Structural determination of large molecules through the reassembly of optimized fragments

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The accurate determination of the optimized structures of large molecules is, computationally quite expensive. As an alternate to the conventional approaches to structural optimization, we have explored the accuracy and speed-up obtained when variants of the fragmentation optimization and recombination method (FORM) are used. Specifically, the method was applied to eight prototypical molecules - n-decane, hexa-alanine, a long conjugate hydrocarbon molecule, a large polar conjugated molecule, large (5,5) armchair single-walled carbon nanotubes, a salen-aluminum complex and a multiply H-bonded system (two conformers of vancomycin aglycon with Di-N-acetyl-L-Lys-D-Ala-D-Ala - without optimizing the structure of the whole molecules. We find that FORM can predict the structure of these molecules with an acceptable accuracy, all at a computational cost that is 2-11 times less than conventional quantum mechanical methods at the Hartree-Fock (HF), density functional theory (DFT) and MP2 level of accuracy. FORM may therefore represent a viable approach for the fast structural predictions of large molecules. (C) 2008 Elsevier Inc. All rights reserved.
Publisher
ELSEVIER SCIENCE INC
Issue Date
2008-10
Language
English
Article Type
Article
Keywords

ELECTRONIC-STRUCTURE METHODS; DENSITY-FUNCTIONAL THEORY; GEOMETRY OPTIMIZATION; CONQUER METHOD; ORBITAL CALCULATIONS; BIOLOGICAL MACROMOLECULES; CONVERGENCE ACCELERATION; ITERATIVE SUBSPACE; TAILORING APPROACH; EFFICIENT METHOD

Citation

JOURNAL OF MOLECULAR GRAPHICS & MODELLING, v.27, no.3, pp.364 - 375

ISSN
1093-3263
DOI
10.1016/j.jmgm.2008.06.004
URI
http://hdl.handle.net/10203/90812
Appears in Collection
CH-Journal Papers(저널논문)
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