Symmetry numbers and chemical reaction rates

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.     

VinaMPI: Facilitating multiple receptor high‐throughput virtual docking on high‐performance computers

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.     

Efficient calculation of SAMPL4 hydration free energies using OMEGA,SZYBKI, QUACPAC,and Zap TK

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.     

Method for the direct determination of available carbohydrates in low-carbohydrate products using high-performance anion exchange chromatography

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.     

Temperature dependence of carbon-13 kinetic isotope effects of importance to global climate change

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.     

Analysis of SM8 and Zap TK calculations and their geometric sensitivity

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.     

Photoinduced charge carrier generation in a poly(3-hexylthiophene) and methanofullerene bulk heterojunction investigated by time-resolved terahertz spectroscopy

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.     

Determination of the enthalpy change for anabolism by four methods

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 C_substrate→C_products+xO₂ with an enthalpy change, ΔH_b. Four methods are proposed for determining ΔH_b: (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, R_SG, and of the product (R_SG ΔH_b). The product (R_SG ΔH_b) equals (−ΔH_CO2R_CO2−R_q) where R_CO2 is the specific rate of CO₂ production by respiration, ΔH_CO2 is the heat of combustion of respiratory substrate per mole of CO₂ and R_q is the specific metabolic heat rate. ΔH_b is then calculated as the ratio (R_SG ΔH_b)/R_SG. (d) From (ΔH_b=−(R_q/R_CO2+ΔH_CO2) [(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. ΔH_b values from all four methods are in reasonable agreement despite the different assumptions involved.     

Optical parametric processes and broadly tunable femtosecond sources

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.