pyEFP: Automatic decomposition of the complex molecular systems into rigid polarizable fragments

Odinokov, A. V.; Dubinets, Nikita O.; Bagatur’yants, A. A.

doi:10.1002/jcc.25149

Cited by 4 publications

(3 citation statements)

References 29 publications

(33 reference statements)

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“…While several algorithms for fragmenting large molecules into smaller molecular fragments have been previously proposed, few are appropriate for generating high-quality torsion scans. Many of these algorithms fall into two categories: fragmenting molecules for synthetic accessibility [22,23,24] and fragmenting molecules to achieve linear scaling for QC calculations [25,26,27,28]. …”

Section: Introductionmentioning

confidence: 99%

Capturing non-local through-bond effects in molecular mechanics force fields I: Fragmenting molecules for quantum chemical torsion scans [Article v1.1]

Stern

Bayly²,

Smith

et al. 2020

Preprint

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Accurate molecular mechanics force fields for small molecules are essential for predicting protein-ligand binding affinities in drug discovery and understanding the biophysics of biomolecular systems. Torsion potentials derived from quantum chemical (QC) calculations are critical for determining the conformational distributions of small molecules, but are computationally expensive and scale poorly with molecular size. To reduce computational cost and avoid the complications of distal through-space intramolecular interactions, molecules are generally fragmented into smaller entities to carry out QC torsion scans. However, torsion potentials, particularly for conjugated bonds, can be strongly affected by through-bond chemistry distal to the torsion itself. Poor fragmentation schemes have the potential to significantly disrupt electronic properties in the region around the torsion by removing important, distal chemistries, leading to poor representation of the parent molecule’s chemical environment and the resulting torsion energy profile. Here we show that a rapidly computable quantity, the fractional Wiberg bond order (WBO), is a sensitive reporter on whether the chemical environment around a torsion has been disrupted. We show that the WBO can be used as a surrogate to assess the robustness of fragmentation schemes and identify conjugated bond sets. We use this concept to construct a validation set by exhaustively fragmenting a set of druglike organic molecules and examine their corresponding WBO distributions derived from accessible conformations that can be used to evaluate fragmentation schemes. To illustrate the utility of the WBO in assessing fragmentation schemes that preserve the chemical environment, we propose a new fragmentation scheme that uses rapidly-computable AM1 WBOs, which are available essentially for free as part of standard AM1-BCC partial charge assignment. This approach can simultaneously maximize the chemical equivalency of the fragment and the substructure in the larger molecule while minimizing fragment size to accelerate QC torsion potential computation for small molecules and reducing undesired through-space steric interactions.

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Section: Introductionmentioning

confidence: 99%

Capturing non-local through-bond effects in molecular mechanics force fields I: Fragmenting molecules for quantum chemical torsion scans [Article v1.1]

Stern

Bayly²,

Smith

et al. 2020

Preprint

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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, 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.…”

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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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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“…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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pyEFP: Automatic decomposition of the complex molecular systems into rigid polarizable fragments

Cited by 4 publications

References 29 publications

Capturing non-local through-bond effects in molecular mechanics force fields I: Fragmenting molecules for quantum chemical torsion scans [Article v1.1]

Capturing non-local through-bond effects in molecular mechanics force fields I: Fragmenting molecules for quantum chemical torsion scans [Article v1.1]

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

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