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Title: Quantum Mechanical Fragment Methods Based on Partitioning Atoms or Partitioning Coordinates

Authors:
 [1];  [1];  [1];  [1];  [1];  [1]
  1. Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455-0431, United States
Publication Date:
Sponsoring Org.:
USDOE
OSTI Identifier:
1252063
Grant/Contract Number:  
FG02-86ER13579
Resource Type:
Published Article
Journal Name:
Accounts of Chemical Research
Additional Journal Information:
Journal Name: Accounts of Chemical Research Journal Volume: 47 Journal Issue: 9; Journal ID: ISSN 0001-4842
Publisher:
American Chemical Society
Country of Publication:
United States
Language:
English

Citation Formats

Wang, Bo, Yang, Ke R., Xu, Xuefei, Isegawa, Miho, Leverentz, Hannah R., and Truhlar, Donald G. Quantum Mechanical Fragment Methods Based on Partitioning Atoms or Partitioning Coordinates. United States: N. p., 2014. Web. doi:10.1021/ar500068a.
Wang, Bo, Yang, Ke R., Xu, Xuefei, Isegawa, Miho, Leverentz, Hannah R., & Truhlar, Donald G. Quantum Mechanical Fragment Methods Based on Partitioning Atoms or Partitioning Coordinates. United States. https://doi.org/10.1021/ar500068a
Wang, Bo, Yang, Ke R., Xu, Xuefei, Isegawa, Miho, Leverentz, Hannah R., and Truhlar, Donald G. Mon . "Quantum Mechanical Fragment Methods Based on Partitioning Atoms or Partitioning Coordinates". United States. https://doi.org/10.1021/ar500068a.
@article{osti_1252063,
title = {Quantum Mechanical Fragment Methods Based on Partitioning Atoms or Partitioning Coordinates},
author = {Wang, Bo and Yang, Ke R. and Xu, Xuefei and Isegawa, Miho and Leverentz, Hannah R. and Truhlar, Donald G.},
abstractNote = {},
doi = {10.1021/ar500068a},
journal = {Accounts of Chemical Research},
number = 9,
volume = 47,
place = {United States},
year = {Mon May 19 00:00:00 EDT 2014},
month = {Mon May 19 00:00:00 EDT 2014}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.1021/ar500068a

Citation Metrics:
Cited by: 22 works
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Works referenced in this record:

Redistributed Charge and Dipole Schemes for Combined Quantum Mechanical and Molecular Mechanical Calculations
journal, May 2005

  • Lin, Hai; Truhlar, Donald G.
  • The Journal of Physical Chemistry A, Vol. 109, Issue 17
  • DOI: 10.1021/jp0446332

An Accurate Calculation of Electronic Contribution to Static Permittivity Tensor for Organic Molecular Crystals on the Basis of the Charge Response Kernel Theory
journal, August 2009

  • Tsutsumi, Jun’ya; Yoshida, Hiroyuki; Murdey, Richard
  • The Journal of Physical Chemistry A, Vol. 113, Issue 32
  • DOI: 10.1021/jp903420w

Appraisal of molecular tailoring approach for large clusters
journal, March 2013

  • Sahu, Nityananda; Yeole, Sachin D.; Gadre, Shridhar R.
  • The Journal of Chemical Physics, Vol. 138, Issue 10
  • DOI: 10.1063/1.4793706

Anchoring the potential energy surface of the cyclic water trimer
journal, January 2004

  • Anderson, Julie A.; Crager, Kelly; Fedoroff, Lisa
  • The Journal of Chemical Physics, Vol. 121, Issue 22
  • DOI: 10.1063/1.1799931

Diabatic Molecular Orbitals, Potential Energies, and Potential Energy Surface Couplings by the 4-fold Way for Photodissociation of Phenol
journal, July 2013

  • Xu, Xuefei; Yang, Ke R.; Truhlar, Donald G.
  • Journal of Chemical Theory and Computation, Vol. 9, Issue 8
  • DOI: 10.1021/ct400447f

Simple formulas for improved point-charge electrostatics in classical force fields and hybrid quantum mechanical/molecular mechanical embedding
journal, January 2008

  • Cisneros, G. A.; Tholander, S. Na-Im; Parisel, O.
  • International Journal of Quantum Chemistry, Vol. 108, Issue 11
  • DOI: 10.1002/qua.21675

Electrostatically embedded many-body method for dipole moments, partial atomic charges, and charge transfer
journal, January 2012

  • Leverentz, Hannah R.; Maerzke, Katie A.; Keasler, Samuel J.
  • Physical Chemistry Chemical Physics, Vol. 14, Issue 21
  • DOI: 10.1039/c2cp24113g

Generalized Hybrid-Orbital Method for Combining Density Functional Theory with Molecular Mechanicals
journal, September 2005


A “critical” appraisal of electrostatic charge models for molecules
journal, April 1994

  • Gadre, Shridhar R.; Pundlik, Savita S.; Shrivastava, Indira H.
  • Proceedings / Indian Academy of Sciences, Vol. 106, Issue 2
  • DOI: 10.1007/BF02840752

Distributed multipole analysis, or how to describe a molecular charge distribution
journal, October 1981


Many-body interaction analysis: Algorithm development and application to large molecular clusters
journal, September 2004

  • Kulkarni, Anant D.; Ganesh, V.; Gadre, Shridhar R.
  • The Journal of Chemical Physics, Vol. 121, Issue 11
  • DOI: 10.1063/1.1780156

Hybrid Models for Combined Quantum Mechanical and Molecular Mechanical Approaches
journal, January 1996

  • Bakowies, Dirk; Thiel, Walter
  • The Journal of Physical Chemistry, Vol. 100, Issue 25
  • DOI: 10.1021/jp9536514

Permutationally invariant potential energy surfaces in high dimensionality
journal, October 2009

  • Braams, Bastiaan J.; Bowman, Joel M.
  • International Reviews in Physical Chemistry, Vol. 28, Issue 4
  • DOI: 10.1080/01442350903234923

Interpolating moving least-squares methods for fitting potential energy surfaces: Improving efficiency via local approximants
journal, December 2007

  • Guo, Yin; Tokmakov, Igor; Thompson, Donald L.
  • The Journal of Chemical Physics, Vol. 127, Issue 21
  • DOI: 10.1063/1.2805084

Computational Chemistry of Polyatomic Reaction Kinetics and Dynamics:  The Quest for an Accurate CH 5 Potential Energy Surface
journal, November 2007

  • Albu, Titus V.; Espinosa-García, Joaquín; Truhlar, Donald G.
  • Chemical Reviews, Vol. 107, Issue 11
  • DOI: 10.1021/cr078026x

Ab initio studies of cyclic water clusters (H 2 O) n , n =1–6. II. Analysis of many‐body interactions
journal, May 1994

  • Xantheas, Sotiris S.
  • The Journal of Chemical Physics, Vol. 100, Issue 10
  • DOI: 10.1063/1.466846

An effective fragment method for modeling solvent effects in quantum mechanical calculations
journal, August 1996

  • Day, Paul N.; Jensen, Jan H.; Gordon, Mark S.
  • The Journal of Chemical Physics, Vol. 105, Issue 5
  • DOI: 10.1063/1.472045

ReaxFF Reactive Force Field for Molecular Dynamics Simulations of Hydrocarbon Oxidation
journal, February 2008

  • Chenoweth, Kimberly; van Duin, Adri C. T.; Goddard, William A.
  • The Journal of Physical Chemistry A, Vol. 112, Issue 5
  • DOI: 10.1021/jp709896w

Generalized Born Solvation Model SM12
journal, December 2012

  • Marenich, Aleksandr V.; Cramer, Christopher J.; Truhlar, Donald G.
  • Journal of Chemical Theory and Computation, Vol. 9, Issue 1
  • DOI: 10.1021/ct300900e

Molecular Tailoring Approach for Simulation of Electrostatic Properties
journal, September 1994

  • Gadre, Shridhar R.; Shirsat, Rajendra N.; Limaye, Ajay C.
  • The Journal of Physical Chemistry, Vol. 98, Issue 37
  • DOI: 10.1021/j100088a013

Global ab initio ground-state potential energy surface of N 4
journal, July 2013

  • Paukku, Yuliya; Yang, Ke R.; Varga, Zoltan
  • The Journal of Chemical Physics, Vol. 139, Issue 4
  • DOI: 10.1063/1.4811653

Efficient Approach to Reactive Molecular Dynamics with Accurate Forces
journal, October 2009

  • Higashi, Masahiro; Truhlar, Donald G.
  • Journal of Chemical Theory and Computation, Vol. 5, Issue 11
  • DOI: 10.1021/ct900301d

The importance of three-body terms in the fragment molecular orbital method
journal, April 2004

  • Fedorov, Dmitri G.; Kitaura, Kazuo
  • The Journal of Chemical Physics, Vol. 120, Issue 15
  • DOI: 10.1063/1.1687334

Electrostatically Embedded Many-Body Expansion for Simulations
journal, December 2007

  • Dahlke, Erin E.; Truhlar, Donald G.
  • Journal of Chemical Theory and Computation, Vol. 4, Issue 1
  • DOI: 10.1021/ct700223r

Electrostatically Embedded Molecular Tailoring Approach and Validation for Peptides
journal, February 2013

  • Isegawa, Miho; Wang, Bo; Truhlar, Donald G.
  • Journal of Chemical Theory and Computation, Vol. 9, Issue 3
  • DOI: 10.1021/ct300845q

Many-Body Effects in Intermolecular Forces
journal, November 1994

  • Elrod, Matthew J.; Saykally, Richard J.
  • Chemical Reviews, Vol. 94, Issue 7
  • DOI: 10.1021/cr00031a010

Application of the Electrostatically Embedded Many-Body Expansion to Microsolvation of Ammonia in Water Clusters
journal, April 2008

  • Sorkin, Anastassia; Dahlke, Erin E.; Truhlar, Donald G.
  • Journal of Chemical Theory and Computation, Vol. 4, Issue 5
  • DOI: 10.1021/ct7003462

Bonding between CO and the MgO(001) surface: A modified picture
journal, February 1994

  • Nygren, Martin A.; Pettersson, Lars G. M.; Barandiarán, Zoila
  • The Journal of Chemical Physics, Vol. 100, Issue 3
  • DOI: 10.1063/1.466553

Perturbation Theory Approach to Intermolecular Potential Energy Surfaces of van der Waals Complexes
journal, November 1994

  • Jeziorski, Bogumil; Moszynski, Robert; Szalewicz, Krzysztof
  • Chemical Reviews, Vol. 94, Issue 7
  • DOI: 10.1021/cr00031a008

Geometry optimization using tuned and balanced redistributed charge schemes for combined quantum mechanical and molecular mechanical calculations
journal, January 2011

  • Wang, Bo; Truhlar, Donald G.
  • Physical Chemistry Chemical Physics, Vol. 13, Issue 22
  • DOI: 10.1039/c0cp02850a

A Generalized Hybrid Orbital (GHO) Method for the Treatment of Boundary Atoms in Combined QM/MM Calculations
journal, June 1998

  • Gao, Jiali; Amara, Patricia; Alhambra, Cristobal
  • The Journal of Physical Chemistry A, Vol. 102, Issue 24
  • DOI: 10.1021/jp9809890

Joyce and Ulysses: integrated and user-friendly tools for the parameterization of intramolecular force fields from quantum mechanical data
journal, January 2013

  • Barone, Vincenzo; Cacelli, Ivo; De Mitri, Nicola
  • Physical Chemistry Chemical Physics, Vol. 15, Issue 11
  • DOI: 10.1039/c3cp44179b

C ONSTRUCTING M ULTIDIMENSIONAL M OLECULAR P OTENTIAL E NERGY S URFACES FROM A B I NITIO D ATA
journal, October 1999


Including Charge Penetration Effects in Molecular Modeling
journal, October 2010

  • Wang, Bo; Truhlar, Donald G.
  • Journal of Chemical Theory and Computation, Vol. 6, Issue 11
  • DOI: 10.1021/ct1003862

Electrostatically Embedded Many-Body Expansion for Large Systems, with Applications to Water Clusters
journal, November 2006

  • Dahlke, Erin E.; Truhlar, Donald G.
  • Journal of Chemical Theory and Computation, Vol. 3, Issue 1
  • DOI: 10.1021/ct600253j

A pseudobond approach to combining quantum mechanical and molecular mechanical methods
journal, January 1999

  • Zhang, Yingkai; Lee, Tai-Sung; Yang, Weitao
  • The Journal of Chemical Physics, Vol. 110, Issue 1
  • DOI: 10.1063/1.478083

Density functional cluster description of ionic materials: Improved boundary conditions for MgO clusters with the help of cation model potentials
journal, January 1997


Assessment of the Pairwise Additive Approximation and Evaluation of Many-Body Terms for Water Clusters
journal, June 2006

  • Dahlke, Erin E.; Truhlar, Donald G.
  • The Journal of Physical Chemistry B, Vol. 110, Issue 22
  • DOI: 10.1021/jp061039e

Electrostatically Embedded Many-Body Approximation for Systems of Water, Ammonia, and Sulfuric Acid and the Dependence of Its Performance on Embedding Charges
journal, May 2009

  • Leverentz, Hannah R.; Truhlar, Donald G.
  • Journal of Chemical Theory and Computation, Vol. 5, Issue 6
  • DOI: 10.1021/ct900095d

Zeolite Structure and Reactivity by Combined Quantum-Chemical−Classical Calculations
journal, July 1999

  • de Vries, Alex H.; Sherwood, Paul; Collins, Simon J.
  • The Journal of Physical Chemistry B, Vol. 103, Issue 29
  • DOI: 10.1021/jp9913012

Parametrization and Validation of Intramolecular Force Fields Derived from DFT Calculations
journal, August 2007

  • Cacelli, Ivo; Prampolini, Giacomo
  • Journal of Chemical Theory and Computation, Vol. 3, Issue 5
  • DOI: 10.1021/ct700113h

Modeling the Kinetics of Bimolecular Reactions
journal, November 2006

  • Fernández-Ramos, Antonio; Miller, James A.; Klippenstein, Stephen J.
  • Chemical Reviews, Vol. 106, Issue 11
  • DOI: 10.1021/cr050205w

Generalized Energy-Based Fragmentation Approach for Computing the Ground-State Energies and Properties of Large Molecules
journal, March 2007

  • Li, Wei; Li, Shuhua; Jiang, Yuansheng
  • The Journal of Physical Chemistry A, Vol. 111, Issue 11
  • DOI: 10.1021/jp067721q

Combined Quantum Mechanical and Molecular Mechanical Methods for Calculating Potential Energy Surfaces: Tuned and Balanced Redistributed-Charge Algorithm
journal, January 2010

  • Wang, Bo; Truhlar, Donald G.
  • Journal of Chemical Theory and Computation, Vol. 6, Issue 2
  • DOI: 10.1021/ct900366m

Optimization of quantum mechanical molecular mechanical partitioning schemes: Gaussian delocalization of molecular mechanical charges and the double link atom method
journal, December 2002

  • Das, Debananda; Eurenius, Kirsten P.; Billings, Eric M.
  • The Journal of Chemical Physics, Vol. 117, Issue 23
  • DOI: 10.1063/1.1520134

A generalized many-body expansion and a unified view of fragment-based methods in electronic structure theory
journal, August 2012

  • Richard, Ryan M.; Herbert, John M.
  • The Journal of Chemical Physics, Vol. 137, Issue 6
  • DOI: 10.1063/1.4742816

Ab-Initio-Based Potential Energy Surfaces for Complex Molecules and Molecular Complexes
journal, May 2010

  • Bowman, J. M.; Braams, B. J.; Carter, S.
  • The Journal of Physical Chemistry Letters, Vol. 1, Issue 12
  • DOI: 10.1021/jz100626h

Quantum mechanical computations on very large molecular systems: The local self-consistent field method: QUANTUM MECHANICAL COMPUTATIONS
journal, March 1994

  • Théry, Vincent; Rinaldi, Daniel; Rivail, Jean-Louis
  • Journal of Computational Chemistry, Vol. 15, Issue 3
  • DOI: 10.1002/jcc.540150303

A Simple, Exact Density-Functional-Theory Embedding Scheme
journal, July 2012

  • Manby, Frederick R.; Stella, Martina; Goodpaster, Jason D.
  • Journal of Chemical Theory and Computation, Vol. 8, Issue 8
  • DOI: 10.1021/ct300544e

The analytical representation of electronic potential-energy surfaces
journal, July 1989


The implementation of a fast and accurate QM/MM potential method in Amber
journal, January 2008

  • Walker, Ross C.; Crowley, Michael F.; Case, David A.
  • Journal of Computational Chemistry, Vol. 29, Issue 7
  • DOI: 10.1002/jcc.20857

Adjusted Connection Atoms for Combined Quantum Mechanical and Molecular Mechanical Methods
journal, November 1999

  • Antes, Iris; Thiel, Walter
  • The Journal of Physical Chemistry A, Vol. 103, Issue 46
  • DOI: 10.1021/jp991771w

Anchor Points Reactive Potential for Bond-Breaking Reactions
journal, February 2014

  • Yang, Ke R.; Xu, Xuefei; Truhlar, Donald G.
  • Journal of Chemical Theory and Computation, Vol. 10, Issue 3
  • DOI: 10.1021/ct401074s

Screened Electrostatically Embedded Many-Body Method
journal, August 2011

  • Tempkin, Jeremy O. B.; Leverentz, Hannah R.; Wang, Bo
  • The Journal of Physical Chemistry Letters, Vol. 2, Issue 17
  • DOI: 10.1021/jz200893t

Simple one-electron quantum capping potentials for use in hybrid QM/MM studies of biological molecules
journal, June 2002

  • DiLabio, Gino A.; Hurley, Margaret M.; Christiansen, Phillip A.
  • The Journal of Chemical Physics, Vol. 116, Issue 22
  • DOI: 10.1063/1.1477182

Atomic Multipole Expansions of Molecular Charge Densities. Electrostatic Potentials
book, January 1981


Computer simulation of zeolite structure and reactivity using embedded cluster methods
journal, January 1997

  • Sherwood, Paul; de Vries, Alex H.; Collins, Simon J.
  • Faraday Discussions, Vol. 106
  • DOI: 10.1039/a701790a

Evaluation of an ab initio quantum mechanical/molecular mechanical hybrid-potential link-atom method
journal, February 2003

  • Amara, Patricia; Field, Martin J.
  • Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta), Vol. 109, Issue 1
  • DOI: 10.1007/s00214-002-0413-3

Evaluation of the Electrostatically Embedded Many-Body Expansion and the Electrostatically Embedded Many-Body Expansion of the Correlation Energy by Application to Low-Lying Water Hexamers
journal, December 2007

  • Dahlke, Erin E.; Leverentz, Hannah R.; Truhlar, Donald G.
  • Journal of Chemical Theory and Computation, Vol. 4, Issue 1
  • DOI: 10.1021/ct700183y

Molecules-in-Molecules: An Extrapolated Fragment-Based Approach for Accurate Calculations on Large Molecules and Materials
journal, April 2011

  • Mayhall, Nicholas J.; Raghavachari, Krishnan
  • Journal of Chemical Theory and Computation, Vol. 7, Issue 5
  • DOI: 10.1021/ct200033b