Evaluation of charge penetration between distributed multipolar expansions

Freitag, Mark Alan; Gordon, Mark S.; Jensen, Jan H.; Stevens, Walter J.

doi:10.1063/1.481370

Cited by 160 publications

(218 citation statements)

References 20 publications

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“…However, even considering a single static configuration, our results cannot be considered as quantitative ones because our methodological approach does not include inter-fragment polarization effects (only a local correction is introduced by the OME reassociation method in the important peptide junction region). A methodology that incorporates inter-fragment polarization effects 69,[81][82][83] and a correction for the charge penetration effect 84 is under development. These improvements are especially important to avoid significant errors when evaluating the internal ion pair energy and also when evaluating the ion pair interaction with the surrounding protein residues and water molecules.…”

Section: Discussionmentioning

confidence: 99%

Electrostatic properties in the catalytic site of papain: A possible regulatory mechanism for the reactivity of the ion pair

et al. 2003

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We present an analysis of the electrostatic properties in the catalytic site of papain (EC 3.4.22.2), an archetype enzyme of the C1 cysteine proteinase family, and we investigate their possible role in the formation, stabilization and regulation of the Cys25 (؊) …His159 (؉) catalytic ion pair. The electrostatic properties were computed using a reassociation method based in multicentered multipolar expansions obtained from ab initio quantum calculations of overlapping protein fragments. Solvent effects were introduced by coupling the use of multicentered multipolar expansions to two continuum boundary element methods to solve the Poisson and the linearized Poisson-Boltzmann equations. The electrostatic profile found in the proton transfer region of papain showed that this enzyme has a well-defined electrostatic environment to favor the formation and stabilization of the catalytic ion pair. The papain catalytic site electrostatic profile can be considered as an electrostatic fingerprint of the papain family with the following characteristics: (i) the presence of a net electric field highly aligned in the (Cys25)-SG3(His159)-ND1 direction; (ii) the electrostatic profile has a saddlepoint character; (iii) it is basically a local environmental effect. Furthermore, our analysis describes a possible regulatory mechanism (the E SG3 ND1 attenuation effect) controlling the ion pair reactivity and permits to infer the Asp57 acidic residue as the most probable candidate to act as the electrostatic modulator. Proteins 2003;52:236 -253.

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Section: Discussionmentioning

confidence: 99%

Electrostatic properties in the catalytic site of papain: A possible regulatory mechanism for the reactivity of the ion pair

et al. 2003

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“…This disadvantage has been addressed to an extent by the use of damping functions that correct the interaction energies at close intermolecular distances. [14][15][16] It has been shown that another possibility for the accurate determination of the intermolecular Coulomb contribution is by interacting the unperturbed frozen densities of the two molecules either numerically 17 or analytically. 18 The latter method is based on the density fitting (DF) formalism (Coulomb fitting), [19][20][21] where the electron density is expanded using Gaussian auxiliary basis sets (ABSs) centered on specific sites on the molecule.…”

Section: Introductionmentioning

confidence: 99%

Generalization of the Gaussian electrostatic model: Extension to arbitrary angular momentum, distributed multipoles, and speedup with reciprocal space methods

Cisneros

Piquemal

Darden

2006

The Journal of Chemical Physics

111

192

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The simulation of biological systems by means of current empirical force fields presents shortcomings due to their lack of accuracy, especially in the description of the nonbonded terms. We have previously introduced a force field based on density fitting termed the Gaussian electrostatic model-0 (GEM-0) J.-P. Piquemal et al. [J. Chem. Phys. 124, 104101 (2006)] that improves the description of the nonbonded interactions. GEM-0 relies on density fitting methodology to reproduce each contribution of the constrained space orbital variation (CSOV) energy decomposition scheme, by expanding the electronic density of the molecule in s-type Gaussian functions centered at specific sites. In the present contribution we extend the Coulomb and exchange components of the force field to auxiliary basis sets of arbitrary angular momentum. Since the basis functions with higher angular momentum have directionality, a reference molecular frame (local frame) formalism is employed for the rotation of the fitted expansion coefficients. In all cases the intermolecular interaction energies are calculated by means of Hermite Gaussian functions using the McMurchie-Davidson [J. Comput. Phys. 26, 218 (1978)] recursion to calculate all the required integrals. Furthermore, the use of Hermite Gaussian functions allows a point multipole decomposition determination at each expansion site. Additionally, the issue of computational speed is investigated by reciprocal space based formalisms which include the particle mesh Ewald (PME) and fast Fourier-Poisson (FFP) methods. Frozen-core (Coulomb and exchange-repulsion) intermolecular interaction results for ten stationary points on the water dimer potential-energy surface, as well as a one-dimensional surface scan for the canonical water dimer, formamide, stacked benzene, and benzene water dimers, are presented. All results show reasonable agreement with the corresponding CSOV calculated reference contributions, around 0.1 and 0.15 kcal/mol error for Coulomb and exchange, respectively. Timing results for single Coulomb energy-force calculations for (H 2 O) n , n=64, 128, 256, 512, and 1024, in periodic boundary conditions with PME and FFP at two different rms force tolerances are also presented. For the small and intermediate auxiliaries, PME shows faster times than FFP at both accuracies and the advantage of PME widens at higher accuracy, while for the largest auxiliary, the opposite occurs.

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“…This shortcoming may be overcome to an extent by using damping functions that correct the intermolecular interaction energy. 18,19 Equation (1) can also be solved without approximations with either numerical or analytical procedures. Gavezzotti has proposed a method that relies on the direct numerical integration over molecular electron density.…”

Section: Introductionmentioning

confidence: 99%

Intermolecular electrostatic energies using density fitting

Cisneros¹,

Piquemal²,

Darden³

2005

The Journal of Chemical Physics

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A method is presented to calculate the electron-electron and nuclear-electron intermolecular Coulomb interaction energy between two molecules by separately fitting the unperturbed molecular electron density of each monomer. This method is based on the variational Coulomb fitting method which relies on the expansion of the ab initio molecular electron density in site-centered auxiliary basis sets. By expanding the electron density of each monomer in this way the integral expressions for the intermolecular electrostatic calculations are simplified, lowering the operation count as well as the memory usage. Furthermore, this method allows the calculation of intermolecular Coulomb interactions with any level of theory from which a one-electron density matrix can be obtained. Our implementation is initially tested by calculating molecular properties with the density fitting method using three different auxiliary basis sets and comparing them to results obtained from ab initio calculations. These properties include dipoles for a series of molecules, as well as the molecular electrostatic potential and electric field for water. Subsequently, the intermolecular electrostatic energy is tested by calculating ten stationary points on the water dimer potential-energy surface. Results are presented for electron densities obtained at four different levels of theory using two different basis sets, fitted with three auxiliary basis sets. Additionally, a one-dimensional electrostatic energy surface scan is performed for four different systems (H 2 O dimer, Mg 2+ -H 2 O, Cu + -H 2 O, and n-methyl-formamide dimer). Our results show a very good agreement with ab initio calculations for all properties as well as interaction energies.

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Evaluation of charge penetration between distributed multipolar expansions

Cited by 160 publications

References 20 publications

Electrostatic properties in the catalytic site of papain: A possible regulatory mechanism for the reactivity of the ion pair

Electrostatic properties in the catalytic site of papain: A possible regulatory mechanism for the reactivity of the ion pair

Generalization of the Gaussian electrostatic model: Extension to arbitrary angular momentum, distributed multipoles, and speedup with reciprocal space methods

Intermolecular electrostatic energies using density fitting

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