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Computing the electric potential of biomolecules: Application of a new method of molecular surface triangulation
Author(s) -
Zauhar R. J.,
Morgan R. S.
Publication year - 1990
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.540110509
Subject(s) - computation , surface (topology) , triangulation , solvation , curvilinear coordinates , molecule , electrostatics , biomolecule , accessible surface area , electric potential , chemistry , computational chemistry , statistical physics , physics , algorithm , materials science , computer science , mathematics , nanotechnology , quantum mechanics , geometry , voltage
A new method is presented for defining a smooth, triangulated analytic surface for biological molecules. The surface produced by the algorithm is well‐suited for use with a recently developed polarizationcharge technique 1 for the computation of the electrostatic potential of solvated molecules, and may also be used for calculations of molecular surface areas and volumes. The new method employs Connolly's definitions of contact, reentrant and saddle surface, 2 but includes modifications that preclude the presence of self‐interesting reentrant surface, and also insure a rigorous decomposition of contact regions into curvilinear finite elements. The triangulation algorithm may be used in conjunction with the electrostatic methods described previously to compute the electric potential of molecules of arbitrary shape in solution. Applications include the estimation of hydration enthalpies, computation of the electrostatic forces associated with solvation, estimation of interactions between separate charged species in solution, and computation of the three‐dimensional form of the molecular electric potential. Test calculations are presented for a double‐stranded dinucleotide, the polypeptide enkephalin, and the protein ferredoxin.