The Effective Fragment Potential Method:  A QM-Based MM Approach to Modeling Environmental Effects in Chemistry

Gordon, Mark S.; Freitag, and Mark A.; Bandyopadhyay, Pradipta; and, Jan H. Jensen; Kairys, Visvaldas; Stevens, Walter J.

doi:10.1021/jp002747h

Cited by 605 publications

(695 citation statements)

References 61 publications

(99 reference statements)

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“…33,34 The final geometry produced by the classical MD equilibration was used as the initial geometry for the FMO-MD equilibration. The FMO-MD equilibration was performed using the NVT ensemble for 500 fs with a 1.0 fs step size and with randomized initial velocities to ensure that the temperature was maintained at 300 K. The Nose−Hoover thermostat with chains 35 was used to control the temperature.…”

Section: Equations Of Fragment Molecular Orbitalmentioning

confidence: 99%

Fragment Molecular Orbital Molecular Dynamics with the Fully Analytic Energy Gradient

Brorsen

Minezawa

et al. 2012

J. Chem. Theory Comput.

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Fragment molecular orbital molecular dynamics (FMO-MD) with periodic boundary conditions is performed on liquid water using the analytic energy gradient, the electrostatic potential point charge approximation, and the electrostatic dimer approximation. Compared to previous FMO-MD simulations of water that used an approximate energy gradient, inclusion of the response terms to provide a fully analytic energy gradient results in better energy conservation in the NVE ensemble for liquid water. An FMO-MD simulation that includes the fully analytic energy gradient and two body corrections (FMO2) gives improved energy conservation compared with a previously calculated FMO-MD simulation with an approximate energy gradient and including up to three body corrections (FMO3). Disciplines Chemistry CommentsReprinted (adapted) ABSTRACT: Fragment molecular orbital molecular dynamics (FMO-MD) with periodic boundary conditions is performed on liquid water using the analytic energy gradient, the electrostatic potential point charge approximation, and the electrostatic dimer approximation. Compared to previous FMO-MD simulations of water that used an approximate energy gradient, inclusion of the response terms to provide a fully analytic energy gradient results in better energy conservation in the NVE ensemble for liquid water. An FMO-MD simulation that includes the fully analytic energy gradient and two body corrections (FMO2) gives improved energy conservation compared with a previously calculated FMO-MD simulation with an approximate energy gradient and including up to three body corrections (FMO3). INTRODUCTION1.1. Fragment Molecular Orbital Method. Much progress has been made recently in improving algorithms for ab initio calculations on large systems. 1,2 One strategy is to use a fragmentation approach, in which a large system of interest is divided into smaller subsystems, and ab initio calculations are performed on these smaller subsystems. 2 One of the most successful and extensively developed fragmentation methods is the fragment molecular orbital (FMO) method 3 proposed by Kitaura et al. in 1999. The FMO method has been implemented for most ab initio and density functional theory (DFT) methods. 4−8 Numerous approximations to the original FMO method have been implemented to improve the efficiency of the calculation. The two most important of these approximations are the electrostatic point charge (ESP-PC) approximation and the electrostatic dimer (ES-DIM) approximation. 9 The ESP-PC approximation calculates the FMO embedded electrostatic potential using point charges rather than two electron integrals, while the ES-DIM approximation calculates the dimer energy of two fragments using point charges rather than using ab initio methods.FMO gradients were developed soon after the introduction of the FMO method. 10 Improvements to the gradient followed that allowed the use of gradients with the ESP-PC approximation 11 and the ES-DIM approximation. 12 Because the dimer (or trimer) density is not iterated to self-consi...

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Section: Equations Of Fragment Molecular Orbitalmentioning

confidence: 99%

Fragment Molecular Orbital Molecular Dynamics with the Fully Analytic Energy Gradient

Brorsen

Minezawa

et al. 2012

J. Chem. Theory Comput.

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“…[51][52][53][54] The EFP method was developed for the water molecule and was designed to reproduce HF results for aqueous solvation while requiring considerably less computational cost. 1,2 The EFP approach has been successfully applied to a variety of problems, including the solvation of small cations, 55 the solvation of the Menshutkin reaction, 56 the solvation of an S N 2 reaction, 57 and the energetics and structures of small water clusters. 58 Recently, Webb and Merrill studied the solvation of small anions (X -(H 2 O) n ) using the EFP method.…”

Section: Introductionmentioning

confidence: 99%

Theoretical Study of the Solvation of Fluorine and Chlorine Anions by Water

Kemp

Gordon

2005

J. Phys. Chem. A

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The solvation of fluoride and chloride anions (F-and Cl-, respectively) by water has been studied using effective fragment potentials (EFPs) for the water molecules and ab initio quantum mechanics for the anions. In particular, the number of water molecules required to fully surround each anion has been investigated. Monte Carlo calculations have been used in an attempt to find the solvated system X-(H2O)n (X = F, Cl) with the lowest energy for each value of n. It is predicted that 18 water molecules are required to form a complete solvation shell around a Cl-anion, where "complete solvation" is interpreted as an ion that is completely surrounded by solvent molecules. Although fewer water molecules may fully solvate the Cl-anion, such structures are higher in energy than partially solvated molecules, up to n ≥ 18. Calculations on the F-anion suggest that 15 water molecules are required for a complete solvation shell. The EFP predictions are in good agreement with the relative energies predicted by ab initio energy calculations at the EFP geometries. Disciplines Chemistry CommentsReprinted (adapted) The solvation of fluoride and chloride anions (F -and Cl -, respectively) by water has been studied using effective fragment potentials (EFPs) for the water molecules and ab initio quantum mechanics for the anions. In particular, the number of water molecules required to fully surround each anion has been investigated. Monte Carlo calculations have been used in an attempt to find the solvated system X -(H 2 O) n (X ) F, Cl) with the lowest energy for each value of n. It is predicted that 18 water molecules are required to form a complete solvation shell around a Cl -anion, where "complete solvation" is interpreted as an ion that is completely surrounded by solvent molecules. Although fewer water molecules may fully solvate the Clanion, such structures are higher in energy than partially solvated molecules, up to n g 18. Calculations on the F -anion suggest that 15 water molecules are required for a complete solvation shell. The EFP predictions are in good agreement with the relative energies predicted by ab initio energy calculations at the EFP geometries.

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“…20,21 One of the strengths of the EFP method is that it allows one to apportion the nonbonded interaction energy into physically meaningful contributions, including Coulombic (electrostatics), induction (polarization), exchange repulsion, dispersion, and charge transfer.…”

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Intramolecular Amide Stacking and Its Competition with Hydrogen Bonding in a Small Foldamer

et al. 2009

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The Effective Fragment Potential Method: A QM-Based MM Approach to Modeling Environmental Effects in Chemistry

Cited by 605 publications

References 61 publications

Fragment Molecular Orbital Molecular Dynamics with the Fully Analytic Energy Gradient

Fragment Molecular Orbital Molecular Dynamics with the Fully Analytic Energy Gradient

Theoretical Study of the Solvation of Fluorine and Chlorine Anions by Water

Intramolecular Amide Stacking and Its Competition with Hydrogen Bonding in a Small Foldamer

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