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Quantum mechanics/molecular mechanics electrostatic embedding with continuous and discrete functions.

ABSTRACT: A quantum mechanics/molecular mechanics (QM/MM) implementation that uses the Gaussian electrostatic model (GEM) as the MM force field is presented. GEM relies on the reproduction of electronic density by using auxiliary basis sets to calculate each component of the intermolecular interaction. This hybrid method has been used, along with a conventional QM/MM (point charges) method, to determine the polarization on the QM subsystem by the MM environment in QM/MM calculations on 10 individual H(2)O dimers and a Mg(2+)-H(2)O dimer. We observe that GEM gives the correct polarization response in cases when the MM fragment has a small charge, while the point charges produce significant over-polarization of the QM subsystem and in several cases present an opposite sign for the polarization contribution. In the case when a large charge is located in the MM subsystem, for example, the Mg(2+) ion, the opposite is observed at small distances. However, this is overcome by the use of a damped Hermite charge, which provides the correct polarization response.

SUBMITTER: Cisneros GA

PROVIDER: S-EPMC2656107 | biostudies-literature | 2006 Jul

REPOSITORIES: biostudies-literature

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Quantum mechanics/molecular mechanics electrostatic embedding with continuous and discrete functions.

Cisneros G Andrés GA Piquemal Jean-Philip JP Darden Thomas A TA

The journal of physical chemistry. B 20060701 28

A quantum mechanics/molecular mechanics (QM/MM) implementation that uses the Gaussian electrostatic model (GEM) as the MM force field is presented. GEM relies on the reproduction of electronic density by using auxiliary basis sets to calculate each component of the intermolecular interaction. This hybrid method has been used, along with a conventional QM/MM (point charges) method, to determine the polarization on the QM subsystem by the MM environment in QM/MM calculations on 10 individual H(2)O ...[more]

PMID: 16836309

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Project description:Direct molecular dynamics (MD) simulation with ab initio quantum mechanical and molecular mechanical (QM/MM) methods is very powerful for studying the mechanism of chemical reactions in a complex environment but also very time-consuming. The computational cost of QM/MM calculations during MD simulations can be reduced significantly using semiempirical QM/MM methods with lower accuracy. To achieve higher accuracy at the ab initio QM/MM level, a correction on the existing semiempirical QM/MM model is an attractive idea. Recently, we reported a neural network (NN) method as QM/MM-NN to predict the potential energy difference between semiempirical and ab initio QM/MM approaches. The high-level results can be obtained using neural network based on semiempirical QM/MM MD simulations, but the lack of direct MD samplings at the ab initio QM/MM level is still a deficiency that limits the applications of QM/MM-NN. In the present paper, we developed a dynamic scheme of QM/MM-NN for direct MD simulations on the NN-predicted potential energy surface to approximate ab initio QM/MM MD. Since some configurations excluded from the database for NN training were encountered during simulations, which may cause some difficulties on MD samplings, an adaptive procedure inspired by the selection scheme reported by Behler [ Behler Int. J. Quantum Chem. 2015 , 115 , 1032 ; Behler Angew. Chem., Int. Ed. 2017 , 56 , 12828 ] was employed with some adaptions to update NN and carry out MD iteratively. We further applied the adaptive QM/MM-NN MD method to the free energy calculation and transition path optimization on chemical reactions in water. The results at the ab initio QM/MM level can be well reproduced using this method after 2-4 iteration cycles. The saving in computational cost is about 2 orders of magnitude. It demonstrates that the QM/MM-NN with direct MD simulations has great potentials not only for the calculation of thermodynamic properties but also for the characterization of reaction dynamics, which provides a useful tool to study chemical or biochemical systems in solution or enzymes.

Project description:In quantum mechanics, the theory of quantum transitions is grounded on the convergence of a series of time-dependent perturbation theory. In nuclear and atomic physics, this series converges because the dynamics of quantum transitions (quantum jumps) are absent by definition. In molecular and chemical physics, on the contrary, the dynamics of "quantum" transitions, being determined by the joint motion of a light electron (or electrons) and very heavy nuclei, are present by definition, and the series of time-dependent perturbation theory becomes singular. An exception is the dynamic problem for stationary states in the Born-Oppenheimer adiabatic approximation, when the electronic subsystem turns out to be "off" from the general dynamic process and therefore is not dynamically full-fledged: it only forms an electric potential in which the nuclei oscillate. Removing the aforementioned singularity can be accomplished in two ways. The first method was consisted of introducing an additional postulate in the form of the Franck-Condon principle into molecular quantum mechanics, in which the adiabatic approximation is used. The second method was proposed by the author and consisted of damping the singular dynamics of the joint motion of an electron and nuclei in the intermediate (transient) state of molecular "quantum" transitions by introducing chaos. This chaos arises only during molecular quantum transitions and is called dozy chaos. Formally, the damping is carried out by replacing an infinitely small imaginary addition in the spectral representation of the complete Green's function of the system with its finite quantity. The damping chaos (dozy chaos) leads to the continuity of the energy spectrum in the molecular transient state, which is a sign of classical mechanics. Meanwhile, the initial and final states of the molecule obey quantum mechanics in the adiabatic approximation. Molecular quantum mechanics, which takes into account the chaotic dynamics of the transient state of molecular "quantum" transitions, can be called quantum-classical (dozy-chaos) mechanics. The efficacy of the damping for the aforementioned singularity was previously shown by dozy-chaos mechanics of elementary electron transfers in condensed matter, which is the simplest case of dozy-chaos mechanics, and its applications to a whole number of problems, especially to the optical spectra in polymethine dyes and their aggregates. This paper provides a regular exposition of this dozy-chaos (quantum-classical) mechanics of the elementary electron transfers. The main results of its applications presented in the introduction are also described.

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Quantum mechanics/molecular mechanics electrostatic embedding with continuous and discrete functions.

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Quantum mechanics/molecular mechanics electrostatic embedding with continuous and discrete functions.

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