Effective Fragment Potential Method for H-Bonding: How To Obtain Parameters for Nonrigid Fragments

Dubinets, Nikita O.; Slipchenko, Lyudmila V.

doi:10.1021/acs.jpca.7b01701

Cited by 6 publications

(10 citation statements)

References 46 publications

(70 reference statements)

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“…The potential in the EFP approach is generated based on ab initio quantum chemical calculations in which the total intermolecular interaction energy is presented as a sum of the following components: electrostatic interaction up to octupoles, polarization, dispersion, exchange repulsion, and charge transfer. One of the advantages of EFP is the possibility to partition large molecules into smaller fragments, generate the potential parameters for the latter, and build the total environment potential from such fragments …”

Section: Methodsmentioning

confidence: 99%

“…One of the advantages of EFP is the possibility to partition large molecules into smaller fragments, 39 generate the potential parameters for the latter, and build the total environment potential from such fragments. 40 Numerical Monte Carlo Calculation of the Hole Mobility. The Monte Carlo calculation of mobility implies that the carrier (hole) performs random jumps over a manifold of pointlike localized states.…”

Section: Marcus Theory For Hopping Charge Transportmentioning

confidence: 99%

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Anisotropic Hole Transport in ap-Quaterphenyl Molecular Crystal: Theory and Simulation

et al. 2021

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A computational procedure is proposed for predicting the charge hopping rate in organic semiconductor crystals. The procedure is verified using a p-quaterphenyl molecular crystal as the test system, in which the thermally activated hole mobility is relatively low, its hole states are localized, and, hence, charge transport is of hopping character. The hole mobility in p-quaterphenyl is simulated by the Monte Carlo method with the hopping probability governed by a Marcus-like rate constant. The microscopic parameters of the Marcus model have been calculated by ab initio multireference quantum chemical method (XMCQDPT/CASSCF). Molecular conformation and crystal environment effects on the Marcus hopping parameters are studied. It is found that different arrangements of monomers typical for the crystal structure provide different hopping parameters and, hence, different hole mobilities in different directions. Monte Carlo simulations of the hole mobility predict that the hole mobility attains its maximum in the [100] direction, where hopping occurs through parallel monomers at the closest distance, which is lower than 0.01 cm2/(V·s).

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Section: Methodsmentioning

confidence: 99%

Section: Marcus Theory For Hopping Charge Transportmentioning

confidence: 99%

Anisotropic Hole Transport in ap-Quaterphenyl Molecular Crystal: Theory and Simulation

et al. 2021

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“…The basis set for MAKEFP was 6‐31G(d,p). The coordinates of the resulting EFP parameters for each fragment were transformed according to the fragment coordinates in the MD cells, and all the coordinate‐dependent parameters were recomputed using the algorithm described in Reference . Next, the fragments were combined into large molecules again, the capping hydrogens were removed, and their charges were uniformly distributed between the neighboring atoms.…”

Section: Methodsmentioning

confidence: 99%

“…Effective fragment potential is an ab initio generated potential, in which total intermolecular interaction energy of the system is presented as a sum of electrostatic (coulombic), polarization (induction), dispersion, exchange repulsion, and charge transfer energies. One of the advantages of EFP method is the possibility of partitioning large environment molecules into smaller fragments, generating potential parameters for them, and constructing the total environment potential from fragment potentials …”

Section: Introductionmentioning

confidence: 99%

Use of effective fragment potentials for simulation of excited states in an inhomogeneous environment

Dubinets

Freidzon

Bagatur’yants

2019

Int J of Quantum Chemistry

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Singlet and triplet spectra of phosphorescent organic light-emitting diode dopants such as bis(2-methyldibenzo[f,h]quinoxaline)(acetylacetonate)iridium(III) in inhomogeneous amorphous hosts are simulated by time-dependent density functional theory (TDDFT) using molecular dynamics and effective fragment potentials (EFPs). The EFPs of the host molecules N,N 0 -di(1-naphthyl)-N,N 0 -diphenyl-(1,1 0 -biphenyl)-4,4 0 -diamine and 4,4 0 -bis(Ncarbazolyl)-1,1 0 -biphenyl are constructed from small fragments. The procedure for breaking large molecules into fragments and constructing an EFP is presented. It is demonstrated that polarizable inhomogeneous environment affects the position, intensity, and width of the spectral bands and, therefore, should be taken into account in accurate simulations of spectral bands.

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“…The EFMO method has been shown to provide accurate energetics in water clusters, griffithsin−carbohydrate complex, and enzymatic catalysis. 46−50 Another possibility, which has been partly explored in our previous work, 9 is to adjust parameters computed at one fragment geometry to other geometries, without explicitly recomputing them. The goal of the present work is to refine and generalize this approach, and provide essential benchmarks.…”

Section: Introductionmentioning

confidence: 99%

Effective Fragment Potentials for Flexible Molecules: Transferability of Parameters and Amino Acid Database

Kim

Bui

Tazhigulov

et al. 2020

J. Chem. Theory Comput.

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An accurate but efficient description of noncovalent interactions is a key to predictive modeling of biological and materials systems. The effective fragment potential (EFP) is an ab initio-based force field that provides a physically meaningful decomposition of noncovalent interactions of a molecular system into Coulomb, polarization, dispersion, and exchange-repulsion components. An EFP simulation protocol consists of two steps, preparing parameters for molecular fragments by a series of ab initio calculations on each individual fragment, and calculation of interaction energy and properties of a total molecular system based on the prepared parameters. As the fragment parameters (distributed multipoles, polarizabilities, localized wave function, etc.) depend on a fragment geometry, straightforward application of the EFP method requires recomputing parameters of each fragment if its geometry changes, for example, during thermal fluctuations of a molecular system. Thus, recomputing fragment parameters can easily become both computational and human bottlenecks and lead to a loss of efficiency of a simulation protocol. An alternative approach, in which fragment parameters are adjusted to different fragment geometries, referred to as “flexible EFP”, is explored here. The parameter adjustment is based on translations and rotations of local coordinate frames associated with fragment atoms. The protocol is validated on extensive benchmark of amino acid dimers extracted from molecular dynamics snapshots of a cryptochrome protein. A parameter database for standard amino acids is developed to automate flexible EFP simulations in proteins. To demonstrate applicability of flexible EFP in large-scale protein simulations, binding energies and vertical electron ionization and electron attachment energies of a lumiflavin chromophore of the cryptochrome protein are computed. The results obtained with flexible EFP are in a close agreement with the standard EFP procedure but provide a significant reduction in computational cost.

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Effective Fragment Potential Method for H-Bonding: How To Obtain Parameters for Nonrigid Fragments

Cited by 6 publications

References 46 publications

Anisotropic Hole Transport in ap-Quaterphenyl Molecular Crystal: Theory and Simulation

Anisotropic Hole Transport in ap-Quaterphenyl Molecular Crystal: Theory and Simulation

Use of effective fragment potentials for simulation of excited states in an inhomogeneous environment

Effective Fragment Potentials for Flexible Molecules: Transferability of Parameters and Amino Acid Database

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