Search

Abstract: A fast and accurate Quantum Mechanics/Molecular Mechanics method is described for thermodynamic simulation of solutes (or active sites in flexible molecules) in polar environments. The solute is described quantum mechanically and is held fixed during averaging over solvent configurations, which are described by Molecular Mechanics. Quantum calculations during simulation are replaced by the evaluation of the response of the solute to the long range electric field of the solvent, using precalculated generalized electric moments and polarizabilities. This results in huge decrease of computational time without affecting the accuracy of the QM/MM results. Implementation in a Monte Carlo program accelerated the simulations of guanine and the phenylalanine dipeptide in TIP3P water by over four orders of magnitude. Polarizability is essential for accuracy. Its inclusion decreases the average signed energy error and its standard deviation from 5.69 to 0.003 and 1.22 to 0.013kcal/mol, respectively, for the dipeptide. Hyperpolarizability contributions are insignificant. [Copyright &y& Elsevier]

A very simple quantum chemical model is proposed to simulate the effect of external forces acting on a single molecule. It involves optimising the geometry of a molecule with an external force applied to selected nuclei. This approach is used to investigate conformational transitions of the pyranose ring, which have been the subject of several atomic force microscopy (AFM) experiments, and to generate a number of previously unknown isomers of azobenzene. [ABSTRACT FROM AUTHOR]

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. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009 [ABSTRACT FROM AUTHOR]