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Nuclear–Electronic Orbital QM/MM Approach: Geometry Optimizations and Molecular Dynamics

Journal Article · · Journal of Chemical Theory and Computation
 [1];  [2];  [2];  [1]
  1. Yale University, New Haven, CT (United States)
  2. University of Washington, Seattle, WA (United States)
+ Show Author Affiliations

Hybrid quantum mechanical/molecular mechanical (QM/MM) methods allow simulations of chemical reactions in atomistic solvent and heterogeneous environments such as proteins. Herein, the nuclear–electronic orbital (NEO) QM/MM approach is introduced to enable the quantization of specified nuclei, typically protons, in the QM region using a method such as NEO-density functional theory (NEO-DFT). This approach includes proton delocalization, polarization, anharmonicity, and zero-point energy in geometry optimizations and dynamics. Expressions for the energies and analytical gradients associated with the NEO-QM/MM method, as well as the previously developed polarizable continuum model (NEO-PCM), are provided. Geometry optimizations of small organic molecules hydrogen bonded to water in either dielectric continuum solvent or explicit atomistic solvent illustrate that aqueous solvation can strengthen hydrogen-bonding interactions for the systems studied, as indicated by shorter intermolecular distances at the hydrogen-bond interface. We then performed a real-time direct dynamics simulation of a phenol molecule in explicit water using the NEO-QM/MM method. Furthermore, these developments and initial examples provide the foundation for future studies of nuclear–electronic quantum dynamics in complex chemical and biological environments.

Research Organization:
Yale University, New Haven, CT (United States); University of Washington, Seattle, WA (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Basic Energy Sciences (BES); National Science Foundation (NSF)
Grant/Contract Number:
SC0023284
OSTI ID:
2554028
Alternate ID(s):
OSTI ID: 2422222
Journal Information:
Journal of Chemical Theory and Computation, Journal Name: Journal of Chemical Theory and Computation Journal Issue: 13 Vol. 19; ISSN 1549-9618
Publisher:
American Chemical SocietyCopyright Statement
Country of Publication:
United States
Language:
English

References (75)

QM/MM Methods for Biomolecular Systems journal January 2009
Dissecting Solvent Effects on Hydrogen Bonding journal June 2022
QM/MM through the 1990s: The First Twenty Years of Method Development and Applications journal July 2014
Energies, structures, and electronic properties of molecules in solution with the C-PCM solvation model journal April 2003
Improving the efficiency and convergence of geometry optimization with the polarizable continuum model: New energy gradients and molecular surface tessellation journal January 2004
Lennard-Jones parameters for the combined QM/MM method using the B3LYP/6-31G*/AMBER potential journal September 2005
MDAnalysis: A toolkit for the analysis of molecular dynamics simulations journal April 2011
A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations journal July 1990
Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models journal October 1992
Exploiting graphical processing units to enable quantum chemistry calculation of large solvated molecules with conductor-like polarizable continuum models journal October 2018
Polarizable continuum model: Polarizable continuum model journal January 2012
The Chronus Quantum software package journal August 2019
Dielectric continuum methods for quantum chemistry journal March 2021
VMD: Visual molecular dynamics journal February 1996
Electrostatic interaction of a solute with a continuum. A direct utilizaion of AB initio molecular potentials for the prevision of solvent effects journal February 1981
Nuclear Quantum Effects in Water and Aqueous Systems: Experiment, Theory, and Current Challenges journal April 2016
Multicomponent Quantum Chemistry: Integrating Electronic and Nuclear Quantum Effects via the Nuclear–Electronic Orbital Method journal April 2020
Solvated Nuclear–Electronic Orbital Structure and Dynamics journal February 2022
INAQS, a Generic Interface for Nonadiabatic QM/MM Dynamics: Design, Implementation, and Validation for GROMACS/Q-CHEM simulations journal July 2022
Multicomponent Coupled Cluster Singles and Doubles Theory within the Nuclear-Electronic Orbital Framework journal November 2018
On the Accuracy of the Direct Method to Calculate pKa from Electronic Structure Calculations journal December 2020
Calculating Free Energy Changes in Continuum Solvation Models journal February 2016
1.14*CM1A-LBCC: Localized Bond-Charge Corrected CM1A Charges for Condensed-Phase Simulations journal January 2017
Multicomponent Orbital-Optimized Perturbation Theory Methods: Approaching Coupled Cluster Accuracy at Lower Cost journal January 2020
Real-Time Time-Dependent Nuclear−Electronic Orbital Approach: Dynamics beyond the Born–Oppenheimer Approximation journal April 2020
Solvent Induced Proton Polarization within the Nuclear−Electronic Orbital Framework journal March 2023
Multicomponent Density Functional Theory: Impact of Nuclear Quantum Effects on Proton Affinities and Geometries journal July 2017
Multicomponent Time-Dependent Density Functional Theory: Proton and Electron Excitation Energies journal March 2018
Simulation of enzyme reactions using valence bond force fields and other hybrid quantum/classical approaches journal November 1993
Molecular Interactions in Solution: An Overview of Methods Based on Continuous Distributions of the Solvent journal November 1994
Proton-Coupled Electron Transfer journal November 2007
Hydrogen Tunneling in Enzymes and Biomimetic Models journal December 2013
The ONIOM Method and Its Applications journal April 2015
Accurate Composite and Fragment-Based Quantum Chemical Models for Large Molecules journal April 2015
Quantum Mechanical Continuum Solvation Models journal August 2005
Benchmarking the Conductor-like Polarizable Continuum Model (CPCM) for Aqueous Solvation Free Energies of Neutral and Ionic Organic Molecules journal October 2004
Fully Integrated Approach to Compute Vibrationally Resolved Optical Spectra: From Small Molecules to Macrosystems journal February 2009
van der Waals Volumes and Radii journal March 1964
Proton Binding to Proteins:  p K a Calculations with Explicit and Implicit Solvent Models journal March 2004
p K a Calculations with QM/MM Free Energy Perturbations journal November 2003
A Critical Evaluation of Different QM/MM Frontier Treatments with SCC-DFTB as the QM Method journal May 2005
p K a Calculations in Solution and Proteins with QM/MM Free Energy Perturbation Simulations:  A Quantitative Test of QM/MM Protocols journal August 2005
Analysis of Nuclear Quantum Effects on Hydrogen Bonding journal February 2007
Density Functional Theory Treatment of Electron Correlation in the Nuclear−Electronic Orbital Approach journal May 2007
A Smooth Solvation Potential Based on the Conductor-Like Screening Model journal December 1999
Frontier Bonds in QM/MM Methods: A Comparison of Different Approaches journal February 2000
Continuum Solvation Models: What Else Can We Learn from Them? journal April 2010
Polarizable Continuum Reaction-Field Solvation Models Affording Smooth Potential Energy Surfaces journal December 2009
Are thermodynamic cycles necessary for continuum solvent calculation of pK a s and reduction potentials? journal January 2015
Practical computation of electronic excitation in solution: vertical excitation model journal January 2011
Multiconfigurational nuclear-electronic orbital approach: Incorporation of nuclear quantum effects in electronic structure calculations journal September 2002
Self—Consistent Molecular Orbital Methods. XII. Further Extensions of Gaussian—Type Basis Sets for Use in Molecular Orbital Studies of Organic Molecules journal March 1972
Ab initio Ehrenfest dynamics journal August 2005
Continuous surface charge polarizable continuum models of solvation. I. General formalism journal March 2010
A smooth, nonsingular, and faithful discretization scheme for polarizable continuum models: The switching/Gaussian approach journal December 2010
Self‐consistent molecular orbital methods. XXIII. A polarization‐type basis set for second‐row elements journal October 1982
Comparison of simple potential functions for simulating liquid water journal July 1983
Time-dependent non-equilibrium dielectric response in QM/continuum approaches journal January 2015
Development of a practical multicomponent density functional for electron-proton correlation to produce accurate proton densities journal September 2017
Multicomponent equation-of-motion coupled cluster singles and doubles: Theory and calculation of excitation energies for positronium hydride journal April 2019
Development of nuclear basis sets for multicomponent quantum chemistry methods journal June 2020
Nuclear–electronic orbital Ehrenfest dynamics journal December 2020
Nuclear–electronic orbital methods: Foundations and prospects journal July 2021
Software for the frontiers of quantum chemistry: An overview of developments in the Q-Chem 5 package journal August 2021
Electronic Born–Oppenheimer approximation in nuclear-electronic orbital dynamics journal March 2023
Potential energy functions for atomic-level simulations of water and organic and biomolecular systems journal May 2005
Quantum nature of the hydrogen bond journal April 2011
Quantum delocalization of protons in the hydrogen-bond network of an enzyme active site journal December 2014
Intrinsically smooth discretisation of Connolly's solvent-excluded molecular surface journal July 2019
GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit journal February 2013
LigParGen web server: an automatic OPLS-AA parameter generator for organic ligands journal April 2017
Analysis of polarization in QM/MM modelling of biologically relevant hydrogen bonds journal September 2008
Density-functional exchange-energy approximation with correct asymptotic behavior journal September 1988
Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density journal January 1988
On the Difference Between Additive and Subtractive QM/MM Calculations journal April 2018

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Related Subjects

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
Geometry optimization
Molecules
QM/MM
Solvation
Solvents