed for the temperature range of 116 K-5000 K using classical statistical mechanics supplemented with high-order quantum corrections. The virial coefficients calculated were compared with the generally less precise available experimental data as well as with values computed from other potentials in the literature {in particular, the recent highly accurate potential of Jäger et al. [J. Chem. Phys. 144, 114304 (2016)]}. The detailed examination in this work suggests that the present theoretical prediction can be applied as reference values in disciplines involving thermophysical and electromagnetic properties of krypton gas.

Time-independent quantum dynamics for diatom-surface scattering

NASA Astrophysics Data System (ADS)

Saalfrank, Peter; Miller, William H.

1993-06-01

Two time-independent quantum reactive scattering methods, namely, the S-matrix Kohn technique to compute the full S-matrix, and the absorbing boundary Green's function method to compute cumulative reaction probabilities, are applied here to the case of diatom-surface scattering. In both cases a discrete variable representation for the operators is used. We test the methods for two- and three-dimensional uncorrugated potential energy surfaces, which have been used earlier by Halstead et al. [J. Chem. Phys. 93, 2359 (1990)] and by Sheng et al. [J. Chem. Phys. 97, 684 (1992)] in studies of H2 dissociating on metal substrates with theoretical techniques different from those applied here. We find overall but not always perfect agreement with these earlier studies. Based on ab initio data and experiment, a new, six-dimensional potential energy surface for the dissociative chemisorption of H2 on Ni(100) is proposed. Two- and three-dimensional cuts through the new potential are performed to illustrate special dynamical aspects of this particular molecule-surface reaction: (i) the role of corrugation effects, (ii) the importance of the ``cartwheel'' rotation of H2, and (iii) the role of the ``helicopter'' degree of freedom for the adsorbing molecule.

Yielding of a model glass former: An interpretation with an effective system of icosahedra

NASA Astrophysics Data System (ADS)

Pinney, Rhiannon; Liverpool, Tanniemola B.; Royall, C. Patrick

2018-03-01

We consider the yielding under simple shear of a binary Lennard-Jones glass former whose super-Arrhenius dynamics are correlated with the formation of icosahedral structures. We recast this glass former as an effective system of icosahedra [Pinney et al., J. Chem. Phys. 143, 244507 (2015), 10.1063/1.4938424]. Looking at the small-strain region of sheared simulations, we observe that shear rates affect the shear localization behavior particularly at temperatures below the glass transition as defined with a fit to the Vogel-Fulcher-Tamman equation. At higher temperature, shear localization starts immediately on shearing for all shear rates. At lower temperatures, faster shear rates can result in a delayed start in shear localization, which begins close to the yield stress. Building from a previous work which considered steady-state shear [Pinney et al., J. Chem. Phys. 143, 244507 (2015), 10.1063/1.4938424], we interpret the response to shear and the shear localization in terms of a local effective temperature with our system of icosahedra. We find that the effective temperatures of the regions undergoing shear localization increase significantly with increasing strain (before reaching a steady-state plateau).

Comment on “Propagation of surface waves on a semi-bounded quantum magnetized collisional plasma” [Phys. Plasmas 20, 122106 (2013)

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

Moradi, Afshin, E-mail: a.moradi@kut.ac.ir

2016-04-15

In a recent article [Niknam et al., Phys. Plasmas 20, 122106 (2013)], Niknam et al. investigated the propagation of TM surface waves on a semi-bounded quantum magnetized collisional plasma in the Faraday configuration (in this case, the magnetic field is parallel to the both of the plasma surface and direction of propagation). Here, we present a fresh look at the problem and show that TM surface waves cannot propagate on surface of the present system. We find in the Faraday configuration the surface waves acquire both TM and TE components due to the cyclotron motion of electrons. Therefore, the mainmore » result of the work by Niknam et al. is incorrect.« less

ChemBank: a small-molecule screening and cheminformatics resource database.

PubMed

Seiler, Kathleen Petri; George, Gregory A; Happ, Mary Pat; Bodycombe, Nicole E; Carrinski, Hyman A; Norton, Stephanie; Brudz, Steve; Sullivan, John P; Muhlich, Jeremy; Serrano, Martin; Ferraiolo, Paul; Tolliday, Nicola J; Schreiber, Stuart L; Clemons, Paul A

2008-01-01

ChemBank (http://chembank.broad.harvard.edu/) is a public, web-based informatics environment developed through a collaboration between the Chemical Biology Program and Platform at the Broad Institute of Harvard and MIT. This knowledge environment includes freely available data derived from small molecules and small-molecule screens and resources for studying these data. ChemBank is unique among small-molecule databases in its dedication to the storage of raw screening data, its rigorous definition of screening experiments in terms of statistical hypothesis testing, and its metadata-based organization of screening experiments into projects involving collections of related assays. ChemBank stores an increasingly varied set of measurements derived from cells and other biological assay systems treated with small molecules. Analysis tools are available and are continuously being developed that allow the relationships between small molecules, cell measurements, and cell states to be studied. Currently, ChemBank stores information on hundreds of thousands of small molecules and hundreds of biomedically relevant assays that have been performed at the Broad Institute by collaborators from the worldwide research community. The goal of ChemBank is to provide life scientists unfettered access to biomedically relevant data and tools heretofore available primarily in the private sector.

Direct observation of bulk Fermi surface at higher Brillouin zones in a heavily hole-doped cuprate

NASA Astrophysics Data System (ADS)

Al-Sawai, W.; Sakurai, Y.; Itou, M.; Barbiellini, B.; Mijnarends, P. E.; Markiewicz, R. S.; Kaprzyk, S.; Gillet, J.-M.; Wakimoto, S.; Fujita, M.; Basak, S.; Lin, H.; Bansil, A.; Yamada, K.

2010-03-01

We have observed the bulk Fermi surface (FS) in an overdoped (x=0.3) single crystal of La2-xSrxCuO4 by using Compton scattering. A 2-D momentum density reconstruction [1] from measured Compton profiles, yields a clear FS signature in a higher Brillouin zone centered at p=(1.5,1.5) a.u. The quantitative agreement with density functional theory (DFT) calculations [2] and momentum density experiment suggests that Fermi-liquid physics is restored in the overdoped regime. We have also measured the 2-D angular correlation of positron annihilation radiation (2D-ACAR) [3] and noticed a similar quantitative agreement with the DFT simulations. However, 2D-ACAR does not give a clear signature of the FS in the extended momentum space in both theory and experiment. Work supported in part by the US DOE.[1] Y. Tanaka et al., Phys. Rev. B 63, 045120 (2001).[2] S. Sahrakorpi et al., Phys. Rev. Lett. 95, 157601 (2005).[3] L. C. Smedskjaer et al., J. Phys. Chem. Solids 52, 1541 (1991).

Comment on "Analysis of single-layer metamaterial absorber with reflection theory" [J. Appl. Phys. 117, 154906 (2015)

NASA Astrophysics Data System (ADS)

Tung, Nguyen Thanh

2016-03-01

In a recent paper, Xiong et al. [J. Appl. Phys. 117, 154906 (2015)] presented the simulated results of a Jerusalem-cross structure in an attempt to elaborate their proposed reflection theory for metamaterial absorbers. Noting that even at non-resonant frequencies the real part of the permeability shows an over-high average value and its imaginary part drops abruptly from positivity to negativity, we argue that their simulated results are unphysical, resulting from an incomplete understanding of the retrieval procedure.

CHEM-Based Self-Deploying Spacecraft Radar Antennas

NASA Technical Reports Server (NTRS)

Sokolowski, Witold; Huang, John; Ghaffarian, Reza

2004-01-01

A document proposes self-deploying spacecraft radar antennas based on cold hibernated elastic memory (CHEM) structures. Described in a number of prior NASA Tech Briefs articles, the CHEM concept is one of utilizing open-cell shape-memory-polymer (SMP) foams to make lightweight structures that can be compressed for storage and can later be expanded, then rigidified for use. A CHEM-based antenna according to the proposal would comprise three layers of microstrip patches and transmission lines interspersed with two flat layers of SMP foam, which would serve as both dielectric spacers and as means of deployment. The SMP foam layers would be fabricated at full size at a temperature below the SMP glass-transition temperature (Tg). The layers would be assembled into a unitary structure, which, at temperature above Tg, would be compacted to much smaller thickness, then rolled up for storage. Next, the structure would be cooled to below Tg and kept there during launch. Upon reaching the assigned position in outer space, the structure would be heated above Tg to make it rebound to its original size and shape. The structure as thus deployed would then be rigidified by natural cooling to below Tg

Ground-state energy of HeH{sup +}

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

Zhou Binglu; Zhu Jiongming; Yan Zongchao

2006-06-15

The nonrelativistic ground-state energy of {sup 4}HeH{sup +} is calculated using a variational method in Hylleraas coordinates. Convergence to a few parts in 10{sup 10} is achieved, which improves the best previous result of Pavanello et al. [J. Chem. Phys. 123, 104306 (2005)]. Expectation values of the interparticle distances are evaluated. Similar results for {sup 3}HeH{sup +} are also presented.

Obadiah Reid | NREL

Science.gov Websites

.; Boltalina, O. V.; Strauss, S. H.; Kopidakis, N.; Rumbles, G. Inter-Fullerene Electronic Coupling Controls .; Noel, N. K.; Reid, O. G.; Rumbles, G.; Kukura, P.; et al. Mechanism for Rapid Growth of Organic Organic Framework. J. Phys. Chem. Lett. 2016, 7, 3660-3665. Reid, O. G.; Yang, M.; Kopidakis, N.; Zhu, K

Simulation of the single-vibronic-level emission spectrum of HPS.

PubMed

Mok, Daniel K W; Lee, Edmond P F; Chau, Foo-tim; Dyke, John M

2014-05-21

We have computed the potential energy surfaces of the X¹A' and ùA" states of HPS using the explicitly correlated multi-reference configuration interaction (MRCI-F12) method, and Franck-Condon factors between the two states, which include anharmonicity and Duschinsky rotation, with the aim of testing the assignment of the recently reported single-vibronic-level (SVL) emission spectrum of HPS [R. Grimminger, D. J. Clouthier, R. Tarroni, Z. Wang, and T. J. Sears, J. Chem. Phys. 139, 174306 (2013)]. These are the highest level calculations on these states yet reported. It is concluded that our spectral simulation supports the assignments of the molecular carrier, the electronic states involved and the vibrational structure of the experimental laser induced fluorescence, and SVL emission spectra proposed by Grimminger et al. [J. Chem. Phys. 139, 174306 (2013)]. However, there remain questions unanswered regarding the relative electronic energies of the two states and the geometry of the excited state of HPS.

Iterative universal state selective correction for the Brillouin-Wigner multireference coupled-cluster theory

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

Banik, Subrata; Ravichandran, Lalitha; Brabec, Jiri

2015-03-21

As a further development of the previously introduced a posteriori Universal State-Selective (USS) corrections [K. Kowalski, J. Chem. Phys. 134, 194107 (2011)] and [Brabec et al., J. Chem. Phys., 136, 124102 (2012)], we suggest an iterative form of the USS correction by means of correcting effective Hamiltonian matrix elements. We also formulate USS corrections via the left Bloch equations. The convergence of the USS corrections with excitation level towards the FCI limit is also investigated. Various forms of the USS and simplified diagonal USSD corrections at the SD and SD(T) levels are numerically assessed on several model systems and onmore » the ozone and tetramethyleneethane molecules. It is shown that the iterative USS correction can successfully replace the previously developed a posteriori BWCC size-extensivity correction, while it is not sensitive to intruder states and performs well also in other cases when the a posteriori one fails, like e.g. for the asymmetric vibration mode of ozone.« less

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

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

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

2015-10-07

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

Using the thermal Gaussian approximation for the Boltzmann operator in semiclassical initial value time correlation functions.

PubMed

Liu, Jian; Miller, William H

2006-12-14

The thermal Gaussian approximation (TGA) recently developed by Frantsuzov et al. [Chem. Phys. Lett. 381, 117 (2003)] has been demonstrated to be a practical way for approximating the Boltzmann operator exp(-betaH) for multidimensional systems. In this paper the TGA is combined with semiclassical (SC) initial value representations (IVRs) for thermal time correlation functions. Specifically, it is used with the linearized SC-IVR (LSC-IVR, equivalent to the classical Wigner model), and the "forward-backward semiclassical dynamics" approximation developed by Shao and Makri [J. Phys. Chem. A 103, 7753 (1999); 103, 9749 (1999)]. Use of the TGA with both of these approximate SC-IVRs allows the oscillatory part of the IVR to be integrated out explicitly, providing an extremely simple result that is readily applicable to large molecular systems. Calculation of the force-force autocorrelation for a strongly anharmonic oscillator demonstrates its accuracy, and calculation of the velocity autocorrelation function (and thus the diffusion coefficient) of liquid neon demonstrates its applicability.

Full Parallel Implementation of an All-Electron Four-Component Dirac-Kohn-Sham Program.

PubMed

Rampino, Sergio; Belpassi, Leonardo; Tarantelli, Francesco; Storchi, Loriano

2014-09-09

A full distributed-memory implementation of the Dirac-Kohn-Sham (DKS) module of the program BERTHA (Belpassi et al., Phys. Chem. Chem. Phys. 2011, 13, 12368-12394) is presented, where the self-consistent field (SCF) procedure is replicated on all the parallel processes, each process working on subsets of the global matrices. The key feature of the implementation is an efficient procedure for switching between two matrix distribution schemes, one (integral-driven) optimal for the parallel computation of the matrix elements and another (block-cyclic) optimal for the parallel linear algebra operations. This approach, making both CPU-time and memory scalable with the number of processors used, virtually overcomes at once both time and memory barriers associated with DKS calculations. Performance, portability, and numerical stability of the code are illustrated on the basis of test calculations on three gold clusters of increasing size, an organometallic compound, and a perovskite model. The calculations are performed on a Beowulf and a BlueGene/Q system.

Quantum Monte Carlo calculations of NiO

NASA Astrophysics Data System (ADS)

Maezono, Ryo; Towler, Mike D.; Needs, Richard. J.

2008-03-01

We describe variational and diffusion quantum Monte Carlo (VMC and DMC) calculations [1] of NiO using a 1024-electron simulation cell. We have used a smooth, norm-conserving, Dirac-Fock pseudopotential [2] in our work. Our trial wave functions were of Slater-Jastrow form, containing orbitals generated in Gaussian-basis UHF periodic calculations. Jastrow factor is optimized using variance minimization with optimized cutoff lengths using the same scheme as our previous work. [4] We apply the lattice regulated scheme [5] to evaluate non-local pseudopotentials in DMC and find the scheme improves the smoothness of the energy-volume curve. [1] CASINO ver.2.1 User Manual, University of Cambridge (2007). [2] J.R. Trail et.al., J. Chem. Phys. 122, 014112 (2005). [3] CRYSTAL98 User's Manual, University of Torino (1998). [4] Ryo Maezono et.al., Phys. Rev. Lett., 98, 025701 (2007). [5] Michele Casula, Phys. Rev. B 74, 161102R (2006).

On the use temperature parameterized rate coefficients in the estimation of non-equilibrium reaction rates

NASA Astrophysics Data System (ADS)

Shizgal, Bernie D.; Chikhaoui, Aziz

2006-06-01

The present paper considers a detailed analysis of the nonequilibrium effects for a model reactive system with the Chapman-Eskog (CE) solution of the Boltzmann equation as well as an explicit time dependent solution. The elastic cross sections employed are a hard sphere cross section and the Maxwell molecule cross section. Reactive cross sections which model reactions with and without activation energy are used. A detailed comparison is carried out with these solutions of the Boltzmann equation and the approximation introduced by Cukrowski and coworkers [J. Chem. Phys. 97 (1992) 9086; Chem. Phys. 89 (1992) 159; Physica A 188 (1992) 344; Chem. Phys. Lett. A 297 (1998) 402; Physica A 275 (2000) 134; Chem. Phys. Lett. 341 (2001) 585; Acta Phys. Polonica B 334 (2003) 3607.] based on the temperature of the reactive particles. We show that the Cukrowski approximation has limited applicability for the large class of reactive systems studied in this paper. The explicit time dependent solutions of the Boltzmann equation demonstrate that the CE approach is valid only for very slow reactions for which the corrections to the equilibrium rate coefficient are very small.

"CHEM"opera for Chemistry Education

ERIC Educational Resources Information Center

Chung, Yong Hee

2013-01-01

"CHEM"opera is an opera blended with demonstrations of chemical reactions. It has been produced and performed twice by chemistry undergraduate students at Hallym University in South Korea. It aims to demonstrate interesting chemical reactions to chemistry students, children and the public and to facilitate their understanding of the role…

Development of the EarthChem Geochronology and Thermochronology database: Collaboration of the EarthChem and EARTHTIME efforts

NASA Astrophysics Data System (ADS)

Walker, J. D.; Ash, J. M.; Bowring, J.; Bowring, S. A.; Deino, A. L.; Kislitsyn, R.; Koppers, A. A.

2009-12-01

One of the most onerous tasks in rigorous development of data reporting and databases for geochronological and thermochronological studies is to fully capture all of the metadata needed to completely document both the analytical work as well as the interpretation effort. This information is available in the data reduction programs used by researchers, but has proven difficult to harvest into either publications or databases. For this reason, the EarthChem and EARTHTIME efforts are collaborating to foster the next generation of data management and discovery for age information by integrating data reporting with data reduction. EarthChem is a community-driven effort to facilitate the discovery, access, and preservation of geochemical data of all types and to support research and enable new and better science. EARTHTIME is also a community-initiated project whose aim is to foster the next generation of high-precision geochronology and thermochoronology. In addition, collaboration with the CRONUS effort for cosmogenic radionuclides is in progress. EarthChem workers have met with groups working on the Ar-Ar, U-Pb, and (U-Th)/He systems to establish data reporting requirements as well as XML schemas to be used for transferring data from reduction programs to database. At present, we have prototype systems working for the U-Pb_Redux, ArArCalc, MassSpec, and Helios programs. In each program, the user can select to upload data and metadata to the GEOCHRON system hosted at EarthChem. There are two additional requirements for upload. The first is having a unique identifier (IGSN) obtained either manually or via web services contained within the reduction program from the SESAR system. The second is that the user selects whether the sample is to be available for discovery (public) or remain hidden (private). Search for data at the GEOCHRON portal can be done using age, method, mineral, or location parameters. Data can be downloaded in the full XML format for ingestion back

Spectral Dissimilarities Between AZULENE(C10H_8) and NAPHTHALENE(C10H_8)

NASA Astrophysics Data System (ADS)

Baba, Masaaki

2010-06-01

Polycyclic aromatic hydrocarbons (PAHs) are of great interest in the molecular structure and excited-state dynamics, and there have been extensive spectroscopic and theoretical studies. Azulene and naphthalene are bicyclic aromatic hydrocarbons composed of odd- and even-membered rings, respectively. First, they were discriminated by a theory of mutual polarizability. Naphthalene is an alternant hydrocarbon, but azulene is not. In contrast, spectral resemblances were found by John Platt et al., and were explained by their simple model of molecular orbital. However, the absorption and emission feature of the S_1 and S_2 states is completely different each other. We have investigated each rotational and vibrational structures, and radiative and nonradiative processes by means of high-resolution spectroscopy and ab initio calculation. The equilibrium structures in the S_0, S_1, and S_2 states are similar. This small structural change upon electronic excitation is common to PAH molecules composed of six-membered rings. The fluorescence quantum yield is high because radiationless transitions such as intersystem crossing (ISC) to the triplet state and internal conversion (IC) to the S_0 state are very slow in the S_1 state. In contrast, the S_1 state of azulene is nonfluorescent and the S_1 ← S_0 excitation energy is abnormally small. We consider that the potential energy curve of a b_2 vibration is shallower in the S_1 state, and therefore the vibronic coupling with the S_0 state is strong to enhance the IC process remarkably. This situation is, of course, due to its peculiar characteristics of odd-membered rings and molecular symmetry, which are completely different from the naphthalene molecule. C. A. Coulson and H. C. Longuet-Higgins, Proc. Roy. Soc. A, 191, 39 (1947) D. E. Mann, J. R. Platt, and H. B. Klevens, J. Chem. Phys., 17, 481 (1949) Y. Semba, M. Baba, et al., J. Chem. Phys., 131, 024303 (2009) K. Yoshida, M. Baba, et al., J. Chem. Phys., 130, 194304 (2009)

Characterization of Acremonium and Isaria ice nuclei

NASA Astrophysics Data System (ADS)

Pummer, Bernhard G.; Pöschl, Ulrich; Fröhlich-Nowoisky, Janine

2014-05-01

.J. et al. (2013) Atmos. Chem. Phys. 13, 6151-6164 Iannone R. et al. (2011) Atmos. Chem. Phys. 11, 1191-1201 Jayaweera K. and Flanagan P. (1982) Geophys. Res. Lett. 9, 94-97 Kieft T.L. and Ruscetti T. (1990) J. Bacteriol. 172, 3519-3523 Morris C.E. et al. (2013) Atmos. Chem. Phys. 13, 4223-4233 Pouleur S. et al. (1992) Appl. Environ. Microbiol. 58, 2960-2964 Pummer B. et al. (2013) Biogeosci. 10, 8083-8091 Tsumuki H. et al. (1995) Ann. Phytopathol. Soc. Jpn. 61, 334-339

Microphysical Properties of Single Secondary Organic Aerosol (SOA) Particles

NASA Astrophysics Data System (ADS)

Rovelli, Grazia; Song, Young-Chul; Pereira, Kelly; Hamilton, Jacqueline; Topping, David; Reid, Jonathan

2017-04-01

water or SVOCs evaporative loss was measured as a function of water activity by fitting the collected light scattering patterns with a generated Mie-Theory library of phase functions.[3] Long trapping experiments (up to >20000 s) allow the observation of slow SVOCs evaporation kinetics at different T and RH conditions. Water condensation/evaporation kinetics experiments onto/from trapped SOA droplets following fast RH step changes (<0.5 s) were also performed in order to evaluate possible kinetics limitations to water diffusion in the condensed phase resulting from the formation of a viscous matrix. [1] Fuzzi et al., Atmos. Chem. Phys. 15, 8217-8299 (2015). [2] Rovelli et al., J. Phys. Chem. A 120, 4376-4388 (2016). [3] Cotterell et al., Phys. Chem. Chem. Phys. 17, 15843-15856 (2015).

The Cl + O3 reaction: a detailed QCT simulation of molecular beam experiments.

PubMed

Menéndez, M; Castillo, J F; Martínez-Haya, B; Aoiz, F J

2015-10-14

We have studied in detail the dynamics of the Cl + O3 reaction in the 1-56 kcal mol(-1) collision energy range using quasi-classical trajectory (QCT) calculations on a recent potential energy surface (PES) [J. F. Castillo et al., Phys. Chem. Chem. Phys., 2011, 13, 8537]. The main goal of this work has been to assess the accuracy of the PES and the reliability of the QCT method by comparison with the existing crossed molecular beam results [J. Zhang and Y. T. Lee J. Phys. Chem. A, 1997, 101, 6485]. For this purpose, we have developed a methodology that allows us to determine the experimental observables in crossed molecular beam experiments (integral and differential cross sections, recoil velocity distributions, scattering angle-recoil velocity polar maps, etc.) as continuous functions of the collision energy. Using these distributions, raw experimental data in the laboratory frame (angular distributions and time-of-flight spectra) have been simulated from first principles with the sole information on the instrumental parameters and taking into account the energy spread. A general good agreement with the experimental data has been found, thereby demonstrating the adequacy of the QCT method and the quality of the PES to describe the dynamics of this reaction at the level of resolution of the existing crossed beam experiments. Some features which are apparent in the differential cross sections have also been analysed in terms of the dynamics of the reaction and its evolution with the collision energy.

Robust SERS Enhancement Factor Statistics Using Rotational Correlation Spectroscopy

DTIC Science & Technology

2012-05-02

Polymer coatings quench the reaction , preventing further aggregation when a Raman active molecule is added. (B) The bulk Raman spectrum of MBA in...Schrof, W. J. Phys. Chem. A 2001, 105, 3673. (12) Jiang, J.; Bosnick, K.; Maillard , M.; Brus, L. J. Phys. Chem. B 2003, 107, 9964. (13) Talley, C. E

Revisiting Deng et al.'s Multiparty Quantum Secret Sharing Protocol

NASA Astrophysics Data System (ADS)

Hwang, Tzonelih; Hwang, Cheng-Chieh; Yang, Chun-Wei; Li, Chuan-Ming

2011-09-01

The multiparty quantum secret sharing protocol [Deng et al. in Chin. Phys. Lett. 23: 1084-1087, 2006] is revisited in this study. It is found that the performance of Deng et al.'s protocol can be much improved by using the techniques of block-transmission and decoy single photons. As a result, the qubit efficiency is improved 2.4 times and only one classical communication, a public discussion, and two quantum communications between each agent and the secret holder are needed rather than n classical communications, n public discussions, and 3n/2 quantum communications required in the original scheme.

Electron-impact excitation of Rydberg and valence electronic states of nitric oxide: II. Integral cross sections

NASA Astrophysics Data System (ADS)

Brunger, M. J.; Campbell, L.; Cartwright, D. C.; Middleton, A. G.; Mojarrabi, B.; Teubner, P. J. O.

2000-02-01

Integral cross sections (ICSs) for the excitation of 18 excited electronic states, and four composite excited electronic states, in nitric oxide (NO) have been determined for incident electron energies of 15, 20, 30, 40 and 50 eV. These ICSs were derived by extrapolating the respective measured differential cross sections (M J Brunger et al 2000 J. Phys. B: At. Mol. Opt. Phys. 33 783) to 0° and 180° and by performing the appropriate integration. Comparison of the present ICSs with the results of those determined in earlier optical emission measurements, and from theoretical calculations is made. At each incident energy considered, the current ICSs are also summed along with the corresponding elastic and rovibrational excitation ICSs from B Mojarrabi et al (1995 J. Phys. B: At. Mol. Opt. Phys. 28 487) and the ionization cross sections from Rapp and Englander-Golden (1965 J. Chem. Phys. 43 1464), to derive an estimate of the grand total cross sections (GTSs) for e- + NO scattering. The GTSs derived in this manner are compared with the results from independent linear transmission experiments and are found to be entirely consistent with them. The present excited electronic state ICS, and those for elastic and rovibrational excitation from Mojarrabi et al , appear to represent the first set of self-consistent cross sections for electron impact scattering from NO.

Statistical mechanical theory for steady state systems. VI. Variational principles

NASA Astrophysics Data System (ADS)

Attard, Phil

2006-12-01

Several variational principles that have been proposed for nonequilibrium systems are analyzed. These include the principle of minimum rate of entropy production due to Prigogine [Introduction to Thermodynamics of Irreversible Processes (Interscience, New York, 1967)], the principle of maximum rate of entropy production, which is common on the internet and in the natural sciences, two principles of minimum dissipation due to Onsager [Phys. Rev. 37, 405 (1931)] and to Onsager and Machlup [Phys. Rev. 91, 1505 (1953)], and the principle of maximum second entropy due to Attard [J. Chem.. Phys. 122, 154101 (2005); Phys. Chem. Chem. Phys. 8, 3585 (2006)]. The approaches of Onsager and Attard are argued to be the only viable theories. These two are related, although their physical interpretation and mathematical approximations differ. A numerical comparison with computer simulation results indicates that Attard's expression is the only accurate theory. The implications for the Langevin and other stochastic differential equations are discussed.

Evaluation of Chem-Crete : final report.

DOT National Transportation Integrated Search

1982-01-01

Two test sections, one on new construction and the other on a maintenance resurfacing project, were installed in the fall of 1980 to evaluate the proprietary product Chem-Crete. Laboratory tests and dynaflect and density measurements were performed o...

Recalculation of the infrared continuum spectrum of the lowest energy triplet transitions in K2

NASA Astrophysics Data System (ADS)

Ligare, Martin; Edmonds, J. Brent

1991-09-01

The observation and identification of the spectra arising from transitions between the lowest energy triplet electronic states of diatomic potassium molecules were made by Huennekens et al. [J. Chem. Phys. 80, 4794 (1984)]. In this letter we recalculate theoretical spectra for these transitions using quasistatic line broadening theory and the recently published ab initio potential energy curves of Jeung and Ross [J. Phys. B 21, 1473 (1988)]. The calculated satellite of the 3Σ+g-3Σ+u transition occurs at 1.105 μm while the satellite is experimentally observed at 1.096 μm. This improved agreement both solidifies the original identification of Huennekens et al. and indicates the accuracy of the recent potential energy curves of Jeung and Ross for the low energy triplet states.

Sources of Water-soluble Organic Aerosol in the Southeastern United States - Evidence of SOA Formed Through Heterogeneous Reactions

NASA Astrophysics Data System (ADS)

Zhang, X.; Weber, R. J.

2010-12-01

. Weber (2010), Water-soluble organic aerosol material and the light-absorption characteristics of aqueous extracts measured over the southeastern United States, Atm. Chem. Phys., 10, 5965-5977. Hennigan, C. J., M. H. Bergin, J. E. Dibb, and R. J. Weber (2008a), Enhanced secondary organic aerosol formation due to water uptake by fine particles, Geophys. Res. Lett., 35, L18801, 18810.11029/12008GL035046. Hennigan, C. J., M. H. Bergin, and R. J. Weber (2008b), Correlations between water-soluble organic aerosol and water vapor: A synergistic effect from biogenic emissions?, Environ. Sci. Tech., 42(24), 9079-9085. Hennigan, C. J., et al. (2008c), On the volatility and production mechanisms of newly formed nitrate and water soluble organic aerosol in Mexico City, Atm. Chem. Phys., 8, 3761-3768. Hennigan, C. J., M. H. Bergin, A. G. Russell, A. Nenes, and R. J. Weber (2009), Gas/particle partitioning of water-soluble organic aerosol in Atlanta, Atm. Chem. Phys., 9, 3613-3628. Zhang, X., A. Hecobian, M. Zheng, N. Frank, and R. J. Weber (2010), Biomass buring impact on PM2.5 over the southeastern U.S.: Intgrating chemically speciated FRM filter measurements, MODIS fire counts and PMF analysis, Atm. Chem. Phys., 10, 6839-6853.

Infrared Spectroscopy of the H2/HD/D2-O2 Van Der Waals Complexes

NASA Astrophysics Data System (ADS)

Raston, Paul; Bunn, Hayley

2016-06-01

Hydrogen is the most abundant element in the universe and oxygen is the third, so understanding the interaction between the two in their different forms is important to understanding astrochemical processes. The interaction between H2 and O2 has been explored in low energy scattering experiments and by far infrared synchrotron spectroscopy of the van der Waals complex. The far infrared spectra suggest a parallel stacked average structure with seven bound rotationally excited states. Here, we present the far infrared spectrum of HD/D2-O2 and the mid infrared spectrum of H2-O2 at 80 K, recorded at the infrared beamline facility of the Australian Synchrotron. We observed 'sharp' peaks in the mid infrared region, corresponding to the end over end rotation of H2-O2, that are comparatively noisier than analogous peaks in the far infrared where the synchrotron light is brightest. The larger reduced mass of HD and D2 compared to H2 is expected to result in more rotational bound states and narrower bands. The latest results in our ongoing efforts to explore this system will be presented. Y. Kalugina, et al., Phys. Chem. Chem. Phys. 14, 16458 (2012) S. Chefdeville et al. Science 341, 1094 (2013) H. Bunn et al. ApJ 799, 65 (2015)

Modeling collective behavior of molecules in nanoscale direct deposition processes

NASA Astrophysics Data System (ADS)

Lee, Nam-Kyung; Hong, Seunghun

2006-03-01

We present a theoretical model describing the collective behavior of molecules in nanoscale direct deposition processes such as dip-pen nanolithography. We show that strong intermolecular interactions combined with nonuniform substrate-molecule interactions can produce various shapes of molecular patterns including fractal-like structures. Computer simulations reveal circular and starlike patterns at low and intermediate densities of preferentially attractive surface sites, respectively. At large density of such surface sites, the molecules form a two-dimensional invasion percolation cluster. Previous experimental results showing anisotropic patterns of various chemical and biological molecules correspond to the starlike regime [P. Manandhar et al., Phys. Rev. Lett. 90, 115505 (2003); J.-H. Lim and C. A. Mirkin, Adv. Mater. (Weinheim, Ger.) 14, 1474 (2002); D. L. Wilson et al., Proc. Natl. Acad. Sci. U.S.A. 98, 13660 (2001); M. Su et al., Appl. Phys. Lett. 84, 4200 (2004); R. McKendry et al., Nano Lett. 2, 713 (2002); H. Zhou et al., Appl. Surf. Sci. 236, 18 (2004); G. Agarwal et al., J. Am. Chem. Soc. 125, 580 (2003)].

Modelling Contribution of Biogenic VOCs to New Particle Formation in the Jülich Plant Atmosphere Chamber

NASA Astrophysics Data System (ADS)

Liao, L.; Boy, M.; Mogensen, D.; Mentel, T. F.; Kleist, E.; Kiendler-Scharr, A.; Tillman, R.; Kulmala, M. T.; Dal Maso, M.

2012-12-01

new aerosol formation in the lower troposphere, developed by Boy, et al. (2006). We first evaluate the modelled results with measurements, and further we investigate the influence of different order of magnitude of terpene mixing ratios, especially isoprene and monoterpenes to the most important parameter of new particles formation, i.e. the formation rate (J1). Also, the influence of varying organic source rates on the sulphuric acid concentration available for particle formation is discussed. M. Boy et al., (2006). Atmos. Chem. Phys., 6, 4499-4517. M. Kulmala et al., (2004). Atmos. Chem. Phys., 4, 557-562. P. Tunved et al., (2006). Science, 14, 261-263. Th. F. Mentel et al., (2009). Atmos. Chem. Phys., 9, 4387-4406.

Ozone Enhancement in the Lower Troposphere over East Asia Observed by OMI: Evidence of Transboundary Pollution Transport from China to Korea and Japan

NASA Astrophysics Data System (ADS)

Hayashida, S.; Ono, A.; Liu, X.; Yang, K.; Kanaya, Y.; Chance, K.

2014-12-01

Liu et al. (2010) developed an algorithm to retrieve ozone profiles from the ground to ~60 km from OMI ultraviolet radiances using the optimal estimation technique (Rogers, 2000). This algorithm is for derivation of an ozone profile divided into 24 layers, with three layers in the troposphere (0-3km, 3-6km, 6-9km). In this study, we report results for the analysis of lower tropospheric ozone over CEC using the OMI ozone profiles mentioned above. First, we show good correlation of OMI-derived ozone with aircraft measurements and ozonesonde measurements. Second, we show significant enhancement of ozone derived from OMI over CEC. To interpret this remarkable enhancement of ozone, we show correlation of ozone with carbon monoxide (CO) and hotspot numbers suggesting the effects of crop burning on ozone enhancement. Third, we also show complementary data obtained in the field campaign at Mt. Tai in 2005 and 2006 (Kayana et al., 2013) to demonstrate ozone enhancement in June every year and show the relationship with residue burning in fields over Shandong and Hebei Provinces. Finally, we show important evidence of transboundary pollution transport from China to Korea and Japan.References:Kanaya, Y., et al. (2013), Atmos. Chem. Phys., 13(16), 8265-8283.Liu, X., et al. (2010), Atmos. Chem. Phys., 10(5), 2521-2537.Rodgers, C. D. (2000), Inverse methods for atmospheric sounding: Theory and practice, World Scientific Publishing, Singapore.

The Ammonia Dimer Revisited

NASA Astrophysics Data System (ADS)

Dawes, Richard; Van Der Avoird, Ad

2012-06-01

The conclusion from microwave spectra by Nelson, Fraser, and Klemperer that the ammonia dimer has a nearly cyclic structure led to much debate about the issue of whether (NH_3)_2 is hydrogen bonded. This structure was surprising because most {ab initio} calculations led to a classical, nearly linear, hydrogen-bonded structure. An obvious explanation of the discrepancy between the outcome of these calculations and the microwave data which led Nelson {et al.} to their ``surprising structure'' might be the effect of vibrational averaging: the electronic structure calculations focus on finding the minimum of the intermolecular potential, the experiment gives a vibrationally averaged structure. Isotope substitution studies seemed to indicate, however, that the complex is nearly rigid. Additional data became available from high-resolution molecular beam far-infrared spectroscopy in the Saykally group. These spectra, displaying large tunneling splittings, indicate that the complex is very floppy. The seemingly contradictory experimental data were explained when it became possible to calculate the vibration-rotation-tunneling (VRT) states of the complex on a six-dimensional intermolecular potential surface. The potential used was a simple model potential, with parameters fitted to the far-infrared data. Now, for the first time, a six-dimensional potential was computed by high level {ab initio} methods and this potential will be used in calculations of the VRT states of (NH_3)_2 and (ND_3)_2. So, we will finally be able to answer the question whether the conclusions from the model calculations are indeed a valid explanation of the experimental data. D. Nelson, G. T. Fraser, and W. Klemperer J. Chem. Phys. 83 6201 (1985) J. G. Loeser, C. A. Schmuttenmaer, R. C. Cohen, M. J. Elrod, D. W. Steyert, R. J. Saykally, R. E. Bumgarner, and G. A. Blake J. Chem. Phys. 97 4727 (1992) E. H. T. Olthof, A. van der Avoird, and P. E. S. Wormer J. Chem. Phys. 101 8430 (1994) E. H. T. Olthof

DPubChem: a web tool for QSAR modeling and high-throughput virtual screening.

PubMed

Soufan, Othman; Ba-Alawi, Wail; Magana-Mora, Arturo; Essack, Magbubah; Bajic, Vladimir B

2018-06-14

High-throughput screening (HTS) performs the experimental testing of a large number of chemical compounds aiming to identify those active in the considered assay. Alternatively, faster and cheaper methods of large-scale virtual screening are performed computationally through quantitative structure-activity relationship (QSAR) models. However, the vast amount of available HTS heterogeneous data and the imbalanced ratio of active to inactive compounds in an assay make this a challenging problem. Although different QSAR models have been proposed, they have certain limitations, e.g., high false positive rates, complicated user interface, and limited utilization options. Therefore, we developed DPubChem, a novel web tool for deriving QSAR models that implement the state-of-the-art machine-learning techniques to enhance the precision of the models and enable efficient analyses of experiments from PubChem BioAssay database. DPubChem also has a simple interface that provides various options to users. DPubChem predicted active compounds for 300 datasets with an average geometric mean and F 1 score of 76.68% and 76.53%, respectively. Furthermore, DPubChem builds interaction networks that highlight novel predicted links between chemical compounds and biological assays. Using such a network, DPubChem successfully suggested a novel drug for the Niemann-Pick type C disease. DPubChem is freely available at www.cbrc.kaust.edu.sa/dpubchem .

Dust Detection by Curiosity ChemCam

NASA Image and Video Library

2013-04-08

The ChemCam instrument on NASA Curiosity Mars rover fired its laser 50 times at its onboard graphite target showing spectral measurements from the first shot, which hit dust on the target, compared to spectral measurements of from the 50th shot.

Unimolecular Reactions of Nitrites and Nitrates.

DTIC Science & Technology

1983-04-01

02 and in the presence of excess NO. A ’similar conclusion was drawn by Kabasakalian and Townley [69) from Iphotolysis of octyl nitrite. McMillan [70...Pimentel, J. Chem. Phys., 29, 883 (1958). 68. P.L. Hanst and J.G. Calvert, 3. Phys. Chem., 63, 2071 (1959). 69. P. Kabasakalian and E.R. Townley , J. Am

Lithium Borides - High Energy Materials

DTIC Science & Technology

2000-02-28

1993. 99, 7983. (32) Pulay P.; Hamilton. T. P. J. Chem. Phys. 1988, 88. 4926 . (33) Frisch. M. J.: Trucks. G. W.; Schlegel. H. B.: Gill, P. M. W...25] P.V. Sudhakar, K. Lammertsma, J. Chem. Phys. 99 (1993) 7929. [26] M.J. van der Woerd, K. Lammertsma, B.J. Duke, H.F. Schaefer , III, J

Quantum Criticality and Superconductivity in β-YbAlB4

NASA Astrophysics Data System (ADS)

Nakatsuji, Satoru

2009-03-01

Heavy fermion systems have provided a number of prototypical compounds to study unconventional superconductivity and non-Fermi-liquid (NFL) states. A long standing issue in the research of heavy fermion superconductivity in 4f intermetallics is the dramatically different behavior between the electron like Ce (4f^1) and hole like Yb (4f^13) compounds. While superconductivity has been found in a number of Ce based heavy fermion compounds, no superconductivity has been reported for the corresponding Yb systems. In this talk, I present our recent finding of the superconductivity in the new heavy fermion system β-YbAlB4 [1-3]. The superconducting transition temperature is 80 mK, and above it, the system exhibits pronounced NFL behavior in the transport and thermodynamic properties [2,3]. Furthermore, the magnetic field dependence of the NFL behavior indicates that the system is a rare example of a pure metal that displays quantum criticality at ambient pressure and under zero magnetic field. Using our latest results, we discuss the detailed properties of superconductivity and quantum criticality. This is the work performed in collaboration with K. Kuga, Y. Matsumoto, T. Tomita, Y. Machida, T. Tayama, T. Sakakibara, Y. Karaki, H. Ishimoto, S. Yonezawa, Y. Maeno, E. Pearson, G. G. Lonzarich, L.Balicas, H. Lee, and Z. Fisk. [4pt] [1] Robin T. Macaluso, Satoru Nakatsuji, Kentaro Kuga, Evan Lyle Thomas, Yo Machida, Yoshiteru Maeno, Zachary Fisk, and Julia Y. Chan, Chem. Mater. 19 1918 (2007). [0pt] [2] S. Nakatsuji, K.Kuga, Y. Machida, T. Tayama, T. Sakakibara, Y. Karaki, H. Ishimoto, S. Yonezawa, Y. Maeno, E. Pearson, G. G. Lonzarich, L.Balicas, H. Lee, and Z. Fisk, Nature Phys 4, 603-607 (2008). [0pt] [3] K. Kuga, Y. Karaki, Y. Matsumoto, Y. Machida, and S. Nakatsuji, Phys. Rev. Lett. 101, 137004 (2008).

Epitaxially Grown Colloidal Crystals of Silica Microspheres on Patterned Substrate of Triangular Arrays

DTIC Science & Technology

2008-07-16

min after addition of binary mixture. Other images are taken (d) after supernatant removal, (e) after ammonia exposure, ( f ) after air-drying and dye...12] J.P. Hoogenboom , D. Derks, P. Vergeer, A. van Blaaderen, J. Chem. Phys. 117 (2002) 11320. [13] A. van Blaaderen, R. Ruel, P. Wiltzius, Nature...Axe, Y. Fujii, Phys. Rev. Lett. 62 (1989) 1524. [19] F . El Azhar, M. Baus, J.P. Ryekaert, E.J. Meijer, J. Chem. Phys. 112 (2000) 5121. [20] M.S

Exploring Physics with Computer Animation and PhysGL

NASA Astrophysics Data System (ADS)

Bensky, T. J.

2016-10-01

This book shows how the web-based PhysGL programming environment (http://physgl.org) can be used to teach and learn elementary mechanics (physics) using simple coding exercises. The book's theme is that the lessons encountered in such a course can be used to generate physics-based animations, providing students with compelling and self-made visuals to aid their learning. Topics presented are parallel to those found in a traditional physics text, making for straightforward integration into a typical lecture-based physics course. Users will appreciate the ease at which compelling OpenGL-based graphics and animations can be produced using PhysGL, as well as its clean, simple language constructs. The author argues that coding should be a standard part of lower-division STEM courses, and provides many anecdotal experiences and observations, that include observed benefits of the coding work.

Chem/bio sensing with non-classical light and integrated photonics.

PubMed

Haas, J; Schwartz, M; Rengstl, U; Jetter, M; Michler, P; Mizaikoff, B

2018-01-29

Modern quantum technology currently experiences extensive advances in applicability in communications, cryptography, computing, metrology and lithography. Harnessing this technology platform for chem/bio sensing scenarios is an appealing opportunity enabling ultra-sensitive detection schemes. This is further facilliated by the progress in fabrication, miniaturization and integration of visible and infrared quantum photonics. Especially, the combination of efficient single-photon sources together with waveguiding/sensing structures, serving as active optical transducer, as well as advanced detector materials is promising integrated quantum photonic chem/bio sensors. Besides the intrinsic molecular selectivity and non-destructive character of visible and infrared light based sensing schemes, chem/bio sensors taking advantage of non-classical light sources promise sensitivities beyond the standard quantum limit. In the present review, recent achievements towards on-chip chem/bio quantum photonic sensing platforms based on N00N states are discussed along with appropriate recognition chemistries, facilitating the detection of relevant (bio)analytes at ultra-trace concentration levels. After evaluating recent developments in this field, a perspective for a potentially promising sensor testbed is discussed for reaching integrated quantum sensing with two fiber-coupled GaAs chips together with semiconductor quantum dots serving as single-photon sources.

A Statistical Physics Analysis of Rock and Concrete Damage Response

DTIC Science & Technology

1991-05-30

condensation after passing through a jet (Levinger et a 1988, Rayane et a 1989) or from an impacted solid by sputtering (Weiland et al 1989). The distribution of...1/3 = 8.5 a2/3 = 15 (figure 13). Fits of similar goodness were achieved to other data obtained by the above authors for Arm and by Rayane et al (1989...Holcman 1 1987 Int. J. Eng. Sc. 25 473 Rayane D, Melinon P, Cabaud B, Hoareau A, Tribollet B and Broyer M 1989 J. Chem. Phys. 90 3295 Rice 11975

Distributed chemical computing using ChemStar: an open source java remote method invocation architecture applied to large scale molecular data from PubChem.

PubMed

Karthikeyan, M; Krishnan, S; Pandey, Anil Kumar; Bender, Andreas; Tropsha, Alexander

2008-04-01

We present the application of a Java remote method invocation (RMI) based open source architecture to distributed chemical computing. This architecture was previously employed for distributed data harvesting of chemical information from the Internet via the Google application programming interface (API; ChemXtreme). Due to its open source character and its flexibility, the underlying server/client framework can be quickly adopted to virtually every computational task that can be parallelized. Here, we present the server/client communication framework as well as an application to distributed computing of chemical properties on a large scale (currently the size of PubChem; about 18 million compounds), using both the Marvin toolkit as well as the open source JOELib package. As an application, for this set of compounds, the agreement of log P and TPSA between the packages was compared. Outliers were found to be mostly non-druglike compounds and differences could usually be explained by differences in the underlying algorithms. ChemStar is the first open source distributed chemical computing environment built on Java RMI, which is also easily adaptable to user demands due to its "plug-in architecture". The complete source codes as well as calculated properties along with links to PubChem resources are available on the Internet via a graphical user interface at http://moltable.ncl.res.in/chemstar/.

Research Investigation Directed Toward Extending the Useful Range of the Electromagnetic Spectrum.

DTIC Science & Technology

1985-12-31

0.33) or a Schwarzschild reflector (N.A. ..- - 1.25, x 36) directly onto the GaAs (100) substrate housed in a stainless steel, 4-window cell. The cell...Department of Energy under contract .. DE-AC-02-78ER04940. (1) G. Karl , P. Kruus and J. Polanyl, J. Chem. Phys. 46,224, (1967). .- (2) G. Karl , P. Kruus, J...Chem. 39, 2244, (1961). (7) G. Karl and J. Polanyl, J. Chem Phys. 38, 271, (1963). (8) H. Okabe, Photochemistrv-of Small Molecules, New York, J

Calculation of Kinetic Data for Processes Leading to UV Signatures

DTIC Science & Technology

1989-03-31

Jv we make use of the numerical algorithm developed by Stodden and Micha 17, extending it to the equations of motion in curvilinear coordinates. To be...in the field of the average potential V(Q). The set of equations (4.13’) have been recently derived by Stodden and Michat 5 in a more tedious.way by...B. Bloom, J. Chem. Phys. 83, 5703 (1985) 5 P. K. Swamninathan, C. D. Stodden , and D. A. Micha, J. Chem. Phys., in press (1989). 6 R. A. Marcus, Chem

Effect of climate change and CO2 inhibition on isoprene emissions in Europe calculated using the ALARO-0 regional climate model

NASA Astrophysics Data System (ADS)

Bauwens, Maite; Müller, Jean-François; Stavrakou, Trisevgeni; De Cruz, Lesley; Van Schaeybroeck, Bert; Termonia, Piet; De Troch, Rozemien; Berckmans, Julie; Hamdi, Rafiq

2017-04-01

11% lower and 26% higher than the present isoprene emissions over Europe. Giot, O. et al.: Validation of the ALARO-0 model within the EURO-CORDEX framework, Geosci. Model Dev. Discuss., 8, 8387-8409, 2015. Guenther, A. et al.: Estimates of global terrestrial isoprene emissions using MEGAN (Model of Emissions of Gases and Aerosols from Nature), Atmos. Chem. Phys., 6, 3181-3210, 2006. Müller, J.-F. et al.: Global isoprene emissions estimated using MEGAN, ECMWF analyses and a detailed canopy environmental model, Atmos. Chem. Phys., 8, 1329-1341, 2008 Stavrakou, T. et al.: Isoprene emissions over Asia 1979-2012 : impact of climate and land use changes, Atmos. Chem. Phys., 14, 4587-4605, 2014.

Structural relaxation of vitreous albite near Tg and implications for transport properties of the supercooled liquid at high pressure

NASA Astrophysics Data System (ADS)

Gaudio, S. J.; Lesher, C. E.

2012-12-01

We estimate the glass transition temperature, Tg, for vitreous/amorphous albite between 0 and 7.7 GPa by tracking the progress of densification following high-temperature annealing experiments with run durations equal to 5τ (when τ=100 s). Tg decreases by 54 K/GPa up to 2.6 GPa, and thereafter shows a weak negative pressure dependence. This behavior mimics the negative pressure dependence of viscosity of albite liquid shown by [1]; however, we do not find a change in the sign of ∂Tg/∂P at least up to 7.7 GPa as reported in some isothermal ∂η/∂P, and ∂DO/∂P data sets. Our high field (21.8 T) 27Al MAS NMR measurements of recovered glasses rapidly quenched from super-Tg conditions possess trace amounts of high coordinated Al at 2.6 GPa and only ˜17% by 5.5 GPa. This suggests that the decrease in Tg (and viscosity at low temperature) results dominantly from topological rearrangement of the supercooled melt structure and not changes to Al or Si coordination number and connectivity of the network. In fact, at Tg from 0 to 8 GPa, the XNBO, or network connectivity, is unchanged [2] and at 7.7 GPa, we find the proportion of high coordinated Al is still ˜35%. Convergence in the timescales of relaxation at Tg(P) and the onset of Na mobility to 6 GPa documented by high-pressure electrical conductivity measurements [3] implies that the fragility of albite melt increases with pressure up to ˜4-5 GPa, without changing the effective polymerization of the melt. In contrast, fragility appears to decrease with pressure in partially depolymerized silicate melts. Such differences in fragility can be used for extrapolation of activation energy based models for viscous flow to high pressure. [1] Kushiro, 1978, EPSL, 41; Brearley et al., 1986, GCA, 50; Brearley and Montana, 1989, GCA, 53; Poe et al., 1997, Science, 276; Suzuki et al., 2002, Phys. Chem. Miner., 29; Funakoshi et al., 2002, J. Phys.: Condens. Matter., 14; Behrens and Schulze, 2003, Am. Min., 88. [2] Lee et

EXAFS and XANES investigation of the ETS-10 microporous titanosilicate.

PubMed

Prestipino, C; Solari, P L; Lamberti, C

2005-07-14

In this work, we report state-of-the-art analysis of both Ti K-edge high-resolution XANES and EXAFS data collected on the ETS-10 molecular sieve at the GILDA BM8 beamline of the ESRF facility. The interatomic distances and the angles obtained in our EXAFS study are in fair agreement with the single-crystal XRD data of Wang and Jacobson (Chem. Commun. 1999, 973) and with the recent ab initio periodic study of Damin et al. (J. Phys. Chem. B 2004, 108, 1328) Differently from previous EXAFS work (J. Phys. Chem. 1996, 100, 449), our study supports a model of ETS-10 where the Ti atoms are bonded with two equivalent axial oxygen atoms. This model is also able to reproduce the edge and the post-edge region of the XANES spectrum. Conversely, the weak but well-defined pre-edge peak at 4971.3 eV can be explained only by assuming that a fraction of Ti atoms are in a local geometry similar to that of the pentacoordinated Ti sites in the ETS-4 structure. These Ti atoms in ETS-10 should be the terminal of the -Ti-O-Ti-O-Ti- chains, of which the actual number is strongly increased by the high crystal defectivity (Ti vacancies).

The Jet-Cooled High-Resolution IR Spectrum of Formic Acid Cyclic Dimer

NASA Astrophysics Data System (ADS)

Goubet, Manuel; Bteich, Sabath; Huet, Therese R.; Pirali, Olivier; Asselin, Pierre; Soulard, Pascale; Jabri, Atef; Roy, P.; Georges, Robert

2017-06-01

As the simplest carboxylic acid, formic acid (FA) is an excellent model molecule to investigate the general properties of carboxylic acids. FA is also an atmospherically and astrophysically relevant molecule. It is well known that its dimeric form is predominant in the gas phase at temperatures below 423 K. The cyclic conformation of the dimer (FACD) is an elementary system to be understood for the concerted hydrogen transfer through equivalent hydrogen bonds, an essential process within biomolecules. The IR range is a crucial spectral region, particularly the far-IR, as it gives a direct access to the intermolecular vibrational modes involved in this process. Moreover, due to its centrosymmetric conformation, the FACD exhibits no pure rotation spectrum and, due to spectral line congestion and Doppler broadening, IR bands cannot be rotationally resolved at room temperature. So far, only parts of the ν_{5}-GS band (C-O stretch) have been observed under jet-cooled conditions using laser techniques. We present here six rotationally resolved IR bands of FACD recorded under jet-cooled conditions using the Jet-AILES apparatus and the QCL spectrometer at MONARIS, including the far-IR ν_{24}-GS band (intermolecular in-plane bending). Splitting due to vibration-rotation-tunneling motions are clearly observed. A full spectral analysis is in progress starting from the GS constants obtained by Goroya et al. and with the support of electronic structure calculations. T. Miyazawa and K. S. Pitzer, J. Am. Chem. Soc. 81, 74, 1959 R. Georges, M. Freytes, D. Hurtmans, I. Kleiner, J. Vander Auwera, M. Herman, Chem. Phys. 305, 187, 2004 M. Ortlieb and M. Havenith, J. Phys. Chem. A 111, 7355, 2007; K. G. Goroya, Y. Zhu, P. Sun and C. Duan, J. Chem. Phys. 140, 164311, 2014 This work is supported by the CaPPA project (Chemical and Physical Properties of the Atmosphere) ANR-11-LABX-0005-01

Heterogeneous Uptake of HO2 Radicals onto Submicron Atmospheric Aerosols

NASA Astrophysics Data System (ADS)

Matthews, P. S.; George, I. J.; Brooks, B.; Whalley, L. K.; Baeza-Romero, M. T.; Heard, D. E.

2012-12-01

dependence was observed. A time dependence has been observed, with higher HO2 uptake coefficients measured at short reaction times with the uptake coefficient decreasing at longer times. A HO2 concentration dependence has also been observed whereby a higher uptake coefficient is measured at lower HO2 concentrations. The time dependence and HO2 concentration dependence may suggest an aerosol saturation mechanism. The HO2 uptake temperature dependence is currently being investigated, as well as uptake on to a wider range of inorganic and organic aerosols. This work was supported by the National Environment Research Council under grant number NE/F020651/1. PSJM is grateful to NERC for a research studentship. References (1) Sommariva, R. et al. Atmos. Chem. Phys.2006, 6, 1135-1153. (2) Whalley, L.K. et al. Atmos. Chem. Phys. 2010, 10, 1555-1576. (3) Mao, J. et al. Atmos. Chem. Phys. 2010, 10, 5823-5838. (4) Jaegle, L. et al. J. Geophys. Atm. 2000, 105, 3877-3892. (5) Taketani, F. et al. J. Phys. Chem. 2008, 112, 2370-2377. (6) Thornton, J. et al. J. Geophys. Atm. 2005, 110, D08309.

Consequences of ChemR23 Heteromerization with the Chemokine Receptors CXCR4 and CCR7

PubMed Central

de Poorter, Cédric; Baertsoen, Kevin; Lannoy, Vincent; Parmentier, Marc; Springael, Jean-Yves

2013-01-01

Recent studies have shown that heteromerization of the chemokine receptors CCR2, CCR5 and CXCR4 is associated to negative binding cooperativity. In the present study, we build on these previous results, and investigate the consequences of chemokine receptor heteromerization with ChemR23, the receptor of chemerin, a leukocyte chemoattractant protein structurally unrelated to chemokines. We show, using BRET and HTRF assays, that ChemR23 forms homomers, and provide data suggesting that ChemR23 also forms heteromers with the chemokine receptors CCR7 and CXCR4. As previously described for other chemokine receptor heteromers, negative binding cooperativity was detected between ChemR23 and chemokine receptors, i.e. the ligands of one receptor competed for the binding of a specific tracer of the other. We also showed, using mouse bone marrow-derived dendritic cells prepared from wild-type and ChemR23 knockout mice, that ChemR23-specific ligands cross-inhibited CXCL12 binding on CXCR4 in a ChemR23-dependent manner, supporting the relevance of the ChemR23/CXCR4 interaction in native leukocytes. Finally, and in contrast to the situation encountered for other previously characterized CXCR4 heteromers, we showed that the CXCR4-specific antagonist AMD3100 did not cross-inhibit chemerin binding in cells co-expressing ChemR23 and CXCR4, demonstrating that cross-regulation by AMD3100 depends on the nature of receptor partners with which CXCR4 is co-expressed. PMID:23469143

Consequences of ChemR23 heteromerization with the chemokine receptors CXCR4 and CCR7.

PubMed

de Poorter, Cédric; Baertsoen, Kevin; Lannoy, Vincent; Parmentier, Marc; Springael, Jean-Yves

2013-01-01

Recent studies have shown that heteromerization of the chemokine receptors CCR2, CCR5 and CXCR4 is associated to negative binding cooperativity. In the present study, we build on these previous results, and investigate the consequences of chemokine receptor heteromerization with ChemR23, the receptor of chemerin, a leukocyte chemoattractant protein structurally unrelated to chemokines. We show, using BRET and HTRF assays, that ChemR23 forms homomers, and provide data suggesting that ChemR23 also forms heteromers with the chemokine receptors CCR7 and CXCR4. As previously described for other chemokine receptor heteromers, negative binding cooperativity was detected between ChemR23 and chemokine receptors, i.e. the ligands of one receptor competed for the binding of a specific tracer of the other. We also showed, using mouse bone marrow-derived dendritic cells prepared from wild-type and ChemR23 knockout mice, that ChemR23-specific ligands cross-inhibited CXCL12 binding on CXCR4 in a ChemR23-dependent manner, supporting the relevance of the ChemR23/CXCR4 interaction in native leukocytes. Finally, and in contrast to the situation encountered for other previously characterized CXCR4 heteromers, we showed that the CXCR4-specific antagonist AMD3100 did not cross-inhibit chemerin binding in cells co-expressing ChemR23 and CXCR4, demonstrating that cross-regulation by AMD3100 depends on the nature of receptor partners with which CXCR4 is co-expressed.

Watching Conformations of Biomolecules: a Microwave Spectroscopy Approach

NASA Astrophysics Data System (ADS)

Lopez, J. C.

2011-06-01

The combination of laser ablation with Fourier transform microwave spectroscopy in supersonic jets (LA-MB-FTMW) has made possible the gas-phase study of solid biomolecules with high melting points. In the experiment, solids are efficiently vaporized by a high-energy laser pulse, supersonically expanded into a evacuated Fabry-Perot cavity and characterised by their rotational spectra. Recent improvements such as the use of picosecond pulse lasers, new ablation nozzles and the extension of the range of the spectrometers to low frequecy have notably increased the sensitivity of our experimental setup. To date different α-, β- and γ-amino acids have been studied using this technique, making possible the characterization of their preferred conformations and gaining insight in the role of intramolecular interactions. Even in conformationally challenging systems the different rotamers of such biomolecules can be identified by rotational spectroscopy as can be illustrated by the assignment of six low-energy conformers in cysteine and aspartic acid, seven in serine and threonine,^a and nine in γ-amino butyric acid (GABA). In all cases the low-energy conformers have been conclusive identified from their experimental rotational and 14N quadrupole coupling constants. The spectra of neurotransmitters and of the nucleic acid bases uracil, thymine, cytosine and guanine have also been studied and their preferred conformers or tautomeric forms determined. The complexes between amino acids and nucleic acid bases with water have also been investigated to obtain information on the possible changes induced in the conformational or tautomeric preferences by the addition of solvent molecules. J. L. Alonso, C. Pérez, M. E. Sanz, J. C. López, S. Blanco, Phys. Chem. Chem. Phys. 11, 617-627 (2009) and references therein M. E. Sanz, J. C. López, J. L. Alonso, Phys. Chem. Chem. Phys., 12, 3573-3578 (2010) S. Blanco, J. C. López, S. Mata and J. L. Alonso, Angew. Chem. Int. Ed. 49, 9187

Bierman {ital et al.}Reply:

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

Bierman, J.D.; Chan, P.; Liang, J.F.

1997-05-01

reply to the Comment by C.H.Dasso et al., Phys. Rev. Lett. 78,XXX(1997). A Reply to the Comment by C.H. Dasso and J. Fern{acute a}ndez-Niello. {copyright} {ital 1997} {ital The American Physical Society}

Accurate thermochemistry and spectroscopy of the oxygen-protonated sulfur dioxide isomers.

PubMed

Puzzarini, Cristina

2011-12-28

Despite the promising relevance of protonated sulfur dioxide in astrophysical and atmospheric fields, its thermochemical and spectroscopic characterization is very limited. High-level quantum-chemical calculations have shown that the most stable isomer is the cis oxygen-protonated sulfur dioxide, HOSO(+), while the trans form is about 2 kcal mol(-1) less stable; even less stable (by about 42 kcal mol(-1)) is the S-protonated isomer [V. Lattanzi et al., J. Chem. Phys., 2010, 133, 194305]. The enthalpy of formation for the cis- and trans-HOSO(+) is presented, based on the well tested HEAT protocol [A. Tajti et al., J. Chem. Phys., 2004, 121, 11599]. Systematically extrapolated ab initio energies, accounting for electron correlation through coupled cluster theory, including up to single, double, triple and quadruple excitations, have been corrected for core-electron correlation, anharmonic zero-point vibrational energy, diagonal Born-Oppenheimer and scalar relativistic effects. As a byproduct, proton affinity of sulfur dioxide and atomization energies have also been obtained at the same levels of theory. Vibrational and rotational spectroscopic properties have been investigated by means of composite schemes that allow us to account for truncation of basis set as well as core correlation. Where available, for both thermochemistry and spectroscopy, very good agreement with experimental data has been observed.

Vibrational spectroscopy via the Caldeira-Leggett model with anharmonic system potentials

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

Gottwald, Fabian; Ivanov, Sergei D., E-mail: sergei.ivanov@uni-rostock.de; Kühn, Oliver

2016-04-28

The Caldeira-Leggett (CL) model, which describes a system bi-linearly coupled to a harmonic bath, has enjoyed popularity in condensed phase spectroscopy owing to its utmost simplicity. However, the applicability of the model to cases with anharmonic system potentials, as it is required for the description of realistic systems in solution, is questionable due to the presence of the invertibility problem [F. Gottwald et al., J. Phys. Chem. Lett. 6, 2722 (2015)] unless the system itself resembles the CL model form. This might well be the case at surfaces or in the solid regime, which we here confirm for a particularmore » example of an iodine molecule in the atomic argon environment under high pressure. For this purpose we extend the recently proposed Fourier method for parameterizing linear generalized Langevin dynamics [F. Gottwald et al., J. Chem. Phys. 142, 244110 (2015)] to the non-linear case based on the CL model and perform an extensive error analysis. In order to judge on the applicability of this model in advance, we give practical empirical criteria and discuss the effect of the potential renormalization term. The obtained results provide evidence that the CL model can be used for describing a potentially broad class of systems.« less

Spectroscopy of the UO+2 cation and the delayed ionization of UO2.

PubMed

Merritt, Jeremy M; Han, Jiande; Heaven, Michael C

2008-02-28

Vibronically resolved spectra for the UO+2 cation have been recorded using the pulsed field ionization zero electron kinetic energy (PFI-ZEKE) technique. For the ground state, long progressions in both the bending and symmetric stretch vibrations were observed. Bend and stretch progressions of the first electronically excited state were also observed, and the origin was found at an energy of 2678 cm(-1) above the ground state zero-point level. This observation is consistent with a recent theoretical prediction [Infante et al., J. Chem. Phys. 127, 124308 (2007)]. The ionization energy for UO2, derived from the PFI-ZEKE spectrum, namely, 6.127(1) eV, is in excellent agreement with the value obtained from an earlier photoionization efficiency measurement. Delayed ionization of UO2 in the gas phase has been reported previously [Han et al., J. Chem. Phys. 120, 5155 (2004)]. Here, we extend the characterization of the delayed ionization process by performing a quantitative study of the ionization rate as a function of the energy above the ionization threshold. The ionization rate was found to be 5 x 10(6) s(-1) at threshold, and increased linearly with increasing energy in the range investigated (0-1200 cm(-1)).

Polyphosphazene Solid Electrolytes.

DTIC Science & Technology

1984-10-01

soL..I’IIN ’ . LAV A - .:.u.s 009 ’-" 4. T .. T. edSutoe .TVCO EO T EI O Polyphosphazene Solid Electrolytes Interim Technical Repor 6. PEAFORMING RG ...Y. T.; Whitmore , D. H. Solid State Ionics 1982, 7, 129. (10) Bauerle, J. E. J. Phys. Chem. Solids 1969, 30, 2657. (11) MacDonald, J. R. J. Chem. Phys

Computer modeling of the optical properties and heating of spherical gold and silica-gold nanoparticles for laser combined imaging and photothermal treatment.

PubMed

Pustovalov, V; Astafyeva, L; Jean, B

2009-06-03

Recently, several groups of investigators (Anderson, Halas, Zharov, El-Sayed and their co-workers (Pitsillides et al 2003 Biophys. J. 84 4023-31, Zharov et al 2003 Appl. Phys. Lett. 83 4897-9, Zharov et al 2004 Proc. SPIE 5319 291-9, Loo et al 2005 Nano Lett. 5 709-11, Gobin et al 2007 Nano Lett. 7 1929-34, Fu et al 2008 Nanotechnology 19 045103, Huang et al 2006 J. Am. Chem. Soc. 128 2115-20, Jain et al 2006 J. Phys. Chem. B 110 7238-48, Jain et al 2007 Nano Today 2 18-29)) demonstrated, through pioneering results, the great potential of laser thermal therapy of cells and tissues conjugated with gold nanoparticles. It was also proposed to use combined diagnostics and therapy on the basis of nanoparticle selection for achievement of efficient contrast for laser imaging applications, as well as for photothermal therapy. However, the current understanding of the relationship between optical properties (absorption, backscattering) of nanoparticles, the efficiency of nanoparticle heating and the possibility to use them for combined imaging and therapy is limited. Here, we report the results of computer modeling of optical absorption and backscattering properties and laser heating of gold and silica-gold spherical nanoparticles for laser combined imaging and photothermal treatment of cells and tissues conjugated with nanoparticles. The efficiencies of nanoparticle heating and backscattering by nanoparticles, depending upon their radii, structure and optical properties of the metal, were investigated. This paper focuses on the analysis and determination of appropriate ranges of nanoparticle sizes for the purposes of laser combined imaging and photothermal treatment. The possibility to use spherical gold and silica-gold nanoparticles in determined ranges of radii for these purposes for laser wavelengths 532 and 800 nm is investigated.

Mechanisms of Laser Induced Reactions in Opaque Heterogeneous Environments

DTIC Science & Technology

1993-11-01

D. Oelkrug, W.P. Hagan, J. Hyslop and F. Wilkinson, Opt. Acta, 1983, 30, 1090. 38. D. Oelkrug, S. Uhl, C.J. Willsher and F. Wilkinson, J. Phys. Chem...Oelkrug D. Hagan W P, Hyslop ]I and Wilkinson F 1983 Opt. Acta 301090 Kessler Rt W and Wilkinson F 1981 J. Chem. Soc.. Fa’aday Trans. 1 77 309 Kossanyi J...under the corrected emission spectrum is a direct evaluation 8 T. Kartens and K. Ki.obs, J. Phys. Chem., 1980 , 84, 1871. of OF. The displacement of the

Compilation of Atomic and Molecular Data Relevant to Gas Lasers. Volume VII.

DTIC Science & Technology

1980-12-01

Schaefer and A. E. Orel, "Potential Energy Curves for Diatomic Zinc and Codmium", J. Chem. Phys. 71, 1122 (1979). 19. M. F. Golde and A. Kuaran...34Chemiluminescence of Argon Bromide. I. The Emission Spectrum of ArBr", J. Chem. Phys. 72, 434 (1980). 20. M. F. Golde and K. Kuaran, "Chemiluminescence of...72, 2469 (1980). (A-4.6 - A-4.17). 3. M. F. Golde and A. Kvaran, "Chemiluminescence of Argon Bromide. I. The Emission Spectrum of Ar Br", J. Chem

ChemTS: an efficient python library for de novo molecular generation.

PubMed

Yang, Xiufeng; Zhang, Jinzhe; Yoshizoe, Kazuki; Terayama, Kei; Tsuda, Koji

2017-01-01

Automatic design of organic materials requires black-box optimization in a vast chemical space. In conventional molecular design algorithms, a molecule is built as a combination of predetermined fragments. Recently, deep neural network models such as variational autoencoders and recurrent neural networks (RNNs) are shown to be effective in de novo design of molecules without any predetermined fragments. This paper presents a novel Python library ChemTS that explores the chemical space by combining Monte Carlo tree search and an RNN. In a benchmarking problem of optimizing the octanol-water partition coefficient and synthesizability, our algorithm showed superior efficiency in finding high-scoring molecules. ChemTS is available at https://github.com/tsudalab/ChemTS.

ChemTS: an efficient python library for de novo molecular generation

PubMed Central

Yang, Xiufeng; Zhang, Jinzhe; Yoshizoe, Kazuki; Terayama, Kei; Tsuda, Koji

2017-01-01

Abstract Automatic design of organic materials requires black-box optimization in a vast chemical space. In conventional molecular design algorithms, a molecule is built as a combination of predetermined fragments. Recently, deep neural network models such as variational autoencoders and recurrent neural networks (RNNs) are shown to be effective in de novo design of molecules without any predetermined fragments. This paper presents a novel Python library ChemTS that explores the chemical space by combining Monte Carlo tree search and an RNN. In a benchmarking problem of optimizing the octanol-water partition coefficient and synthesizability, our algorithm showed superior efficiency in finding high-scoring molecules. ChemTS is available at https://github.com/tsudalab/ChemTS. PMID:29435094

ChemTS: an efficient python library for de novo molecular generation

NASA Astrophysics Data System (ADS)

Yang, Xiufeng; Zhang, Jinzhe; Yoshizoe, Kazuki; Terayama, Kei; Tsuda, Koji

2017-12-01

Automatic design of organic materials requires black-box optimization in a vast chemical space. In conventional molecular design algorithms, a molecule is built as a combination of predetermined fragments. Recently, deep neural network models such as variational autoencoders and recurrent neural networks (RNNs) are shown to be effective in de novo design of molecules without any predetermined fragments. This paper presents a novel Python library ChemTS that explores the chemical space by combining Monte Carlo tree search and an RNN. In a benchmarking problem of optimizing the octanol-water partition coefficient and synthesizability, our algorithm showed superior efficiency in finding high-scoring molecules. ChemTS is available at https://github.com/tsudalab/ChemTS.

Synthetic chemerin-derived peptides suppress inflammation through ChemR23

PubMed Central

Cash, Jenna L.; Hart, Rosie; Russ, Andreas; Dixon, John P.C.; Colledge, William H.; Doran, Joanne; Hendrick, Alan G.; Carlton, Mark B.L.; Greaves, David R.

2008-01-01

Chemerin is a chemotactic protein that binds to the G protein–coupled receptor, ChemR23. We demonstrate that murine chemerin possesses potent antiinflammatory properties that are absolutely dependent on proteolytic processing. A series of peptides was designed, and only those identical to specific C-terminal chemerin sequences exerted antiinflammatory effects at picomolar concentrations in vitro. One of these, chemerin15 (C15; A140-A154), inhibited macrophage (MΦ) activation to a similar extent as proteolyzed chemerin, but exhibited reduced activity as a MΦ chemoattractant. Intraperitoneal administration of C15 (0.32 ng/kg) to mice before zymosan challenge conferred significant protection against zymosan-induced peritonitis, suppressing neutrophil (63%) and monocyte (62%) recruitment with a concomitant reduction in proinflammatory mediator expression. Importantly, C15 was unable to ameliorate zymosan-induced peritonitis in ChemR23−/− mice, demonstrating that C15's antiinflammatory effects are entirely ChemR23 dependent. In addition, administration of neutralizing anti-chemerin antibody before zymosan challenge resulted in a significant exacerbation of peritoneal inflammation (up to 170%), suggesting an important endogenous antiinflammatory role for chemerin-derived species. Collectively, these results show that chemerin-derived peptides may represent a novel therapeutic strategy for the treatment of inflammatory diseases through ChemR23. PMID:18391062

Dirac bubble potential for He-He and inadequacies in the continuum: Comparing an analytic model with elastic collision experiments

NASA Astrophysics Data System (ADS)

Chrysos, Michael

2017-01-01

We focus on the long-pending issue of the inadequacy of the Dirac bubble potential model in the description of He-He interactions in the continuum [L. L. Lohr and S. M. Blinder, Int. J. Quantum Chem. 53, 413 (1995)]. We attribute this failure to the lack of a potential wall to mimic the onset of the repulsive interaction at close range separations. This observation offers the explanation to why this excessively simple model proves incapable of quantitatively reproducing previous experimental findings of glory scattering in He-He, although being notorious for its capability of reproducing several distinctive features of the atomic and isotopic helium dimers and trimers [L. L. Lohr and S. M. Blinder, Int. J. Quantum Chem. 90, 419 (2002)]. Here, we show that an infinitely high, energy-dependent potential wall of properly calculated thickness rc(E) taken as a supplement to the Dirac bubble potential suffices for agreement with variable-energy elastic collision cross section experiments for 4He-4He, 3He-4He, and 3He-3He [R. Feltgen et al., J. Chem. Phys. 76, 2360 (1982)]. In the very low energy regime, consistency is found between the Dirac bubble potential (to which our extended model is shown to reduce) and cold collision experiments [J. C. Mester et al., Phys. Rev. Lett. 71, 1343 (1993)]; this consistency, which in this regime lends credence to the Dirac bubble potential, was never noticed by its authors. The revised model being still analytic is of high didactical value while expected to increase in predictive power relative to other appraisals.

Refinement of pressure calibration for multi-anvil press experiments

NASA Astrophysics Data System (ADS)

Ono, S.

2016-12-01

Accurate characterization of the pressure and temperature environment in high-pressure apparatuses is of essential importance when we apply laboratory data to the study of the Earth's interior. Recently, the synchrotron X-ray source can be used for the high-pressure experiments, and the in situ pressure calibration has been a common technique. However, this technique cannot be used in the laboratory-based experiments. Even now, the conventional pressure calibration is of great interest to understand the Earth's interior. Several high-pressure phase transitions used as the pressure calibrants in the laboratory-based multi-anvil experiments have been investigated. Precise determinations of phase boundaries of CaGeO3 [1], Fe2SiO4 [2], SiO2, and Zr [3] were performed by the multi-anvil press or the diamond anvil cell apparatuses combined with the synchrotron X-ray diffraction technique. The transition pressures in CaGeO3 (garnet-perovskite), Fe2SiO4 (alfa-gamma), and SiO2 (coesite-stishovite) were in general agreement with those reported by previous studies. However, significant discrepancies for the slopes, dP/dT, of these transitions between our and previous studies were confirmed. In the case of Zr study [3], our experimental results elucidate the inconsistency in the transition pressure between omega and beta phase in Zr observed in previous studies. [1] Ono et al. (2011) Phys. Chem. Minerals, 38, 735-740.[2] Ono et al. (2013) Phys. Chem. Minerals, 40, 811-816.[3] Ono & Kikegawa (2015) J. Solid State Chem., 225, 110-113.

A History of ChemMatters Magazine

ERIC Educational Resources Information Center

Tinnesand, Michael J.

2007-01-01

ChemMatters, the chemistry magazine published since 1983, has always provided interesting topics for chemistry students. The American Chemical Society publishes the magazine and many well-known authors like Isaac Asimov, Glen Seaborg and Derek Davenport have contributed to the magazine and the magazine has succeeded in its goal of demystifying…

Stripe-teeth metamaterial Al- and Nb-based rectennas (Presentation Recording)

NASA Astrophysics Data System (ADS)

Osgood, Richard M.; Giardini, Stephen A.; Carlson, Joel B.; Joghee, Prabhuram; O'Hayre, Ryan P.; Diest, Kenneth; Rothschild, Mordechai

2015-09-01

Unlike a semiconductor, where the absorption is limited by the band gap, a "microrectenna array" could theoretically very efficiently rectify any desired portion of the infrared frequency spectrum (25 - 400 THz). We investigated vertical metal-insulator-metal (MIM) diodes that rectify vertical high-frequency fields produced by a metamaterial planar stripe-teeth Al or Au array (above the diodes), similar to stripe arrays that have demonstrated near-perfect absorption in the infrared due to critical coupling [1]. Using our design rules that maximize asymmetry (and therefore the component of the electric field pointed into the substrate, analogous to Second Harmonic Generation), we designed, fabricated, and analyzed these metamaterial-based microrectenna arrays. NbOx and Al2O3 were produced by anodization and ALD, respectively. Smaller visible-light Pt-NbOx-Nb rectennas have produced output power when illuminated by visible (514 nm) light [2]. The resonances of these new Au/NbOx/Nb and Al/Al2O3/Al microrectenna arrays, with larger dimensions and more complex nanostructures than in Ref. 1, were characterized by microscopic FTIR microscopy and agreed well with FDTD models, once the experimental refractive index values were entered into the model. Current-voltage measurements were carried out, showed that the Al/Al2O3/Al diodes have very large barrier heights and breakdown voltages, and were compared to our model of the MIM diode. We calculate expected THz-rectification using classical [3] and quantum [4] rectification models, and compare to measurements of direct current output, under infrared illumination. [1] C. Wu, et. al., Phys. Rev. B 84 (2011) 075102. [2] R. M. Osgood III, et. al., Proc. SPIE 8096, 809610 (2011). [3] A. Sanchez, et. al., J. Appl. Phys. 49 (1978) 5270. [4] J. R. Tucker and M. J. Feldman, Rev. of Mod. Phys. 57, (1985)1055.

General, Unified, Multiscale Modeling to Predict the Sensitivity of Energetic Materials

DTIC Science & Technology

2011-10-05

Time dependence of molecular carbon cluster size in solid methane shocked with a piston velocity up =11 km /s. The initial temperature and density were...Galilean in- variant in configuration space, but the kinetic energy of the system depends on the scalar product of the total momentum with U. To... dependent superheating of the x-component shock direction of kinetic energy . This 224513-4 Dawes et al. J. Chem. Phys. 131, 224513 2009 Author

Three dimensional atom-diatom quantum reactive scattering calculations using absorbing potential: speed up of the propagation scheme.

PubMed

Stoecklin, T

2008-09-01

In this paper a new propagation scheme is proposed for atom-diatom reactive calculations using a negative imaginary potential (NIP) within a time independent approach. It is based on the calculation of a rotationally adiabatic basis set, the neglected coupling terms being re-added in the following step of the propagation. The results of this approach, which we call two steps rotationally adiabatic coupled states calculations (2-RACS), are compared to those obtained using the adiabatic DVR method (J. C. Light and Z. Bazic, J. Chem. Phys., 1987, 87, 4008; C. Leforestier, J. Chem. Phys., 1991, 94, 6388), to the NIP coupled states results of the team of Baer (D. M. Charutz, I. Last and M. Baer, J. Chem. Phys., 1997, 106, 7654) and to the exact results obtained by Zhang (J. Z. H. Zhang and W. H. Miller, J. Chem. Phys., 1989, 91, 1528) for the D + H(2) reaction. The example of implementation of our method of computation of the adiabatic basis will be given here in the coupled states approximation, as this method has proved to be very efficient in many cases and is quite fast.

Fragmentation Pathways of Lithiated Hexose Monosaccharides

NASA Astrophysics Data System (ADS)

Abutokaikah, Maha T.; Frye, Joseph W.; Tschampel, John; Rabus, Jordan M.; Bythell, Benjamin J.

2018-05-01

We characterize the primary fragmentation reactions of three isomeric lithiated D-hexose sugars (glucose, galactose, and mannose) utilizing tandem mass spectrometry, regiospecific labeling, and theory. We provide evidence that these three isomers populate similar fragmentation pathways to produce the abundant cross-ring cleavage peaks (0,2A1 and 0,3A1). These pathways are highly consistent with the prior literature (Hofmeister et al. J. Am. Chem. Soc. 113, 5964-5970, 1991, Bythell et al. J. Am. Soc. Mass Spectrom. 28, 688-703, 2017, Rabus et al. Phys. Chem. Chem. Phys. 19, 25643-25652, 2017) and the present labeling data. However, the structure-specific energetics and rate-determining steps of these reactions differ as a function of precursor sugar and anomeric configuration. The lowest energy water loss pathways involve loss of the anomeric oxygen to furnish B1 ions. For glucose and galactose, the lithiated α-anomers generate ketone structures at C2 in a concerted reaction involving a 1,2-migration of the C2-H to the anomeric carbon (C1). In contrast, the β-anomers are predicted to form 1,3-anhydroglucose/galactose B1 ion structures. Initiation of the water loss reactions from each anomeric configuration requires distinct reactive conformers, resulting in different product ion structures. Inversion of the stereochemistry at C2 has marked consequences. Both lithiated mannose forms expel water to form 1,2-anhydromannose B1 ions with the newly formed epoxide group above the ring. Additionally, provided water loss is not instantaneous, the α-anomer can also isomerize to generate a ketone structure at C2 in a concerted reaction involving a 1,2-migration of the C2-H to C1. This product is indistinguishable to that from α-glucose. The energetics and interplay of these pathways are discussed. [Figure not available: see fulltext.

O2(X3 Sigma- sub g) and O2(a1 Delta sub g) Charge Exchange with Simple Ions (Postprint)

DTIC Science & Technology

2014-06-03

5218 (2007). 2A. Midey, I. Dotan, and A. A. Viggiano, J. Phys. Chem. A 112, 3040 (2008). 3A. Midey, I. Dotan, J. V. Seeley , and A. A. Viggiano, Int. J...2003). 9A. J. Midey, A. Viggiano, P. Zhang, S. Irle, and K. Morokuma, J. Phys. Chem. A 110, 3080 (2006). 10P. M. Hierl, I. Dotan, J. V. Seeley , J. M

Cation or Solvent-Induced Supermolecular Phthalocyanine Formation: Crown Ether Substituted Phthalocyanines.

DTIC Science & Technology

1987-06-01

38.) of slightly bluish green powder (Anal, see Table I). tH NMR(CDCl 3 ) 8.02(8H,s), 4.7-3.6(64H,m), - 3.41(2H,s). ZnCRPc was obtained by reaction of...J.P.; Bencosme, S.; Evitt, E., Sessler, J. Chem. Phys. 1984, 86, 161. Mialoco, C.; Giannotti, A., Maillard , P.; Momeuteau, M. Chem. Phys. Lett. 1984

A Converse Approach to NMR Chemical Shifts for Norm-Conserving Pseudopotentials

NASA Astrophysics Data System (ADS)

Lopez, Graham; Ceresoli, Davide; Marzari, Nicola; Thonhauser, Timo

2010-03-01

Building on the recently developed converse approach for the ab-initio calculation of NMR chemical shifts [1], we present a corresponding framework that is suitable in connection with norm-conserving pseudopotentials. Our approach uses the GIPAW transformation [2] to set up a formalism where the derivative of the orbital magnetization [3] is taken with respect to a microscopic, localized magnetic dipole in the presence of pseudopotentials. The advantages of our method are that it is conceptually simple, the need for a linear-response framework is avoided, and it is applicable to large systems. We present results for calculations of several well-studied systems, including the carbon, hydrogen, fluorine, and phosphorus shifts in various molecules and solids. Our results are in very good agreement with both linear-response calculations and experimental results.[4pt] [1] T. Thonhauser et al., J. Chem. Phys. 131, 101101 (2009).[2] C. J. Pickard and F. Mauri, Phys. Rev. B 63, 245101 (2001).[3] T. Thonhauser et al., Phys. Rev. Lett. 95, 137205 (2005).

Communication: An accurate global potential energy surface for the ground electronic state of ozone

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

Dawes, Richard, E-mail: dawesr@mst.edu, E-mail: hguo@unm.edu; Lolur, Phalgun; Li, Anyang

We report a new full-dimensional and global potential energy surface (PES) for the O + O{sub 2} → O{sub 3} ozone forming reaction based on explicitly correlated multireference configuration interaction (MRCI-F12) data. It extends our previous [R. Dawes, P. Lolur, J. Ma, and H. Guo, J. Chem. Phys. 135, 081102 (2011)] dynamically weighted multistate MRCI calculations of the asymptotic region which showed the widely found submerged reef along the minimum energy path to be the spurious result of an avoided crossing with an excited state. A spin-orbit correction was added and the PES tends asymptotically to the recently developed long-rangemore » electrostatic model of Lepers et al. [J. Chem. Phys. 137, 234305 (2012)]. This PES features: (1) excellent equilibrium structural parameters, (2) good agreement with experimental vibrational levels, (3) accurate dissociation energy, and (4) most-notably, a transition region without a spurious reef. The new PES is expected to allow insight into the still unresolved issues surrounding the kinetics, dynamics, and isotope signature of ozone.« less

Numerical study of the effects of surface topography and chemistry on the wetting transition using the string method.

PubMed

Zhang, Yanan; Ren, Weiqing

2014-12-28

Droplets on a solid surface patterned with microstructures can exhibit the composite Cassie-Baxter (CB) state or the wetted Wenzel state. The stability of the CB state is determined by the energy barrier separating it from the wetted state. In this work, we study the CB to Wenzel transition using the string method [E et al., J. Chem. Phys. 126, 164103 (2007); W. Ren and E. Vanden-Eijnden, J. Chem. Phys. 138, 134105 (2013)]. We compute the transition states and energy barriers for a three-dimensional droplet on patterned surfaces. The liquid-vapor coexistence is modeled using the mean field theory. Numerical results are obtained for surfaces patterned with straight pillars and nails, respectively. It is found that on both type of surfaces, wetting occurs via infiltration of the liquid in a single groove. The reentrant geometry of nails creates large energy barrier for the wetting of the solid surface compared to straight pillars. We also study the effect of surface chemistry, pillar height, and inter-pillar spacing on the energy barrier and compare it with nails.

Monolayer Adsorption of Ar and Kr on Graphite: Theoretical Isotherms and Spreading Pressures

PubMed

Mulero; Cuadros

1997-02-01

The validity of analytical equations for two-dimensional fluids in the prediction of monolayer adsorption isotherms and spreading pressures of rare gases on graphite is analyzed. The statistical mechanical theory of Steele is used to relate the properties of the adsorbed and two-dimensional fluids. In such theory the model of graphite is a perfectly flat surface, which means that only the first order contribution of the fluid-solid interactions are taken into account. Two analytical equations for two-dimensional Lennard-Jones fluids are used: one proposed by Reddy-O'Shea, based in the fit on pressure and potential energy computer simulated results, and other proposed by Cuadros-Mulero, based in the fit of the Helmholtz free energy calculated from computer simulated results of the radial distribution function. The theoretical results are compared with experimental results of Constabaris et al. (J. Chem. Phys. 37, 915 (1962)) for Ar and of Putnam and Fort (J. Phys. Chem. 79, 459 (1975)) for Kr. Good agreement is found using both equations in both cases.

On the zeroth-order hamiltonian for CASPT2 calculations of spin crossover compounds.

PubMed

Vela, Sergi; Fumanal, Maria; Ribas-Ariño, Jordi; Robert, Vincent

2016-04-15

Complete active space self-consistent field theory (CASSCF) calculations and subsequent second-order perturbation theory treatment (CASPT2) are discussed in the evaluation of the spin-states energy difference (ΔH(elec)) of a series of seven spin crossover (SCO) compounds. The reference values have been extracted from a combination of experimental measurements and DFT + U calculations, as discussed in a recent article (Vela et al., Phys Chem Chem Phys 2015, 17, 16306). It is definitely proven that the critical IPEA parameter used in CASPT2 calculations of ΔH(elec), a key parameter in the design of SCO compounds, should be modified with respect to its default value of 0.25 a.u. and increased up to 0.50 a.u. The satisfactory agreement observed previously in the literature might result from an error cancellation originated in the default IPEA, which overestimates the stability of the HS state, and the erroneous atomic orbital basis set contraction of carbon atoms, which stabilizes the LS states. © 2015 Wiley Periodicals, Inc.

Re-examination of the Cs2 ground singlet X1Σg+ and triplet a3Σu+ states

NASA Astrophysics Data System (ADS)

Sovkov, Vladimir B.; Xie, Feng; Lyyra, A. Marjatta; Ahmed, Ergin H.; Ma, Jie; Jia, Suotang

2017-09-01

This paper clarifies the disagreement in the depth of the potential energy curve of the cesium dimer singlet ground state which has lasted for nearly a decade. We point out that the origin of this disagreement must be a technical misprint in the values of the three binding energies reported by Danzl et al. [Science 321, 1062 (2008)], while the X1Σg+ state potential reported by Coxon and Hajigeorgiou [J. Chem. Phys. 132, 094105 (2010)], based on experimental data by Amiot and Dulieu [J. Chem. Phys. 117, 5155 (2002)], is quite correct. We have recalculated the potential energy function of the triplet ground state a3Σu+ by using the available experimental data spanning both the attractive and the repulsive branches so that the potential energy function complies asymptotically with the singlet ground state X1Σg+ potential energy function by Coxon and Hajigeorgiou. This is important for the simulation of the near dissociation properties such as Feshbach resonances, which are typically observed in modern experiments with ultracold atoms and molecules.

Trajectory dynamics study of the Ar + CH4 dissociation reaction at high temperatures: the importance of zero-point-energy effects.

PubMed

Marques, J M C; Martínez-Núñez, E; Fernandez-Ramos, A; Vazquez, S A

2005-06-23

Large-scale classical trajectory calculations have been performed to study the reaction Ar + CH4--> CH3 +H + Ar in the temperature range 2500 < or = T/K < or = 4500. The potential energy surface used for ArCH4 is the sum of the nonbonding pairwise potentials of Hase and collaborators (J. Chem. Phys. 2001, 114, 535) that models the intermolecular interaction and the CH4 intramolecular potential of Duchovic et al. (J. Phys. Chem. 1984, 88, 1339), which has been modified to account for the H-H repulsion at small bending angles. The thermal rate coefficient has been calculated, and the zero-point energy (ZPE) of the CH3 product molecule has been taken into account in the analysis of the results; also, two approaches have been applied for discarding predissociative trajectories. In both cases, good agreement is observed between the experimental and trajectory results after imposing the ZPE of CH3. The energy-transfer parameters have also been obtained from trajectory calculations and compared with available values estimated from experiment using the master equation formalism; in general, the agreement is good.

Normal Mode Analysis on the Relaxation of AN Excited Nitromethane Molecule in Argon Bath

NASA Astrophysics Data System (ADS)

Rivera-Rivera, Luis A.; Wagner, Albert F.

2017-06-01

In our previous work [Rivera-Rivera et al. J. Chem. Phys. 142, 014303 (2015).] classical molecular dynamics simulations followed, in an Ar bath, the relaxation of nitromethane (CH_3NO_2) instantaneously excited by statistically distributing 50 kcal/mol among all its internal degrees of freedom. The 300 K Ar bath was at pressures of 10 to 400 atm. Both rotational and vibrational energies exhibited multi-exponential decay. This study explores mode-specific mechanisms at work in the decay process. With the separation of rotation and vibration developed by Rhee and Kim [J. Chem. Phys. 107, 1394 (1997).], one can show that the vibrational kinetic energy decomposes only into vibrational normal modes while the rotational and Coriolis energies decompose into both vibrational and rotational normal modes. Then the saved CH_3NO_2 positions and momenta can be converted into mode-specific energies whose decay over 1000 ps can be monitored. The results identify vibrational and rotational modes that promote/resist energy lost and drive multi-exponential behavior. In addition to mode-specificity, the results show disruption of IVR with increasing pressure.

Numerical study of the effects of surface topography and chemistry on the wetting transition using the string method

NASA Astrophysics Data System (ADS)

Zhang, Yanan; Ren, Weiqing

2014-12-01

Droplets on a solid surface patterned with microstructures can exhibit the composite Cassie-Baxter (CB) state or the wetted Wenzel state. The stability of the CB state is determined by the energy barrier separating it from the wetted state. In this work, we study the CB to Wenzel transition using the string method [E et al., J. Chem. Phys. 126, 164103 (2007); W. Ren and E. Vanden-Eijnden, J. Chem. Phys. 138, 134105 (2013)]. We compute the transition states and energy barriers for a three-dimensional droplet on patterned surfaces. The liquid-vapor coexistence is modeled using the mean field theory. Numerical results are obtained for surfaces patterned with straight pillars and nails, respectively. It is found that on both type of surfaces, wetting occurs via infiltration of the liquid in a single groove. The reentrant geometry of nails creates large energy barrier for the wetting of the solid surface compared to straight pillars. We also study the effect of surface chemistry, pillar height, and inter-pillar spacing on the energy barrier and compare it with nails.

Numerical study of the effects of surface topography and chemistry on the wetting transition using the string method

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

Zhang, Yanan, E-mail: ynzhang@suda.edu.cn; Ren, Weiqing, E-mail: matrw@nus.edu.sg; Institute of High Performance Computing, Singapore 138632

2014-12-28

Droplets on a solid surface patterned with microstructures can exhibit the composite Cassie-Baxter (CB) state or the wetted Wenzel state. The stability of the CB state is determined by the energy barrier separating it from the wetted state. In this work, we study the CB to Wenzel transition using the string method [E et al., J. Chem. Phys. 126, 164103 (2007); W. Ren and E. Vanden-Eijnden, J. Chem. Phys. 138, 134105 (2013)]. We compute the transition states and energy barriers for a three-dimensional droplet on patterned surfaces. The liquid-vapor coexistence is modeled using the mean field theory. Numerical results aremore » obtained for surfaces patterned with straight pillars and nails, respectively. It is found that on both type of surfaces, wetting occurs via infiltration of the liquid in a single groove. The reentrant geometry of nails creates large energy barrier for the wetting of the solid surface compared to straight pillars. We also study the effect of surface chemistry, pillar height, and inter-pillar spacing on the energy barrier and compare it with nails.« less

Worldwide biogenic soil NOx emission estimates from OMI NO2 observations and the GEOS-Chem model

NASA Astrophysics Data System (ADS)

Vinken, Geert; Boersma, Folkert; Maasakkers, Bram; Martin, Randall

2014-05-01

Bacteria in soils are an important source of biogenic nitrogen oxides (NOx = NO + NO2), which are important precursors for ozone (O3) formation. Furthermore NOx emissions contribute to increased nitrogen deposition and particulate matter formation. Bottom-up estimates of global soil NOx emissions range from 4 to 27 Tg N / yr, reflecting our incomplete knowledge of emission factors and processes driving these emissions. In this study we used, for the first time, OMI NO2 columns on all continents to reduce the uncertainty in soil NOx emissions. Regions and months dominated by soil NOx emissions were identified using a filtering scheme in the GEOS-Chem chemistry transport model. Consequently, we compared OMI observed NO2 observed columns to GEOS-Chem simulated columns and provide constraints for these months in 11 regions. This allows us to provide a top-down emission inventory for 2005 for soil NOx emissions from all continents. Our total global soil NOx emission inventory amounts to 10 Tg N / yr. Our estimate is 4% higher than the GEOS-Chem a priori (Hudman et al., 2012), but substantial regional differences exist (e.g. +20% for Sahel and India; and -40% for mid-USA). We furthermore observed a stronger seasonal cycle in the Sahel region, indicating directions for possible future improvements to the parameterization currently used in GEOS-Chem. We validated NO2 concentrations simulated with this new top-down inventory against surface NO2 measurements from monitoring stations in Africa, the USA and Europe. On the whole, we conclude that simulations with our new top-down inventory better agree with measurements. Our work shows that satellite retrieved NO2 columns can improve estimates of soil NOx emissions over sparsely monitored remote rural areas. We show that the range in previous estimates of soil NOx emissions is too large, and global emissions are most likely around 10 Tg N/yr, in agreement with the most recent parameterizations.

Hydrogen-bond symmetrization in methane and hydrogen hydrates in the Mbar range

NASA Astrophysics Data System (ADS)

Bove, L. E.; Ranieri, U.; Gaal, R.; Finocchi, F.; Kuhs, W. F.; Falenty, A.; Klotz, S.; Gillet, P.

2016-12-01

Ice-VII and ice-X phases are the most stable forms of ice at high temperature and extreme pressures, typical of the interiors of satellites and planets. The phase transition between them is a prototypical case of quantum-driven phenomenon, as it can be described as a quantum delocalization of protons in the middle of O-O distances. Recent studies on LiCl- and NaCl-doped ice 1-3 have shown that the presence of salt inclusions in the ice lattice suppresses the quantum behavior of protons, hindering the appearance of the symmetric phase, and possibly suppressing the predicted high temperature superionic phase. This finding stimulated the investigation of similar effects in other water-based compounds, which are thought to be present in icy bodies, namely hydrogen and methane high pressure hydrates. Few experiments have been performed in the past to identify signatures of the hydrogen-bond symmetrization in methane and hydrogen hydrates without reaching conclusive results4,5. Here we present new results on the hydrogen-bond symmetrization of methane and hydrogen hydrates using Raman scattering in the Mbar range and semiclassical simulations including nuclear quantum effects. 1 Bove L. E. et al., E_ect of salt on the H-bond symmetrization in ice, Proc. Natl. Acad. Sci. USA 112, 8216, 2015 ; 2. Bronstein Y. et al., Quantum versus classical protons in pure and salty ice under pressure, Phys. Rev. B 93, 024104, 2016. 3. Klotz S. et al., Ice VII from aqueous salt solutions: From a glass to a crystal with broken H-bonds, Nature Sci. Rep. , in press. 4. Tanaka T. et al., Phase changes of _lled ice Ih methane hydrate under low temperature and high pressure, J. Chem. Phys. 139, 104701, 2013 5. Hirai H. et al., Structural changes of _lled ice Ic hydrogen hydrate under low temperatures and high pressures from 5 to 50 GPa, J. Chem. Phys. 137, 074505, 2012

ChemDoodle Web Components: HTML5 toolkit for chemical graphics, interfaces, and informatics.

PubMed

Burger, Melanie C

2015-01-01

ChemDoodle Web Components (abbreviated CWC, iChemLabs, LLC) is a light-weight (~340 KB) JavaScript/HTML5 toolkit for chemical graphics, structure editing, interfaces, and informatics based on the proprietary ChemDoodle desktop software. The library uses and WebGL technologies and other HTML5 features to provide solutions for creating chemistry-related applications for the web on desktop and mobile platforms. CWC can serve a broad range of scientific disciplines including crystallography, materials science, organic and inorganic chemistry, biochemistry and chemical biology. CWC is freely available for in-house use and is open source (GPL v3) for all other uses.Graphical abstractAdd interactive 2D and 3D chemical sketchers, graphics, and spectra to websites and apps with ChemDoodle Web Components.

FastChem: An ultra-fast equilibrium chemistry

NASA Astrophysics Data System (ADS)

Kitzmann, Daniel; Stock, Joachim

2018-04-01

FastChem is an equilibrium chemistry code that calculates the chemical composition of the gas phase for given temperatures and pressures. Written in C++, it is based on a semi-analytic approach, and is optimized for extremely fast and accurate calculations.

The PubChem chemical structure sketcher

PubMed Central

2009-01-01

PubChem is an important public, Web-based information source for chemical and bioactivity information. In order to provide convenient structure search methods on compounds stored in this database, one mandatory component is a Web-based drawing tool for interactive sketching of chemical query structures. Web-enabled chemical structure sketchers are not new, being in existence for years; however, solutions available rely on complex technology like Java applets or platform-dependent plug-ins. Due to general policy and support incident rate considerations, Java-based or platform-specific sketchers cannot be deployed as a part of public NCBI Web services. Our solution: a chemical structure sketching tool based exclusively on CGI server processing, client-side JavaScript functions, and image sequence streaming. The PubChem structure editor does not require the presence of any specific runtime support libraries or browser configurations on the client. It is completely platform-independent and verified to work on all major Web browsers, including older ones without support for Web2.0 JavaScript objects. PMID:20298522

Effect of wall-mediated hydrodynamic fluctuations on the kinetics of a Brownian nanoparticle

NASA Astrophysics Data System (ADS)

Yu, Hsiu-Yu; Eckmann, David M.; Ayyaswamy, Portonovo S.; Radhakrishnan, Ravi

2016-12-01

The reactive flux formalism (Chandler 1978 J. Chem. Phys. 68, 2959-2970. (doi:10.1063/1.436049)) and the subsequent development of methods such as transition path sampling have laid the foundation for explicitly quantifying the rate process in terms of microscopic simulations. However, explicit methods to account for how the hydrodynamic correlations impact the transient reaction rate are missing in the colloidal literature. We show that the composite generalized Langevin equation (Yu et al. 2015 Phys. Rev. E 91, 052303. (doi:10.1103/PhysRevE.91.052303)) makes a significant step towards solving the coupled processes of molecular reactions and hydrodynamic relaxation by examining how the wall-mediated hydrodynamic memory impacts the two-stage temporal relaxation of the reaction rate for a nanoparticle transition between two bound states in the bulk, near-wall and lubrication regimes.

Reply to "Comment on `Simple improvements to classical bubble nucleation models'"

NASA Astrophysics Data System (ADS)

Tanaka, Kyoko K.; Tanaka, Hidekazu; Angélil, Raymond; Diemand, Jürg

2016-08-01

We reply to the Comment by Schmelzer and Baidakov [Phys. Rev. E 94, 026801 (2016)]., 10.1103/PhysRevE.94.026801 They suggest that a more modern approach than the classic description by Tolman is necessary to model the surface tension of curved interfaces. Therefore we now consider the higher-order Helfrich correction, rather than the simpler first-order Tolman correction. Using a recent parametrization of the Helfrich correction provided by Wilhelmsen et al. [J. Chem. Phys. 142, 064706 (2015)], 10.1063/1.4907588, we test this description against measurements from our simulations, and find an agreement stronger than what the pure Tolman description offers. Our analyses suggest a necessary correction of order higher than the second for small bubbles with radius ≲1 nm. In addition, we respond to other minor criticism about our results.

Model analysis of secondary organic aerosol formation by glyoxal in laboratory studies: the case for photoenhanced chemistry.

PubMed

Sumner, Andrew J; Woo, Joseph L; McNeill, V Faye

2014-10-21

The reactive uptake of glyoxal by atmospheric aerosols is believed to be a significant source of secondary organic aerosol (SOA). Several recent laboratory studies have been performed with the goal of characterizing this process, but questions remain regarding the effects of photochemistry on SOA growth. We applied GAMMA (McNeill et al. Environ. Sci. Technol. 2012, 46, 8075-8081), a photochemical box model with coupled gas-phase and detailed aqueous aerosol-phase chemistry, to simulate aerosol chamber studies of SOA formation by the uptake of glyoxal by wet aerosol under dark and irradiated conditions (Kroll et al. J. Geophys. Res. 2005, 110 (D23), 1-10; Volkamer et al. Atmos. Chem. Phys. 2009, 9, 1907-1928; Galloway et al. Atmos. Chem. Phys. 2009, 9, 3331- 306 3345 and Geophys. Res. Lett. 2011, 38, L17811). We find close agreement between simulated SOA growth and the results of experiments conducted under dark conditions using values of the effective Henry's Law constant of 1.3-5.5 × 10(7) M atm(-1). While irradiated conditions led to the production of some organic acids, organosulfates, and other oxidation products via well-established photochemical mechanisms, these additional product species contribute negligible aerosol mass compared to the dark uptake of glyoxal. Simulated results for irradiated experiments therefore fell short of the reported SOA mass yield by up to 92%. This suggests a significant light-dependent SOA formation mechanism that is not currently accounted for by known bulk photochemistry, consistent with recent laboratory observations of SOA production via photosensitizer chemistry.

Fast computation of molecular random phase approximation correlation energies using resolution of the identity and imaginary frequency integration

NASA Astrophysics Data System (ADS)

Eshuis, Henk; Yarkony, Julian; Furche, Filipp

2010-06-01

The random phase approximation (RPA) is an increasingly popular post-Kohn-Sham correlation method, but its high computational cost has limited molecular applications to systems with few atoms. Here we present an efficient implementation of RPA correlation energies based on a combination of resolution of the identity (RI) and imaginary frequency integration techniques. We show that the RI approximation to four-index electron repulsion integrals leads to a variational upper bound to the exact RPA correlation energy if the Coulomb metric is used. Auxiliary basis sets optimized for second-order Møller-Plesset (MP2) calculations are well suitable for RPA, as is demonstrated for the HEAT [A. Tajti et al., J. Chem. Phys. 121, 11599 (2004)] and MOLEKEL [F. Weigend et al., Chem. Phys. Lett. 294, 143 (1998)] benchmark sets. Using imaginary frequency integration rather than diagonalization to compute the matrix square root necessary for RPA, evaluation of the RPA correlation energy requires O(N4 log N) operations and O(N3) storage only; the price for this dramatic improvement over existing algorithms is a numerical quadrature. We propose a numerical integration scheme that is exact in the two-orbital case and converges exponentially with the number of grid points. For most systems, 30-40 grid points yield μH accuracy in triple zeta basis sets, but much larger grids are necessary for small gap systems. The lowest-order approximation to the present method is a post-Kohn-Sham frequency-domain version of opposite-spin Laplace-transform RI-MP2 [J. Jung et al., Phys. Rev. B 70, 205107 (2004)]. Timings for polyacenes with up to 30 atoms show speed-ups of two orders of magnitude over previous implementations. The present approach makes it possible to routinely compute RPA correlation energies of systems well beyond 100 atoms, as is demonstrated for the octapeptide angiotensin II.

Fast computation of molecular random phase approximation correlation energies using resolution of the identity and imaginary frequency integration.

PubMed

Eshuis, Henk; Yarkony, Julian; Furche, Filipp

2010-06-21

The random phase approximation (RPA) is an increasingly popular post-Kohn-Sham correlation method, but its high computational cost has limited molecular applications to systems with few atoms. Here we present an efficient implementation of RPA correlation energies based on a combination of resolution of the identity (RI) and imaginary frequency integration techniques. We show that the RI approximation to four-index electron repulsion integrals leads to a variational upper bound to the exact RPA correlation energy if the Coulomb metric is used. Auxiliary basis sets optimized for second-order Møller-Plesset (MP2) calculations are well suitable for RPA, as is demonstrated for the HEAT [A. Tajti et al., J. Chem. Phys. 121, 11599 (2004)] and MOLEKEL [F. Weigend et al., Chem. Phys. Lett. 294, 143 (1998)] benchmark sets. Using imaginary frequency integration rather than diagonalization to compute the matrix square root necessary for RPA, evaluation of the RPA correlation energy requires O(N(4) log N) operations and O(N(3)) storage only; the price for this dramatic improvement over existing algorithms is a numerical quadrature. We propose a numerical integration scheme that is exact in the two-orbital case and converges exponentially with the number of grid points. For most systems, 30-40 grid points yield muH accuracy in triple zeta basis sets, but much larger grids are necessary for small gap systems. The lowest-order approximation to the present method is a post-Kohn-Sham frequency-domain version of opposite-spin Laplace-transform RI-MP2 [J. Jung et al., Phys. Rev. B 70, 205107 (2004)]. Timings for polyacenes with up to 30 atoms show speed-ups of two orders of magnitude over previous implementations. The present approach makes it possible to routinely compute RPA correlation energies of systems well beyond 100 atoms, as is demonstrated for the octapeptide angiotensin II.

Study of Spin Splitting in GaN/AlGaN Quantum Wells

DTIC Science & Technology

2009-05-11

plasma-assisted molecular - beam epitaxy ”, Jap. J. Appl. Phys. 47, 891 (2008), we have grown M-plane GaN films with self-assembled C-plane GaN nanopillars...on a γ-LiAlO2 substrate by plasma-assisted molecular - beam epitaxy . The diameters of the basal plane of the nanopillars are about 200 to 900 nm and...Line defects of M-plane GaN grown on γ-LiAlO2 by plasma-assisted molecular beam epitaxy ”, Appl. Phys. Lett. 92 pp.202106 (2008), we studied the

Simulation of particle diversity and mixing state over Greater Paris: a model-measurement inter-comparison.

PubMed

Zhu, Shupeng; Sartelet, Karine N; Healy, Robert M; Wenger, John C

2016-07-18

Air quality models are used to simulate and forecast pollutant concentrations, from continental scales to regional and urban scales. These models usually assume that particles are internally mixed, i.e. particles of the same size have the same chemical composition, which may vary in space and time. Although this assumption may be realistic for continental-scale simulations, where particles originating from different sources have undergone sufficient mixing to achieve a common chemical composition for a given model grid cell and time, it may not be valid for urban-scale simulations, where particles from different sources interact on shorter time scales. To investigate the role of the mixing state assumption on the formation of particles, a size-composition resolved aerosol model (SCRAM) was developed and coupled to the Polyphemus air quality platform. Two simulations, one with the internal mixing hypothesis and another with the external mixing hypothesis, have been carried out for the period 15 January to 11 February 2010, when the MEGAPOLI winter field measurement campaign took place in Paris. The simulated bulk concentrations of chemical species and the concentrations of individual particle classes are compared with the observations of Healy et al. (Atmos. Chem. Phys., 2013, 13, 9479-9496) for the same period. The single particle diversity and the mixing-state index are computed based on the approach developed by Riemer et al. (Atmos. Chem. Phys., 2013, 13, 11423-11439), and they are compared to the measurement-based analyses of Healy et al. (Atmos. Chem. Phys., 2014, 14, 6289-6299). The average value of the single particle diversity, which represents the average number of species within each particle, is consistent between simulation and measurement (2.91 and 2.79 respectively). Furthermore, the average value of the mixing-state index is also well represented in the simulation (69% against 59% from the measurements). The spatial distribution of the mixing

Can we define an asymptotic value for the ice active surface site density for heterogeneous ice nucleation?

NASA Astrophysics Data System (ADS)

Niedermeier, Dennis; Augustin-Bauditz, Stefanie; Hartmann, Susan; Wex, Heike; Ignatius, Karoliina; Stratmann, Frank

2015-04-01

active surface site density, which we named ns*, for the investigated feldspar sample. The comparison of these results with those of other studies elucidates the general feasibility of determining such an asymptotic value and also show that the value of ns* strongly depends on the method of the particle surface area determination. Acknowledgement This work is partly funded by the Federal Ministry of Education and Research (BMBF - project CLOUD 12) and by the German Research Foundation (DFG project WE 4722/1-1, part of the research unit INUIT, FOR 1525). D. Niedermeier acknowledges financial support from the Alexander von Humboldt-foundation. References Augustin et al.: Immersion freezing of birch pollen washing water, Atmos. Chem. Phys., 13, 10989-11003, doi:10.5194/acp-13-10989-2013, 2013. Hartmann et al.: Immersion freezing of ice nucleation active protein complexes, Atmos. Chem. Phys., 13, 5751-5766, doi:10.5194/acp-13-5751-2013, 2013. Murray et al.: Ice nucleation by particles immersed in supercooled cloud droplets, Chem. Soc. Rev., 41, 6519-6554, 2012. Wex et al.: Intercomparing different devices for the investigation of ice nucleating particles using Snomax® as test substance, Atmos. Chem. Phys. Discuss., 14, 22321-22384, doi:10.5194/acpd-14-22321-2014, 2014.

Exploring the High-Pressure Behavior of PETN: A Combined Quantum Mechanical and Experimental Study

DTIC Science & Technology

2006-11-01

calculations to explore the hypothesized compression-induced polymorphic phase transition [Gruzdkov 2004]. The initial crystal in these Figure 4...Scuseria, G.E., and Chabalowski, C.F. 2004: An ab Initio Study of Solid Nitromethane, HMX , RDX , and CL20: Successes and Failures of DFT. J. Phys. Chem... RDX , HMX , HNIW, and PETN Crystals. J. Phys. Chem. B, 103, 6783. Trotter, J., 1963: Bond lengths and angles in Pentaerythritol Tetranitrate. Acta

High-Pressure Synchrotron Infrared Absorption and Raman Spectroscopy of ζ-N_2

NASA Astrophysics Data System (ADS)

Gregoryanz, E.; Goncharov, A. F.; Mao, H. K.; Hemley, R. J.

2000-03-01

Infrared mid-IR and Raman spectra of high-pressure, low-temperature phases of solid nitrogen have been measured to above 40 GPa. The transition to the lower-symmetry ordered phase ζ at 21 GPa, reported by Schiferl et al. [1]. has been confirmed. We observe three Raman-active and two IR components of the nu2 stretching mode (disk-like molecules) and only one Raman-active component of the nu1 mode (sphere-like molecules). All the vibron modes increase frequency with pressure. The structure of ζ-N2 phase is discussed. [1] Schiferl et al., J. Phys. Chem., 89, 2324 (1985).

ChemCam rock laser for Mars Science Laboratory "Curiosity"

ScienceCinema

Wiens, Roger

2018-02-06

Los Alamos has a long history of space-related instruments, tied primarily to its role in defense-related treaty verification. Space-based detectors have helped determine the differences between signals from lightning bolts and potential nuclear explosions. LANL-developed gamma-ray detection instruments first revealed the existence of what we now know as gamma-ray bursts, an exciting area of astrophysical research. And the use of LANL instruments on varied space missions continues with such products as the ChemCam rock laser for NASA, shown here. The Engineering Model of the ChemCam Mars Science Laboratory rover instrument arrived at NASA's Jet Propulsion Laboratory on February 6, 2008. The Flight Model was shipped in August, 2010 for installation on the rover at JPL. ChemCam will use imaging and laser-induced breakdown spectroscopy (LIBS) to determine rock and soil compositions on Mars, up to 9 meters from the rover. The engineering model is being integrated into the rover test bed for the development and testing of the rover software. The actual flight model components were concurrently assembled at Los Alamos and in Toulouse, France. The Mars Science Laboratory is scheduled to launch in 2011. Animations courtesy of JPL/NASA.

Metal-enhanced chemiluminescence from chromium, copper, nickel, and zinc nanodeposits: Evidence for a second enhancement mechanism in metal-enhanced fluorescence

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

Weisenberg, Micah; Zhang Yongxia; Geddes, Chris D.

Over the past decade metal-fluorophore interactions, metal-enhanced fluorescence, have attracted significant research attention, with the technology now becoming common place in life science applications. In this paper, we address the underlying mechanisms of metal-enhanced fluorescence (MEF) and experimentally show using chemiluminescence solutions that MEF is indeed underpinned by two complimentary mechanisms, consistent with the recent reports by Geddes and co-workers [Zhang et al., J. Phys. Chem. C 113, 12095 (2009)] and their enhanced fluorescence hypothesis.

Temperature Dependence on the Low and High Frequency Raman Scattering from Liquid Water.

DTIC Science & Technology

1986-10-01

elaboration of the Young- Westerdahl (YW) thermodynamic model, assuming conservation of hydrogen-bonded (HB) and nonhydrogen-bonded (NHB = bent and/or...Al*= -RB, and AS’ = RC. previously.3 The total integrated BE corrected Raman intensities, I/ Young and Westerdahl (YW) successfully used Eq. (1to...Scherer. M. K. Go. and S. Kint. 1. Phys. Chem. 78. 1304 (1974). in wudb xetdfrv! .Ti ekplrztion 3T. F. Young and R. P. Westerdahl . ARL 135. Office of

Electron mass stopping power in H2

NASA Astrophysics Data System (ADS)

Fursa, Dmitry V.; Zammit, Mark C.; Threlfall, Robert L.; Savage, Jeremy S.; Bray, Igor

2017-08-01

Calculations of electron mass stopping power (SP) of electrons in H2 have been performed using the convergent close-coupling method for incident electron energies up to 2000 eV. Convergence of the calculated SP has been established by increasing the size of the close-coupling expansion from 9 to 491 states. Good agreement was found with the SP measurements of Munoz et al. [Chem. Phys. Lett. 433, 253 (2007), 10.1016/j.cplett.2006.10.114].

Advanced Zinc Phosphate Conversion and Pre-Ceramic Polymetallosiloxane Coatings for Corrosion Protection of Steel and Aluminum, and Characteristics of Polyphenyletheretherketone-Based Materials

DTIC Science & Technology

1992-09-24

which the trivalent ion is the principal oxidation state, preferentially reacts with hydroxylated organosilane to form the Al-O-Si linkage at a low... tig front the carboxylic acid, COOH, in the p(AA) [6j. The spectra for all of the cobalt- and nickel-incorporated Zn-Ph samples show a slight...to study bonding in chromium , manganese, iron, and cobalt compounds J Chem Phys 57 (1972) pp 973-982 1 1 Lindberg, B.J. et at. Molecular

Contrasting two different interpretations of the dynamics in binary glass forming mixtures

NASA Astrophysics Data System (ADS)

Valenti, S.; Capaccioli, S.; Ngai, K. L.

2018-02-01

In a series of papers on binary glass-forming mixtures of tripropyl phosphate (TPP) with polystyrene (PS), Kahlau et al. [J. Chem. Phys. 140, 044509 (2014)] and Bock et al. [J. Chem. Phys. 139, 064508 (2013); J. Chem. Phys. 140, 094505 (2014); and J. Non-Cryst. Solids 407, 88-97 (2015)] presented the data on the dynamics of the two components studied over the entire composition range by several experimental methods. From these sets of data, obtained by multiple experimental techniques on mixtures with a large difference ΔTg ≈ 200 K between the glass transition temperatures of two starting glass formers, they obtained two α-relaxations, α1 and α2. The temperature dependence of the slower α1 is Vogel-Fulcher like, but the faster α2 is Arrhenius. We have re-examined their data and show that their α2-relaxation is the Johari-Goldstein (JG) β-relaxation with Arrhenius T-dependence admixed with a true α2-relaxation having a stronger temperature dependence. In support of our interpretation of their data, we made dielectric measurements at elevated pressures P to show that the ratio of the α1 and α2 relaxation times, τα1(T,P)/τα2(T,P), is invariant to variations of T and P, while τα1(T,P) is kept constant. This property proves unequivocally that the α2-relaxation is the JG β-relaxation, the precursor of the α1-relaxation. Subsequently, the true but unresolved α2-relaxation is recovered, and its relaxation times with much stronger temperature dependence are deduced, as expected for the α-relaxation of the TPP component. The results are fully compatible with those found in another binary mixture of methyltetrahydrofuran with tristyrene and PS with ΔTg ≈ 283 K, even larger than ΔTg ≈ 200 K of the mixture of TPP with PS, and in several polymer blends. The contrast between the two very different interpretations brought out in this paper is deemed beneficial for further progress in this research area.

Comment on ``Anisotropy studies of molecular-beam-epitaxy-grown Co(111) thin films by ferromagnetic resonance'' [J. Appl. Phys. 75, 6492 (1994)

NASA Astrophysics Data System (ADS)

Artman, J. O.

1995-05-01

The magnetic free energy expression E used to calculate ferromagnetic resonance frequencies by F. Schreiber et al., J. Appl. Phys. 75, 6492 (1994) is examined. The expression is correct for hexagonal site symmetry films but not for any type of cubic symmetry film. The correct expression, including both K1c and K2c anisotropy contributions, for E with H in the basal plane of a (111) film is given in the text.

Performance of the JULES land surface model for UK Biogenic VOC emissions

NASA Astrophysics Data System (ADS)

Hayman, Garry; Comyn-Platt, Edward; Vieno, Massimo; Langford, Ben

2017-04-01

:10.1111/j.1469-8137.2009.02859.x; (3) Grote and Niinemets, 2008: Plant Biol., 10, 8, doi:10.1055/s-2007-964975; (4) Best et al., 2011: Geosci. Model Dev., 4, 677, doi:10.5194/gmd-4-677-2011; (5) Clark et al., 2011: Geosci. Model Dev., 4, 701, doi:10.5194/gmd-4-701-2011; (6) Pacifico et al., 2011: Atmos. Chem. Phys., 11, 4371, doi:10.5194/acp-11-4371-2011; [7] Simpson et al., 2012: Atmos. Chem. Phys., 12, 7825, doi: 10.5194/acp-12-7825-2012; [8] Vieno et al., 2016: Atmos. Chem. Phys., 16, 265, doi: 10.5194/acp-16-265-2016.

Assessing changes in stratospheric mean age of air and fractional release using historical trace gas observations

NASA Astrophysics Data System (ADS)

Laube, Johannes; Bönisch, Harald; Engel, Andreas; Röckmann, Thomas; Sturges, William

2014-05-01

Large-scale stratospheric transport is pre-dominantly governed by the Brewer-Dobson circulation. Due to climatic change a long-term acceleration of this residual stratospheric circulation has been proposed (e.g. Austin et al.,2006). Observational evidence has revealed indications for temporary changes (e.g. Bönisch et al., 2011) but a confirmation of a significant long-term trend is missing so far (e.g. Engel et al., 2009). A different aspect is a possible long-term change in the break-down of chemically important species such as chlorofluorocarbons as proposed by Butchart et al. 2001. Recent studies show significant differences adding up to more than 20 % in the chlorine released from such compounds (Newman et al., 2007; Laube et al., 2013). We here use a data set of three long-lived trace gases, namely SF6, CF2Cl2, and N2O, as measured in whole-air samples collected during balloon and aircraft flights between 1975 and 2011, to assess changes in stratospheric transport and chemistry. For this purpose we utilise the mean stratospheric transit times (or mean ages of air) in combination with a measure of the chemical decomposition (i.e. fractional release factors). We also evaluate the influence of different trend correction methods on these quantities and explore their variability with latitude, altitude, and season. References Austin, J. & Li, F.: On the relationship between the strength of the Brewer-Dobson circulation and the age of stratospheric air, Geophys. Res. Lett., 33, L17807, 2006. Bönisch, H., Engel, A., Birner, Th., Hoor, P., Tarasick, D. W., and Ray, E. A.: On the structural changes in the Brewer-Dobson circulation after 2000, Atmos. Chem. Phys., 11, 3937-3948, 2011. Butchart, N. & Scaife, A. A. Removal of chlorofluorocarbons by increased mass exchange between the stratosphere and troposphere in a changing climate. Nature, 410, 799-802, 2001. Engel, A., Möbius, T., Bönisch, H., Schmidt, U., Heinz, R., Levin, I., Atlas, E., Aoki, S., Nakazawa, T

Torsional Angle Driver (TorAD) System for HyperChem/Excel

NASA Astrophysics Data System (ADS)

Starkey, Ronald

1999-02-01

The torsional angle driver system for HyperChem/Excel is a package of several Excel spreadsheets and macro programs to be used with HyperChem to obtain and plot information, such as total energy, for the conformations that result from a 360° rotation about a torsional angle system in a molecule. The TorAD system also includes several HyperChem scripts to facilitate its use. TorAD was developed for use in the undergraduate organic chemistry laboratory. The results obtained with TorAD could be obtained manually with HyperChem, but it would take considerable time and would not be instructive to the students. Use of the TorAD system allows students to spend their time on the more important aspect of conformation analysisinterpretation of results. The Excel spreadsheet/macro programs in TorAD include:

· Tor_xl_a and tor_xl obtain and plot the total energy at 5° torsional-angle intervals. The calculation method, the torsional-angle restraint, and the structure to be used at each angle can be set by the user. The advanced version, tor_xl_a, which requires HyperChem 4.5 or later, also allows torsional-angle structures to be saved for later recall as individual structures or, using a HyperChem script, in a movie format. It also provides a rapid scan of the 360° rotation where only single-point calculations, rather than geometry optimizations, are performed. The tor_xl system will perform routine tasks in a manner suitable for most instructional settings. · Tor_Comp performs molecular mechanics optimizations at 5° intervals and obtains and plots four energy parameters (total, torsional, nonbonded, and bond [bend plus stretch] energy) as a function of torsional angle. The calculation method and the restraint can be specified. · TorDipol produces a plot of the total energy and the calculated dipole moment at 5° steps of the torsional angle. The default calculation is the semi-empirical AM

Thermal equation of state of Molybdenum determined from in situ synchrotron X-ray diffraction with laser-heated diamond anvil cells

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

Huang, Xiaoli; Li, Fangfei; Zhou, Qiang

Here we report that the equation of state (EOS) of Mo is obtained by an integrated technique of laser-heated DAC and synchrotron X-ray diffraction. The cold compression and thermal expansion of Mo have been measured up to 80 GPa at 300 K, and 92 GPa at 3470 K, respectively. The P-V-T data have been treated with both thermodynamic and Mie–Gruneisen-Debye methods for the thermal EOS inversion. The results are self-consistent and in agreement with the static multi-anvil compression data of Litasov et al. (J. Appl. Phys. 113, 093507 (2013)) and the theoretical data of Zeng et al. (J. Phys. Chem.more » B 114, 298 (2010)). Furthermore, these high pressure and high temperature (HPHT) data with high precision firstly complement and close the gap between the resistive heating and the shock compression experiment.« less

Thermal equation of state of Molybdenum determined from in situ synchrotron X-ray diffraction with laser-heated diamond anvil cells

DOE PAGES

Huang, Xiaoli; Li, Fangfei; Zhou, Qiang; ...

2016-02-17

Here we report that the equation of state (EOS) of Mo is obtained by an integrated technique of laser-heated DAC and synchrotron X-ray diffraction. The cold compression and thermal expansion of Mo have been measured up to 80 GPa at 300 K, and 92 GPa at 3470 K, respectively. The P-V-T data have been treated with both thermodynamic and Mie–Gruneisen-Debye methods for the thermal EOS inversion. The results are self-consistent and in agreement with the static multi-anvil compression data of Litasov et al. (J. Appl. Phys. 113, 093507 (2013)) and the theoretical data of Zeng et al. (J. Phys. Chem.more » B 114, 298 (2010)). Furthermore, these high pressure and high temperature (HPHT) data with high precision firstly complement and close the gap between the resistive heating and the shock compression experiment.« less

Calibrating the ChemCam LIBS for Carbonate Minerals on Mars

DOE R&D Accomplishments Database

Wiens, Roger C.; Clegg, Samuel M.; Ollila, Ann M.; Barefield, James E.; Lanza, Nina; Newsom, Horton E.

2009-01-01

The ChemCam instrument suite on board the NASA Mars Science Laboratory (MSL) rover includes the first LIBS instrument for extraterrestrial applications. Here we examine carbonate minerals in a simulated martian environment using the LIDS technique in order to better understand the in situ signature of these materials on Mars. Both chemical composition and rock type are determined using multivariate analysis (MVA) techniques. Composition is confirmed using scanning electron microscopy (SEM) techniques. Our initial results suggest that ChemCam can recognize and differentiate between carbonate materials on Mars.

Hydrogen adsorption strength and sites in the metal organic framework MOF5: Comparing experiment and model calculations

NASA Astrophysics Data System (ADS)

Mulder, F. M.; Dingemans, T. J.; Schimmel, H. G.; Ramirez-Cuesta, A. J.; Kearley, G. J.

2008-07-01

Hydrogen adsorption in porous, high surface area, and stable metal organic frameworks (MOF's) appears a novel route towards hydrogen storage materials [N.L. Rosi, J. Eckert, M. Eddaoudi, D.T. Vodak, J. Kim, M. O'Keeffe, O.M. Yaghi, Science 300 (2003) 1127; J.L.C. Rowsell, A.R. Millward, K. Sung Park, O.M. Yaghi, J. Am. Chem. Soc. 126 (2004) 5666; G. Ferey, M. Latroche, C. Serre, F. Millange, T. Loiseau, A. Percheron-Guegan, Chem. Commun. (2003) 2976; T. Loiseau, C. Serre, C. Huguenard, G. Fink, F. Taulelle, M. Henry, T. Bataille, G. Férey, Chem. Eur. J. 10 (2004) 1373]. A prerequisite for such materials is sufficient adsorption interaction strength for hydrogen adsorbed on the adsorption sites of the material because this facilitates successful operation under moderate temperature and pressure conditions. Here we report detailed information on the geometry of the hydrogen adsorption sites, based on the analysis of inelastic neutron spectroscopy (INS). The adsorption energies for the metal organic framework MOF5 equal about 800 K for part of the different sites, which is significantly higher than for nanoporous carbon materials (˜550 K) [H.G. Schimmel, G.J. Kearley, M.G. Nijkamp, C.T. Visser, K.P. de Jong, F.M. Mulder, Chem. Eur. J. 9 (2003) 4764], and is in agreement with what is found in first principles calculations [T. Sagara, J. Klassen, E. Ganz, J. Chem. Phys. 121 (2004) 12543; F.M. Mulder, T.J. Dingemans, M. Wagemaker, G.J. Kearley, Chem. Phys. 317 (2005) 113]. Assignments of the INS spectra is realized using comparison with independently published model calculations [F.M. Mulder, T.J. Dingemans, M. Wagemaker, G.J. Kearley, Chem. Phys. 317 (2005) 113] and structural data [T. Yildirim, M.R. Hartman, Phys. Rev. Lett. 95 (2005) 215504].

e-Phys: a suite of intracellular neurophysiology programs integrating COM (component object model) technologies.

PubMed

Nguyen, Quoc-Thang; Miledi, Ricardo

2003-09-30

Current computer programs for intracellular recordings often lack advanced data management, are usually incompatible with other applications and are also difficult to adapt to new experiments. We have addressed these shortcomings in e-Phys, a suite of electrophysiology applications for intracellular recordings. The programs in e-Phys use Component Object Model (COM) technologies available in the Microsoft Windows operating system to provide enhanced data storage, increased interoperability between e-Phys and other COM-aware applications, and easy customization of data acquisition and analysis thanks to a script-based integrated programming environment. Data files are extensible, hierarchically organized and integrated in the Windows shell by using the Structured Storage technology. Data transfers to and from other programs are facilitated by implementing the ActiveX Automation standard and distributed COM (DCOM). ActiveX Scripting allows experimenters to write their own event-driven acquisition and analysis programs in the VBScript language from within e-Phys. Scripts can reuse components available from other programs on other machines to create distributed meta-applications. This paper describes the main features of e-Phys and how this package was used to determine the effect of the atypical antipsychotic drug clozapine on synaptic transmission at the neuromuscular junction.

Cubic ice and large humidity with respect to ice in cold cirrus clouds

NASA Astrophysics Data System (ADS)

Bogdan, A.; Loerting, T.

2009-04-01

-cloud water supersaturations" in the upper-tropospheric cold cirrus clouds. Using instead the value of Hc→h ? 50 J/mol (Handa et al., 1986; Mayer and Hallbrucker, 1987) the calculation gives that Pc is only ~3% larger than that of Ph. Recently it has been reported that emulsified water droplets freeze to cubic ice when being cooled at a rate of 10 K/min (Murray and Bertram, 2006,). We prepared emulsified droplets using the same emulsification technique and studied them with a differential scanning calorimeter (DSC) between 278 and 180 K using a scanning rate of 10 K/min. During the warming of the samples we observed a very broad, tiny exothermal peak approximately between 230 and 260 K. Kohl et al. (2000) observed exothermal peak at ~230 K during the warming at 30 K/min of several samples of hyperquenched glassy water (HGW) prepared at temperature between 130 and 190 K. They attributed this peak to the cubic-to-hexagonal ice transition and estimated Hc→h to be between ~33 and 75 J/mol. Johari (2005) used the value of Hc→h ? 37 J/mol. Assuming that in our case the broad peak between 230 and 260 K is also due to the cubic-to-hexagonal ice transition we obtained approximately between 10 and 25 J/mol for Hc→h. This low enthalpy of transformation suggests that cubic ice in the atmosphere contains many hexagonal stacking faults. Using these values of Hc→h for cubic ice as produced at atmospheric cooling rates, the above mentioned formula gives that Pc is larger than that of Ph only by ~1%. We, therefore, suggest that the difference in the water vapor pressures between ice Ic and ice Ih is small and does not play a significant role in the elevation of RHi in cold cirrus clouds. Murphy, D. M., and T. Koop (2005), Q. J. R. Meteorol. Soc. 131, 1539-1565. Shilling, J. E. et al. (2006). Geophys. Res. Lett. 33, L17801, doi:1029/2006GL026671. Handa, P. Y., D. D. Klug, and E. Whalley (1986). J. Chem. Phys. 84, 7009-7010. Mayer, E., and A. Hallbrucker (1987), Nature

Water Accommodation on Bare and Coated Ice

NASA Astrophysics Data System (ADS)

Kong, Xiangrui

2015-04-01

The Nordic Centre of Excellence CRAICC. Reference: X.R. Kong, P. Papagiannakopoulos, E.S. Thomson, J.B.C. Pettersson, Water Accommodation and Desorption Kinetics on Ice, J. Phys. Chem. A, 118 (2014) 3973-3979. E.S. Thomson, X. Kong, N. Markovic, P. Papagiannakopoulos, J.B.C. Pettersson, Collision dynamics and uptake of water on alcohol-covered ice, Atmos. Chem. Phys. 13 (2013) 2223-2233. P. Papagiannakopoulos, X.R. Kong, E.S. Thomson, J.B.C. Pettersson, Water Interactions with Acetic Acid Layers on Ice and Graphite, J. Phys. Chem. B, (2014) doi: 10.1021/jp503552w.

Torsional, Vibrational and Vibration-Torsional Levels in the S_{1} and Ground Cationic D_{0}^{+} States of Para-Xylene

NASA Astrophysics Data System (ADS)

Gardner, Adrian M.; Tuttle, William Duncan; Groner, Peter; Wright, Timothy G.

2017-06-01

Insight gained from examining the "pure" torsional, vibrational and vibration-torsional (vibtor) levels of the single rotor molecules: toluene (methylbenzene) and para-fluorotoluene (pFT), is applied to the double rotor para-xylene (p-dimethylbenzene) molecule . Resonance-enhanced multiphoton ionization (REMPI) spectroscopy and zero-kinetic-energy (ZEKE) spectroscopy are employed in order to investigate the S_{1} and ground cationic states of para-xylene. Observed transitions are assigned in the full molecular symmetry group (G_{72}) for the first time. J. R. Gascooke, E. A. Virgo, and W. D. Lawrance, J. Chem. Phys., 143, 044313 (2015). A. M. Gardner, W. D. Tuttle, L. Whalley, A. Claydon, J. H. Carter and T. G. Wright, J. Chem. Phys., 145, 124307 (2016). A. M. Gardner, W. D. Tuttle, P. Groner and T. G. Wright, J. Chem. Phys., (2017, in press).

Drilled Hole and ChemCam Marks at Cumberland

NASA Image and Video Library

2013-06-05

The Chemistry and Camera ChemCam instrument on NASA Mars rover Curiosity was used to check the composition of gray tailings from the hole in rock target Cumberland that the rover drilled on May 19, 2013.

Thermodynamics of Supercooled and Glassy Water

NASA Astrophysics Data System (ADS)

Debenedetti, Pablo G.

1998-03-01

The behavior of metastable water at low temperatures is unusual. The isothermal compressibility, the isobaric heat capacity, and the magnitude of the thermal expansion coefficient increase sharply upon supercooling, and structural relaxation becomes extremely sluggish at temperatures far above the glass transition(Angell, C.A., Annu. Rev. Phys. Chem., 34, 593, 1983)(Debenedetti, P.G., Metastable Liquids. Concepts and Principles, Princeton University Press, 1996). Water has two distinct glassy phases, low- and high-density amorphous ice (LDA, HDA). The transition between LDA and HDA is accompanied by sharp volume and enthalpy changes, and appears to be first-order(Mishima, O., L.D.Calvert, and E. Whalley, Nature, 314, 76, 1985)(Mishima, O., J. Chem. Phys., 100, 5910, 1994). The understanding of these observations in terms of an underlying global phase behavior remains incomplete(Speedy, R.J., J. Phys. Chem., 86, 982, 1982)(Poole, P.H., F. Sciortino, U. Essman, and H.E. Stanley, Nature, 360, 324, 1992)(Sastry, S., P.G. Debenedetti, F. Sciortino, and H.E. Stanley, Phys. Rev. E, 53, 6144, 1996)(Tanaka, H., Nature, 380, 328, 1996)(Xie, Y., K.F. Ludwig, G. Morales, D.E. Hare, and C.M. Sorensen, Phys. Rev. Lett., 71, 2050, 1993). Microscopic theories and computer simulations suggest several scenarios that can reproduce some experimental observations. Interesting and novel ideas have resulted from this body of theoretical work, such as the possibility of liquid-liquid immiscibility in a pure substance(Poole, P.H., F.Sciortino, T.Grande, H.E. Stanley, and C.A. Angell, Phys. Rev. Lett., 73, 1632, 1994)(Roberts, C.J., and P.G. Debenedetti, J. Chem. Phys., 105, 658, 1996)(Roberts, C.J., P.G. Debenedetti, and A.Z. Panagiotopoulos, Phys. Rev. Lett., 77, 4386, 1996)(Harrington, S., R. Zhang, P.H. Poole, F. Sciortino, and H.E. Stanley, Phys. Rev. Lett., 78, 2409, 1997). In this talk I will review the experimental facts, discuss their theoretical interpretation, and identify key

Effects of Solvation on One- and Two-Photon Spectra of Coumarin Derivatives: A Time-Dependent Density Functional Theory Study (Postprint)

DTIC Science & Technology

2007-01-01

2003. 15 A. Barik , S. Nath, and H. Pal, J . Chem. Phys. 119, 10202 2003. 16 A. Fisher, C. Cremer, and E. H. K. Stelzer, Appl. Opt. 34, 1989 1995...Hardened Materials Branch //Signature// TIM J . SCHUMACHER, Chief Survivability and Sensor Materials Division This...coumarin 152, 152A, 522, 153, 307, and 151. 094303-2 Nguyen, Day, and Pachter J . Chem. Phys. 126, 094303 2007 Downloaded 06 Nov 2007 to 134.131.125.49

Science and Technology Text Mining: Comparative Analysis of the Research Impact Assessment Literature and the Journal of the American Chemical Society

DTIC Science & Technology

2003-08-15

Their analyses confirmed Swanson’s results, and showed that FISH OIL and EICOSAPENTAENOIC ACID (one of fish oil’s main chemical constituents) offered...therefore true candidates for discovery. They finally arrive at FISH OIL, and EICOSAPENTAENOIC ACID (one of fish oil’s main chemical constituents...CHEM 250 ; BIOPOLYMERS 242 ; LANGMUIR 239 ; MOL-PHYS 233 ; 24 PHYS-REV-B 232 ; ANAL-CHEM 225 ; INT-J-MASS-SPECTROM 222 ; NUCLEIC- ACIDS -RES 222 ; J

Molecular based equation of state for shocked liquid nitromethane.

PubMed

Desbiens, Nicolas; Bourasseau, Emeric; Maillet, Jean-Bernard; Soulard, Laurent

2009-07-30

An approach is proposed to obtain the equation of state of unreactive shocked liquid nitromethane. Unlike previous major works, this equation of state is not based on extended integration schemes [P.C. Lysne, D.R. Hardesty, Fundamental equation of state of liquid nitromethane to 100 kbar, J. Chem. Phys. 59 (1973) 6512]. It does not follow the way proposed by Winey et al. [J.M. Winey, G.E. Duvall, M.D. Knudson, Y.M. Gupta, Equation of state and temperature measurements for shocked nitromethane, J. Chem. Phys. 113 (2000) 7492] where the specific heat C(v), the isothermal bulk modulus B(T) and the coefficient of thermal pressure (deltaP/deltaT)(v) are modeled as functions of temperature and volume using experimental data. In this work, we compute the complete equation of state by microscopic calculations. Indeed, by means of Monte Carlo molecular simulations, we have proposed a new force field for nitromethane that lead to a good description of shock properties [N. Desbiens, E. Bourasseau, J.-B. Maillet, Potential optimization for the calculation of shocked liquid nitromethane properties, Mol. Sim. 33 (2007) 1061; A. Hervouët, N. Desbiens, E. Bourasseau, J.-B. Maillet, Microscopic approaches to liquid nitromethane detonation properties, J. Phys. Chem. B 112 (2008) 5070]. Particularly, it has been shown that shock temperatures and second shock temperatures are accurately reproduced which is significative of the quality of the potential. Here, thermodynamic derivative properties are computed: specific heats, Grüneisen parameter, sound velocity among others, along the Hugoniot curve. This work constitutes to our knowledge the first determination of the equation of state of an unreactive shocked explosive by molecular simulations.

Curiosity ChemCam Analyzes Rocks, Soils and Dust

NASA Image and Video Library

2013-04-08

This diagram shows how materials analyzed by the ChemCam instrument on NASA Curiosity Mars rover during the first 100 Martian days of the mission differed with regard to hydrogen content horizontal axis and alkali vertical axis.

Aerosol Processing in Mixed-Phase Clouds in ECHAM5-HAM: Comparison of Single-Column Model Simulations to Observations

NASA Astrophysics Data System (ADS)

Hoose, C.; Lohmann, U.; Stier, P.; Verheggen, B.; Weingartner, E.; Herich, H.

2007-12-01

The global aerosol-climate model ECHAM5-HAM (Stier et al., 2005) has been extended by an explicit treatment of cloud-borne particles. Two additional modes for in-droplet and in-crystal particles are introduced, which are coupled to the number of cloud droplet and ice crystal concentrations simulated by the ECHAM5 double-moment cloud microphysics scheme (Lohmann et al., 2007). Transfer, production and removal of cloud-borne aerosol number and mass by cloud droplet activation, collision scavenging, aqueous-phase sulfate production, freezing, melting, evaporation, sublimation and precipitation formation are taken into account. The model performance is demonstrated and validated with observations of the evolution of total and interstitial aerosol concentrations and size distributions during three different mixed-phase cloud events at the alpine high-altitude research station Jungfraujoch (Switzerland) (Verheggen et al, 2007). Although the single-column simulations can not be compared one-to-one with the observations, the governing processes in the evolution of the cloud and aerosol parameters are captured qualitatively well. High scavenged fractions are found during the presence of liquid water, while the release of particles during the Bergeron-Findeisen process results in low scavenged fractions after cloud glaciation. The observed coexistence of liquid and ice, which might be related to cloud heterogeneity at subgrid scales, can only be simulated in the model when forcing non-equilibrium conditions. References: U. Lohmann et al., Cloud microphysics and aerosol indirect effects in the global climate model ECHAM5-HAM, Atmos. Chem. Phys. 7, 3425-3446 (2007) P. Stier et al., The aerosol-climate model ECHAM5-HAM, Atmos. Chem. Phys. 5, 1125-1156 (2005) B. Verheggen et al., Aerosol partitioning between the interstitial and the condensed phase in mixed-phase clouds, Accepted for publication in J. Geophys. Res. (2007)

Transferability of polarizable models for ion-water electrostatic interaction

NASA Astrophysics Data System (ADS)

Masia, Marco

2009-06-01

Studies of ion-water systems at condensed phase and at interfaces have pointed out that molecular and ionic polarization plays an important role for many phenomena ranging from hydrogen bond dynamics to water interfaces' structure. Classical and ab initio Molecular Dynamics simulations reveal that induced dipole moments at interfaces (e.g. air-water and water-protein) are usually high, hinting that polarizable models to be implemented in classical force fields should be very accurate in reproducing the electrostatic properties of the system. In this paper the electrostatic properties of three classical polarizable models for ion-water interaction are compared with ab initio results both at gas and condensed phase. For Li+- water and Cl--water dimers the reproducibility of total dipole moments obtained with high level quantum chemical calculations is studied; for the same ions in liquid water, Car-Parrinello Molecular Dynamics simulations are used to compute the time evolution of ionic and molecular dipole moments, which are compared with the classical models. The PD2-H2O model developed by the author and coworkers [Masia et al. J. Chem. Phys. 2004, 121, 7362] together with the gaussian intermolecular damping for ion-water interaction [Masia et al. J. Chem. Phys. 2005, 123, 164505] showed to be the fittest in reproducing the ab initio results from gas to condensed phase, allowing for force field transferability.

Approximating Matsubara dynamics using the planetary model: Tests on liquid water and ice

NASA Astrophysics Data System (ADS)

Willatt, Michael J.; Ceriotti, Michele; Althorpe, Stuart C.

2018-03-01

Matsubara dynamics is the quantum-Boltzmann-conserving classical dynamics which remains when real-time coherences are taken out of the exact quantum Liouvillian [T. J. H. Hele et al., J. Chem. Phys. 142, 134103 (2015)]; because of a phase-term, it cannot be used as a practical method without further approximation. Recently, Smith et al. [J. Chem. Phys. 142, 244112 (2015)] developed a "planetary" model dynamics which conserves the Feynman-Kleinert (FK) approximation to the quantum-Boltzmann distribution. Here, we show that for moderately anharmonic potentials, the planetary dynamics gives a good approximation to Matsubara trajectories on the FK potential surface by decoupling the centroid trajectory from the locally harmonic Matsubara fluctuations, which reduce to a single phase-less fluctuation particle (the "planet"). We also show that the FK effective frequency can be approximated by a direct integral over these fluctuations, obviating the need to solve iterative equations. This modification, together with use of thermostatted ring-polymer molecular dynamics, allows us to test the planetary model on water (gas-phase, liquid, and ice) using the q-TIP4P/F potential surface. The "planetary" fluctuations give a poor approximation to the rotational/librational bands in the infrared spectrum, but a good approximation to the bend and stretch bands, where the fluctuation lineshape is found to be motionally narrowed by the vibrations of the centroid.

Rate coefficients from quantum and quasi-classical cumulative reaction probabilities for the S(1D) + H2 reaction

NASA Astrophysics Data System (ADS)

Jambrina, P. G.; Lara, Manuel; Menéndez, M.; Launay, J.-M.; Aoiz, F. J.

2012-10-01

Cumulative reaction probabilities (CRPs) at various total angular momenta have been calculated for the barrierless reaction S(1D) + H2 → SH + H at total energies up to 1.2 eV using three different theoretical approaches: time-independent quantum mechanics (QM), quasiclassical trajectories (QCT), and statistical quasiclassical trajectories (SQCT). The calculations have been carried out on the widely used potential energy surface (PES) by Ho et al. [J. Chem. Phys. 116, 4124 (2002), 10.1063/1.1431280] as well as on the recent PES developed by Song et al. [J. Phys. Chem. A 113, 9213 (2009), 10.1021/jp903790h]. The results show that the differences between these two PES are relatively minor and mostly related to the different topologies of the well. In addition, the agreement between the three theoretical methodologies is good, even for the highest total angular momenta and energies. In particular, the good accordance between the CRPs obtained with dynamical methods (QM and QCT) and the statistical model (SQCT) indicates that the reaction can be considered statistical in the whole range of energies in contrast with the findings for other prototypical barrierless reactions. In addition, total CRPs and rate coefficients in the range of 20-1000 K have been calculated using the QCT and SQCT methods and have been found somewhat smaller than the experimental total removal rates of S(1D).

Approximating Matsubara dynamics using the planetary model: Tests on liquid water and ice.

PubMed

Willatt, Michael J; Ceriotti, Michele; Althorpe, Stuart C

2018-03-14

Matsubara dynamics is the quantum-Boltzmann-conserving classical dynamics which remains when real-time coherences are taken out of the exact quantum Liouvillian [T. J. H. Hele et al., J. Chem. Phys. 142, 134103 (2015)]; because of a phase-term, it cannot be used as a practical method without further approximation. Recently, Smith et al. [J. Chem. Phys. 142, 244112 (2015)] developed a "planetary" model dynamics which conserves the Feynman-Kleinert (FK) approximation to the quantum-Boltzmann distribution. Here, we show that for moderately anharmonic potentials, the planetary dynamics gives a good approximation to Matsubara trajectories on the FK potential surface by decoupling the centroid trajectory from the locally harmonic Matsubara fluctuations, which reduce to a single phase-less fluctuation particle (the "planet"). We also show that the FK effective frequency can be approximated by a direct integral over these fluctuations, obviating the need to solve iterative equations. This modification, together with use of thermostatted ring-polymer molecular dynamics, allows us to test the planetary model on water (gas-phase, liquid, and ice) using the q-TIP4P/F potential surface. The "planetary" fluctuations give a poor approximation to the rotational/librational bands in the infrared spectrum, but a good approximation to the bend and stretch bands, where the fluctuation lineshape is found to be motionally narrowed by the vibrations of the centroid.

Bounds on quantum collapse models from matter-wave interferometry: calculational details

NASA Astrophysics Data System (ADS)

Toroš, Marko; Bassi, Angelo

2018-03-01

We present a simple derivation of the interference pattern in matter-wave interferometry predicted by a class of quantum master equations. We apply the obtained formulae to the following collapse models: the Ghirardi-Rimini-Weber (GRW) model, the continuous spontaneous localization (CSL) model together with its dissipative (dCSL) and non-Markovian generalizations (cCSL), the quantum mechanics with universal position localization (QMUPL), and the Diósi-Penrose (DP) model. We discuss the separability of the dynamics of the collapse models along the three spatial directions, the validity of the paraxial approximation, and the amplification mechanism. We obtain analytical expressions both in the far field and near field limits. These results agree with those already derived in the Wigner function formalism. We compare the theoretical predictions with the experimental data from two recent matter-wave experiments: the 2012 far-field experiment of Juffmann T et al (2012 Nat. Nanotechnol. 7 297-300) and the 2013 Kapitza-Dirac-Talbot-Lau (KDTL) near-field experiment of Eibenberger et al (2013 Phys. Chem. Chem. Phys. 15 14696-700). We show the region of the parameter space for each collapse model that is excluded by these experiments. We show that matter-wave experiments provide model-insensitive bounds that are valid for a wide family of dissipative and non-Markovian generalizations.

Gaussian basis sets for use in correlated molecular calculations. XI. Pseudopotential-based and all-electron relativistic basis sets for alkali metal (K-Fr) and alkaline earth (Ca-Ra) elements

NASA Astrophysics Data System (ADS)

Hill, J. Grant; Peterson, Kirk A.

2017-12-01

New correlation consistent basis sets based on pseudopotential (PP) Hamiltonians have been developed from double- to quintuple-zeta quality for the late alkali (K-Fr) and alkaline earth (Ca-Ra) metals. These are accompanied by new all-electron basis sets of double- to quadruple-zeta quality that have been contracted for use with both Douglas-Kroll-Hess (DKH) and eXact 2-Component (X2C) scalar relativistic Hamiltonians. Sets for valence correlation (ms), cc-pVnZ-PP and cc-pVnZ-(DK,DK3/X2C), in addition to outer-core correlation [valence + (m-1)sp], cc-p(w)CVnZ-PP and cc-pwCVnZ-(DK,DK3/X2C), are reported. The -PP sets have been developed for use with small-core PPs [I. S. Lim et al., J. Chem. Phys. 122, 104103 (2005) and I. S. Lim et al., J. Chem. Phys. 124, 034107 (2006)], while the all-electron sets utilized second-order DKH Hamiltonians for 4s and 5s elements and third-order DKH for 6s and 7s. The accuracy of the basis sets is assessed through benchmark calculations at the coupled-cluster level of theory for both atomic and molecular properties. Not surprisingly, it is found that outer-core correlation is vital for accurate calculation of the thermodynamic and spectroscopic properties of diatomic molecules containing these elements.

Speed dependence of CH335Cl-O2 line-broadening parameters probed on rotational transitions: Measurements and semi-classical calculations

NASA Astrophysics Data System (ADS)

Buldyreva, J.; Margulès, L.; Motiyenko, R. A.; Rohart, F.

2013-11-01

Relaxation parameters for K-components (K≤6) of six J→J+1 rotational transitions (J=6, 10, 17, 22, 31 and 33) of CH335Cl perturbed by O2 are measured at room temperature with Voigt, speed-dependent Voigt and Galatry profiles in order to probe the speed-dependence effects. With respect to the previous study of CH335Cl-N2 system [Guinet et al., J Quant Spectrosc Radiat Transfer 2012;113:1113], higher active-gas pressures are reached, providing better signal-to-noise ratios, and the exact expression of the Beer-Lambert law is introduced in the fitting procedure, leading, among other advantages, to much more realistic low-pressure results. The broadening parameters of the considered lines are also computed by a semi-classical method for various relative velocities of colliders and the powers characterizing the dependence of the collisional cross-sections on relative speeds are deduced as functions of the rotational numbers J and K. Additional calculations performed with the Maxwell-Boltzmann distribution of velocities show no significant difference with the earlier results [Buldyreva et al., Phys Chem Chem Phys 2011;13:20326] obtained within the mean thermal velocity approximation. Weighted sums of the presently measured Voigt-profile O2-broadening parameters and of the previously published N2-broadening ones are calculated to yield experimental air-broadening coefficients for spectroscopic databases.

Why is MP2-Water "Cooler" and "Denser" than DFT-Water?

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

Willow, Soohaeng Y.; Zeng, Xiao Cheng; Xantheas, Sotiris S.

To maintain water in the liquid phase at the correct (1 g/cm3) density during first-principles simulations, density-functional theory (DFT) with a dispersionless generalized-gradient-approximation (GGA) functional requires a much higher temperature and pressure than the ambient conditions. Conversely, ab initio second-order many-body perturbation (MP2) calculations of liquid water performed by Del Ben et al. [J. Chem. Phys. Lett. 4, 3753 (2013); J. Chem. Phys. 143, 054506 (2015)] and by us [Willow et al., Sci. Rep. 5, 14358 (2015)] required a lower temperature and a negative pressure than DFT to keep water liquid. Here, we present a unifying explanation of these trendsmore » derived from classical water simulations using a polarizable force field with different sets of parameters. We show that the calculated temperature and pressure of the liquid phase are strongly correlated with the polarizability of water and the dispersion interaction, respectively. In DFT/GGA, the polarizability and thus the induced dipole moments and the hydrogen-bond strength are all overestimated. This hinders the rotational motion of molecules and requires a higher temperature for water to be liquid. In MP2 and DFT/GGA, the dispersion interaction is stronger and weaker (or lacking), respectively. This explains why liquid water contracts uniformly and becomes too dense in MP2, whereas the opposite is the case for dispersionless DFT/GGA.« less

Pure AlN layers in metal-polar AlGaN/AlN/GaN and AlN/GaN heterostructures grown by low-temperature ammonia-based molecular beam epitaxy

NASA Astrophysics Data System (ADS)

Kaun, Stephen W.; Mazumder, Baishakhi; Fireman, Micha N.; Kyle, Erin C. H.; Mishra, Umesh K.; Speck, James S.

2015-05-01

When grown at a high temperature (820 °C) by ammonia-based molecular beam epitaxy (NH3-MBE), the AlN layers of metal-polar AlGaN/AlN/GaN heterostructures had a high GaN mole fraction (∼0.15), as identified by atom probe tomography in a previous study (Mazumder et al 2013 Appl. Phys. Lett. 102 111603). In the study presented here, growth at low temperature (<740 °C) by NH3-MBE yielded metal-polar AlN layers that were essentially pure at the alloy level. The improved purity of the AlN layers grown at low temperature was correlated to a dramatic increase in the sheet density of the two-dimensional electron gas (2DEG) at the AlN/GaN heterointerface. Through application of an In surfactant, metal-polar AlN(3.5 nm)/GaN and AlGaN/AlN(2.5 nm)/GaN heterostructures grown at low temperature yielded low 2DEG sheet resistances of 177 and 285 Ω/□, respectively.

PubChem3D: Conformer generation

PubMed Central

2011-01-01

Background PubChem, an open archive for the biological activities of small molecules, provides search and analysis tools to assist users in locating desired information. Many of these tools focus on the notion of chemical structure similarity at some level. PubChem3D enables similarity of chemical structure 3-D conformers to augment the existing similarity of 2-D chemical structure graphs. It is also desirable to relate theoretical 3-D descriptions of chemical structures to experimental biological activity. As such, it is important to be assured that the theoretical conformer models can reproduce experimentally determined bioactive conformations. In the present study, we investigate the effects of three primary conformer generation parameters (the fragment sampling rate, the energy window size, and force field variant) upon the accuracy of theoretical conformer models, and determined optimal settings for PubChem3D conformer model generation and conformer sampling. Results Using the software package OMEGA from OpenEye Scientific Software, Inc., theoretical 3-D conformer models were generated for 25,972 small-molecule ligands, whose 3-D structures were experimentally determined. Different values for primary conformer generation parameters were systematically tested to find optimal settings. Employing a greater fragment sampling rate than the default did not improve the accuracy of the theoretical conformer model ensembles. An ever increasing energy window did increase the overall average accuracy, with rapid convergence observed at 10 kcal/mol and 15 kcal/mol for model building and torsion search, respectively; however, subsequent study showed that an energy threshold of 25 kcal/mol for torsion search resulted in slightly improved results for larger and more flexible structures. Exclusion of coulomb terms from the 94s variant of the Merck molecular force field (MMFF94s) in the torsion search stage gave more accurate conformer models at lower energy windows. Overall

PubChem atom environments.

PubMed

Hähnke, Volker D; Bolton, Evan E; Bryant, Stephen H

2015-01-01

Atom environments and fragments find wide-spread use in chemical information and cheminformatics. They are the basis of prediction models, an integral part in similarity searching, and employed in structure search techniques. Most of these methods were developed and evaluated on the relatively small sets of chemical structures available at the time. An analysis of fragment distributions representative of most known chemical structures was published in the 1970s using the Chemical Abstracts Service data system. More recently, advances in automated synthesis of chemicals allow millions of chemicals to be synthesized by a single organization. In addition, open chemical databases are readily available containing tens of millions of chemical structures from a multitude of data sources, including chemical vendors, patents, and the scientific literature, making it possible for scientists to readily access most known chemical structures. With this availability of information, one can now address interesting questions, such as: what chemical fragments are known today? How do these fragments compare to earlier studies? How unique are chemical fragments found in chemical structures? For our analysis, after hydrogen suppression, atoms were characterized by atomic number, formal charge, implicit hydrogen count, explicit degree (number of neighbors), valence (bond order sum), and aromaticity. Bonds were differentiated as single, double, triple or aromatic bonds. Atom environments were created in a circular manner focused on a central atom with radii from 0 (atom types) up to 3 (representative of ECFP_6 fragments). In total, combining atom types and atom environments that include up to three spheres of nearest neighbors, our investigation identified 28,462,319 unique fragments in the 46 million structures found in the PubChem Compound database as of January 2013. We could identify several factors inflating the number of environments involving transition metals, with many

Mw Systematic Study of Alkaloids: the Distorted Tropane of Scopoline

NASA Astrophysics Data System (ADS)

Ecija, Patricia; Cocinero, Emilio J.; Basterretxea, Francisco J.; Fernandez, Jose A.; Castano, Fernando; Lesarri, Alberto

2013-06-01

Tropane alkaloids have diverse pharmacological uses and are well-known for their neurostimulant activity. Previous structure-activity-relationship established correlations between bioactivity and several aspects of ligand conformation and stereochemistry, including delicate intramolecular effects like nitrogen inversion^{a}. We have initiated a series of structural studies on tropane alkaloids^{b}, aimed to discerning their intrinsic stereochemical properties using rotational spectroscopy in supersonic jets^{c}. Here we extend these studies to the epoxytropanes, initially motivated to interrogate the influence of the epoxy group on nitrogen inversion and ring conformation. The rotational spectrum evidences a single structure in the gas phase, providing a first description of the (three ring) structurally-distorted tropane in scopoline. The determined rotational parameters of scopoline reveal the structural consequences of the intramolecular cyclation of scopine, which breaks the original epoxy group and creates a new ether bridge and a 7β-hydroxytropane configuration. The hydroxyl group further stabilizes the molecule by an O-H \\cdots N intramolecular hydrogen bond, which, in turn, forces the N-methyl group to the less stable axial form^{b}. The experimental work was supported by ab initio and DFT calculations. ^{a} i) S.Singh, Chem. Rev. 100, 925 (2000); ii) A. Krunic, D. Pan, W.J. Dunn III, S.V.S. Miariappan, Bioorg. & Med. Chem. 17, 811 (2009). ^{b} E.J. Cocinero, A. Lesarri, P. écija, J.-U. Grabow, J.A. Fernández, F. Castaño, Phys. Chem. Chem. Phys. 12, 6076 (2010). ^{c} E.J. Cocinero, A. Lesarri, P. écija, J.-U. Grabow, J.A. Fernández, F. Castaño, Phys. Chem. Chem. Phys. 12, 12486 (2010).

ChemCam rock laser for Mars Science Laboratory "Curiosity"

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

Wiens, Roger

2010-09-03

Los Alamos has a long history of space-related instruments, tied primarily to its role in defense-related treaty verification. Space-based detectors have helped determine the differences between signals from lightning bolts and potential nuclear explosions. LANL-developed gamma-ray detection instruments first revealed the existence of what we now know as gamma-ray bursts, an exciting area of astrophysical research. And the use of LANL instruments on varied space missions continues with such products as the ChemCam rock laser for NASA, shown here. The Engineering Model of the ChemCam Mars Science Laboratory rover instrument arrived at NASA's Jet Propulsion Laboratory on February 6, 2008.more » The Flight Model was shipped in August, 2010 for installation on the rover at JPL. ChemCam will use imaging and laser-induced breakdown spectroscopy (LIBS) to determine rock and soil compositions on Mars, up to 9 meters from the rover. The engineering model is being integrated into the rover test bed for the development and testing of the rover software. The actual flight model components were concurrently assembled at Los Alamos and in Toulouse, France. The Mars Science Laboratory is scheduled to launch in 2011. Animations courtesy of JPL/NASA.« less

ChemCam Rock Laser for the Mars Science Laboratory

ScienceCinema

LANL

2017-12-09

Los Alamos has a long history of space-related instr... Los Alamos has a long history of space-related instruments, tied primarily to its role in defense-related treaty verification. Space-based detectors have helped determine the differences between signals from lightning bolts and potential nuclear explosions. LANL-developed gamma-ray detection instruments first revealed the existence of what we now know as gamma-ray bursts, an exciting area of astrophysical research. And the use of LANL instruments on varied space missions continues with such products as the ChemCam rock laser for NASA, shown here. The Engineering Model of the ChemCam Mars Science Laboratory rover instrument arrived at NASA's Jet Propulsion Laboratory on February 6, 2008. ChemCam will use imaging and laser-induced breakdown spectroscopy (LIBS) to determine rock and soil compositions on Mars, up to 9 meters from the rover. The engineering model is being integrated into the rover test bed for the development and testing of the rover software. The actual flight model components are concurrently being assembled at Los Alamos and in Toulouse, France, and will be delivered to JPL in July. The Mars Science Laboratory is scheduled to launch in 2009. Animations courtesy of JPL/NASA.

Analysis of experimental nucleation data for silver and SiO using scaled nucleation theory

NASA Astrophysics Data System (ADS)

Hale, Barbara N.; Kemper, Paul; Nuth, Joseph A.

1989-10-01

The experimental vapor phase nucleation data of Nuth et al., for silver [J. A. Nuth, K. A. Donnelly, B. Donn, and L. U. Lilleleht, J. Chem. Phys. 77, 2639 (1982)] and SiO [J. A. Nuth and B. Donn, J. Chem. Phys. 85, 1116 (1986)] are reanalyzed using a scaled model for homogeneous nucleation [B. N. Hale, Phys. Rev. A 33, 4156 (1986)]. The approximation is made that the vapor pressure at the nucleation site is not diminished significantly from that at the source (crucible). It is found that the data for ln S have a temperature dependence consistent with the scaled theory ln S≊ΓΩ3/2 [Tc/T-1]3/2, and predict critical temperatures 3800±200 K for silver and 3700±200 K for SiO. One can also extract an effective excess surface entropy per atom Ω=2.1±0.1 and an effective surface tension σ≊1500-0.45T ergs/cm2 for the small silver clusters (assuming a range of nucleation rates from 105 to 1011 cm-3 s-1). The corresponding values for SiO are Ω≊1.7±0.1 and σ≊820-0.22T ergs/cm2 (assuming a range of nucleation rates from 109 to 1012 cm-3 s-1).

Characterising Brazilian biomass burning emissions using WRF-Chem with MOSAIC sectional aerosol

NASA Astrophysics Data System (ADS)

Archer-Nicholls, S.; Lowe, D.; Darbyshire, E.; Morgan, W. T.; Bela, M. M.; Pereira, G.; Trembath, J.; Kaiser, J. W.; Longo, K. M.; Freitas, S. R.; Coe, H.; McFiggans, G.

2015-03-01

The South American Biomass Burning Analysis (SAMBBA) field campaign took detailed in situ flight measurements of aerosol during the 2012 dry season to characterise biomass burning aerosol and improve understanding of its impacts on weather and climate. Developments have been made to the Weather Research and Forecast model with chemistry (WRF-Chem) model to improve the representation of biomass burning aerosol in the region, by coupling a sectional aerosol scheme to the plume-rise parameterisation. Brazilian Biomass Burning Emissions Model (3BEM) fire emissions are used, prepared using PREP-CHEM-SRC, and mapped to CBM-Z and MOSAIC species. Model results have been evaluated against remote sensing products, AERONET sites, and four case studies of flight measurements from the SAMBBA campaign. WRF-Chem predicted layers of elevated aerosol loadings (5-20 μg sm-3) of particulate organic matter at high altitude (6-8 km) over tropical forest regions, while flight measurements showed a sharp decrease above 2-4 km altitude. This difference was attributed to the plume-rise parameterisation overestimating injection height. The 3BEM emissions product was modified using estimates of active fire size and burned area for the 2012 fire season, which reduced the fire size. The enhancement factor for fire emissions was increased from 1.3 to 5 to retain reasonable aerosol optical depths (AODs). The smaller fire size lowered the injection height of the emissions, but WRF-Chem still showed elevated aerosol loadings between 4-5 km altitude. Over eastern cerrado (savannah-like) regions, both modelled and measured aerosol loadings decreased above approximately 4 km altitude. Compared with MODIS satellite data and AERONET sites, WRF-Chem represented AOD magnitude well (between 0.3-1.5) over western tropical forest fire regions in the first half of the campaign, but tended to over-predict them in the second half, when precipitation was more significant. Over eastern cerrado regions, WRF-Chem

Characterising Brazilian biomass burning emissions using WRF-Chem with MOSAIC sectional aerosol

NASA Astrophysics Data System (ADS)

Archer-Nicholls, S.; Lowe, D.; Darbyshire, E.; Morgan, W. T.; Bela, M. M.; Pereira, G.; Trembath, J.; Kaiser, J. W.; Longo, K. M.; Freitas, S. R.; Coe, H.; McFiggans, G.

2014-09-01

The South American Biomass Burning Analysis (SAMBBA) field campaign took detailed in-situ flight measurements of aerosol during the 2012 dry season to characterise biomass burning aerosol and improve understanding of its impacts on weather and climate. Developments have been made to the Weather research and Forecast model with chemistry (WRF-Chem) model to improve the representation of biomass burning aerosol in the region by coupling a sectional aerosol scheme to the plume rise parameterisation. Brazilian Biomass Burning Emissions Model (3BEM) fire emissions are used, prepared using PREP-CHEM-SRC, and mapped to CBM-Z and MOSAIC species. Model results have been evaluated against remote sensing products, AERONET sites, and four case studies of flight measurements from the SAMBBA campaign. WRF-Chem predicted layers of elevated aerosol loadings (5-20 μg sm-3) of particulate organic matter at high altitude (6-8 km) over tropical forest regions, while flight measurements showed a sharp decrease above 2-4 km altitude. This difference was attributed to the plume-rise parameterisation overestimating injection height. The 3BEM emissions product was modified using estimates of active fire size and burned area for the 2012 fire season, which reduced the fire size. The enhancement factor for fire emissions was increased from 1.3 to 5 to retain reasonable aerosol optical depths (AOD). The smaller fire size lowered the injection height of the emissions, but WRF-Chem still showed elevated aerosol loadings between 4-5 km altitude. Over eastern Cerrado (savannah-like) regions, both modelled and measured aerosol loadings decreased above approximately 4 km altitude. Compared with MODIS satellite data and AERONET sites, WRF-Chem represented AOD magnitude well (between 0.3-1.5) over western tropical forest fire regions in the first half of the campaign, but tended to over-predict them in the second half, when precipitation was more significant. Over eastern Cerrado regions, WRF-Chem

Poly (acrylonitrile - co -1-vinylimidazole): A New Melt Processable Carbon Fiber Precursor

DTIC Science & Technology

2011-01-01

changed fromwhite to brown and then black during stabilization as expected. The stabi- lized black copolymers were insoluble in DMF, showing good...Paliwal DK, Bajaj P. J Appl Polym Sci 1996;59:1819. [9] Bhanu VA, Rangarajan P, Wiles K, Bortner M, Sankarpandian M, Godshall D, et al. Polymer 2002;43:4841...AA. Carbon 2005;43:1065e72. [23] Bajaj P, Roopanwal AK. J Macromol Sci Rev Macromol Chem Phys 1997;C37:97. [24] Mukundan T, Bhanu VA, Wiles KB, Johnson

Visualization of Two-Phase Fluid Distribution Using Laser Induced Exciplex Fluorescence

NASA Astrophysics Data System (ADS)

Kim, J. U.; Darrow, J.; Schock, H.; Golding, B.; Nocera, D.; Keller, P.

1998-03-01

Laser-induced exciplex (excited state complex) fluorescence has been used to generate two-dimensional images of dispersed liquid and vapor phases with spectrally resolved two-color emissions. In this method, the vapor phase is tagged by the monomer fluorescence while the liquid phase is tracked by the exciplex fluorescence. A new exciplex visualization system consisting of DMA and 1,4,6-TMN in an isooctane solvent was developed.(J.U. Kim et al., Chem. Phys. Lett. 267, 323-328 (1997)) The direct ca

Ultrafast Chemical Dynamics of Reactions in Beams

DTIC Science & Technology

1994-04-14

Wave Packet Motion in Dissociative Reactions: Up to 40 Picoseconds. P. Cong, A. Mokhtari , and A. H. Zewail Chem. Phys. Lett., 172.109 (1990) 3. Direct...Femtosecond Mapping of the Trajectories in a Chemical Reaction. A. Mokhtari , P. Cong, J. L. Herek, and A. H. Zewail Nature, 348 225 (1990) 4...to 40 Picoseconds. P. Cong. A. Mokhtari , and A. H. Zewail Chem. Phys. Left., 172. 109 (1990) 8 4. Femtosecond Selective Control of Wave Packet

Impact of Backbone Rigidity on the Photomechanical Response of Glassy, Azobenzene-Functionalized Polyimides (Postprint)

DTIC Science & Technology

2014-01-13

Y .; Choi, H . H .; Hwang , H . K.; Kim, Y .; Lee , S .; Jang, S . H .; Kakimoto, M.; Takezoe, H . Jpn. J. Appl. Phys., Part 1: Regul. Pap. Short Notes Rev... H .; Vaia, R. A.; Tan, L. S .; White, T. J. Angew. Chem., Int. Ed. 2012, 51 (17), 4117−4121. (6) Wang, D. H .; Lee , K. M.; Yu, Z. N .; Koerner, H .; Vaia...J. Macromol. Chem. Phys. 2013, 214 (11), 1189−1194. (8) Wang, D. H .; Lee , K. M.;

Tropospheric ozone using an emission tagging technique in the CAM-Chem and WRF-Chem models

NASA Astrophysics Data System (ADS)

Lupascu, A.; Coates, J.; Zhu, S.; Butler, T. M.

2017-12-01

Tropospheric ozone is a short-lived climate forcing pollutant. High concentration of ozone can affect human health (cardiorespiratory and increased mortality due to long-term exposure), and also it damages crops. Attributing ozone concentrations to the contributions from different sources would indicate the effects of locally emitted or transported precursors on ozone levels in specific regions. This information could be used as an important component of the design of emissions reduction strategies by indicating which emission sources could be targeted for effective reductions, thus reducing the burden of ozone pollution. Using a "tagging" approach within the CAM-Chem (global) and WRF-Chem (regional) models, we can quantify the contribution of individual emission of NOx and VOC precursors on air quality. Hence, when precursor emissions of NOx are tagged, we have seen that the largest contributors on ozone levels are the anthropogenic sources, while in the case of precursor emissions of VOCs, the biogenic sources and methane account for more than 50% of ozone levels. Further, we have extended the NOx tagging method in order to investigate continental source region contributions to concentrations of ozone over various receptor regions over the globe, with a zoom over Europe. In general, summertime maximum ozone in most receptor regions is largely attributable to local emissions of anthropogenic NOx and biogenic VOC. During the rest of the year, especially during springtime, ozone in most receptor regions shows stronger influences from anthropogenic emissions of NOx and VOC in remote source regions.

Spark Generated by ChemCam Laser During Tests

NASA Image and Video Library

2010-09-21

The ChemCam instrument for NASA Mars Science Laboratory mission uses a pulsed laser beam to vaporize a pinhead-size target, producing a flash of light from the ionized material plasma that can be analyzed to identify chemical elements in the target.

Recent results from the ILL NSEs

NASA Astrophysics Data System (ADS)

Farago, Bela

2007-07-01

In this paper I will try to present some recent results on less usual subjects, which I believe are forward pointing to fields which might develop faster as new sources/instruments become available. The first deals with an assembly of spherical microemulsions which under certain conditions self-organize themselves into a cubic phase. Applying contrast variation and covering the large dynamical range of NSE we just start to be able to identify the different kind of relaxations present [B. Molle, et al., Phys. Rev. Lett. 90 (2003) 068305]. The second shows a nice example of diffusion of alkane chains in porous material (zeolite). Here high resolution and high intensity were needed to pinpoint the predicted “window” effect [H. Jobic, et al., Angew. Chem. Int. Ed. 43(3) (2004) 364]. Finally some results on PMMA/PEO polymer blend will be shown, where the high count rate and simultaneous multi-Q measurement on IN11C made the experiment possible. Still improved resolution would be very welcome to fully extract all possible information [B. Farago, et al., Phys. Rev. E 72 (2005) 031809].

Properties of Organic Liquids when Simulated with Long-Range Lennard-Jones Interactions.

PubMed

Fischer, Nina M; van Maaren, Paul J; Ditz, Jonas C; Yildirim, Ahmet; van der Spoel, David

2015-07-14

In order to increase the accuracy of classical computer simulations, existing methodologies may need to be adapted. Hitherto, most force fields employ a truncated potential function to model van der Waals interactions, sometimes augmented with an analytical correction. Although such corrections are accurate for homogeneous systems with a long cutoff, they should not be used in inherently inhomogeneous systems such as biomolecular and interface systems. For such cases, a variant of the particle mesh Ewald algorithm (Lennard-Jones PME) was already proposed 20 years ago (Essmann et al. J. Chem. Phys. 1995, 103, 8577-8593), but it was implemented only recently (Wennberg et al. J. Chem. Theory Comput. 2013, 9, 3527-3537) in a major simulation code (GROMACS). The availability of this method allows surface tensions of liquids as well as bulk properties to be established, such as density and enthalpy of vaporization, without approximations due to truncation. Here, we report on simulations of ≈150 liquids (taken from a force field benchmark: Caleman et al. J. Chem. Theory Comput. 2012, 8, 61-74) using three different force fields and compare simulations with and without explicit long-range van der Waals interactions. We find that the density and enthalpy of vaporization increase for most liquids using the generalized Amber force field (GAFF, Wang et al. J. Comput. Chem. 2004, 25, 1157-1174) and the Charmm generalized force field (CGenFF, Vanommeslaeghe et al. J. Comput. Chem. 2010, 31, 671-690) but less so for OPLS/AA (Jorgensen and Tirado-Rives, Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 6665-6670), which was parametrized with an analytical correction to the van der Waals potential. The surface tension increases by ≈10(-2) N/m for all force fields. These results suggest that van der Waals attractions in force fields are too strong, in particular for the GAFF and CGenFF. In addition to the simulation results, we introduce a new version of a web server, http

ScrubChem: Cleaning of PubChem Bioassay Data to Create Diverse and Massive Bioactivity Datasets for Use in Modeling Applications (SOT)

EPA Science Inventory

The PubChem Bioassay database is a non-curated public repository with bioactivity data from 64 sources, including: ChEMBL, BindingDb, DrugBank, Tox21, NIH Molecular Libraries Screening Program, and various academic, government, and industrial contributors. However, this data is d...

Slowest kinetic modes revealed by metabasin renormalization

NASA Astrophysics Data System (ADS)

Okushima, Teruaki; Niiyama, Tomoaki; Ikeda, Kensuke S.; Shimizu, Yasushi

2018-02-01

Understanding the slowest relaxations of complex systems, such as relaxation of glass-forming materials, diffusion in nanoclusters, and folding of biomolecules, is important for physics, chemistry, and biology. For a kinetic system, the relaxation modes are determined by diagonalizing its transition rate matrix. However, for realistic systems of interest, numerical diagonalization, as well as extracting physical understanding from the diagonalization results, is difficult due to the high dimensionality. Here, we develop an alternative and generally applicable method of extracting the long-time scale relaxation dynamics by combining the metabasin analysis of Okushima et al. [Phys. Rev. E 80, 036112 (2009), 10.1103/PhysRevE.80.036112] and a Jacobi method. We test the method on an illustrative model of a four-funnel model, for which we obtain a renormalized kinematic equation of much lower dimension sufficient for determining slow relaxation modes precisely. The method is successfully applied to the vacancy transport problem in ionic nanoparticles [Niiyama et al., Chem. Phys. Lett. 654, 52 (2016), 10.1016/j.cplett.2016.04.088], allowing a clear physical interpretation that the final relaxation consists of two successive, characteristic processes.

Characteristic features of a high-energy x-ray spectra estimation method based on the Waggener iterative perturbation principle

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

Iwasaki, Akira; Kubota, Mamoru; Hirota, Junichi

2006-11-15

We have redeveloped a high-energy x-ray spectra estimation method reported by Iwasaki et al. [A. Iwasaki, H. Matsutani, M. Kubota, A. Fujimori, K. Suzaki, and Y. Abe, Radiat. Phys. Chem. 67, 81-91 (2003)]. The method is based on the iterative perturbation principle to minimize differences between measured and calculated transmission curves, originally proposed by Waggener et al. [R. G. Waggener, M. M. Blough, J. A. Terry, D. Chen, N. E. Lee, S. Zhang, and W. D. McDavid, Med. Phys. 26, 1269-1278 (1999)]. The method can estimate spectra applicable for media at least from water to lead using only about tenmore » energy bins. Estimating spectra of 4-15 MV x-ray beams from a linear accelerator, we describe characteristic features of the method with regard to parameters including the prespectrum, number of transmission measurements, number of energy bins, energy bin widths, and artifactual bipeaked spectrum production.« less

Alternative first-principles calculation of entropy for liquids

DOE PAGES

Meyer, Edmund R.; Ticknor, Christopher; Kress, Joel D.; ...

2016-04-15

Here, w present an alternative method for interpreting the velocity autocorrelation function (VACF) of a fluid with application to extracting the entropy in a manner similar to the methods developed by Lin et al. [J. Chem. Phys. 119, 11792 (2003)] and improved upon by Desjarlais [Phys. Rev. E 88, 062145 (2013)]. The liquid VACF is decomposed into two components, one gas and one solid, and each contribution's entropic portion is calculated. But, we fit both the gas and solid portions of the VACF in the time domain. This approach is applied to a single-component liquid (a two-phase model of liquidmore » Al at the melt line) and two different two-component systems: a superionic-to-superionic (bcc to fcc) phase transition in H 2 O at high temperatures and pressures and a metastable liquid state of MgO. Finally, for all three examples, comparisons to existing results in the literature demonstrate the validity of our alternative.« less

Calcium Sulfate Characterized by ChemCam/Curiosity at Gale Crater, Mars

NASA Technical Reports Server (NTRS)

Nachon, M.; Clegg, S. N.; Mangold, N.; Schroeder, S.; Kah, L. C.; Dromart, G.; Ollila, A.; Johnson, J. R.; Oehler, D. Z.; Bridges, J. C.;

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

Williams, S.; Rohlfing, E.A.; Rahn, L.A.

We present analytical signal expressions for each two-color resonant four-wave mixing (TC-RFWM) scheme that can be used for double-resonance molecular spectroscopy in the limit of weak fields (no saturation). The theoretical approach employs time-independent, diagrammatic perturbation theory and a spherical tensor analysis in an extension of recent treatments of degenerate four-wave mixing [S. Williams, R. N. Zare, and L. A. Rahn, J. Chem. Phys. {bold 101}, 1072 (1994)] and TC-RFWM for the specific case of stimulated emission pumping [S. Williams {ital et al.}, J. Chem. Phys. {bold 102}, 8342 (1995)]. Under the assumption that the relaxation of the population, themore » orientation, and the alignment are the same, simple analytic expressions are derived for commonly used experimental configurations. The TC-RFWM signal is found to be a product of a concentration term, a one-photon molecular term, a line shape function, and a laboratory-frame geometric factor. These expressions are intended to facilitate the practical analysis of TC-RFWM spectra by clarifying, for example, the dependence on beam polarizations and rotational branch combinations. {copyright} {ital 1997 American Institute of Physics.}« less

FTIR spectroscopy and thermodynamics of hydrogen adsorbed in a cross-linked polymer.

PubMed

Spoto, Giuseppe; Vitillo, Jenny G; Cocina, Donato; Damin, Alessandro; Bonino, Francesca; Zecchina, Adriano

2007-09-28

The adsorption of H(2) in a cross-linked poly(styrene-co-divinylbenzene) (St-DVB) microporous polymer (BET surface area 920 m(2) g(-1)) is studied by volumetric and gravimetric methods, FTIR spectroscopy at variable temperature (300-14 K) and ab initio calculations. At 77 K the polymer reversibly stores up to 1.3 mass% H(2) at a pressure of 1 bar and 1.8 mass% at 10 bar. The adsorption process involves the specific interaction of H(2) with the structural phenyl rings through weak dispersive forces. The interacting molecules become IR active and give rise to vibrational and rotational-vibrational manifestations which are affected by the temperature, the contact time and the H(2) equilibrium pressure. The spectra of the H(2)/St-DVB system reported here represent the first IR evidence of the adsorption of hydrogen on unsaturated molecules. The adsorption enthalpy is evaluated by the VTIR (variable temperature IR spectroscopy) method (C. Otero Areán et al., Phys. Chem. Chem. Phys., 2007, DOI: 10.1039/b615535a) and compared with the results of ab initio calculations for the H(2)/benzene interaction and with literature data.

Spectroscopic Manifestation of Vibrationally-Mediated Structure Change in the Isolated Formate Monohydrate

NASA Astrophysics Data System (ADS)

Denton, Joanna K.; Wolke, Conrad T.; Gorlova, Olga; Gerardi, Helen; McCoy, Anne B.; Johnson, Mark

2016-06-01

The breadth of the OH stretching manifold observed in the IR for bulk water is commonly attributed to the thermal population of excited states and the presence of many configurations within the water network. Here, I use carboxylate species as a rigid framework to isolate a single water molecule in the gas phase and cold ion vibrational pre-dissociation spectroscopy to explore excited state contributions to bandwidth. The spectrum of the carboxylate monohydrate exhibits a signature series of peaks in the OH stretching region of this system, providing an archetypal model to study vibrationally adiabatic mode separation. Previous analysis of this behavior accounts for the extensive progression in a Franck-Condon formalism involving displaced vibrationally adiabatic potentials. In this talk I will challenge this prediction by using isotopic substation to systematically change the level structure within these potentials. This picture quantitatively accounts for the diffuse spectrum of this complex at elevated temperature providing a convenient spectroscopic reporter for the temperature of ions in a trap. E. M. Myshakin, K. D. Jordan, E. L. Sibert III, M. A. Johnson J. Chem. Phys. 119, 10138 (2003) W.H. Robertson, et al. J. Phys Chem. 107, 6527 (2003)

Nucleus-size pinning for determination of nucleation free-energy barriers and nucleus geometry

NASA Astrophysics Data System (ADS)

Sharma, Abhishek K.; Escobedo, Fernando A.

2018-05-01

Classical Nucleation Theory (CNT) has recently been used in conjunction with a seeding approach to simulate nucleation phenomena at small-to-moderate supersaturation conditions when large free-energy barriers ensue. In this study, the conventional seeding approach [J. R. Espinosa et al., J. Chem. Phys. 144, 034501 (2016)] is improved by a novel, more robust method to estimate nucleation barriers. Inspired by the interfacial pinning approach [U. R. Pedersen, J. Chem. Phys. 139, 104102 (2013)] used before to determine conditions where two phases coexist, the seed of the incipient phase is pinned to a preselected size to iteratively drive the system toward the conditions where the seed becomes a critical nucleus. The proposed technique is first validated by estimating the critical nucleation conditions for the disorder-to-order transition in hard spheres and then applied to simulate and characterize the highly non-trivial (prolate) morphology of the critical crystal nucleus in hard gyrobifastigia. A generalization of CNT is used to account for nucleus asphericity and predict nucleation free-energy barriers for gyrobifastigia. These predictions of nuclei shape and barriers are validated by independent umbrella sampling calculations.

Electron Anisotropy as a Signature of Mode Specific Isomerization in Vinylidene

NASA Astrophysics Data System (ADS)

Gibson, Stephen T.; Laws, Benjamin A.; Mabbs, Richard; Neumark, Daniel; Lineberger, Carl; Field, Robert W.

2016-06-01

he nature of the isomerization process that turns vinylidene into acetylene has been awaiting advances in experimental methods, to better define fractionation widths beyond those available in the seminal 1989 photoelectron spectrum measurement. This has proven a challenge. The technique of velocity-map imaging (VMI) is one avenue of approach. Images of electrons photodetached from vinylidene negative-ions, at various wavelengths, 1064 nm shown, provide more detail, including unassigned structure, but only an incremental improvement in the instrument line width. Intriguingly, the VMIs demonstrate a mode dependent variation in the electron anisotropy. Most notable in the figure, the inner-ring transition clusters are discontinuously, more isotropic. Electron anisotropy may provide an alternative key to examine the character of vinylidene transitions, mediating the necessity for an extreme resolution measurement. Vibrational dependent anisotropy has previously been observed in diatomic photoelectron spectra, associated with the coupling of electronic and nuclear motions. Research supported by the Australian Research Council Discovery Project Grant DP160102585. K. M. Ervin, J. Ho, and W. C. Lineberger, J. Chem. Phys. 91, 5974 (1989). doi:10.1063/1.457415 M. van Duzor et al. J. Chem. Phys. 133, 174311 (2010). doi:10.1063/1.3493349

The calculated in vitro and in vivo chlorophyll a absorption bandshape.

PubMed Central

Zucchelli, Giuseppe; Jennings, Robert C; Garlaschi, Flavio M; Cinque, Gianfelice; Bassi, Roberto; Cremonesi, Oliviero

2002-01-01

The room temperature absorption bandshape for the Q transition region of chlorophyll a is calculated using the vibrational frequency modes and Franck-Condon (FC) factors obtained by line-narrowing spectroscopies of chlorophyll a in a glassy (Rebane and Avarmaa, Chem. Phys. 1982; 68:191-200) and in a native environment (Gillie et al., J. Phys. Chem. 1989; 93:1620-1627) at low temperatures. The calculated bandshapes are compared with the absorption spectra of chlorophyll a measured in two different solvents and with that obtained in vivo by a mutational analysis of a chlorophyll-protein complex. It is demonstrated that the measured distributions of FC factors can account for the absorption bandshape of chlorophyll a in a hexacoordinated state, whereas, when pentacoordinated, reduced FC coupling for vibrational frequencies in the range 540-850 cm(-1) occurs. The FC factor distribution for pentacoordinated chlorophyll also describes the native chlorophyll a spectrum but, in this case, either a low-frequency mode (nu < 200 cm(-1)) must be added or else the 262-cm(-1) mode must increase in coupling by about one order of magnitude to describe the skewness of the main absorption bandshape. PMID:11751324

Communication: Correct charge transfer in CT complexes from the Becke'05 density functional

NASA Astrophysics Data System (ADS)

Becke, Axel D.; Dale, Stephen G.; Johnson, Erin R.

2018-06-01

It has been known for over twenty years that density functionals of the generalized-gradient approximation (GGA) type and exact-exchange-GGA hybrids with low exact-exchange mixing fraction yield enormous errors in the properties of charge-transfer (CT) complexes. Manifestations of this error have also plagued computations of CT excitation energies. GGAs transfer far too much charge in CT complexes. This error has therefore come to be called "delocalization" error. It remains, to this day, a vexing unsolved problem in density-functional theory (DFT). Here we report that a 100% exact-exchange-based density functional known as Becke'05 or "B05" [A. D. Becke, J. Chem. Phys. 119, 2972 (2003); 122, 064101 (2005)] predicts excellent charge transfers in classic CT complexes involving the electron donors NH3, C2H4, HCN, and C2H2 and electron acceptors F2 and Cl2. Our approach is variational, as in our recent "B05min" dipole moments paper [Dale et al., J. Chem. Phys. 147, 154103 (2017)]. Therefore B05 is not only an accurate DFT for thermochemistry but is promising as a solution to the delocalization problem as well.

Energy Decomposition Analysis Based on Absolutely Localized Molecular Orbitals for Large-Scale Density Functional Theory Calculations in Drug Design.

PubMed

Phipps, M J S; Fox, T; Tautermann, C S; Skylaris, C-K

2016-07-12

We report the development and implementation of an energy decomposition analysis (EDA) scheme in the ONETEP linear-scaling electronic structure package. Our approach is hybrid as it combines the localized molecular orbital EDA (Su, P.; Li, H. J. Chem. Phys., 2009, 131, 014102) and the absolutely localized molecular orbital EDA (Khaliullin, R. Z.; et al. J. Phys. Chem. A, 2007, 111, 8753-8765) to partition the intermolecular interaction energy into chemically distinct components (electrostatic, exchange, correlation, Pauli repulsion, polarization, and charge transfer). Limitations shared in EDA approaches such as the issue of basis set dependence in polarization and charge transfer are discussed, and a remedy to this problem is proposed that exploits the strictly localized property of the ONETEP orbitals. Our method is validated on a range of complexes with interactions relevant to drug design. We demonstrate the capabilities for large-scale calculations with our approach on complexes of thrombin with an inhibitor comprised of up to 4975 atoms. Given the capability of ONETEP for large-scale calculations, such as on entire proteins, we expect that our EDA scheme can be applied in a large range of biomolecular problems, especially in the context of drug design.

Vibrational spectra of water solutions of azoles from QM/MM calculations: effects of solvation.

PubMed

Tanzi, Luana; Ramondo, Fabio; Guidoni, Leonardo

2012-10-18

Using microsolvation models and mixed quantum/classical ab initio molecular dynamics simulations, we investigate the vibrational properties of two azoles in water solution: pyrazole and oxazole. The effects of the water-azole hydrogen bonding are rationalized by an extensive comparison between structural parameters and harmonic frequencies obtained by microsolvation models. Following the effective normal-mode analysis introduced by Martinez et al. [Martinez et al., J. Chem. Phys. 2006, 125, 144106], we identify the vibrational frequencies of the solutes using the decomposition of the vibrational density of states of the gas phase and solution dynamics. The calculated shifts from gas phase to solution are fairly in agreement with the available experimental data.

Aqueous aerosol may build up large upper tropospheric ice supersaturation

NASA Astrophysics Data System (ADS)

Bogdan, Anatoli; Molina, Mario J.

2010-05-01

freeze at 194 and 186 K, respectively, the calculated clear-sky Si can exceed 80%. Although our Si values are smaller than the largest observed value of Si ≈ 100%, they are nevertheless larger than the Si ≈ 67% predicted by the WAC at 185 K. Our results can give an impetus for the study of whether multi-component aqueous aerosol, which besides inorganic components also contains organics, may produce the observed Si ≈ 100%. Krämer, M., Schiller, C., Afchine, A., Bauer, R., Gensch, I., Mangold, A.., Schlicht, S., Spelten, N., Sitnikov, N., Borrmann, S., de Reus, M., Spichtinger, P. (2009), Atmos. Chem. Phys. 9, 3505. Lawson, R. P., Pilson, B., Baker, B., Mo, Q., Jensen, E., Pfister, L., Bui, P. (2008), Atmos. Chem. Phys. 8, 1609. Koop, T., Luo, B., Tsias, A., Peter, T. (2000), Nature, 406, 611. Bogdan, A. and Moilna, M. J. (2010), J. Phys. Chem. A (Published online: 5 February). Carslaw, K. S., Wirth, M., Tsias, A., Luo, B. P., Dörnbrack, A., Leutbecher, M., Volkert, H., Renger, W., Bacmeister, J. T., Peter, T. (1998), J. Geophys. Res. 103, 5785. Clegg, S. L., Brimblecombe, P., Wexler, A. S. (1998), J. Phys. Chem. A 102, 2137.

Heterogeneous reaction kinetics and mechanism of the nitration of aerosolized protein by O3 and NO2

NASA Astrophysics Data System (ADS)

Shiraiwa, Manabu; Sosedova, Yulia; Rouvière, Aurélie; Ammann, Markus; Pöschl, Ulrich

2010-05-01

detection limit (γNO2 < ~10-6). The γNO2 by BSA is of the order of 10-5, strongly depending on gas phase ozone concentration, which indicates that O3 plays an important role in NO2 uptake. The γNO2 by deliquesced NaCl is one order of magnitude smaller, which is likely to be attributed to the formation of gas phase NO3 and N2O5, as neither O3 nor NO2 is expected to rapidly react with deliquesced NaCl. This amount of uptake is considered to be maximum contribution of gas phase NO3 radicals and N2O5 to uptake of 13N-labeled species by protein particles. The possible mechanisms of high NO2 uptake by protein particles are: 1) surface reaction between adsorbed O3 and NO2 forming NO3 radicals on the surface which react with protein [5], 2) O3 first reacts with protein forming intermediates, followed by reaction with NO2. Further experiments and modelling are under way. REFERENCES [1] Franze et al., Environ. Sci. Tech., 39, 1673 (2005). [2] Sosedova et al., J. Phys. Chem A., 113, 10979 (2009). [3] Mikhailov et al., Atmos. Chem. Phys., 4, 323 (2004). [4] Mikhailov et al., Atmos. Chem. Phys., 9, 9491 (2009). [5] Shiraiwa et al., Atmos. Chem. Phys., 9, 9571 (2009)

ChemCam Mast Unit Being Prepared for Laser Firing

NASA Image and Video Library

2010-12-23

Researchers prepare for a test of the Chemistry and Camera ChemCam instrument that will fly on NASA Mars Science Laboratory mission; researchers are preparing the instrument mast unit for a laser firing test.

ChemCalc: a building block for tomorrow's chemical infrastructure.

PubMed

Patiny, Luc; Borel, Alain

2013-05-24

Web services, as an aspect of cloud computing, are becoming an important part of the general IT infrastructure, and scientific computing is no exception to this trend. We propose a simple approach to develop chemical Web services, through which servers could expose the essential data manipulation functionality that students and researchers need for chemical calculations. These services return their results as JSON (JavaScript Object Notation) objects, which facilitates their use for Web applications. The ChemCalc project http://www.chemcalc.org demonstrates this approach: we present three Web services related with mass spectrometry, namely isotopic distribution simulation, peptide fragmentation simulation, and molecular formula determination. We also developed a complete Web application based on these three Web services, taking advantage of modern HTML5 and JavaScript libraries (ChemDoodle and jQuery).

Harnessing Solar Power: Novel Strategies for Rational Design of Photocatalysts and Photovoltaic Materials

DTIC Science & Technology

2015-09-01

Complex 2 ( LH2 ) of Rhodobacter sphaeroides with Two- Dimensional Spectroscopy” J. Chem. Phys. 139, 155101 2013. A.F. Fidler, V.P. Singh, P.D. Long...P.D. Dahlberg, and G.S. Engel, “Time Scales of Coherent Dynamics in the Light-Harvesting Complex 2 ( LH2 ) of Rhodobacter sphaeroides” J. Phys. Chem...Spectroscopy of the Light-harvesting Complex LH2 ” Opt. Lett. 36:9 1665-1667 2011 E. Harel, A.F. Fidler, and G.S. Engel, “Single-Shot GRadient

Unraveling the Nature of Chemical Reactivity of Complex Systems

DTIC Science & Technology

2009-01-13

28 J. Zhou, J. J. Lin, W. Shiu, and K. Liu, J. Chem. Phys. 119, 4997 2003. 29 S. C. Althorpe, F. Fernandez - Alonso , B. D. Bean, J. D. Ayers, A. E...Truhlar DG, Espinosa- Garcia J (2000) Potential energy surface, thermal, and state-selected rate coefficients, and kinetic isotope effects for Cl CH43...HCl CH3. J Chem Phys 112:9375–9389. 22. Rangel C, Navarrete M, Corchado JC, Espinosa- Garcia J (2006) Potential energy surface, kinetics, and

Direct Observation of NF(X) Using Laser-Induced Fluorescence: Kinetics of the NF 3 Sigma(-) Ground State

DTIC Science & Technology

1990-08-06

HEIDNER III, J. S. HOLLOWAY, H . HELVAJIAN , AND J. B. KOFFEND Aerophysics Laboratory Laboratory Operations The Aerospace Corporation El Segundo, CA 90245...91, 3658 (1987). 14. E. Quinones, J. Habdas, and D. W. Setser, J. Phys. Chem. 91, 5155 (1987). 15. R. F. Heidner III, H . Helvajian , and J. B. Koffend...J. Chem. Phys. 87, 1520 (1987). 16. R. F. Heidner, H . Helvajian , J. S. Holloway, and J. B. Koffend (to be published). 17. F. A. Johnson and C. B

Extent of Fock-exchange mixing for a hybrid van der Waals density functional?

NASA Astrophysics Data System (ADS)

Jiao, Yang; Schröder, Elsebeth; Hyldgaard, Per

2018-05-01

The vdW-DF-cx0 exchange-correlation hybrid design [K. Berland et al., J. Chem. Phys. 146, 234106 (2017)] has a truly nonlocal correlation component and aims to facilitate concurrent descriptions of both covalent and non-covalent molecular interactions. The vdW-DF-cx0 design mixes a fixed ratio, a, of the Fock exchange into the consistent-exchange van der Waals density functional, vdW-DF-cx [K. Berland and P. Hyldgaard, Phys. Rev. B 89, 035412 (2014)]. The mixing value a is sometimes taken as a semi-empirical parameter in hybrid formulations. Here, instead, we assert a plausible optimum average a value for the vdW-DF-cx0 design from a formal analysis; A new, independent determination of the mixing a is necessary since the Becke fit [A. D. Becke, J. Chem. Phys. 98, 5648 (1993)], yielding a' = 0.2, is restricted to semilocal correlation and does not reflect non-covalent interactions. To proceed, we adapt the so-called two-legged hybrid construction [K. Burke et al., Chem. Phys. Lett. 265, 115 (1997)] to a starting point in the vdW-DF-cx functional. For our approach, termed vdW-DF-tlh, we estimate the properties of the adiabatic-connection specification of the exact exchange-correlation functional, by combining calculations of the Fock exchange and of the coupling-constant variation in vdW-DF-cx. We find that such vdW-DF-tlh hybrid constructions yield accurate characterizations of molecular interactions (even if they lack self-consistency). The accuracy motivates trust in the vdW-DF-tlh determination of system-specific values of the Fock-exchange mixing. We find that an average value a' = 0.2 best characterizes the vdW-DF-tlh description of covalent and non-covalent interactions, although there exists some scatter. This finding suggests that the original Becke value, a' = 0.2, also represents an optimal average Fock-exchange mixing for the new, truly nonlocal-correlation hybrids. To enable self-consistent calculations, we furthermore define and test a zero

VizieR Online Data Catalog: H3O+ and D3O+ rota

NASA Astrophysics Data System (ADS)

Owens, A.; Yurchenko, S. N.; Polyansky, O. L.; Ovsyannikov, R. I.; Thiel, W.; Spirko, V.

2018-01-01

Given the astronomical relevance of H3O+, and a good set of accurately measured experimental data (Uy, White & Oka 1997JMoSp.183..240U; Araki, Ozeki & Saito 1999, Mol. Phys., 97, 177); Tang & Oka 1999JMoSp.196..120T ; Furuya & Saito 2005A&A...441.1039F; Yu et al. 2009ApJS..180..119Y; Yu & Pearson 2014ApJ...786..133Y), we find it worthwhile to carry out a comprehensive study of hydronium, H316O+ (also referred to as H3O+), and its two symmetric top isotopologues, H318O+ and D316O+. To do this we employ a highly accurate variational approach, which was recently applied to ammonia (Owens et al. 2015MNRAS.450.3191O). Like NH3 (Jansen, Bethlem & Ubachs 2014JChPh.140a0901J; Spirko 2014, J. Phys. Chem. Lett., 5, 919; Owens et al. 2015MNRAS.450.3191O), there is a possibility to find transitions with strongly anomalous sensitivities caused by the Δk=+/-3 interactions (see Papousek et al. 1986JMoSt.141..361P), which have not yet been considered. (11 data files).

HExpoChem: a systems biology resource to explore human exposure to chemicals.

PubMed

Taboureau, Olivier; Jacobsen, Ulrik Plesner; Kalhauge, Christian; Edsgärd, Daniel; Rigina, Olga; Gupta, Ramneek; Audouze, Karine

2013-05-01

Humans are exposed to diverse hazardous chemicals daily. Although an exposure to these chemicals is suspected to have adverse effects on human health, mechanistic insights into how they interact with the human body are still limited. Therefore, acquisition of curated data and development of computational biology approaches are needed to assess the health risks of chemical exposure. Here we present HExpoChem, a tool based on environmental chemicals and their bioactivities on human proteins with the objective of aiding the qualitative exploration of human exposure to chemicals. The chemical-protein interactions have been enriched with a quality-scored human protein-protein interaction network, a protein-protein association network and a chemical-chemical interaction network, thus allowing the study of environmental chemicals through formation of protein complexes and phenotypic outcomes enrichment. HExpoChem is available at http://www.cbs.dtu.dk/services/HExpoChem-1.0/.

Improving and assessing vapour pressure estimation methods for organic compounds of atmospheric relevance using a Knudsen Effusion Mass Spectrometer (KEMS)

NASA Astrophysics Data System (ADS)

Booth, A. M.; Topping, D. O.; McFiggans, G. B.; Garforth, A.; Percival, C. J.

2009-12-01

functional groups and interaction parameters, derived from experimental data, to reliably predict boiling points and vapour pressures. A sensitivity study was undertaken to establish the impact of the new experimentally determined vapour pressures on partitioning models. Jacobson, M.C., et al. Rev Geophys, 38 (2), 267-294, 2000. Houghton et al. Climate Change 2001: The Scientific Basis. Contribution of Working Group 1 to the Third Assessment Report of the IPCC., 881 pp., Cambridge University Press, 2001. Johnson, D. , et al. Atmo. Chem. Phys., Vol. 6, 419-431, 2006 Yu, J. Z., et al. J Atmos Chem. 34, 207-258, 1999 Booth, A.M. et al Atmos. Meas. Tech.,2,355-361, 2009 Nanoolal, Y. et al Fluid Phase Equilibria, 269,117-133., 2008. Barley, M. et al Atmos. Chem. Phys., -,to be submitted.

ChemScreener: A Distributed Computing Tool for Scaffold based Virtual Screening.

PubMed

Karthikeyan, Muthukumarasamy; Pandit, Deepak; Vyas, Renu

2015-01-01

In this work we present ChemScreener, a Java-based application to perform virtual library generation combined with virtual screening in a platform-independent distributed computing environment. ChemScreener comprises a scaffold identifier, a distinct scaffold extractor, an interactive virtual library generator as well as a virtual screening module for subsequently selecting putative bioactive molecules. The virtual libraries are annotated with chemophore-, pharmacophore- and toxicophore-based information for compound prioritization. The hits selected can then be further processed using QSAR, docking and other in silico approaches which can all be interfaced within the ChemScreener framework. As a sample application, in this work scaffold selectivity, diversity, connectivity and promiscuity towards six important therapeutic classes have been studied. In order to illustrate the computational power of the application, 55 scaffolds extracted from 161 anti-psychotic compounds were enumerated to produce a virtual library comprising 118 million compounds (17 GB) and annotated with chemophore, pharmacophore and toxicophore based features in a single step which would be non-trivial to perform with many standard software tools today on libraries of this size.

The Aharonov-Bohm effect and Tonomura et al. experiments: Rigorous results

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

Ballesteros, Miguel; Weder, Ricardo

The Aharonov-Bohm effect is a fundamental issue in physics. It describes the physically important electromagnetic quantities in quantum mechanics. Its experimental verification constitutes a test of the theory of quantum mechanics itself. The remarkable experiments of Tonomura et al. ['Observation of Aharonov-Bohm effect by electron holography', Phys. Rev. Lett 48, 1443 (1982) and 'Evidence for Aharonov-Bohm effect with magnetic field completely shielded from electron wave', Phys. Rev. Lett 56, 792 (1986)] are widely considered as the only experimental evidence of the physical existence of the Aharonov-Bohm effect. Here we give the first rigorous proof that the classical ansatz of Aharonovmore » and Bohm of 1959 ['Significance of electromagnetic potentials in the quantum theory', Phys. Rev. 115, 485 (1959)], that was tested by Tonomura et al., is a good approximation to the exact solution to the Schroedinger equation. This also proves that the electron, that is, represented by the exact solution, is not accelerated, in agreement with the recent experiment of Caprez et al. in 2007 ['Macroscopic test of the Aharonov-Bohm effect', Phys. Rev. Lett. 99, 210401 (2007)], that shows that the results of the Tonomura et al. experiments can not be explained by the action of a force. Under the assumption that the incoming free electron is a Gaussian wave packet, we estimate the exact solution to the Schroedinger equation for all times. We provide a rigorous, quantitative error bound for the difference in norm between the exact solution and the Aharonov-Bohm Ansatz. Our bound is uniform in time. We also prove that on the Gaussian asymptotic state the scattering operator is given by a constant phase shift, up to a quantitative error bound that we provide. Our results show that for intermediate size electron wave packets, smaller than the ones used in the Tonomura et al. experiments, quantum mechanics predicts the results observed by Tonomura et al. with an error bound smaller

Multi-scale simulation of quantum dot formation in Al/Al (110) homoepitaxy

NASA Astrophysics Data System (ADS)

Tiwary, Yogesh; Fichthorn, Kristen

2007-03-01

In experimental studies of Al(110) homoepitaxy, it is observed that over a certain temperature window (330-500K), 3D huts, up to 50 nm high with well defined and smooth (111) and (100) facets, form and self-organize over the micron scale [1]. The factors leading to this kinetic self-organization are currently unclear. To understand how these structures form and evolve, we simulated multi-layer, homoepitaxial growth on Al(110) using ab initio kinetic Monte Carlo (KMC). At the high temperatures, where nano-huts form, the KMC simulations are slow. To tackle this problem, we use a technique developed by Devita & Sander [2], in which isolated adatoms make multiple moves in one step. We achieve high efficiency with this algorithm and we explore very high temperatures on large simulation lattices. We uncover a variety of interesting morphologies (Ripples, mounds, smooth surface, huts) that depend on the growth temperature. By varying the barriers for various rate processes, we discern the factors that determine hut sizes, aspect ratios, and self-organization. [1] F. Buatier de Mongeot, W. Zhu, A. Molle, R. Buzio, C. Boragno, U. Valbusa, E. Wang, and Z. Zhang, Phys. Rev. Lett. 91, 016102 (2003). [2] J.P. Devita & L.M. Sander, Phys. Rev. B 72, 205421 (2005).

Magnetic exchange couplings from noncollinear perturbation theory: dinuclear CuII complexes.

PubMed

Phillips, Jordan J; Peralta, Juan E

2014-08-07

To benchmark the performance of a new method based on noncollinear coupled-perturbed density functional theory [J. Chem. Phys. 138, 174115 (2013)], we calculate the magnetic exchange couplings in a series of triply bridged ferromagnetic dinuclear Cu(II) complexes that have been recently synthesized [Phys. Chem. Chem. Phys. 15, 1966 (2013)]. We find that for any basis-set the couplings from our noncollinear coupled-perturbed methodology are practically identical to those of spin-projected energy-differences when a hybrid density functional approximation is employed. This demonstrates that our methodology properly recovers a Heisenberg description for these systems, and is robust in its predictive power of magnetic couplings. Furthermore, this indicates that the failure of density functional theory to capture the subtle variation of the exchange couplings in these complexes is not simply an artifact of broken-symmetry methods, but rather a fundamental weakness of current approximate density functionals for the description of magnetic couplings.

Bridging single and multireference coupled cluster theories with universal state selective formalism

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

Bhaskaran-Nair, Kiran; Kowalski, Karol

2013-05-28

The universal state selective (USS) multireference approach is used to construct new energy functionals which offers a unique possibility of bridging single and multireference coupled cluster theories (SR/MRCC). These functionals, which can be used to develop iterative and non-iterative approaches, utilize a special form of the trial wavefunctions, which assure additive separability (or size-consistency) of the USS energies in the non-interacting subsystem limit. When the USS formalism is combined with approximate SRCC theories, the resulting formalism can be viewed as a size-consistent version of the method of moments of coupled cluster equations (MMCC) employing a MRCC trial wavefunction. Special casesmore » of the USS formulations, which utilize single reference state specific CC (V.V. Ivanov, D.I. Lyakh, L. Adamowicz, Phys. Chem. Chem. Phys. 11, 2355 (2009)) and tailored CC (T. Kinoshita, O. Hino, R.J. Bartlett, J. Chem. Phys. 123, 074106 (2005)) expansions are also discussed.« less

Integral cross sections for electron impact excitation of the 1Σ+u and 1Πu electronic states in CO2

NASA Astrophysics Data System (ADS)

Kawahara, H.; Kato, H.; Hoshino, M.; Tanaka, H.; Campbell, L.; Brunger, M. J.

2008-04-01

We apply the method of Kim (2007 J. Chem. Phys. 126 064305) in order to derive integral cross sections for the 1Σ+u and 1Πu states of CO2, from our corresponding earlier differential cross section measurements (Green et al 2002 J. Phys. B: At. Mol. Opt. Phys. 35 567). The energy range of this work is 20 200 eV. In addition, the BEf-scaling approach is used to calculate integral cross sections for these same states, from their respective thresholds to 5000 eV. In general, good agreement is found between the experimental integral cross sections and those calculated within the BEf-scaling paradigm, over the entire common energy range. Finally, we employ our calculated integral cross sections to determine the electron energy transfer rates for these states, for a thermal electron energy distribution. Such transfer rates are in principle important for understanding the phenomena in atmospheres where CO2 is a dominant constituent, such as on Mars and Venus.

Rotational Spectroscopy of 4-HYDROXY-2-BUTYNENITRILE

NASA Astrophysics Data System (ADS)

Motiyenko, R. A.; Margulès, L.; Guillemin, J.-C.

2015-06-01

Recently we studied the rotational spectrum of hydroxyacetonitrile (HOCH_2CN, HAN) in order to provide a firm basis for its possible detection in the interstellar medium Different plausible pathways of the formation of HAN in the interstellar conditions were proposed; however, up to now, the searches for this molecule were unsuccessful. To continue the study of nitriles that represent an astrophysical interest we present in this talk the analysis of the rotational spectrum of 4-hydroxy-2-butynenitrile (HOCH_2CC-CN, HBN), the next molecule in the series of hydroxymethyl nitriles. Using the Lille spectrometer the spectrum of HBN was measured in the frequency range 50 -- 500 GHz. From the spectroscopic point of view HBN molecule is rather similar to HAN, because of -OH group tunnelling in gauche conformation. As it was previously observed for HAN, due to this large amplitude motion, the splittings in the rotational spectra of HBN are easily resolved making the spectral analysis more difficult. Additional difficulties arise from the near symmetric top character of HBN (κ = -0.996), and very dense spectrum because of relatively small values of rotational constants and a number of low-lying excited vibrational states. The analysis carried out in the frame of reduced axis system approach of Pickett allows to fit within experimental accuracy all the rotational transitions in the ground vibrational state. Thus, the results of the present study provide a reliable catalog of frequency predictions for HBN. The support of the Action sur Projets de l'INSU PCMI, and ANR-13-BS05-0008-02 IMOLABS is gratefully acknowledged Margulès L., Motiyenko R.A., Guillemin J.-C. 68th ISMS, 2013, TI12. Danger G. et al. Phys. Chem. Chem. Phys. 2014, 16, 3360. Pickett H.M. J. Chem. Phys. 1972, 56, 1715.

Experimental and Computational Investigations of the Threshold Photoelectron Spectrum of the HCCN Radical

NASA Astrophysics Data System (ADS)

Gans, B.; Falvo, Cyril; Coudert, L. H.; Garcia, Gustavo A.; Küger, J.; Loison, J.-C.

2017-06-01

The HCCN radical, already detected in the interstellar medium, is also important for nitrile chemistry in Titan's atmosphere. Quite recently the photoionization spectrum of the radical has been recorded using mass selected threshold photoelectron (TPE) spectroscopy and this provided us with the first spectroscopic information about the HCCN} cation. Modeling such a spectrum requires accounting for the non-rigidity of HCCN and for the Renner-Teller effect in HCCN+. In its ^3A'' electronic ground state, HCCN is a non-rigid molecule as the potential for the \\angle{HCC} bending angle is very shallow. Vibronic couplings with the same bending angle leads, in the ^2Π electronic ground state of HCCN+, to a strong Renner-Teller effect giving rise to a bent ^2A' and a quasi-linear ^2A'' state. In this paper the photoionization spectrum of the HCCN radical is simulated. The model developped treats the \\angle{HCC} bending angle as a large amplitude coordinate in both the radical and the cation and accounts for the overall rotation and the Renner-Teller couplings. Gaussian quadrature are used to calculate matrix elements of the three potential energy functions retrieved through ab initio calculations and rovibrational operators going to infinity for the linear configuration are treated rigorously. The HCCN TPE spectrum is computed with the above model calculating all rotational components and choosing the appropriate lineshape. This synthetic spectrum will be shown in the paper and compared with the experimental one.^b Guélin and Cernicharo, A&A 244 (1991) L21 Loison et al., Icarus 247 (2015) 218 Garcia, Krüger, Gans, Falvo, Coudert, and Loison, J. Chem. Phys. (2017) submitted Koput, J. Phys. Chem. A 106 (2002) 6183 Zhao, Zhang, and Sun, J. Phys. Chem. A 112 (2008) 12125

Excess electron is trapped in a large single molecular cage C60F60.

PubMed

Wang, Yin-Feng; Li, Zhi-Ru; Wu, Di; Sun, Chia-Chung; Gu, Feng-Long

2010-01-15

A new kind of solvated electron systems, sphere-shaped e(-)@C60F60 (I(h)) and capsule-shaped e(-)@C60F60 (D6h), in contrast to the endohedral complex M@C60, is represented at the B3LYP/6-31G(d) + dBF (diffusive basis functions) density functional theory. It is proven, by examining the singly occupied molecular orbital (SOMO) and the spin density map of e(-)@C60F60, that the excess electron is indeed encapsulated inside the C60F60 cage. The shape of the electron cloud in SOMO matches with the shape of C60F60 cage. These cage-like single molecular solvated electrons have considerably large vertical electron detachment energies VDE of 4.95 (I(h)) and 4.67 eV (D6h) at B3LYP/6-31+G(3df) + dBF level compared to the VDE of 3.2 eV for an electron in bulk water (Coe et al., Int Rev Phys Chem 2001, 20, 33) and that of 3.66 eV for e(-)@C20F20 (Irikura, J Phys Chem A 2008, 112, 983), which shows their higher stability. The VDE of the sphere-shaped e(-)@C60F60 (I(h)) is greater than that of the capsule-shaped e(-)@C60F60 (D6h), indicating that the excess electron prefers to reside in the cage with the higher symmetry to form the more stable solvated electron. It is also noticed that the cage size [7.994 (I(h)), 5.714 and 9.978 A (D6h) in diameter] is much larger than that (2.826 A) of (H2O)20- dodecahedral cluster (Khan, Chem Phys Lett 2005, 401, 85). Copyright 2009 Wiley Periodicals, Inc.

Droplet Growth Kinetics in Various Environments

NASA Astrophysics Data System (ADS)

Raatikainen, T. E.; Lathem, T. L.; Moore, R.; Lin, J. J.; Cerully, K. M.; Padro, L.; Lance, S.; Cozic, J.; Anderson, B. E.; Nenes, A.

2012-12-01

The largest uncertainties in the effects of atmospherics aerosols on the global radiation budget are related to their indirect effects on cloud properties (IPCC, the Fourth Assessment Report of the Intergovernmental Panel on Climate Change, 2007). Cloud formation is a kinetic process where the resulting cloud properties depend on aerosol properties and meteorological parameters such as updraft velocity (e.g. McFiggans et al., Atmos. Chem. Phys., 6, 2593-2649, 2006). Droplet growth rates are limited by the water vapor diffusion, but additional kinetic limitations, e.g., due to organic surface films, slow solute dissociation or highly viscous or glassy aerosol states have been hypothesized. Significant additional kinetic limitations can lead to increased cloud droplet number concentration, thus the effect is similar to those of increased aerosol number concentration or changes in vertical velocity (e.g. Nenes et al., Geophys. Res. Lett., 29, 1848, 2002). There are a few studies where slow droplet growth has been observed (e.g. Ruehl et al., Geophys. Res. Lett., 36, L15814, 2009), however, little is currently known about their global occurrence and magnitude. Cloud micro-physics models often describe kinetic limitations by an effective water vapor uptake coefficient or similar parameter. Typically, determining aerosol water vapor uptake coefficients requires experimental observations of droplet growth which are interpreted by a numerical droplet growth model where the uptake coefficient is an adjustable parameter (e.g. Kolb et al., Atmos. Chem. Phys., 10, 10561-10605, 2010). Such methods have not been practical for high time-resolution or long term field measurements, until a model was recently developed for analyzing Droplet Measurement Technologies (DMT) cloud condensation nuclei (CCN) counter data (Raatikainen et al., Atmos. Chem. Phys., 12, 4227-4243, 2012). Model verification experiments showed that the calibration aerosol droplet size can be predicted accurately

Research in Electronics - JSEP (Joint Services Electronics Program)

DTIC Science & Technology

1982-04-01

intramolecular V-E coupling in ir laser excited polyatomicso, J. Chem. Phys. 25, 5311 (1981). 5. H . Helvajian and C. Wittig, nVibrational quenching of HgBr(X...Phys. Chem. 86, 438 (1982). 13. H . Helvajian and C. Wittig, "Collisional deexcitation of Hg(6 3po) by HgBr(X), Br(4 2p)8, and Br2(X): evidence for ion...Distribution List. Sincerely, William H . Steier Director Enclosures fJS (j A Y j LI I .. . . . ... rJ .. .. -.. ,1L Lu. UNIVERSITY OF SOUTHERN

Chemerin15 inhibits neutrophil-mediated vascular inflammation and myocardial ischemia-reperfusion injury through ChemR23

PubMed Central

Cash, Jenna L; Bena, Stefania; Headland, Sarah E; McArthur, Simon; Brancaleone, Vincenzo; Perretti, Mauro

2013-01-01

Neutrophil activation and adhesion must be tightly controlled to prevent complications associated with excessive inflammatory responses. The role of the anti-inflammatory peptide chemerin15 (C15) and the receptor ChemR23 in neutrophil physiology is unknown. Here, we report that ChemR23 is expressed in neutrophil granules and rapidly upregulated upon neutrophil activation. C15 inhibits integrin activation and clustering, reducing neutrophil adhesion and chemotaxis in vitro. In the inflamed microvasculature, C15 rapidly modulates neutrophil physiology inducing adherent cell detachment from the inflamed endothelium, while reducing neutrophil recruitment and heart damage in a murine myocardial infarction model. These effects are mediated through ChemR23. We identify the C15/ChemR23 pathway as a new regulator and thus therapeutic target in neutrophil-driven pathologies. PMID:23999103

Investigation of a Particle into Liquid Sampler to Study the Formation & Ageing of Secondary Organic Aerosol

NASA Astrophysics Data System (ADS)

Pereira, K. L.; Hamilton, J. F.; Rickard, A. R.; Bloss, W. J.; Alam, M. S.; Camredon, M.; Munoz, A.; Vazquez, M.; Rodenas, M.; Vera, T.; Borrás, E.

2012-12-01

reports of the atmospheric degradation of Methyl Chavicol. Methyl Chavicol oxidation was investigated using a series of photosmog and ozonolysis experiments with varying ratios of NOx:VOC. An extensive range of instruments were used to monitor radical and product formation [including: LIF (HOx intermediates), LOPAP (HONO), FT-IR, PTR-MS, GC-FID, and SMPS]. Samples were collected using the PILS at 30 minute intervals with filters taken at the end of each experiment for comparison. A number of key oxidation products have been identified. Time profiles can be used to determine the importance of first, second & higher oxidation products and may indicate which species are undergoing oxidation or heterogeneous reactions during aerosol ageing. This data will allow for modelled vs. measured SOA composition comparison, with the potential to determine the rates of reactions for the condensed phase oxidation products formed. References Bouvier-Brown et al., Atmos. Chem. Phys. 9, 2061-2074, 2009. Goldstein and Galbally, Environ. Sci. Technol. 41, 1514-1521, 2007. Hallquist et al., Atmos. Chem. Phys. 9, 5155-5236, 2009. Lee et al., J. Geophys. Res. 111, D17305, 2006. Misztal et al., Atmos. Chem. Phys. Discuss. 10, 1517-1557, 2010. Solomon et al., Climate Change 2007: IPCC Report. Cambridge, 2007. Zhang et al., Geophys. Res. Lett. 34, L13801, 2007.

Handheld Chem/Biosensor Using Extreme Conformational Changes in Designed Binding Proteins to Enhance Surface Plasmon Resonance (SPR)

DTIC Science & Technology

2016-04-01

AFCEC-CX-TY-TR-2016-0007 HANDHELD CHEM/ BIOSENSOR USING EXTREME CONFORMATIONAL CHANGES IN DESIGNED BINDING PROTEINS TO ENHANCE SURFACE PLASMON...Include area code) 03/24/2016 Abstract 08/14/2015--03/31/2016 Handheld chem/ biosensor using extreme conformational changes in designed binding...Baltimore, Maryland on 17-21 April 2016. We propose the development of a highly sensitive handheld chem/ biosensor device using a novel class of engineered

Study of thermal properties of the metastable supersaturated vapor with the integral equation method

NASA Astrophysics Data System (ADS)

Nie, Chu; Geng, Jun; Marlow, W. H.

2008-02-01

Pressure, excess chemical potential, and excess free energy data for different densities of the supersaturated argon vapor at reduced temperatures from 0.7 to 1.2 are obtained by solving the integral equation with perturbation correction to the radial distribution function [F. Lado, Phys. Rev. 135, A1013 (1964)]. For those state points where there is no solution, the integral equation is solved with the interaction between argon atoms modeled by Lennard-Jones potential plus a repulsive potential with one controlling parameter, αexp(-r /σ) and in the end, all the thermal properties are mapped back to the α =0 case. Our pressure data and the spinodal obtained from the current method are compared with a molecular dynamics simulation study [A. Linhart et al., J. Chem. Phys. 122, 144506 (2005)] of the same system.

Soil diversity and hydration as observed by ChemCam at Gale crater, Mars

USGS Publications Warehouse

Meslin, P.-Y.; Gasnault, O.; Forni, O.; Schroder, S.; Cousin, A.; Berger, G.; Clegg, S.M.; Lasue, J.; Maurice, S.; Sautter, V.; Le Mouélic, S.; Wiens, R.C.; Fabre, C.; Goetz, W.; Bish, D.L.; Mangold, N.; Ehlmann, B.; Lanza, N.; Harri, A.-M.; Anderson, Ryan Bradley; Rampe, E.; McConnochie, T.H.; Pinet, P.; Blaney, D.; ,; Archer, D.; Barraclough, B.; Bender, S.; Blake, D.; Blank, J.G.; Bridges, N.; Clark, B. C.; DeFlores, L.; Delapp, D.; Dromart, G.; Dyar, M.D.; Fisk, M. R.; Gondet, B.; Grotzinger, J.; Herkenhoff, K.; Johnson, J.; Lacour, J.-L.; Langevin, Y.; Leshin, L.; Lewin, E.; Madsen, M.B.; Melikechi, N.; Mezzacappa, Alissa; Mischna, M.A.; Moores, J.E.; Newsom, H.; Ollila, A.; ,; Renno, N.; Sirven, J.B.; Tokar, R.; de la Torre, M.; d'Uston, L.; Vaniman, D.; Yingst, A.

2013-01-01

The ChemCam instrument, which provides insight into martian soil chemistry at the submillimeter scale, identified two principal soil types along the Curiosity rover traverse: a fine-grained mafic type and a locally derived, coarse-grained felsic type. The mafic soil component is representative of widespread martian soils and is similar in composition to the martian dust. It possesses a ubiquitous hydrogen signature in ChemCam spectra, corresponding to the hydration of the amorphous phases found in the soil by the CheMin instrument. This hydration likely accounts for an important fraction of the global hydration of the surface seen by previous orbital measurements. ChemCam analyses did not reveal any significant exchange of water vapor between the regolith and the atmosphere. These observations provide constraints on the nature of the amorphous phases and their hydration.

Soil diversity and hydration as observed by ChemCam at Gale crater, Mars.

PubMed

Meslin, P-Y; Gasnault, O; Forni, O; Schröder, S; Cousin, A; Berger, G; Clegg, S M; Lasue, J; Maurice, S; Sautter, V; Le Mouélic, S; Wiens, R C; Fabre, C; Goetz, W; Bish, D; Mangold, N; Ehlmann, B; Lanza, N; Harri, A-M; Anderson, R; Rampe, E; McConnochie, T H; Pinet, P; Blaney, D; Léveillé, R; Archer, D; Barraclough, B; Bender, S; Blake, D; Blank, J G; Bridges, N; Clark, B C; DeFlores, L; Delapp, D; Dromart, G; Dyar, M D; Fisk, M; Gondet, B; Grotzinger, J; Herkenhoff, K; Johnson, J; Lacour, J-L; Langevin, Y; Leshin, L; Lewin, E; Madsen, M B; Melikechi, N; Mezzacappa, A; Mischna, M A; Moores, J E; Newsom, H; Ollila, A; Perez, R; Renno, N; Sirven, J-B; Tokar, R; de la Torre, M; d'Uston, L; Vaniman, D; Yingst, A

2013-09-27

The ChemCam instrument, which provides insight into martian soil chemistry at the submillimeter scale, identified two principal soil types along the Curiosity rover traverse: a fine-grained mafic type and a locally derived, coarse-grained felsic type. The mafic soil component is representative of widespread martian soils and is similar in composition to the martian dust. It possesses a ubiquitous hydrogen signature in ChemCam spectra, corresponding to the hydration of the amorphous phases found in the soil by the CheMin instrument. This hydration likely accounts for an important fraction of the global hydration of the surface seen by previous orbital measurements. ChemCam analyses did not reveal any significant exchange of water vapor between the regolith and the atmosphere. These observations provide constraints on the nature of the amorphous phases and their hydration.

Post-Hartree-Fock studies of the He/Mg(0001) interaction: Anti-corrugation, screening, and pairwise additivity

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

Lara-Castells, María Pilar de, E-mail: Pilar.deLara.Castells@csic.es; Fernández-Perea, Ricardo; Madzharova, Fani

2016-06-28

The adsorption of noble gases on metallic surfaces represents a paradigmatic case of van-der-Waals (vdW) interaction due to the role of screening effects on the corrugation of the interaction potential [J. L. F. Da Silva et al., Phys. Rev. Lett. 90, 066104 (2003)]. The extremely small adsorption energy of He atoms on the Mg(0001) surface (below 3 meV) and the delocalized nature and mobility of the surface electrons make the He/Mg(0001) system particularly challenging, even for state-of-the-art vdW-corrected density functional-based (vdW-DFT) approaches [M. P. de Lara-Castells et al., J. Chem. Phys. 143, 194701 (2015)]. In this work, we meet thismore » challenge by applying two different procedures. First, the dispersion-corrected second-order Möller-Plesset perturbation theory (MP2C) approach is adopted, using bare metal clusters of increasing size. Second, the method of increments [H. Stoll, J. Chem. Phys. 97, 8449 (1992)] is applied at coupled cluster singles and doubles and perturbative triples level, using embedded cluster models of the metal surface. Both approaches provide clear evidences of the anti-corrugation of the interaction potential: the He atom prefers on-top sites, instead of the expected hollow sites. This is interpreted as a signature of the screening of the He atom by the metal for the on-top configuration. The strong screening in the metal is clearly reflected in the relative contribution of successively deeper surface layers to the main dispersion contribution. Aimed to assist future dynamical simulations, a pairwise potential model for the He/surface interaction as a sum of effective He–Mg pair potentials is also presented, as an improvement of the approximation using isolated He–Mg pairs.« less

Post-Hartree-Fock studies of the He/Mg(0001) interaction: Anti-corrugation, screening, and pairwise additivity

NASA Astrophysics Data System (ADS)

de Lara-Castells, María Pilar; Fernández-Perea, Ricardo; Madzharova, Fani; Voloshina, Elena

2016-06-01

The adsorption of noble gases on metallic surfaces represents a paradigmatic case of van-der-Waals (vdW) interaction due to the role of screening effects on the corrugation of the interaction potential [J. L. F. Da Silva et al., Phys. Rev. Lett. 90, 066104 (2003)]. The extremely small adsorption energy of He atoms on the Mg(0001) surface (below 3 meV) and the delocalized nature and mobility of the surface electrons make the He/Mg(0001) system particularly challenging, even for state-of-the-art vdW-corrected density functional-based (vdW-DFT) approaches [M. P. de Lara-Castells et al., J. Chem. Phys. 143, 194701 (2015)]. In this work, we meet this challenge by applying two different procedures. First, the dispersion-corrected second-order Möller-Plesset perturbation theory (MP2C) approach is adopted, using bare metal clusters of increasing size. Second, the method of increments [H. Stoll, J. Chem. Phys. 97, 8449 (1992)] is applied at coupled cluster singles and doubles and perturbative triples level, using embedded cluster models of the metal surface. Both approaches provide clear evidences of the anti-corrugation of the interaction potential: the He atom prefers on-top sites, instead of the expected hollow sites. This is interpreted as a signature of the screening of the He atom by the metal for the on-top configuration. The strong screening in the metal is clearly reflected in the relative contribution of successively deeper surface layers to the main dispersion contribution. Aimed to assist future dynamical simulations, a pairwise potential model for the He/surface interaction as a sum of effective He-Mg pair potentials is also presented, as an improvement of the approximation using isolated He-Mg pairs.

OrChem - An open source chemistry search engine for Oracle(R).

PubMed

Rijnbeek, Mark; Steinbeck, Christoph

2009-10-22

Registration, indexing and searching of chemical structures in relational databases is one of the core areas of cheminformatics. However, little detail has been published on the inner workings of search engines and their development has been mostly closed-source. We decided to develop an open source chemistry extension for Oracle, the de facto database platform in the commercial world. Here we present OrChem, an extension for the Oracle 11G database that adds registration and indexing of chemical structures to support fast substructure and similarity searching. The cheminformatics functionality is provided by the Chemistry Development Kit. OrChem provides similarity searching with response times in the order of seconds for databases with millions of compounds, depending on a given similarity cut-off. For substructure searching, it can make use of multiple processor cores on today's powerful database servers to provide fast response times in equally large data sets. OrChem is free software and can be redistributed and/or modified under the terms of the GNU Lesser General Public License as published by the Free Software Foundation. All software is available via http://orchem.sourceforge.net.

OrChem - An open source chemistry search engine for Oracle®

PubMed Central

2009-01-01

Background Registration, indexing and searching of chemical structures in relational databases is one of the core areas of cheminformatics. However, little detail has been published on the inner workings of search engines and their development has been mostly closed-source. We decided to develop an open source chemistry extension for Oracle, the de facto database platform in the commercial world. Results Here we present OrChem, an extension for the Oracle 11G database that adds registration and indexing of chemical structures to support fast substructure and similarity searching. The cheminformatics functionality is provided by the Chemistry Development Kit. OrChem provides similarity searching with response times in the order of seconds for databases with millions of compounds, depending on a given similarity cut-off. For substructure searching, it can make use of multiple processor cores on today's powerful database servers to provide fast response times in equally large data sets. Availability OrChem is free software and can be redistributed and/or modified under the terms of the GNU Lesser General Public License as published by the Free Software Foundation. All software is available via http://orchem.sourceforge.net. PMID:20298521

Erratum: Hansen et al (2014).

PubMed

2015-04-01

In the article by Hansen AW, Dahl-Petersen I, Helge JW, et al, "Validation of an Internet-Based Long Version of the International Physical Activity Questionnaire in Danish Adults Using Combined Accelerometry and Heart Rate Monitoring," in J Phys Act Health, 11(3), p. 654, the DOI was listed incorrectly (10.1123/jpah.2012-0040a). This error has been fixed. The publisher apologizes for the error.

Quantifying Black Carbon emissions in high northern latitudes using an Atmospheric Bayesian Inversion

NASA Astrophysics Data System (ADS)

Evangeliou, Nikolaos; Thompson, Rona; Stohl, Andreas; Shevchenko, Vladimir P.

2016-04-01

Black carbon (BC) is the main light absorbing aerosol species and it has important impacts on air quality, weather and climate. The major source of BC is incomplete combustion of fossil fuels and the burning of biomass or bio-fuels (soot). Therefore, to understand to what extent BC affects climate change and pollutant dynamics, accurate knowledge of the emissions, distribution and variation of BC is required. Most commonly, BC emission inventory datasets are built by "bottom up" approaches based on activity data and emissions factors, but these methods are considered to have large uncertainty (Cao et al, 2006). In this study, we have used a Bayesian Inversion to estimate spatially resolved BC emissions. Emissions are estimated monthly for 2014 and over the domain from 180°W to 180°E and 50°N to 90°N. Atmospheric transport is modeled using the Lagrangian Particle Dispersion Model, FLEXPART (Stohl et al., 1998; 2005), and the inversion framework, FLEXINVERT, developed by Thompson and Stohl, (2014). The study domain is of particular interest concerning the identification and estimation of BC sources. In contrast to Europe and North America, where BC sources are comparatively well documented as a result of intense monitoring, only one station recording BC concentrations exists in the whole of Siberia. In addition, emissions from gas flaring by the oil industry have been geographically misplaced in most emission inventories and may be an important source of BC at high latitudes since a significant proportion of the total gas flared occurs at these high latitudes (Stohl et al., 2013). Our results show large differences with the existing BC inventories, whereas the estimated fluxes improve modeled BC concentrations with respect to observations. References Cao, G. et al. Atmos. Environ., 40, 6516-6527, 2006. Stohl, A. et al. Atmos. Environ., 32(24), 4245-4264, 1998. Stohl, A. et al. Atmos. Chem. Phys., 5(9), 2461-2474, 2005. Stohl, A. et al. Atmos. Chem. Phys., 13

New Perspectives on the Search for a Parity Violation Effect in Chiral Molecules

NASA Astrophysics Data System (ADS)

Auguste, F.; Tokunaga, S. K.; Shelkovnikov, A.; Daussy, C.; Amy-Klein, A.; Chardonnet, C.; Darquie, B.

2013-06-01

Parity violation (PV) effects have so far never been observed in chiral molecules. Originating from the weak interaction, PV should lead to frequency differences in the rovibrational spectra of the two enantiomers of a chiral molecule. However the smallness of the effect represents a very difficult experimental challenge. We propose to compare the rovibrational spectra (around 10 μm) of two enantiomers, recorded using the ultra-high resolution spectroscopy technique of Doppler-free two-photon Ramsey interferometry in a supersonic molecular beam. With an alternate beam of left- and right-handed molecules and thanks to our expertise in the control of the absolute frequency of the probe CO_2 lasers, we should reach a fractional sensitivity better around 10^{-15} (a few tens of millihertz), on the frequency difference between enantiomers. We will review our latest results on the high-resolution spectroscopy, either in cell or in a supersonic beam, of methyltrioxorhenium. B. Darquié, C. Stoeffler, A. Shelkovnikov, C. Daussy, A. Amy-Klein, C. Chardonnet, S. Zrig, L. Guy, J. Crassous, P. Soulard, P. Asselin, T. R. Huet, P. Schwerdtfeger, R. Bast and T. Saue, Chirality 22, 870 (2010). C. Stoeffler, B. Darquié, A. Shelkovnikov, C. Daussy, A. Amy-Klein, C. Chardonnet, L. Guy, J. Crassous, T. R. Huet, P. Soulard and P. Asselin, Phys. Chem. Chem. Phys. 13, 854 (2011). N. Saleh, S. Zrig, L. Guy, R. Bast, T. Saue, B. Darquié and J. Crassous, submitted to Phys. Chem. Chem. Phys. (2013).

Far-Infrared Spectroscopy of Syn-Vinyl Alcohol

NASA Astrophysics Data System (ADS)

Raston, Paul; Bunn, Hayley

2016-06-01

Vinyl alcohol has been extensively studied in both the microwave and mid-IR spectral regions, where 9 out of 15 vibrational modes have been identified. Here we present the first far-IR spectrum of vinyl alcohol, collected below 700 wn at the Australian Synchrotron. The high resolution (0.001 wn) spectrum reveals the νb{11} and νb{15} fundamentals of syn-vinyl alcohol at 489 wn and 407 wn, in addition to two hot bands of the νb{15} mode at 369 wn and 323 wn. High J transitions in the R-branch of the νb{15} band were found to be perturbed by an a-axis Coriolis interaction with the nearby νb{11} state. The νb{15} torsional mode of syn-vinyl alcohol was fit using a Watson's A-reduced Hamiltonian to yield rotational, centrifugal distortion, and Coriolis coupling parameters. S. Saito, Chem. Phys. Lett. 42, 3 (1976) M. Rodler et al., J. Am. Chem. Soc. 106, 4029 (1948) Y. Koga et al., J. Mol. Spec. 145, 315 (1991) D-L. Joo et al., J. Mol. Spec. 197, 68 (1999)

Full Configuration Interaction Quantum Monte Carlo and Diffusion Monte Carlo: A Comparative Study of the 3D Homogeneous Electron Gas

NASA Astrophysics Data System (ADS)

Shepherd, James J.; López Ríos, Pablo; Needs, Richard J.; Drummond, Neil D.; Mohr, Jennifer A.-F.; Booth, George H.; Grüneis, Andreas; Kresse, Georg; Alavi, Ali

2013-03-01

Full configuration interaction quantum Monte Carlo1 (FCIQMC) and its initiator adaptation2 allow for exact solutions to the Schrödinger equation to be obtained within a finite-basis wavefunction ansatz. In this talk, we explore an application of FCIQMC to the homogeneous electron gas (HEG). In particular we use these exact finite-basis energies to compare with approximate quantum chemical calculations from the VASP code3. After removing the basis set incompleteness error by extrapolation4,5, we compare our energies with state-of-the-art diffusion Monte Carlo calculations from the CASINO package6. Using a combined approach of the two quantum Monte Carlo methods, we present the highest-accuracy thermodynamic (infinite-particle) limit energies for the HEG achieved to date. 1 G. H. Booth, A. Thom, and A. Alavi, J. Chem. Phys. 131, 054106 (2009). 2 D. Cleland, G. H. Booth, and A. Alavi, J. Chem. Phys. 132, 041103 (2010). 3 www.vasp.at (2012). 4 J. J. Shepherd, A. Grüneis, G. H. Booth, G. Kresse, and A. Alavi, Phys. Rev. B. 86, 035111 (2012). 5 J. J. Shepherd, G. H. Booth, and A. Alavi, J. Chem. Phys. 136, 244101 (2012). 6 R. Needs, M. Towler, N. Drummond, and P. L. Ríos, J. Phys.: Condensed Matter 22, 023201 (2010).

Applications and Implications of Fractional Dynamics for Dielectric Relaxation

NASA Astrophysics Data System (ADS)

Hilfer, R.

This article summarizes briefly the presentation given by the author at the NATO Advanced Research Workshop on "Broadband Dielectric Spectroscopy and its Advanced Technological Applications", held in Perpignan, France, in September 2011. The purpose of the invited presentation at the workshop was to review and summarize the basic theory of fractional dynamics (Hilfer, Phys Rev E 48:2466, 1993; Hilfer and Anton, Phys Rev E Rapid Commun 51:R848, 1995; Hilfer, Fractals 3(1):211, 1995; Hilfer, Chaos Solitons Fractals 5:1475, 1995; Hilfer, Fractals 3:549, 1995; Hilfer, Physica A 221:89, 1995; Hilfer, On fractional diffusion and its relation with continuous time random walks. In: Pekalski et al. (eds) Anomalous diffusion: from basis to applications. Springer, Berlin, p 77, 1999; Hilfer, Fractional evolution equations and irreversibility. In: Helbing et al. (eds) Traffic and granular flow'99. Springer, Berlin, p 215, 2000; Hilfer, Fractional time evolution. In: Hilfer (ed) Applications of fractional calculus in physics. World Scientific, Singapore, p 87, 2000; Hilfer, Remarks on fractional time. In: Castell and Ischebeck (eds) Time, quantum and information. Springer, Berlin, p 235, 2003; Hilfer, Physica A 329:35, 2003; Hilfer, Threefold introduction to fractional derivatives. In: Klages et al. (eds) Anomalous transport: foundations and applications. Wiley-VCH, Weinheim, pp 17-74, 2008; Hilfer, Foundations of fractional dynamics: a short account. In: Klafter et al. (eds) Fractional dynamics: recent advances. World Scientific, Singapore, p 207, 2011) and demonstrate its relevance and application to broadband dielectric spectroscopy (Hilfer, J Phys Condens Matter 14:2297, 2002; Hilfer, Chem Phys 284:399, 2002; Hilfer, Fractals 11:251, 2003; Hilfer et al., Fractional Calc Appl Anal 12:299, 2009). It was argued, that broadband dielectric spectroscopy might be useful to test effective field theories based on fractional dynamics.

On interfacial properties of tetrahydrofuran: Atomistic and coarse-grained models from molecular dynamics simulation

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

Garrido, J. M.; Algaba, J.; Blas, F. J., E-mail: felipe@uhu.es

2016-04-14

We have determined the interfacial properties of tetrahydrofuran (THF) from direct simulation of the vapor-liquid interface. The molecules are modeled using six different molecular models, three of them based on the united-atom approach and the other three based on a coarse-grained (CG) approach. In the first case, THF is modeled using the transferable parameters potential functions approach proposed by Chandrasekhar and Jorgensen [J. Chem. Phys. 77, 5073 (1982)] and a new parametrization of the TraPPE force fields for cyclic alkanes and ethers [S. J. Keasler et al., J. Phys. Chem. B 115, 11234 (2012)]. In both cases, dispersive and coulombicmore » intermolecular interactions are explicitly taken into account. In the second case, THF is modeled as a single sphere, a diatomic molecule, and a ring formed from three Mie monomers according to the SAFT-γ Mie top-down approach [V. Papaioannou et al., J. Chem. Phys. 140, 054107 (2014)]. Simulations were performed in the molecular dynamics canonical ensemble and the vapor-liquid surface tension is evaluated from the normal and tangential components of the pressure tensor along the simulation box. In addition to the surface tension, we have also obtained density profiles, coexistence densities, critical temperature, density, and pressure, and interfacial thickness as functions of temperature, paying special attention to the comparison between the estimations obtained from different models and literature experimental data. The simulation results obtained from the three CG models as described by the SAFT-γ Mie approach are able to predict accurately the vapor-liquid phase envelope of THF, in excellent agreement with estimations obtained from TraPPE model and experimental data in the whole range of coexistence. However, Chandrasekhar and Jorgensen model presents significant deviations from experimental results. We also compare the predictions for surface tension as obtained from simulation results for all the models with

Combustion Synthesis Reaction Behavior of Cold-Rolled Ni/Al and Ti/Al Multilayers

DTIC Science & Technology

2011-04-01

6   Figure 4 . Combustion synthesis process of the cold-rolled Ni/Al multilayer foils: (a) reaction front of the displacement of the reaction...Reactive Nanostructured Foil Used as a Heat Source for Joining Titanium . J. Appl. Phys. 2004, 96 ( 4 ), 2336–2342. 16. Wang, J.; Besnoin, E...2011 2. REPORT TYPE Final 3. DATES COVERED (From - To) January 2006–January 2008 4 . TITLE AND SUBTITLE Combustion Synthesis Reaction Behavior of

Excited state of protonated benzene and toluene

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

Esteves-López, Natalia; Dedonder-Lardeux, Claude; Jouvet, Christophe, E-mail: Christophe.jouvet@univ-amu.fr

We present photo-fragmentation electronic spectra of the simplest protonated aromatic molecules, protonated benzene and toluene, recorded under medium resolution conditions and compared with the photo-fragmentation spectrum of protonated pyridine. Despite the resolution and cold temperature achieved in the experiment, the electronic spectra of protonated benzene and toluene are structure-less, thus intrinsically broadened. This is in agreement with the large geometrical changes and the fast dynamic toward internal conversion predicted by ab initio calculations for protonated benzene [Rode et al., J. Phys. Chem. A 113, 5865–5873 (2009)].

A New Transition in the Spectrum of YCl: Rotational Analysis of the K1Π- X1Σ +UV Band System

NASA Astrophysics Data System (ADS)

Xin, Ju; Klynning, Lennart

1996-02-01

The absorption spectrum of the yttrium monochloride molecule (YCl) produced in a King-type furnace has been recorded at high resolution using a 5-m Fastie spectrograph. A new band system in the UV region (centered at 3291 Å) has been found and rotationally analyzed. The transition has been assigned toK1Π-X1Σ+, in accordance with the labeling of the YCl electronic states by Langhoffet al.(J. Chem. Phys.89,396-407, 1988) in their theoretical work. Molecular constants for the new state are presented.

Photoinduced Partial Unfolding of Tubulin Bound to Meso-tetrakis(sulfonatophenyl) Porphyrin Leads to Inhibition of Microtubule Formation In Vitro

DTIC Science & Technology

2013-07-30

H. Nettles, B . Cornett, K . H. Downing, and E. Nogales, Proc. Natl. Acad. Sci. 98, 5312–5316 (2001). B . McMicken et al.: Photoinduced unfolding of...and R. K . Pandey, Chem Soc Rev. 40, 340–362 (2011). [23] B . C. Wilson and M. S. Patterson, Phys Med Biol. 53, R61–R109 (2008). [24] E. D. Sternberg, D... K . Subbarao and R. C. MacDonald, Analyst 118, 913–916 (1993). [30] F. V. Bright and C. Munson, Anal. Chim. Acta 500, 71–104 (2003). [31] Z. Li, T. Lu

Communication: Hypothetical ultralow-density ice polymorphs

NASA Astrophysics Data System (ADS)

Matsui, Takahiro; Hirata, Masanori; Yagasaki, Takuma; Matsumoto, Masakazu; Tanaka, Hideki

2017-09-01

More than 300 kinds of porous ice structures derived from zeolite frameworks and space fullerenes are examined using classical molecular dynamics simulations. It is found that a hypothetical zeolitic ice phase is less dense and more stable than the sparse ice structures reported by Huang et al. [Chem. Phys. Lett. 671, 186 (2017)]. In association with the zeolitic ice structure, even less dense structures, "aeroices," are proposed. It is found that aeroices are the most stable solid phases of water near the absolute zero temperature under negative pressure.

Molecular dynamics simulations of collision-induced absorption: Implementation in LAMMPS

NASA Astrophysics Data System (ADS)

Fakhardji, W.; Gustafsson, M.

2017-02-01

We pursue simulations of collision-induced absorption in a mixture of argon and xenon gas at room temperature by means of classical molecular dynamics. The established theoretical approach (Hartmann et al. 2011 J. Chem. Phys. 134 094316) is implemented with the molecular dynamics package LAMMPS. The bound state features in the absorption spectrum are well reproduced with the molecular dynamics simulation in comparison with a laboratory measurement. The magnitude of the computed absorption, however, is underestimated in a large part of the spectrum. We suggest some aspects of the simulation that could be improved.

Low-lying singlet states of carotenoids having 8-13 conjugated double bonds as determined by electronic absorption spectroscopy

NASA Astrophysics Data System (ADS)

Wang, Peng; Nakamura, Ryosuke; Kanematsu, Yasuo; Koyama, Yasushi; Nagae, Hiroyoshi; Nishio, Tomohiro; Hashimoto, Hideki; Zhang, Jian-Ping

2005-07-01

Electronic absorption spectra were recorded at room temperature in solutions of carotenoids having different numbers of conjugated double bonds, n = 8-13, including a spheroidene derivatives, neurosporene, spheroidene, lycopene, anhydrorhodovibrin and spirilloxanthin. The vibronic states of 1Bu+(v=0-4), 2Ag-(v=0-3), 3Ag- (0) and 1Bu- (0) were clearly identified. The arrangement of the four electronic states determined by electronic absorption spectroscopy was identical to that determined by measurement of resonance Raman excitation profiles [K. Furuichi et al., Chem. Phys. Lett. 356 (2002) 547] for carotenoids in crystals.

The role of 2-methylglyceric acid and oligomer formation in the multiphase processing of secondary organic aerosol from isoprene and methacrolein photooxidation (CUMULUS project)

NASA Astrophysics Data System (ADS)