Quantum chemistry in parallel with PQS
ABSTRACT This article describes the capabilities and performance of the latest release (version 4.0) of the Parallel Quantum Solutions (PQS) ab initio program package. The program was first released in 1998 and evolved from the TEXAS program package developed by Pulay and coworkers in the late 1970s. PQS was designed from the start to run on Linux-based clusters (which at the time were just becoming popular) with all major functionality being (a) fully parallel; and (b) capable of carrying out calculations on large-by ab initio standards-molecules, our initial aim being at least 100 atoms and 1000 basis functions with only modest memory requirements. With modern hardware and recent algorithmic developments, full accuracy, high-level calculations (DFT, MP2, CI, and Coupled-Cluster) can be performed on systems with up to several thousand basis functions on small (4-32 node) Linux clusters. We have also developed a graphical user interface with a model builder, job input preparation, parallel job submission, and post-job visualization and display. (c) 2008 Wiley Periodicals, Inc. J Comput Chem, 2008.
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ABSTRACT: DFT optimization and DFT-MD studies are carried out on αβ-glucose surrounded by ten explicit water molecules and the glucose/water super-molecule completely enclosed by an implicit solvation model, COSMO. A set of twenty one starting configurations of the explicit waters were first optimized empirically with the AMB06C/TIP3P force field, and further optimized using a reduced basis set (B3LYP/4-31G) on the sugar carbon atoms and the larger B3LYP/6-31+G∗ level on all other atoms. Glucose hydroxymethyl conformations included gg, gt, and tg forms, with the hydroxyl group’s conformations counter clockwise, ‘r’, and clockwise, ‘c’, forms. The empirical force field optimized configurations were in general agreement with the DFT results in hydrogen bonding distances from glucose to water molecules, but not in such good agreement in water molecule orientation, a result of lack of lone-pair orientation within the TIP3P force field. The individual energies of all components of the super-molecule complex (i.e. water-water, water-glucose), with and without COSMO, allows analysis of the hydration and interaction energies. Examination of the hydroxyl and hydroxymethyl low energy conformations suggests that the hydrated configurations with gg-r and gg-c conformers are preferred in water. DFT-MD is carried out on all configurations leading to understanding of the lifetimes of water molecule contact with glucose. The results suggest that no water molecule remains at any one specific site around glucose for a significant time, water molecules migrating off and moving around the molecule within several picoseconds.Computational and Theoretical Chemistry 02/2014; 1029:57-67. DOI:10.1016/j.comptc.2013.12.007 · 1.37 Impact Factor
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ABSTRACT: Six conformers of alpha-cysteine were identified by matrix isolation IR spectroscopy combined with NIR laser irradiation. Five of these conformers are identical with five out of six conformers recently identified by microwave spectroscopy. The sixth conformer observed in the present study is a short-lived conformer, which decays by H-atom tunneling; its half-life in a 12 K N2 matrix is 1.0 x 10 3 ± 3.0 x10 2 s. This study proves that matrix isolation IR spectroscopy combined with NIR laser irradiation is a suitable method to identify conformers of a complex system for which computations predict several dozens of conformers, and that the reliability of this method for conformational assignment is comparable to that of microwave spectroscopy.The Journal of Physical Chemistry B 01/2014; 118(8). DOI:10.1021/jp412550q · 3.38 Impact Factor
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ABSTRACT: A series of neutral and protonated five-membered ring cyclic ketene acetals have been examined computationally for any trends in nucleophilicity in the exocyclic methylene and for their ground state geometries. A total of 58 different species were examined, 29 neutral molecules and the corresponding 29 protonated species. The heteroatoms that were used in the heterocyclic ring were a combination of nitrogen, phosphorus, and arsenic from the pnictogen family and oxygen, sulfur, and selenium from the chalcogen family. All geometries were initially optimized at using density functional theory and all stationary points were confirmed to be either minima or transition states through vibrational analysis. All the geometries were consequentially optimized using Møller–Plesset second order perturbation theory with a polarized triple zeta basis set. The main focus of the study was the nucleophilicity of the exocyclic methylene carbon atom and its dependence on heteroatom substitution. As probes for nucleophilicity, the proton affinities of the neutral species, the bond lengths of the exocyclic double bond, and atomic charges were used. The study also resulted in some interesting molecular geometries.Structural Chemistry 02/2014; 25(1). DOI:10.1007/s11224-013-0338-6 · 1.90 Impact Factor