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.