Nuclear-Electronic Orbital Quantum Mechanical/Molecular Mechanical Real-Time Dynamics

Overview

Journal J Phys Chem Lett

Publisher American Chemical Society

Specialty Chemistry

Date 2023 Oct 19

PMID 37857272

Authors

Mathew Chow

Tao E Li

Sharon Hammes-Schiffer

Affiliations

Soon will be listed here.

Abstract

Simulating the nuclear-electronic quantum dynamics of large-scale molecular systems in the condensed phase is key for studying biologically and chemically important processes such as proton transfer and proton-coupled electron transfer reactions. Herein, the real-time nuclear-electronic orbital time-dependent density functional theory (RT-NEO-TDDFT) approach is combined with a hybrid quantum mechanical/molecular mechanical (QM/MM) strategy to enable the accurate description of coupled nuclear-electronic quantum dynamics in the presence of heterogeneous environments such as solvent or proteins. The densities of the electrons and quantum protons are propagated in real time, while the other nuclei are propagated classically on the instantaneous electron-proton vibronic surface. This approach is applied to phenol bound to lysozyme, intramolecular proton transfer in malonaldehyde, and nonequilibrium excited-state intramolecular proton transfer in -hydroxybenzaldehyde. These examples illustrate that the RT-NEO-TDDFT framework, coupled with an atomistic representation of the environment, allows the simulation of condensed-phase systems that exhibit significant nuclear quantum effects.

Citing Articles

Nuclear Quantum Effects in Quantum Mechanical/Molecular Mechanical Free Energy Simulations of Ribonucleotide Reductase.

Chow M, Reinhardt C, Hammes-Schiffer S J Am Chem Soc. 2024; 146(48):33258-33264.

PMID: 39566052 PMC: 11625381. DOI: 10.1021/jacs.4c13955.

References

Zhao L, Wildman A, Pavosevic F, Tully J, Hammes-Schiffer S, Li X . Excited State Intramolecular Proton Transfer with Nuclear-Electronic Orbital Ehrenfest Dynamics. J Phys Chem Lett. 2021; 12(14):3497-3502. DOI: 10.1021/acs.jpclett.1c00564. View

Pavosevic F, Hammes-Schiffer S . Multicomponent equation-of-motion coupled cluster singles and doubles: Theory and calculation of excitation energies for positronium hydride. J Chem Phys. 2019; 150(16):161102. DOI: 10.1063/1.5094035. View

Makri N . Modular path integral methodology for real-time quantum dynamics. J Chem Phys. 2018; 149(21):214108. DOI: 10.1063/1.5058223. View

Pronk S, Pall S, Schulz R, Larsson P, Bjelkmar P, Apostolov R . GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics. 2013; 29(7):845-54. PMC: 3605599. DOI: 10.1093/bioinformatics/btt055. View

Chow M, Lambros E, Li X, Hammes-Schiffer S . Nuclear-Electronic Orbital QM/MM Approach: Geometry Optimizations and Molecular Dynamics. J Chem Theory Comput. 2023; 19(13):3839-3848. DOI: 10.1021/acs.jctc.3c00361. View

You Z, Mewes J, Dreuw A, Herbert J . Comparison of the Marcus and Pekar partitions in the context of non-equilibrium, polarizable-continuum solvation models. J Chem Phys. 2015; 143(20):204104. DOI: 10.1063/1.4936357. View

Li X, Govind N, Isborn C, DePrince 3rd A, Lopata K . Real-Time Time-Dependent Electronic Structure Theory. Chem Rev. 2020; 120(18):9951-9993. DOI: 10.1021/acs.chemrev.0c00223. View

Cofer-Shabica D, Menger M, Ou Q, Shao Y, Subotnik J, Faraji S . INAQS, a Generic Interface for Nonadiabatic QM/MM Dynamics: Design, Implementation, and Validation for GROMACS/Q-CHEM simulations. J Chem Theory Comput. 2022; 18(8):4601-4614. DOI: 10.1021/acs.jctc.2c00204. View

Habershon S, Manolopoulos D, Markland T, Miller 3rd T . Ring-polymer molecular dynamics: quantum effects in chemical dynamics from classical trajectories in an extended phase space. Annu Rev Phys Chem. 2013; 64:387-413. DOI: 10.1146/annurev-physchem-040412-110122. View

10.

Pavosevic F, Rousseau B, Hammes-Schiffer S . Multicomponent Orbital-Optimized Perturbation Theory Methods: Approaching Coupled Cluster Accuracy at Lower Cost. J Phys Chem Lett. 2020; 11(4):1578-1583. DOI: 10.1021/acs.jpclett.0c00090. View

11.

Tomasi J, Mennucci B, Cammi R . Quantum mechanical continuum solvation models. Chem Rev. 2005; 105(8):2999-3093. DOI: 10.1021/cr9904009. View

12.

Yu Q, Pavosevic F, Hammes-Schiffer S . Development of nuclear basis sets for multicomponent quantum chemistry methods. J Chem Phys. 2020; 152(24):244123. DOI: 10.1063/5.0009233. View

13.

Xu X, Chen Z, Yang Y . Molecular Dynamics with Constrained Nuclear Electronic Orbital Density Functional Theory: Accurate Vibrational Spectra from Efficient Incorporation of Nuclear Quantum Effects. J Am Chem Soc. 2022; 144(9):4039-4046. DOI: 10.1021/jacs.1c12932. View

14.

Jorgensen W, Tirado-Rives J . Potential energy functions for atomic-level simulations of water and organic and biomolecular systems. Proc Natl Acad Sci U S A. 2005; 102(19):6665-70. PMC: 1100738. DOI: 10.1073/pnas.0408037102. View

15.

Brunk E, Rothlisberger U . Mixed Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulations of Biological Systems in Ground and Electronically Excited States. Chem Rev. 2015; 115(12):6217-63. DOI: 10.1021/cr500628b. View

16.

Lee , Yang , PARR . Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Phys Rev B Condens Matter. 1988; 37(2):785-789. DOI: 10.1103/physrevb.37.785. View

17.

Tao Z, Yu Q, Roy S, Hammes-Schiffer S . Direct Dynamics with Nuclear-Electronic Orbital Density Functional Theory. Acc Chem Res. 2021; 54(22):4131-4141. DOI: 10.1021/acs.accounts.1c00516. View

18.

Pavosevic F, Culpitt T, Hammes-Schiffer S . Multicomponent Quantum Chemistry: Integrating Electronic and Nuclear Quantum Effects via the Nuclear-Electronic Orbital Method. Chem Rev. 2020; 120(9):4222-4253. DOI: 10.1021/acs.chemrev.9b00798. View

19.

Zhou Y, Wang S, Li Y, Zhang Y . Born-Oppenheimer Ab Initio QM/MM Molecular Dynamics Simulations of Enzyme Reactions. Methods Enzymol. 2016; 577:105-18. PMC: 4986621. DOI: 10.1016/bs.mie.2016.05.013. View

20.

Yang Y, Culpitt T, Hammes-Schiffer S . Multicomponent Time-Dependent Density Functional Theory: Proton and Electron Excitation Energies. J Phys Chem Lett. 2018; 9(7):1765-1770. DOI: 10.1021/acs.jpclett.8b00547. View