Literature DB >> 26641295

Pseudospectral Local Second-Order Møller-Plesset Methods for Computation of Hydrogen Bonding Energies of Molecular Pairs.

George A Kaminski1,2,3, Jon R Maple1,2,3, Robert B Murphy1,2,3, Dale A Braden1,2,3, Richard A Friesner1,2,3.   

Abstract

We present a methodology for computing the binding energy of molecular dimers based on extrapolation of pseudospectral local second-order Moller-Plesset (MP2), or PS-LMP2, energies to the basis set limit. The extrapolation protocol is based on carrying out PS-LMP2 calculations with the Dunning cc-pVTZ (-f) and cc-pVQZ (-g) basis sets and then using a simple two-parameter function to compute the final basis set limit results. The function is parametrized to ultralarge basis set MP2 calculations for 5 molecular pairs taken from the literature and then tested by calculating results for a set of formamide dimers for which such calculations have also been carried out. The results agree to within ca. 0.2 kcal/mol with the conventional MP2 large basis set calculations. A specialized, but relatively simple, protocol is described for eliminating noise due to overcompleteness of the basis set. Timing results are presented for the LMP2 calculations, and comparisons are made with the LMP2 methodology of the QChem program. CPU time required by each of the methods scales as N(3), where N is the number of the basis functions, with the PS-LMP2 approach displaying a 2- to 3-fold advantage in the prefactor. We also discuss one set of test cases for which the PS-LMP2 results disagree with those obtained from an alternative type of MP2 calculation, N-methyl acetamide (NMA) dimers, and show that the results for liquid-state simulations using polarizable parameters derived by fitting to the PS-LMP2 binding energies appear to produce better results when compared with experimental data. The convergence issues associated with the alternative MP2 formulation remain to be investigated.

Entities:  

Year:  2005        PMID: 26641295     DOI: 10.1021/ct049880o

Source DB:  PubMed          Journal:  J Chem Theory Comput        ISSN: 1549-9618            Impact factor:   6.006


  12 in total

Review 1.  Integrated Modeling Program, Applied Chemical Theory (IMPACT).

Authors:  Jay L Banks; Hege S Beard; Yixiang Cao; Art E Cho; Wolfgang Damm; Ramy Farid; Anthony K Felts; Thomas A Halgren; Daniel T Mainz; Jon R Maple; Robert Murphy; Dean M Philipp; Matthew P Repasky; Linda Y Zhang; Bruce J Berne; Richard A Friesner; Emilio Gallicchio; Ronald M Levy
Journal:  J Comput Chem       Date:  2005-12       Impact factor: 3.376

2.  Importance of electrostatic polarizability in calculating cysteine acidity constants and copper(I) binding energy of Bacillus subtilis CopZ.

Authors:  Timothy H Click; Sergei Y Ponomarev; George A Kaminski
Journal:  J Comput Chem       Date:  2012-02-27       Impact factor: 3.376

3.  Parameterization of a B3LYP specific correction for non-covalent interactions and basis set superposition error on a gigantic dataset of CCSD(T) quality non-covalent interaction energies.

Authors:  Severin T Schneebeli; Arteum D Bochevarov; Richard A Friesner
Journal:  J Chem Theory Comput       Date:  2011-03-08       Impact factor: 6.006

4.  Developing multisite empirical force field models for Pt(II) and cisplatin.

Authors:  John P Cvitkovic; George A Kaminski
Journal:  J Comput Chem       Date:  2016-11-11       Impact factor: 3.376

5.  Polarizable Simulations with Second order Interaction Model (POSSIM) force field: Developing parameters for alanine peptides and protein backbone.

Authors:  Sergei Y Ponomarev; George A Kaminski
Journal:  J Chem Theory Comput       Date:  2011-05-10       Impact factor: 6.006

6.  Polarizable Simulations with Second order Interaction Model - force field and software for fast polarizable calculations: Parameters for small model systems and free energy calculations.

Authors:  George A Kaminski; Sergei Y Ponomarev; Aibing B Liu
Journal:  J Chem Theory Comput       Date:  2009-10-05       Impact factor: 6.006

7.  Development of a pharmacophore for cruzain using oxadiazoles as virtual molecular probes: quantitative structure-activity relationship studies.

Authors:  Anacleto S de Souza; Marcelo T de Oliveira; Adriano D Andricopulo
Journal:  J Comput Aided Mol Des       Date:  2017-08-09       Impact factor: 3.686

8.  Effects of lysine substitution on stability of polyalanine alpha-helix.

Authors:  Sergei Y Ponomarev; Qina Sa; George A Kaminski
Journal:  J Chem Theory Comput       Date:  2012-10-02       Impact factor: 6.006

9.  Modeling MEK4 Kinase Inhibitors through Perturbed Electrostatic Potential Charges.

Authors:  Rama K Mishra; Kristine K Deibler; Matthew R Clutter; Purav P Vagadia; Matthew O'Connor; Gary E Schiltz; Raymond Bergan; Karl A Scheidt
Journal:  J Chem Inf Model       Date:  2019-10-14       Impact factor: 4.956

10.  Reproducing basic pKa values for turkey ovomucoid third domain using a polarizable force field.

Authors:  Timothy H Click; George A Kaminski
Journal:  J Phys Chem B       Date:  2009-06-04       Impact factor: 2.991

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