Literature DB >> 32105473

Charting Hydrogen Bond Anisotropy.

Diogo Santos-Martins1, Stefano Forli1.   

Abstract

A hydrogen bond (HB) is an essential interaction in countless phenomena, regulating the chemistry of life. HBs are characterized by two features, strength and directionality, with a high degree of heterogeneity across different chemical groups. These characteristics are dependent on the electronic configuration of the atoms involved in the interaction, which, in turn, is influenced strongly by the local molecular environment. Studies based on the analysis of HB in the solid phase, such as X-ray crystallography, suffer from significant biases due to packing forces. These will tend to better describe strong HBs at the expenses of weak ones, which will be either distorted or under-represented. Using quantum mechanics (QM), we calculated interaction energies for about a hundred acceptors and donors in a rigorously defined set of geometries. We performed 180,000 independent QM calculations, covering all relevant angular components, mapping strength and directionality in a context free from external biases, with both single-site and cooperative HBs. By quantifying directionality, we show that there is no correlation with strength; therefore, these two components need to be addressed separately. Results demonstrate that there are very strong HB acceptors (e.g., dimethyl sulfoxide) with nearly isotropic interactions and weak ones (e.g., thioacetone) with a sharp directional profile. Similarly, groups can have comparable directional propensity but be very distant in the strength spectrum (e.g., thioacetone and pyridine). Results provide a new perspective on the way HB directionality is described, with implications for biophysics and molecular recognition that ultimately can influence chemical biology, protein engineering, and drug design.

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Year:  2020        PMID: 32105473      PMCID: PMC7325729          DOI: 10.1021/acs.jctc.9b01248

Source DB:  PubMed          Journal:  J Chem Theory Comput        ISSN: 1549-9618            Impact factor:   6.006


  42 in total

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Journal:  J Phys Chem B       Date:  2010-03-04       Impact factor: 2.991

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Journal:  J Chem Theory Comput       Date:  2011-12-13       Impact factor: 6.006

5.  A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu.

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6.  Theoretical Calculation of Hydrogen-Bonding Strength for Drug Molecules.

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Review 8.  A medicinal chemist's guide to molecular interactions.

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Authors:  Peng Zhou; Feifei Tian; Fenglin Lv; Zhicai Shang
Journal:  Proteins       Date:  2009-07

10.  Theoretical prediction of hydrogen-bond basicity pKBHX using quantum chemical topology descriptors.

Authors:  Anthony J Green; Paul L A Popelier
Journal:  J Chem Inf Model       Date:  2014-02-04       Impact factor: 4.956

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  2 in total

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2.  The importance of intramolecular hydrogen bonds on the translocation of the small drug piracetam through a lipid bilayer.

Authors:  João T S Coimbra; Ralph Feghali; Rui P Ribeiro; Maria J Ramos; Pedro A Fernandes
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  2 in total

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