Convergence Properties of the Normal Mode Optimization and Its Combination with Molecular Geometry Constraints

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Title:Convergence Properties of the Normal Mode Optimization and Its Combination with Molecular Geometry Constraints
Creators:
Bouř, Petr
Journal or Publication Title:
Collection of Czechoslovak Chemical Communications, 70, 9, pp. 1315-1340
Uncontrolled Keywords:Peptides, <i>Ab initio</i> calculations, Molecular modeling, Vibrational normal modes, Vibrational spectroscopy, Geometry optimization, Beta sheet

Abstract

Optimization in the normal mode coordinates has been established as a useful tool for modeling of vibrational spectra (<i>J. Chem. Phys</i>. <strong>2002</strong>, <i>117</i>, 4126). In this work the algorithm is extended with the aid of harmonic penalty functions to allow for multiple restraints of geometry parameters, such as bond lengths, bond and dihedral angles, and for simultaneous optimization of more molecules. Additionally, geometry optimization when atomic nuclei are maintained on the constant electrostatic potential surface was implemented and its applications for solvent models are discussed. Model systems include small molecules, water cluster, antiparallel β-sheet peptide containing intermolecular hydrogen bonds, periodic α-helix and a parallel β-sheet segments. The normal mode method provided better numerical stability than the conventional redundant internal coordinates, especially for weakly hydrogen-bonded systems, while the speed of the optimization was found similar as for the Cartesian coordinates. <p>

Title:Convergence Properties of the Normal Mode Optimization and Its Combination with Molecular Geometry Constraints
Creators:
Bouř, Petr
Uncontrolled Keywords:Peptides, <i>Ab initio</i> calculations, Molecular modeling, Vibrational normal modes, Vibrational spectroscopy, Geometry optimization, Beta sheet
Divisions:Life and Chemical Sciences > Institute of Organic Chemistry and Biochemistry > Collection of Czechoslovak Chemical Communications
Journal or Publication Title:Collection of Czechoslovak Chemical Communications
Volume:70
Number:9
Page Range:pp. 1315-1340
ISSN:0010-0765
E-ISSN:1212-6950
Publisher:Institute of Organic Chemistry and Biochemistry
Related URLs:
URLURL Type
http://dx.doi.org/10.1135/cccc20051315UNSPECIFIED
ID Code:2414
Item Type:Article
Deposited On:06 Feb 2009 17:18
Last Modified:06 Feb 2009 16:18

Citation

Bouř, Petr (2005) Convergence Properties of the Normal Mode Optimization and Its Combination with Molecular Geometry Constraints. Collection of Czechoslovak Chemical Communications, 70 (9). pp. 1315-1340. ISSN 0010-0765

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