jp075566p_si_002.txt (10.09 kB)
General Methodology to Optimize Damping Functions to Account for Charge Penetration Effects in Electrostatic Calculations Using Multicentered Multipolar Expansions
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posted on 2008-01-17, 00:00 authored by Araken S. Werneck, Tarcísio M. Rocha Filho, Laurent E. DardenneWe developed a methodology to optimize exponential damping functions to account for charge penetration
effects when computing molecular electrostatic properties using the multicentered multipolar expansion method
(MME). This methodology is based in the optimization of a damping parameter set using a two-step fast
local fitting procedure and the ab initio (Hartree−Fock/6-31G** and 6-31G**+) electrostatic potential
calculated in a set of concentric grid of points as reference. The principal aspect of the methodology is a first
local fitting step which generates a focused initial guess to improve the performance of a simplex method
avoiding the use of multiple runs and the choice of initial guesses. Three different strategies for the determination
of optimized damping parameters were tested in the following studies: (1) investigation of the error in the
calculation of the electrostatic interaction energy for five hydrogen-bonded dimers at standard and nonstandard
hydrogen-bonded geometries and at nonequilibrium geometries; (2) calculation of the electrostatic molecular
properties (potential and electric field) for eight small molecular systems (methanol, ammonia, water,
formamide, dichloromethane, acetone, dimethyl sulfoxide, and acetonitrile) and for the 20 amino acids. Our
results show that the methodology performs well not only for small molecules but also for relatively larger
molecular systems. The analysis of the distinct parameter sets associated with different optimization strategies
show that (i) a specific parameter set is more suitable and more general for electrostatic interaction energy
calculations, with an average absolute error of 0.46 kcal/mol at hydrogen-bond geometries; (ii) a second
parameter set is more suitable for electrostatic potential and electric field calculations at and outside the van
der Waals (vdW) envelope, with an average error decrease >72% at the vdW surface. A more general amino
acid damping parameter set was constructed from the original damping parameters derived for the small
fragments and for the amino acids. This damping set is more insensitive to protein backbone and residue
side-chain conformational changes and can be very useful for future docking and molecular dynamics protein
simulations using ab initio based polarizable classical methods.
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dynamics protein simulationsmethodologyoptimization strategies showvan der WaalsCharge Penetration EffectsgeometrieOptimize Damping Functionsmulticentered multipolar expansion methodMulticentered Multipolar ExpansionsWeMMEacidinteraction energy calculationsparametercharge penetration effectsab initio
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