Applicability of Effective Fragment Potential Version 2-Molecular Dynamics (EFP2-MD) Simulations for Predicting Dynamic Liquid Properties Including the Supercritical Fluid Phase

Kuroki, Nahoko; Mori, Hirotoshi

doi:10.1021/acs.jpcb.8b07446

Cited by 5 publications

(5 citation statements)

References 42 publications

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“…The object of this study is to clarify the electronic fluctuation and the temporal evolution of intermolecular interactions in TMAO aqueous solution with a realistic condition of concentration. For this purpose, we focused on solute-solvent interactions and applied the ab initio effective fragment potential-molecular dynamics simulation (EFP-MD), which is particularly suited to performing nanosecond-order AIMD simulations for systems containing several thousand atoms [25][26][27][28][29][30] , for dilute aqueous TMAO solutions (0.18 mol L −1 ). For comparison, a…”

mentioning

confidence: 99%

Electronic fluctuation difference between trimethylamine N-oxide and tert-butyl alcohol in water

Kuroki

Uchino

Funakura

et al. 2022

Sci Rep

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Although small organic molecules in cells have been considered important to control the functions of proteins, their electronic fluctuation and the intermolecular interaction, which is physicochemical origin of the molecular functions, under physiological conditions, i.e., dilute aqueous solutions (0.18 mol L−1), has never been clarified due to the lack of observation methods with both accuracy and efficiency. Herein, the time evolutions of the interactions in dilute aqueous trimethylamine N-oxide (TMAO) and tert-butyl alcohol (TBA) solutions were analyzed via ab initio molecular dynamics simulations accelerated with the fragment molecular theory. It has been known that TMAO and TBA have similar structures, but opposite physiological functions to stabilize and destabilize proteins. It was clarified that TMAO induced stable polarization and charge-transfer interactions with water molecules near the hydrophilic group, and water molecules were caught even near the CH3– group. Those should affect protein stabilization. Understanding the solution dynamics will contribute to artificial chaperone design in next generation medicine.

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confidence: 99%

Electronic fluctuation difference between trimethylamine N-oxide and tert-butyl alcohol in water

Kuroki

Uchino

Funakura

et al. 2022

Sci Rep

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“…In effect, the CT energy component is sometimes ignored when applying EFP2 to chemical problems. [36][37][38][44][45][46][47][48][49] In fact, EFP2 CT term is available only in the GAMESS (US) quantum chemistry program, 42 whereas it is neither supported in the official release of the recent LIBEFP library for linking quantum chemistry packages with the EFP2 functionalities, 50 nor in the Q-CHEM quantum chemistry program, 51 contrary to the remaining electrostatic, exchange-repulsion, induction and dispersion EFP2 terms.…”

Section: Introductionmentioning

confidence: 99%

Ab Initio Effective One-Electron Potential Operators:Applications for Charge-Transfer Energy in Effective Fragment Potentials

Bednarska¹,

Chołuj²,

Góra³

et al. 2020

Preprint

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The concept of effective one-electron potentials (EOP) has proven to be extremely useful in efficient description of electronic structure of chemical systems, especially extended molecular aggregates such as interacting molecules in condensed phases. Here, a general method for EOP-based elimination of electron repulsion integrals (ERIs) is presented, that is tuned towards the fragment-based calculation methodologies such as the second generation of the effective fragment potentials (EFP2) method. Two general types of the EOP operator matrix elements are distinguished and treated either via the distributed multipole expansion or the extended density fitting schemes developed in this work. The EOP technique is then applied to reduce the high computational costs of the effective fragment charge-transfer (CT) terms being the bottleneck of EFP2 potentials. The alternative EOP-based CT energy model is proposed, derived within the framework of intermolecular perturbation theory with Hartree–Fock non-interacting reference wavefunctions, compatible with the original EFP2 formulation. It is found that the computational cost of the EFP2 total interaction energy calculation can be reduced by up to 38 times when using the EOP-based formulation of CT energy, as compared to the original EFP2 scheme, without compromising the accuracy for a wide range of weakly interacting neutral and ionic molecular fragments. The proposed model can thus be used routinely within the EFP2 framework.

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“…In effect, the CT energy component is often ignored in some applications. 35,38,39,[43][44][45][46][47][48] In fact, EFP2 CT term is available only in the GAMESS US quantum chemistry program, 41 whereas it is neither supported in the official release of the recent LIBEFP library for linking quantum chemistry packages with the EFP2 functionalities, 49 nor in the Q-CHEM quantum chemistry program, 50 contrary to electrostatic, exchange-repulsion, induction and dispersion EFP2 terms.…”

Section: Introductionmentioning

confidence: 99%

Ab initio effective one‐electron potential operators: Applications for charge‐transfer energy in effective fragment potentials

et al. 2020

View full text Add to dashboard Cite

The concept of effective one‐electron potentials (EOPs) has proven to be extremely useful in efficient description of electronic structure of chemical systems, especially extended molecular aggregates such as interacting molecules in condensed phases. Here, a general method for EOP‐based elimination of electron repulsion integrals is presented, that is tuned toward the fragment‐based calculation methodologies such as the second generation of the effective fragment potentials (EFP2) method. Two general types of the EOP operator matrix elements are distinguished and treated either via the distributed multipole expansion or the extended density fitting (DF) schemes developed in this work. The EOP technique is then applied to reduce the high computational costs of the effective fragment charge‐transfer (CT) terms being the bottleneck of EFP2 potentials. The alternative EOP‐based CT energy model is proposed, derived within the framework of intermolecular perturbation theory with Hartree–Fock noninteracting reference wavefunctions, compatible with the original EFP2 formulation. It is found that the computational cost of the EFP2 total interaction energy calculation can be reduced by up to 38 times when using the EOP‐based formulation of CT energy, as compared to the original EFP2 scheme, without compromising the accuracy for a wide range of weakly interacting neutral and ionic molecular fragments. The proposed model can thus be used routinely within the EFP2 framework.

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Applicability of Effective Fragment Potential Version 2-Molecular Dynamics (EFP2-MD) Simulations for Predicting Dynamic Liquid Properties Including the Supercritical Fluid Phase

Cited by 5 publications

References 42 publications

Electronic fluctuation difference between trimethylamine N-oxide and tert-butyl alcohol in water

Electronic fluctuation difference between trimethylamine N-oxide and tert-butyl alcohol in water

Ab Initio Effective One-Electron Potential Operators:Applications for Charge-Transfer Energy in Effective Fragment Potentials

Ab initio effective one‐electron potential operators: Applications for charge‐transfer energy in effective fragment potentials

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