Tabu search based strategies for conformational search.

Julius-Maximillians-Universität Würzburg, Institut für Organische Chemie, Am Hubland, 97074 Würzburg, Germany.
The Journal of Physical Chemistry A (Impact Factor: 2.77). 09/2009; 113(43):11699-705. DOI: 10.1021/jp9028084
Source: PubMed

ABSTRACT This paper presents an application of the new nonlinear global optimization routine gradient only tabu search (GOTS) to conformational search problems. It is based on the tabu search strategy which tries to determine the global minimum of a function by the steepest descent-modest ascent strategy. The refinement of ranking procedure of the original GOTS method and the exploitation of simulated annealing elements are described, and the modifications of the GOTS algorithm necessary to adopt it to conformation searches are explained. The utility of the GOTS for conformational search problems is tested using various examples.

  • [Show abstract] [Hide abstract]
    ABSTRACT: The presented program package, Conformational Analysis and Search Tool (CAST) allows the accurate treatment of large and flexible (macro) molecular systems. For the determination of thermally accessible minima CAST offers the newly developed TabuSearch algorithm, but algorithms such as Monte Carlo (MC), MC with minimization, and molecular dynamics are implemented as well. For the determination of reaction paths, CAST provides the PathOpt, the Nudge Elastic band, and the umbrella sampling approach. Access to free energies is possible through the free energy perturbation approach. Along with a number of standard force fields, a newly developed symmetry-adapted perturbation theory-based force field is included. Semiempirical computations are possible through DFTB+ and MOPAC interfaces. For calculations based on density functional theory, a Message Passing Interface (MPI) interface to the Graphics Processing Unit (GPU)-accelerated TeraChem program is available. The program is available on request. © 2014 Wiley Periodicals, Inc.
    Journal of Computational Chemistry 07/2014; · 3.84 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: We present a computational investigation of the conformational response of phycocyanobilin (PCB) to the ability of solvents to form hydrogen bonds. PCB is the chromophore of several proteins in light harvesting complexes. We determine the conformational distributions in different solvents (methanol and hexamethylphosphoramide HMPT) by means of ab initio molecular dynamics simulations and characterize them via ab initio calculations of NMR chemical shift patterns. The computed trajectories and spectroscopic fingerprints illustrate that the energy landscape is very complex and exhibits various conformations of similar energy. We elucidate the strong influence of the solvent characteristics on the structural and spectroscopic parameters. Specifically, we predict a cis-trans isomerization of phycocyanobilin upon switching from the aprotic to the protic solvent, which explains an experimentally observed change in the NMR patterns. In the context of technological molecular recognition, solvent induced conformational switching can be considered a precursor mechanism to the recognition of single molecules.
    Physical Chemistry Chemical Physics 02/2014; · 4.20 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: The current status of global optimization in computational molecular science is characterized in this article by focusing on one particular area, evolutionary algorithms applied to cluster structure optimization. Other algorithms and application areas are also mentioned briefly, indicating a widespread use of global optimization techniques in every conceivable branch of computational molecular science. © 2011 John Wiley & Sons, Ltd. WIREs Comput Mol Sci 2011 1 879–887 DOI: 10.1002/wcms.70
    Wiley Interdisciplinary Reviews: Computational Molecular Science. 11/2011; 1(6).


1 Download