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Antonio Fernández-Ramos Benjamin A. Ellingson Rubén Meana-Pañeda Jorge M. C. Marques Donald G. Truhlar 《Theoretical chemistry accounts》2007,118(4):813-826
This article shows how to evaluate rotational symmetry numbers for different molecular configurations and how to apply them
to transition state theory. In general, the symmetry number is given by the ratio of the reactant and transition state rotational
symmetry numbers. However, special care is advised in the evaluation of symmetry numbers in the following situations: (i)
if the reaction is symmetric, (ii) if reactants and/or transition states are chiral, (iii) if the reaction has multiple conformers
for reactants and/or transition states and, (iv) if there is an internal rotation of part of the molecular system. All these
four situations are treated systematically and analyzed in detail in the present article. We also include a large number of
examples to clarify some complicated situations, and in the last section we discuss an example involving an achiral diasteroisomer. 相似文献
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Sally R. Ellingson Jeremy C. Smith Jerome Baudry 《Journal of computational chemistry》2013,34(25):2212-2221
The program VinaMPI has been developed to enable massively large virtual drug screens on leadership‐class computing resources, using a large number of cores to decrease the time‐to‐completion of the screen. VinaMPI is a massively parallel Message Passing Interface (MPI) program based on the multithreaded virtual docking program AutodockVina, and is used to distribute tasks while multithreading is used to speed‐up individual docking tasks. VinaMPI uses a distribution scheme in which tasks are evenly distributed to the workers based on the complexity of each task, as defined by the number of rotatable bonds in each chemical compound investigated. VinaMPI efficiently handles multiple proteins in a ligand screen, allowing for high‐throughput inverse docking that presents new opportunities for improving the efficiency of the drug discovery pipeline. VinaMPI successfully ran on 84,672 cores with a continual decrease in job completion time with increasing core count. The ratio of the number of tasks in a screening to the number of workers should be at least around 100 in order to have a good load balance and an optimal job completion time. The code is freely available and downloadable. Instructions for downloading and using the code are provided in the Supporting Information. © 2013 Wiley Periodicals, Inc. 相似文献
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Benjamin A. Ellingson Matthew T. Geballe Stanislaw Wlodek Christopher I. Bayly A. Geoffrey Skillman Anthony Nicholls 《Journal of computer-aided molecular design》2014,28(3):289-298
Several submissions for the SAMPL4 hydration free energy set were calculated using OpenEye tools, including many that were among the top performing submissions. All of our best submissions used AM1BCC charges and Poisson–Boltzmann solvation. Three submissions used a single conformer for calculating the hydration free energy and all performed very well with mean unsigned errors ranging from 0.94 to 1.08 kcal/mol. These calculations were very fast, only requiring 0.5–2.0 s per molecule. We observed that our two single-conformer methodologies have different types of failure cases and that these differences could be exploited for determining when the methods are likely to have substantial errors. 相似文献
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Ellingson D Potts B Anderson P Burkhardt G Ellefson W Sullivan D Jacobs W Ragan R 《Journal of AOAC International》2010,93(6):1897-1904
An improved method for direct determination of available carbohydrates in low-level products has been developed and validated for a low-carbohydrate soy infant formula. The method involves modification of an existing direct determination method to improve specificity, accuracy, detection levels, and run times through a more extensive enzymatic digestion to capture all available (or potentially available) carbohydrates. The digestion hydrolyzes all common sugars, starch, and starch derivatives down to their monosaccharide components, glucose, fructose, and galactose, which are then quantitated by high-performance anion-exchange chromatography with photodiode array detection. Method validation consisted of specificity testing and 10 days of analyzing various spike levels of mixed sugars, maltodextrin, and corn starch. The overall RSD was 4.0% across all sample types, which contained within-day and day-to-day components of 3.6 and 3.4%, respectively. Overall average recovery was 99.4% (n = 10). Average recovery for individual spiked samples ranged from 94.1 to 106% (n = 10). It is expected that the method could be applied to a variety of low-carbohydrate foods and beverages. 相似文献
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Lin H Zhao Y Ellingson BA Pu J Truhlar DG 《Journal of the American Chemical Society》2005,127(9):2830-2831
We report here a theoretical study of the 13C kinetic isotope effect (KIE) and its temperature dependence for the reaction OH + CH4 --> H2O + CH3, the major sink of atmospheric methane in the troposphere. The KIE values at various atmospherically significant temperatures were determined by direct dynamics using variational transition state theory with multidimensional tunneling contributions (VTST/MT). The potential energy surfaces (PESs) were generated by hybrid density functional theory as well as by recently developed doubly hybrid density functional theory methods. Comparisons of our calculated KIEs with experimental data and theoretical values in the literature reveal the critical contributions due to multidimensional tunneling and torsion anharmonicity as well as the critical issue of the choice of internal rotational axis. 相似文献
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Benjamin A. Ellingson A. Geoffrey Skillman Anthony Nicholls 《Journal of computer-aided molecular design》2010,24(4):335-342
A prospective study of aqueous solvation energies was done using the SM8 and Zap TK models for a variety of geometries. CM4M
charges calculated with M06 and M06-2X were found to yield similar results for the SM8 model. Zap TK calculations were primarily
done with AM1BCC charges but limited attempts to use charges derived from DFT showed promise. The OMEGA application quickly
generated conformations that performed well with both solvation models, while the use of computationally expensive DFT optimized
geometries yielded increased RMSE and MSE. It is shown that increasing levels of gas phase geometry optimization yield increasingly
unfavorable solvation energy for single conformer models. 相似文献
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Ai X Beard MC Knutsen KP Shaheen SE Rumbles G Ellingson RJ 《The journal of physical chemistry. B》2006,110(50):25462-25471
We report on the ultrafast photoinduced charge separation processes in varying compositions of poly(3-hexylthiophene) (P3HT) blended with the electron acceptor [6,6]-phenyl-C61-butyric acid methyl ester (PCBM). Through the use of time-resolved terahertz spectroscopy, the time- and frequency-dependent complex photoconductivity is measured for samples with PCBM weight fractions (WPCBM) of 0, 0.2, 0.5, and 0.8. By analysis of the frequency-dependent complex conductivity, both the charge carrier yield and the average charge carrier mobility have been determined analytically and indicate a short (<0.2 nm) carrier mean free path and a suppressed long-range transport that is characteristic of carrier localization. Studies on pure films of P3HT demonstrate that charge carrier generation is an intrinsic feature of the polymer that occurs on the time scale of the excitation light, and this is attributed to the dissociation of bound polaron pairs that reside on adjacent polymer chains due to interchain charge transfer. Both interchain and interfacial charge transfer contribute to the measured photoconductivity from the blended samples; interfacial charge transfer increases as a function of increasing PCBM. The addition of PCBM to the polymer films surprisingly does not dramatically increase the production of charge carriers within the first 2 ps. However, charge carriers in the 0.2 and 0.5 blended films survive to much longer times than those in the P3HT and 0.8 films. 相似文献
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Derek Ellingson Aaron Olson Sannali Matheson Richard S. Criddle Bruce N. Smith Lee D. Hansen 《Thermochimica Acta》2003,400(1-2):79-85
The enthalpy change for anabolism is needed to model the growth/respiration relation in plants. If all CO2 production is assigned to catabolism, the anabolic reaction becomes Csubstrate→Cproducts+xO2 with an enthalpy change, ΔHb. Four methods are proposed for determining ΔHb: (a) From the difference in the heats of combustion of substrate and anabolic products (i.e. newly grown tissue). (b) From the composition of newly grown tissue and application of Thornton’s rule. (c) From independently measured values of the specific growth rate, RSG, and of the product (RSG ΔHb). The product (RSG ΔHb) equals (−ΔHCO2RCO2−Rq) where RCO2 is the specific rate of CO2 production by respiration, ΔHCO2 is the heat of combustion of respiratory substrate per mole of CO2 and Rq is the specific metabolic heat rate. ΔHb is then calculated as the ratio (RSG ΔHb)/RSG. (d) From (ΔHb=−(Rq/RCO2+ΔHCO2) [(1−)/] where is the substrate carbon conversion efficiency obtained from a total carbon balance. The first three methods have been tested and compared on oat seedlings and the last on corn seedlings. ΔHb values from all four methods are in reasonable agreement despite the different assumptions involved. 相似文献
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The basic concepts of optical parametric processes and recent results on broadly tunable high-repetition rate femtosecond Optical Parametric Oscillators (fs OPO) are reviewed. Ti:Sapphire-Laser pumped KTP, KTA, and CTA fs OPOs and intracavity-doubled fs KTP OPO in particular are discussed. 相似文献