Literature DB >> 12594791

Ab initio quality one-electron properties of large molecules: development and testing of molecular tailoring approach.

K Babu1, Shridhar R Gadre.   

Abstract

The development of a linear-scaling method, viz. "molecular tailoring approach" with an emphasis on accurate computation of one-electron properties of large molecules is reported. This method is based on fragmenting the reference macromolecule into a number of small, overlapping molecules of similar size. The density matrix (DM) of the parent molecule is synthesized from the individual fragment DMs, computed separately at the Hartree-Fock (HF) level, and is used for property evaluation. In effect, this method reduces the O(N(3)) scaling order within HF theory to an n.O(N'(3)) one, where n is the number of fragments and N', the average number of basis functions in the fragment molecules. An algorithm and a program in FORTRAN 90 have been developed for an automated fragmentation of large molecular systems. One-electron properties such as the molecular electrostatic potential, molecular electron density along with their topography, as well as the dipole moment are computed using this approach for medium and large test chemical systems of varying nature (tocopherol, a model polypeptide and a silicious zeolite). The results are compared qualitatively and quantitatively with the corresponding actual ones for some cases. This method is also extended to obtain MP2 level DMs and electronic properties of large systems and found to be equally successful. Copyright 2003 Wiley Periodicals, Inc. J Comput Chem 24: 484-495, 2003

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Year:  2003        PMID: 12594791     DOI: 10.1002/jcc.10206

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


  6 in total

Review 1.  The MOD-QM/MM Method: Applications to Studies of Photosystem II and DNA G-Quadruplexes.

Authors:  M Askerka; J Ho; E R Batista; J A Gascón; V S Batista
Journal:  Methods Enzymol       Date:  2016-07-15       Impact factor: 1.600

2.  An Angular Overlap Model for Cu(II) Ion in the AMOEBA Polarizable Force Field.

Authors:  Jin Yu Xiang; Jay W Ponder
Journal:  J Chem Theory Comput       Date:  2014       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.  A valence bond model for aqueous Cu(II) and Zn(II) ions in the AMOEBA polarizable force field.

Authors:  Jin Yu Xiang; Jay W Ponder
Journal:  J Comput Chem       Date:  2012-12-05       Impact factor: 3.376

5.  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

6.  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

  6 in total

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