Literature DB >> 16836440

A new algorithm for molecular fragmentation in quantum chemical calculations.

Ryan P A Bettens1, Adrian M Lee.   

Abstract

In this study, we present a "black-box" method for fragmenting a molecule with a well-defined Kekulé or valence-bond structure into a significant number of smaller fragment molecules that are more amenable to high level quantum chemical calculations. By taking an appropriate linear combination of the fragment energies, we show that it is possible in many cases to obtain highly accurate total energies when compared to the total energy of the full molecule. Our method is derived from the approach reported by Deev and Collins, but it contains significant unique elements, including an isodesmic approach to the fragmentation process. Using a method such as that described in this work it is in principle possible to obtain very accurate total energies of systems containing hundreds, if not thousands, of atoms as the approach is subject to massive parallelization.

Year:  2006        PMID: 16836440     DOI: 10.1021/jp062104n

Source DB:  PubMed          Journal:  J Phys Chem A        ISSN: 1089-5639            Impact factor:   2.781


  5 in total

1.  The electrostatic embedding contribution to DFT calculations of ligand-amino acid residues interaction.

Authors:  Tamires C da Silva Ribeiro; Marcelo L Lyra; Vinícius Manzoni
Journal:  J Mol Model       Date:  2018-07-19       Impact factor: 1.810

2.  Electrostatically Embedded Many-Body Expansion for Neutral and Charged Metalloenzyme Model Systems.

Authors:  Elbek K Kurbanov; Hannah R Leverentz; Donald G Truhlar; Elizabeth A Amin
Journal:  J Chem Theory Comput       Date:  2011-11-29       Impact factor: 6.006

3.  The Kernel Energy Method: Construction of 3 & 4 tuple Kernels from a List of Double Kernel Interactions.

Authors:  Lulu Huang; Lou Massa
Journal:  Theochem       Date:  2010-12

4.  Analysis of the Errors in the Electrostatically Embedded Many-Body Expansion of the Energy and the Correlation Energy for Zn and Cd Coordination Complexes with Five and Six Ligands and Use of the Analysis to Develop a Generally Successful Fragmentation Strategy.

Authors:  Elbek K Kurbanov; Hannah R Leverentz; Donald G Truhlar; Elizabeth A Amin
Journal:  J Chem Theory Comput       Date:  2013-06-11       Impact factor: 6.006

5.  MoD-QM/MM Structural Refinement Method: Characterization of Hydrogen Bonding in the Oxytricha nova G-Quadruplex.

Authors:  Junming Ho; Michael B Newcomer; Christina M Ragain; Jose A Gascon; Enrique R Batista; J Patrick Loria; Victor S Batista
Journal:  J Chem Theory Comput       Date:  2014-10-08       Impact factor: 6.006

  5 in total

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