An improved methodology to compute surface site interaction points using high density molecular electrostatic potential surfaces

The theoretical calculation of Surface Site Interaction Points (SSIP) has been used successfully in some applications in the solid and liquid phase. In this work we propose a new set of optimizations for the search of SSIP using the Molecular Electrostatic Potential Surfaces (MEPS) calculated with Density Functional Theory and B3LYP/6‐31*G basis set. The measures that have been implemented are based on the search for the best agreement between experimental H‐bond donor and acceptor parameters (α and β) and the MEPS extremes exploring a range of electron density levels. Additionally, a parameterization as a function of atom types has been performed. The results show that the MEPS calculated at 0.01 au electron density level slightly improves the correlation with experimental data in comparison with the calculation over other density values. This fact is related to the bigger contribution of local electrostatics at higher density levels. The refinement has provided significant improvements to the correlation between theoretical and experimental data. Moreover, the proposed calculation over 0.01 au is six times faster on average than the computation at 0.002 au. The proposed methodology has been developed with the purpose to obtain high precision SSIP in a fast way and to improve their applications in virtual cocrystal screening, calculation of free energies in solution and molecular docking. © 2018 Wiley Periodicals, Inc.

[1]  J. Platts,et al.  Hydrogen bond structural group constants. , 2001, The Journal of organic chemistry.

[2]  C. Hunter,et al.  Virtual Screening Identifies New Cocrystals of Nalidixic Acid , 2014 .

[3]  C. Hunter,et al.  Polarisation effects on the solvation properties of alcohols† †Electronic supplementary information (ESI) available: Experimental and computational details. See DOI: 10.1039/c7sc04890d , 2017, Chemical science.

[4]  J. Murray,et al.  Molecular Surfaces, van der Waals Radii and Electrostatic Potentials in Relation to Noncovalent Interactions , 2009 .

[5]  A. Bacchi,et al.  Sampling rifamycin conformational variety by cruising through crystal forms: implications for polymorph screening and for biological models , 2008 .

[6]  Christopher A. Hunter,et al.  Virtual cocrystal screening , 2011 .

[7]  William F. Eddy,et al.  A New Convex Hull Algorithm for Planar Sets , 1977, TOMS.

[8]  F. P. Preparata,et al.  Convex hulls of finite sets of points in two and three dimensions , 1977, CACM.

[9]  C. Hunter,et al.  Quantifying intermolecular interactions: guidelines for the molecular recognition toolbox. , 2004, Angewandte Chemie.

[10]  Josep L. Rosselló,et al.  A surface site interaction point methodology for macromolecules and huge molecular databases , 2017, J. Comput. Chem..

[11]  A. Bondi van der Waals Volumes and Radii , 1964 .

[12]  C. Hunter,et al.  Cocrystals of spironolactone and griseofulvin based on an in silico screening method , 2017 .

[13]  Jan H. Jensen Molecular Modeling Basics , 2010 .

[14]  Bosco K. Ho,et al.  HOLLOW: Generating Accurate Representations of Channel and Interior Surfaces in Molecular Structures , 2008, BMC Structural Biology.

[15]  Beatriz Pateiro-López,et al.  Generalizing the Convex Hull of a Sample: The R Package alphahull , 2010 .

[16]  M. L. Connolly Analytical molecular surface calculation , 1983 .

[17]  C. Hunter A surface site interaction model for the properties of liquids at equilibrium , 2013 .

[18]  Eleanor J. Gardiner,et al.  Footprinting molecular electrostatic potential surfaces for calculation of solvation energies. , 2013, Physical chemistry chemical physics : PCCP.

[19]  David P. Dobkin,et al.  The quickhull algorithm for convex hulls , 1996, TOMS.

[20]  A. Chouaih,et al.  Theoretical and Experimental Electrostatic Potential around the m-Nitrophenol Molecule , 2015, Molecules.

[21]  M. Schroeder,et al.  LIGSITEcsc: predicting ligand binding sites using the Connolly surface and degree of conservation , 2006, BMC Structural Biology.