skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Parametrization of Combined Quantum Mechanical and Molecular Mechanical Methods: Bond-Tuned Link Atoms

Journal Article · · Molecules
ORCiD logo [1];  [1];  [1]
  1. Univ. of Minnesota, Minneapolis, MN (United States). Dept. of Chemistry
+ Show Author Affiliations

Combined quantum mechanical and molecular mechanical (QM/MM) methods are the most powerful available methods for high-level treatments of subsystems of very large systems. The treatment of the QM-MM boundary strongly affects the accuracy of QM/MM calculations. For QM/MM calculations having covalent bonds cut by the QM-MM boundary, it has been proposed previously to use a scheme with system-specific tuned fluorine link atoms. Here, we propose a broadly parametrized scheme where the parameters of the tuned F link atoms depend only on the type of bond being cut. In the proposed new scheme, the F link atom is tuned for systems with a certain type of cut bond at the QM-MM boundary instead of for a specific target system, and the resulting link atoms are call bond-tuned link atoms. In principle, the bond-tuned link atoms can be as convenient as the popular H link atoms, and they are especially well adapted for high-throughput and accurate QM/MM calculations. Here, we present the parameters for several kinds of cut bonds along with a set of validation calculations that confirm that the proposed bond-tuned link-atom scheme can be as accurate as the system-specific tuned F link-atom scheme.

Research Organization:
Energy Frontier Research Centers (EFRC) (United States). Energy Frontier Research Center for Inorganometallic Catalyst Design (ICDC); Univ. of Minnesota, Minneapolis (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Basic Energy Sciences (BES)
Grant/Contract Number:
SC0012702
OSTI ID:
1510997
Journal Information:
Molecules, Vol. 23, Issue 6; ISSN 1420-3049
Publisher:
MDPICopyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 8 works
Citation information provided by
Web of Science

References (59)

Tuned and Balanced Redistributed Charge Scheme for Combined Quantum Mechanical and Molecular Mechanical (QM/MM) Methods and Fragment Methods: Tuning Based on the CM5 Charge Model journal December 2012
Redistributed Charge and Dipole Schemes for Combined Quantum Mechanical and Molecular Mechanical Calculations journal May 2005
Density Functionals with Broad Applicability in Chemistry journal February 2008
Quantum Mechanical/Molecular Mechanical Simulation Study of the Mechanism of Hairpin Ribozyme Catalysis journal April 2008
Quantum Mechanics/Molecular Mechanics Modeling of Enzymatic Processes: Caveats and Breakthroughs journal December 2015
Temperature Dependence of the Kinetic Isotope Effects in Thymidylate Synthase. A Theoretical Study journal May 2011
A combinedab initio quantum mechanical and molecular mechanical method for carrying out simulations on complex molecular systems: Applications to the CH3Cl + Cl? exchange reaction and gas phase protonation of polyethers journal December 1986
Hybrid Models for Combined Quantum Mechanical and Molecular Mechanical Approaches journal January 1996
QM/MM Studies into the H 2 O 2 -Dependent Activity of Lytic Polysaccharide Monooxygenases: Evidence for the Formation of a Caged Hydroxyl Radical Intermediate journal January 2018
Modified Carbon Pseudopotential for Use in ONIOM Calculations of Alkyl-Substituted Metallocenes † ‡ journal December 2008
Cavity-induced enantioselectivity reversal in a chiral metal–organic framework Brønsted acid catalyst journal January 2012
Development and application of ab initio QM/MM methods for mechanistic simulation of reactions in solution and in enzymes journal March 2009
QM/MM Methods for Biomolecular Systems journal January 2009
The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other functionals journal July 2007
Dioxygen binding to Fe-MOF-74: microscopic insights from periodic QM/MM calculations journal December 2016
Generalized Hybrid Orbital (GHO) Method for Combining Ab Initio Hartree−Fock Wave Functions with Molecular Mechanics journal January 2004
Computational Design of a Time-Dependent Histone Deacetylase 2 Selective Inhibitor journal January 2015
Ab initio relativistic effective potentials with spin‐orbit operators. I. Li through Ar journal March 1985
Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94 journal April 1996
QM/MM Analysis Suggests That Alkaline Phosphatase (AP) and Nucleotide Pyrophosphatase/Phosphodiesterase Slightly Tighten the Transition State for Phosphate Diester Hydrolysis Relative to Solution: Implication for Catalytic Promiscuity in the AP Superfamily journal December 2011
Geometry optimization using tuned and balanced redistributed charge schemes for combined quantum mechanical and molecular mechanical calculations journal January 2011
Multiscale Model for a Metal–Organic Framework: High-Spin Rebound Mechanism in the Reaction of the Oxoiron(IV) Species of Fe-MOF-74 journal April 2015
QM/MM: what have we learned, where are we, and where do we go from here? journal July 2006
Q UANTUM M ECHANICAL M ETHODS FOR E NZYME K INETICS journal October 2002
Investigation of pure inductive effects on benzene ring by 13C NMR chemical shifts: A theoretical study using fictitious nuclear charges of hydrogen atoms (‘H∗ method’) journal February 2007
A Generalized Hybrid Orbital (GHO) Method for the Treatment of Boundary Atoms in Combined QM/MM Calculations journal June 1998
Application of quantum mechanics/molecular mechanics methods in the study of enzymatic reaction mechanisms: Application of QM/MM methods
  • Sousa, Sérgio Filipe; Ribeiro, António J. M.; Neves, Rui P. P.
  • Wiley Interdisciplinary Reviews: Computational Molecular Science, Vol. 7, Issue 2 https://doi.org/10.1002/wcms.1281
journal September 2016
Compound I Reactivity Defines Alkene Oxidation Selectivity in Cytochrome P450cam journal January 2010
A pseudobond approach to combining quantum mechanical and molecular mechanical methods journal January 1999
Chemical Ligation and Isotope Labeling to Locate Dynamic Effects during Catalysis by Dihydrofolate Reductase journal June 2015
Artificial reaction coordinate “tunneling” in free-energy calculations: The catalytic reaction of RNase H journal August 2009
Frontier Orbital Consistent Quantum Capping Potential (FOC-QCP) for Bulky Ligand of Transition Metal Complexes journal March 2008
Calculation of Vibrational Shifts of Nitrile Probes in the Active Site of Ketosteroid Isomerase upon Ligand Binding journal December 2012
Variational optimization of effective atom centered potentials for molecular properties journal January 2005
Hybrid atomistic simulation methods for materials systems journal January 2009
A computational and experimental study of O-glycosylation. Catalysis by human UDP-GalNAc polypeptide:GalNAc transferase-T2 journal January 2014
Structures and Mechanisms of the Carbonyl-ene Reaction between MOF-11 Encapsulated Formaldehyde and Propylene: An ONIOM Study journal June 2008
Combined Quantum Mechanical and Molecular Mechanical Methods for Calculating Potential Energy Surfaces: Tuned and Balanced Redistributed-Charge Algorithm journal January 2010
Hybrid Quantum Mechanics/Molecular Mechanics Investigation of (salen)Mn for use in Metal−Organic Frameworks journal November 2010
A combined experimental and quantum chemical study of CO2 adsorption in the metal–organic framework CPO-27 with different metals journal January 2013
Quantum mechanical computations on very large molecular systems: The local self-consistent field method: QUANTUM MECHANICAL COMPUTATIONS journal March 1994
Charge Model 5: An Extension of Hirshfeld Population Analysis for the Accurate Description of Molecular Interactions in Gaseous and Condensed Phases
  • Marenich, Aleksandr V.; Jerome, Steven V.; Cramer, Christopher J.
  • Journal of Chemical Theory and Computation, Vol. 8, Issue 2, p. 527-541 https://doi.org/10.1021/ct200866d
journal February 2012
Hybrid computational approaches for deriving quantum mechanical insights into metal–organic frameworks journal June 2017
Transition States in a Protein Environment − ONIOM QM:MM Modeling of Isopenicillin N Synthesis journal December 2008
Adjusted Connection Atoms for Combined Quantum Mechanical and Molecular Mechanical Methods journal November 1999
A new method for modelling spectator chemical groups in ab initio calculations: effective group potentials
  • Alary, Fabienne; Poteau, Romuald; Heully, Jean-Louis
  • Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta), Vol. 104, Issue 3-4 https://doi.org/10.1007/s002140000138
journal July 2000
Mixed Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulations of Biological Systems in Ground and Electronically Excited States journal April 2015
Simple one-electron quantum capping potentials for use in hybrid QM/MM studies of biological molecules journal June 2002
The H∗ method: hydrogen atoms with a fictitious nuclear charge. A versatile theoretical tool for study of atom and group properties as substituents: electronegativity and partition of σ and π contributions journal July 2004
P450 Enzymes: Their Structure, Reactivity, and Selectivity—Modeled by QM/MM Calculations journal February 2010
Theoretical Modeling of Large Molecular Systems. Advances in the Local Self Consistent Field Method for Mixed Quantum Mechanics/Molecular Mechanics Calculations journal December 2012
Diels–Alder reaction: A theoretical comprehensive study of substituent effects using the ‘H* method’ journal January 2006
QM/MM: What Have We Learned, Where Are We, and Where Do We Go from Here? journal May 2007
Discovering and understanding materials through computation journal May 2021
Variational optimization of effective atom centered potentials for molecular properties text January 2005
Chemical Ligation and Isotope Labeling to Locate Dynamic Effects during Catalysis by Dihydrofolate Reductase journal June 2015
A simple scheme of estimating substitution or substituent effects in the ab initio MO method based on the shift operator journal September 1990
The mechanism of an asymmetric ring-opening reaction of epoxide with amine catalyzed by a metal–organic framework: insights from combined quantum mechanics and molecular mechanics calculations journal January 2017
Combined quantum mechanical and molecular mechanical method for metal–organic frameworks: proton topologies of NU-1000 journal January 2018

Cited By (2)

Computational Studies of Photocatalysis with Metal–Organic Frameworks journal September 2019
Towards large scale hybrid QM/MM dynamics of complex systems with advanced point dipole polarizable embeddings journal January 2019

Similar Records

Application of quantum mechanics/molecular mechanics methods in the study of enzymatic reaction mechanisms
Journal Article · Thu Sep 01 00:00:00 EDT 2016 · Wiley Interdisciplinary Reviews: Computational Molecular Science · OSTI ID:1510997
+4 more
Link molecule method for quantum mechanical/molecular mechanical hybrid simulations
Journal Article · Fri Aug 10 00:00:00 EDT 2007 · Journal of Computational Physics · OSTI ID:1510997
+2 more
Accurate non-bonded potentials based on periodic quantum mechanics calculations for use in molecular simulations of materials and systems
Journal Article · Fri Oct 18 00:00:00 EDT 2019 · Journal of Chemical Physics · OSTI ID:1510997
+4 more

Related Subjects

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
electrostatics
molecular modeling
multiscale modeling
QM/MM