Center for Molecular Modeling - Y. Shao

Advances in molecular quantum chemistry contained in the Q-Chem 4 program package

wim — Mon, 16 Feb 2015 13:43:16 +0000

Y. Shao, et al., A. Ghysels

Molecular Physics

113 (2), 184-215

2015

Abstract

A summary of the technical advances that are incorporated in the fourth major release of the Q-Chem quantum chemistry program is provided, covering approximately the last seven years. These include developments in density functional theory methods and algorithms, nuclear magnetic resonance (NMR) property evaluation, coupled cluster and perturbation theories, methods for electronically excited and open-shell species, tools for treating extended environments, algorithms for walking on potential surfaces, analysis tools, energy and electron transfer modelling, parallel computing capabilities, and graphical user interfaces. In addition, a selection of example case studies that illustrate these capabilities is given. These include extensive benchmarks of the comparative accuracy of modern density functionals for bonded and non-bonded interactions, tests of attenuated second order Møller–Plesset (MP2) methods for intermolecular interactions, a variety of parallel performance benchmarks, and tests of the accuracy of implicit solvation models. Some specific chemical examples include calculations on the strongly correlated Cr2 dimer, exploring zeolite-catalysed ethane dehydrogenation, energy decomposition analysis of a charged ter-molecular complex arising from glycerol photoionisation, and natural transition orbitals for a Frenkel exciton state in a nine-unit model of a self-assembling nanotube.

DOI

http://dx.doi.org/10.1080/00268976.2014.952696

Private attachment

15_MolPhys_113(2)184_YihanShao.pdf

Vibrational subsystem analysis: A method for probing free energies and correlations in the harmonic limit

wim — Mon, 03 Oct 2011 09:58:51 +0000

H. Lee Woodcock III, W. Zheng, A. Ghysels, Y. Shao, J. Kong, B.R. Brooks

Journal of Chemical Physics

129 (21), 214109

2008

Abstract

A new vibrational subsystem analysis (VSA) method is presented for coupling global motion to a local subsystem while including the inertial effects of the environment. The premise of the VSA method is a partitioning of a system into a smaller region of interest and a usually larger part referred to as environment. This method allows the investigation of local-global coupling, a more accurate estimation of vibrational free energy contribution for parts of a large system, and the elimination of the “tip effect” in elastic network model calculations. Additionally, the VSA method can be used as a probe of specific degrees of freedom that may contribute to free energy differences. The VSA approach can be employed in many ways, but it will likely be most useful for estimating activation free energies in QM/MM reaction path calculations. Four examples are presented to demonstrate the utility of this method.

DOI

http://dx.doi.org/10.1063/1.3013558

Private attachment

08 j. chem. phys. 129(21)214109 woodcock.pdf

Efficient Calculation of QM/MM Frequencies with the Mobile Block Hessian

wim — Tue, 23 Aug 2011 07:07:28 +0000

A. Ghysels, H. Lee Woodcock III, J.D. Larkin, B.T. Miller, Y. Shao, J. Kong, D. Van Neck, V. Van Speybroeck, M. Waroquier, B.R. Brooks

Journal of Chemical Theory and Computation (JCTC)

7 (2), 496–514

2011

Abstract

The calculation of the analytical second derivative matrix (Hessian) is the bottleneck for vibrational analysis in QM/MM systems when an electrostatic embedding scheme is employed. Even with a small number of QM atoms in the system, the presence of MM atoms increases the computational cost dramatically: the long-range Coulomb interactions require that additional coupled perturbed self-consistent field (CPSCF) equations need to be solved for each MM atom displacement. This paper presents an extension to the Mobile Block Hessian (MBH) formalism for QM/MM calculations with blocks in the MM region and its implementation in a parallel version of the Q-Chem/CHARMM interface. MBH reduces both the CPU time and the memory requirements compared to the standard full Hessian QM/MM analysis, without the need to use a cutoff distance for the electrostatic interactions. Special attention is given to the treatment of link atoms which are usually present when the QM/MM border cuts through a covalent bond. Computational efficiency improvements are highlighted using a reduced chorismate mutase enzyme system, consisting of 24 QM atoms and 306 MM atoms, as a test example. In addition, the drug bortezomib, used for cancer treatment of myeloma, has been studied as a test case with multiple MBH block choices and both a QM and QM/MM description. The accuracy of the calculated Hessians is quantified by imposing Eckart constraints, which allows for the assessment of numerical errors in second derivative procedures. The results show that MBH within the QM/MM description not only is a computationally attractive method but also produces accurate results.

DOI

http://dx.doi.org/10.1021/ct100473f

Private attachment

11 j chem theory comp 7, 496 ghysels.pdf

Normal mode calculations with the QM/MM full Hessian and the Mobile Block Hessian (MBH) method

wim — Tue, 18 Oct 2011 06:59:12 +0000

A. Ghysels, H. Lee Woodcock III, Y. Shao, B.R. Brooks, V. Van Speybroeck, D. Van Neck, M. Waroquier

Poster

Conference / event / venue

7th Canadian Computational Chemistry Conference

Halifax, Canada

Monday, 20 July, 2009 to Friday, 24 July, 2009

Normal mode calculations with the QM/MM full Hessian and the Mobile Block Hessian (MBH) method

wim — Mon, 17 Oct 2011 14:09:25 +0000

A. Ghysels, H. Lee Woodcock III, Y. Shao, B.R. Brooks, V. Van Speybroeck, D. Van Neck, M. Waroquier

Poster

Conference / event / venue

Quantum Chemistry in Belgium 9th edition

Louvain-la-Neuve, Belgium

Tuesday, 26 January, 2010

Abstract

2010 QBC9 ghysels.pdf

Efficient calculation of QM/MM frequencies with the Mobile Block Hessian

wim — Mon, 17 Oct 2011 13:45:19 +0000

A. Ghysels, H. Lee Woodcock III, Y. Shao, B.R. Brooks, D. Van Neck, V. Van Speybroeck, M. Waroquier

Poster

Conference / event / venue

Gordon Research Conference - Computational Chemistry

Les Diablerets, Switzerland

Sunday, 29 August, 2010 to Friday, 3 September, 2010

Abstract

2010 efficient calculation NAMIAM.pdf

The evaluation of the QM/MM full Hessian and some applications

wim — Mon, 17 Oct 2011 09:54:02 +0000

H. Lee Woodcock III, A. Ghysels, Y. Shao, J. Kong, B.R. Brooks

Talk

Conference / event / venue

238th ACS National Meeting

Washington DC

Sunday, 16 August, 2009 to Thursday, 20 August, 2009

Abstract

2009 abstract ACS_AnGhysels.pdf

Efficient calculation of QM/MM frequencies with the Mobile Block Hessian method

wim — Mon, 17 Oct 2011 08:30:55 +0000

A. Ghysels, H. Lee Woodcock III, Y. Shao, J. Kong, B.R. Brooks, D. Van Neck, V. Van Speybroeck, M. Waroquier

Talk

Conference / event / venue

North American Meeting on Industrial and Applied Mathematics (NAMIAM)

Huatulco, Mexico

Monday, 6 December, 2010 to Saturday, 11 December, 2010

Abstract

2010 efficient calculation NAMIAM.pdf