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    Embracing chemical and structural diversity with UCONGA: A universal conformer generation and analysis program (2017)

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    Type of Content
    Journal Article
    UC Permalink
    https://hdl.handle.net/10092/105241
    
    Publisher's DOI/URI
    http://doi.org/10.1016/j.jmgm.2017.09.007
    
    Publisher
    Elsevier BV
    ISSN
    1093-3263
    1873-4243
    Language
    eng
    Collections
    • Science: Journal Articles [1179]
    Authors
    Gunby, Nathaniel cc
    Masters, Sarah cc
    Crittenden, Deborah cc
    show all
    Abstract

    © 2017 Elsevier Inc. Molecular properties depend on molecular structure, so the first step in any computational chemistry investigation is to generate all thermally accessible conformers. Typically it is necessary to make a trade-off between the number of conformers to be explored and the accuracy of the method used to calculate their energies. Ab initio potential energy surface scans can, in principle, be applied to any molecule, but their conformational cost scales poorly with both molecular size and dimensionality of the search space. Specialized conformer generation techniques rely on parameterized force fields and may also use knowledge-based rules for generating conformers, and are typically only available for drug-like organic molecules. Neither approach is well-suited to generating or identifying chemically sensible conformers for larger non-organic molecules. The Universal CONformer Generation and Analysis (UCONGA) program package fills this niche. It requires no parameters other than built-in atomic van der Waals radii to generate comprehensive ensembles of sterically-allowed conformers, for molecules of arbitrary composition and connectivity. Analysis scripts are provided to identify representative structures from clusters of similar conformers, which may be further refined by subsequent geometry optimization. This approach is particularly useful for molecules not described by parameterized force fields, as it minimizes the number of computationally intensive ab initio calculations required to characterize the conformer ensemble. We anticipate that UCONGA will be particularly useful for computational and structural chemists studying flexible non-drug-like molecules.

    Citation
    Gunby NR, Masters SL, Crittenden DL (2017). Embracing chemical and structural diversity with UCONGA: A universal conformer generation and analysis program. Journal of Molecular Graphics and Modelling. 77. 286-294.
    This citation is automatically generated and may be unreliable. Use as a guide only.
    Keywords
    Software; Molecular conformation; Computer simulation; Drug design; Structural chemistry; Inorganic chemistry
    ANZSRC Fields of Research
    34 - Chemical sciences::3407 - Theoretical and computational chemistry::340701 - Computational chemistry
    34 - Chemical sciences::3401 - Analytical chemistry::340199 - Analytical chemistry not elsewhere classified
    46 - Information and computing sciences::4601 - Applied computing::460104 - Applications in physical sciences
    Rights
    All rights reserved unless otherwise stated
    http://hdl.handle.net/10092/17651

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