Literature DB >> 18715046

A gradient-directed Monte Carlo approach to molecular design.

Xiangqian Hu1, David N Beratan, Weitao Yang.   

Abstract

The recently developed linear combination of atomic potentials (LCAP) approach [M. Wang et al., J. Am. Chem. Soc. 128, 3228 (2006)] allows continuous optimization in a discrete chemical space, and thus is useful in the design of molecules for targeted properties. To address further challenges arising from the rugged, continuous property surfaces in the LCAP approach, we develop a gradient-directed Monte Carlo (GDMC) strategy as an augmentation to the original LCAP optimization method. The GDMC method retains the power of exploring molecular space by utilizing local gradient information computed from the LCAP approach to jump between discrete molecular structures. It also allows random MC moves to overcome barriers between local optima on property surfaces. The combined GDMC-LCAP approach is demonstrated here for optimizing nonlinear optical properties in a class of donor-acceptor substituted benzene and porphyrin frameworks. Specifically, one molecule with four nitrogen atoms in the porphyrin ring was found to have a larger first hyperpolarizability than structures with the conventional porphyrin motif.

Entities:  

Year:  2008        PMID: 18715046     DOI: 10.1063/1.2958255

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  4 in total

1.  A gradient-directed Monte Carlo method for global optimization in a discrete space: application to protein sequence design and folding.

Authors:  Xiangqian Hu; David N Beratan; Weitao Yang
Journal:  J Chem Phys       Date:  2009-10-21       Impact factor: 3.488

2.  Computational design, synthesis and biological evaluation of para-quinone-based inhibitors for redox regulation of the dual-specificity phosphatase Cdc25B.

Authors:  Shahar Keinan; William D Paquette; John J Skoko; David N Beratan; Weitao Yang; Sunita Shinde; Paul A Johnston; John S Lazo; Peter Wipf
Journal:  Org Biomol Chem       Date:  2008-07-15       Impact factor: 3.876

3.  Stochastic voyages into uncharted chemical space produce a representative library of all possible drug-like compounds.

Authors:  Aaron M Virshup; Julia Contreras-García; Peter Wipf; Weitao Yang; David N Beratan
Journal:  J Am Chem Soc       Date:  2013-05-02       Impact factor: 15.419

4.  iQSPR in XenonPy: A Bayesian Molecular Design Algorithm.

Authors:  Stephen Wu; Guillaume Lambard; Chang Liu; Hironao Yamada; Ryo Yoshida
Journal:  Mol Inform       Date:  2019-11-05       Impact factor: 3.353

  4 in total

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