Literature DB >> 17299773

Gaussian induced dipole polarization model.

Dennis Elking1, Tom Darden, Robert J Woods.   

Abstract

A new induced dipole polarization model based on interacting Gaussian charge densities is presented. In contrast to the original induced point dipole model, the Gaussian polarization model is capable of finite interactions at short distances. Aspects of convergence related to the Gaussian model will be explored. The Gaussian polarization model is compared with the damped Thole-induced dipole model and the point dipole model. It will be shown that the Gaussian polarization model performs slightly better than the Thole model in terms of fitting to molecular polarizability tensors. An advantage of the model based on Gaussian charge distribution is that it can be easily generalized to other multipole moments and provide effective damping for both permanent electrostatic and polarization models. Finally, a method of parameterizing polarizabilities is presented. This method is based on probing a molecule with point charges and fitting polarizabilities to electrostatic potential. In contrast to the generic atom type polarizabilities fit to molecular polarizability tensors, probed polarizabilities are significantly more accurate in terms of reproducing molecular polarizability tensors and electrostatic potential, while retaining conformational transferability.

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Year:  2007        PMID: 17299773      PMCID: PMC2176076          DOI: 10.1002/jcc.20574

Source DB:  PubMed          Journal:  J Comput Chem        ISSN: 0192-8651            Impact factor:   3.376


  9 in total

Review 1.  Potential energy functions: from consistent force fields to spectroscopically determined polarizable force fields.

Authors:  Kim Palmo; Berit Mannfors; Noemi G Mirkin; Samuel Krimm
Journal:  Biopolymers       Date:  2003-03       Impact factor: 2.505

2.  Development of a polarizable force field for proteins via ab initio quantum chemistry: first generation model and gas phase tests.

Authors:  George A Kaminski; Harry A Stern; B J Berne; Richard A Friesner; Yixiang X Cao; Robert B Murphy; Ruhong Zhou; Thomas A Halgren
Journal:  J Comput Chem       Date:  2002-12       Impact factor: 3.376

3.  OPEP: a tool for the optimal partitioning of electric properties.

Authors:  János G Angyán; Christophe Chipot; François Dehez; Christof Hättig; Georg Jansen; Claude Millot
Journal:  J Comput Chem       Date:  2003-06       Impact factor: 3.376

4.  Many-body force field models based solely on pairwise Coulomb screening do not simultaneously reproduce correct gas-phase and condensed-phase polarizability limits.

Authors:  Timothy J Giese; Darrin M York
Journal:  J Chem Phys       Date:  2004-06-01       Impact factor: 3.488

5.  Improved Formulas for the Calculation of the Electrostatic Contribution to the Intermolecular Interaction Energy from Multipolar Expansion of the Electronic Distribution.

Authors:  Jean-Philip Piquemal; Nohad Gresh; Claude Giessner-Prettre
Journal:  J Phys Chem A       Date:  2003-12-04       Impact factor: 2.781

6.  On the performance of molecular polarization methods. II. Water and carbon tetrachloride close to a cation.

Authors:  Marco Masia; Michael Probst; Rossend Rey
Journal:  J Chem Phys       Date:  2005-10-22       Impact factor: 3.488

7.  From dimer to condensed phases at extreme conditions: accurate predictions of the properties of water by a Gaussian charge polarizable model.

Authors:  Patrice Paricaud; Milan Predota; Ariel A Chialvo; Peter T Cummings
Journal:  J Chem Phys       Date:  2005-06-22       Impact factor: 3.488

8.  Towards a force field based on density fitting.

Authors:  Jean-Philip Piquemal; G Andrés Cisneros; Peter Reinhardt; Nohad Gresh; Thomas A Darden
Journal:  J Chem Phys       Date:  2006-03-14       Impact factor: 3.488

9.  Consistent treatment of inter- and intramolecular polarization in molecular mechanics calculations.

Authors:  Pengyu Ren; Jay W Ponder
Journal:  J Comput Chem       Date:  2002-12       Impact factor: 3.376

  9 in total
  31 in total

1.  Generalized and efficient algorithm for computing multipole energies and gradients based on Cartesian tensors.

Authors:  Dejun Lin
Journal:  J Chem Phys       Date:  2015-09-21       Impact factor: 3.488

2.  Numerical fitting of molecular properties to Hermite Gaussians.

Authors:  G Andrés Cisneros; Dennis Elking; Jean-Philip Piquemal; Thomas A Darden
Journal:  J Phys Chem A       Date:  2007-11-01       Impact factor: 2.781

3.  Contracted auxiliary Gaussian basis integral and derivative evaluation.

Authors:  Timothy J Giese; Darrin M York
Journal:  J Chem Phys       Date:  2008-02-14       Impact factor: 3.488

Review 4.  Classical electrostatics for biomolecular simulations.

Authors:  G Andrés Cisneros; Mikko Karttunen; Pengyu Ren; Celeste Sagui
Journal:  Chem Rev       Date:  2013-08-27       Impact factor: 60.622

5.  Recent Force Field Strategies for Intrinsically Disordered Proteins.

Authors:  Junxi Mu; Hao Liu; Jian Zhang; Ray Luo; Hai-Feng Chen
Journal:  J Chem Inf Model       Date:  2021-02-16       Impact factor: 4.956

Review 6.  Molecular simulations of carbohydrates and protein-carbohydrate interactions: motivation, issues and prospects.

Authors:  Elisa Fadda; Robert J Woods
Journal:  Drug Discov Today       Date:  2010-06-08       Impact factor: 7.851

Review 7.  Predicting the Structures of Glycans, Glycoproteins, and Their Complexes.

Authors:  Robert J Woods
Journal:  Chem Rev       Date:  2018-08-09       Impact factor: 60.622

8.  Efficient formulation of polarizable Gaussian multipole electrostatics for biomolecular simulations.

Authors:  Haixin Wei; Ruxi Qi; Junmei Wang; Piotr Cieplak; Yong Duan; Ray Luo
Journal:  J Chem Phys       Date:  2020-09-21       Impact factor: 3.488

9.  Fluorescence of tryptophan in designed hairpin and Trp-cage miniproteins: measurements of fluorescence yields and calculations by quantum mechanical molecular dynamics simulations.

Authors:  Andrew W McMillan; Brandon L Kier; Irene Shu; Aimee Byrne; Niels H Andersen; William W Parson
Journal:  J Phys Chem B       Date:  2013-02-04       Impact factor: 2.991

10.  Revisiting the myths of protein interior: studying proteins with mass-fractal hydrophobicity-fractal and polarizability-fractal dimensions.

Authors:  Anirban Banerji; Indira Ghosh
Journal:  PLoS One       Date:  2009-10-16       Impact factor: 3.240

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