DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: The Fragment Molecular Orbital Method Based on Long-Range Corrected Density-Functional Tight-Binding

Abstract

The presently available linear scaling approaches to density-functional tight-binding (DFTB) based on the fragment molecular orbital (FMO) method are severely impacted by the problem of artificial charge transfer due to the self-interaction error (SIE), which hampers the simulation of zwitterionic systems such as biopolymers or ionic liquids. Here we report an extension of FMO-DFTB where we included a long-range corrected (LC) functional designed to mitigate the DFTB SIE, called the FMO-LC-DFTB method, resulting in a robust method which succeeds in simulating zwitterionic systems. Both energy and analytic gradient are developed for the gas phase and the polarizable continuum model of solvation. The scaling of FMO-LC-DFTB with system size N is shown to be almost linear, O(N1.13–1.28), and its numerical accuracy is established for a variety of representative systems including neutral and charged polypeptides. It is shown that pair interaction energies between fragments for two mini-proteins are in excellent agreement with results from long-range corrected density functional theory. The new method was employed in long time scale (1 ns) molecular dynamics simulations of the tryptophan cage protein (PDB: 1L2Y) in the gas phase for four different protonation states and in stochastic global minimum structure searches for 1-ethyl-3-methylimidazolium nitrate ionic liquid clustersmore » containing up to 2300 atoms.« less

Authors:
ORCiD logo [1]; ORCiD logo [2]; ORCiD logo [3]; ORCiD logo [4]; ORCiD logo [5]; ORCiD logo [6]
  1. Univ. of Tennessee, Knoxville, TN (United States)
  2. Kyoto Univ., Kyoto (Japan)
  3. National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba (Japan)
  4. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
  5. Univ. Claude Bernard Lyon 1, Villeurbanne (France)
  6. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Univ. of Tennessee, Knoxville, TN (United States)
Publication Date:
Research Org.:
Energy Frontier Research Centers (EFRC) (United States). Fluid Interface Reactions, Structures and Transport Center (FIRST); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES)
OSTI Identifier:
1512513
Alternate Identifier(s):
OSTI ID: 1566991
Grant/Contract Number:  
AC05-00OR22725
Resource Type:
Accepted Manuscript
Journal Name:
Journal of Chemical Theory and Computation
Additional Journal Information:
Journal Volume: 15; Journal Issue: 5; Journal ID: ISSN 1549-9618
Publisher:
American Chemical Society
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY

Citation Formats

Vuong, Van Quan, Nishimoto, Yoshio, Fedorov, Dmitri G., Sumpter, Bobby G., Niehaus, Thomas A., and Irle, Stephan. The Fragment Molecular Orbital Method Based on Long-Range Corrected Density-Functional Tight-Binding. United States: N. p., 2019. Web. doi:10.1021/acs.jctc.9b00108.
Vuong, Van Quan, Nishimoto, Yoshio, Fedorov, Dmitri G., Sumpter, Bobby G., Niehaus, Thomas A., & Irle, Stephan. The Fragment Molecular Orbital Method Based on Long-Range Corrected Density-Functional Tight-Binding. United States. https://doi.org/10.1021/acs.jctc.9b00108
Vuong, Van Quan, Nishimoto, Yoshio, Fedorov, Dmitri G., Sumpter, Bobby G., Niehaus, Thomas A., and Irle, Stephan. Thu . "The Fragment Molecular Orbital Method Based on Long-Range Corrected Density-Functional Tight-Binding". United States. https://doi.org/10.1021/acs.jctc.9b00108. https://www.osti.gov/servlets/purl/1512513.
@article{osti_1512513,
title = {The Fragment Molecular Orbital Method Based on Long-Range Corrected Density-Functional Tight-Binding},
author = {Vuong, Van Quan and Nishimoto, Yoshio and Fedorov, Dmitri G. and Sumpter, Bobby G. and Niehaus, Thomas A. and Irle, Stephan},
abstractNote = {The presently available linear scaling approaches to density-functional tight-binding (DFTB) based on the fragment molecular orbital (FMO) method are severely impacted by the problem of artificial charge transfer due to the self-interaction error (SIE), which hampers the simulation of zwitterionic systems such as biopolymers or ionic liquids. Here we report an extension of FMO-DFTB where we included a long-range corrected (LC) functional designed to mitigate the DFTB SIE, called the FMO-LC-DFTB method, resulting in a robust method which succeeds in simulating zwitterionic systems. Both energy and analytic gradient are developed for the gas phase and the polarizable continuum model of solvation. The scaling of FMO-LC-DFTB with system size N is shown to be almost linear, O(N1.13–1.28), and its numerical accuracy is established for a variety of representative systems including neutral and charged polypeptides. It is shown that pair interaction energies between fragments for two mini-proteins are in excellent agreement with results from long-range corrected density functional theory. The new method was employed in long time scale (1 ns) molecular dynamics simulations of the tryptophan cage protein (PDB: 1L2Y) in the gas phase for four different protonation states and in stochastic global minimum structure searches for 1-ethyl-3-methylimidazolium nitrate ionic liquid clusters containing up to 2300 atoms.},
doi = {10.1021/acs.jctc.9b00108},
journal = {Journal of Chemical Theory and Computation},
number = 5,
volume = 15,
place = {United States},
year = {Thu Apr 18 00:00:00 EDT 2019},
month = {Thu Apr 18 00:00:00 EDT 2019}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Citation Metrics:
Cited by: 29 works
Citation information provided by
Web of Science

Save / Share:

Works referenced in this record:

Rethinking amide bond synthesis
journal, December 2011

  • Pattabiraman, Vijaya R.; Bode, Jeffrey W.
  • Nature, Vol. 480, Issue 7378
  • DOI: 10.1038/nature10702

Metal–Organic Frameworks in Biomedicine
journal, September 2011

  • Horcajada, Patricia; Gref, Ruxandra; Baati, Tarek
  • Chemical Reviews, Vol. 112, Issue 2, p. 1232-1268
  • DOI: 10.1021/cr200256v

Mixed Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulations of Biological Systems in Ground and Electronically Excited States
journal, April 2015

  • Brunk, Elizabeth; Rothlisberger, Ursula
  • Chemical Reviews, Vol. 115, Issue 12
  • DOI: 10.1021/cr500628b

Brønsted Acidity in Metal–Organic Frameworks
journal, June 2015


Acidic Ionic Liquids
journal, May 2016


Acid-base properties and catalytic activity of metal-organic frameworks: A view from spectroscopic and semiempirical methods
journal, April 2016


Multiscale Studies on Ionic Liquids
journal, February 2017


Ionic Liquid Designed for PEDOT:PSS Conductivity Enhancement
journal, April 2018

  • de Izarra, Ambroise; Park, Seongjin; Lee, Jinhee
  • Journal of the American Chemical Society, Vol. 140, Issue 16
  • DOI: 10.1021/jacs.7b10306

Large-Scale Computations in Chemistry: A Bird’s Eye View of a Vibrant Field
journal, April 2015

  • Akimov, Alexey V.; Prezhdo, Oleg V.
  • Chemical Reviews, Vol. 115, Issue 12
  • DOI: 10.1021/cr500524c

Challenges in large scale quantum mechanical calculations: Challenges in large scale quantum mechanical calculations
journal, November 2016

  • Ratcliff, Laura E.; Mohr, Stephan; Huhs, Georg
  • Wiley Interdisciplinary Reviews: Computational Molecular Science, Vol. 7, Issue 1
  • DOI: 10.1002/wcms.1290

Construction of tight-binding-like potentials on the basis of density-functional theory: Application to carbon
journal, May 1995


Self-consistent-charge density-functional tight-binding method for simulations of complex materials properties
journal, September 1998

  • Elstner, M.; Porezag, D.; Jungnickel, G.
  • Physical Review B, Vol. 58, Issue 11, p. 7260-7268
  • DOI: 10.1103/PhysRevB.58.7260

DFTB3: Extension of the Self-Consistent-Charge Density-Functional Tight-Binding Method (SCC-DFTB)
journal, March 2011

  • Gaus, Michael; Cui, Qiang; Elstner, Marcus
  • Journal of Chemical Theory and Computation, Vol. 7, Issue 4
  • DOI: 10.1021/ct100684s

Development and use of quantum mechanical molecular models. 76. AM1: a new general purpose quantum mechanical molecular model
journal, June 1985

  • Dewar, Michael J. S.; Zoebisch, Eve G.; Healy, Eamonn F.
  • Journal of the American Chemical Society, Vol. 107, Issue 13
  • DOI: 10.1021/ja00299a024

Optimization of parameters for semiempirical methods II. Applications
journal, March 1989


Optimization of parameters for semiempirical methods I. Method
journal, March 1989


Optimization of parameters for semiempirical methods V: Modification of NDDO approximations and application to 70 elements
journal, September 2007


Semiempirical Quantum-Chemical Orthogonalization-Corrected Methods: Theory, Implementation, and Parameters
journal, January 2016

  • Dral, Pavlo O.; Wu, Xin; Spörkel, Lasse
  • Journal of Chemical Theory and Computation, Vol. 12, Issue 3
  • DOI: 10.1021/acs.jctc.5b01046

Semiempirical Quantum Mechanical Methods for Noncovalent Interactions for Chemical and Biochemical Applications
journal, April 2016


Description of non-covalent interactions in SCC-DFTB methods
journal, January 2017

  • Miriyala, Vijay Madhav; Řezáč, Jan
  • Journal of Computational Chemistry, Vol. 38, Issue 10
  • DOI: 10.1002/jcc.24725

Toward Accurate Conformational Energies of Smaller Peptides and Medium-Sized Macrocycles: MPCONF196 Benchmark Energy Data Set
journal, February 2018

  • Řezáč, Jan; Bím, Daniel; Gutten, Ondrej
  • Journal of Chemical Theory and Computation, Vol. 14, Issue 3
  • DOI: 10.1021/acs.jctc.7b01074

Random versus Systematic Errors in Reaction Enthalpies Computed Using Semiempirical and Minimal Basis Set Methods
journal, April 2018

  • Kromann, Jimmy C.; Welford, Alexander; Christensen, Anders S.
  • ACS Omega, Vol. 3, Issue 4
  • DOI: 10.1021/acsomega.8b00189

DFTB Parameters for the Periodic Table, Part 2: Energies and Energy Gradients from Hydrogen to Calcium
journal, October 2015

  • Oliveira, Augusto F.; Philipsen, Pier; Heine, Thomas
  • Journal of Chemical Theory and Computation, Vol. 11, Issue 11
  • DOI: 10.1021/acs.jctc.5b00702

Unraveling the plasma-material interface with real time diagnosis of dynamic boron conditioning in extreme tokamak plasmas
journal, July 2017

  • Domínguez-Gutiérrez, F. Javier; Bedoya, Felipe; Krstić, Predrag S.
  • Nuclear Fusion, Vol. 57, Issue 8
  • DOI: 10.1088/1741-4326/aa7b17

DFTB+, a Sparse Matrix-Based Implementation of the DFTB Method
journal, July 2007

  • Aradi, B.; Hourahine, B.; Frauenheim, Th.
  • The Journal of Physical Chemistry A, Vol. 111, Issue 26
  • DOI: 10.1021/jp070186p

Density functional tight binding
journal, March 2014

  • Elstner, Marcus; Seifert, Gotthard
  • Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, Vol. 372, Issue 2011
  • DOI: 10.1098/rsta.2012.0483

The fragment molecular orbital method: theoretical development, implementation in GAMESS, and applications: Fragment molecular orbital method in GAMESS
journal, June 2017

  • Fedorov, Dmitri G.
  • Wiley Interdisciplinary Reviews: Computational Molecular Science, Vol. 7, Issue 6
  • DOI: 10.1002/wcms.1322

Density-Functional Tight-Binding Combined with the Fragment Molecular Orbital Method
journal, October 2014

  • Nishimoto, Yoshio; Fedorov, Dmitri G.; Irle, Stephan
  • Journal of Chemical Theory and Computation, Vol. 10, Issue 11
  • DOI: 10.1021/ct500489d

Large-Scale Quantum-Mechanical Molecular Dynamics Simulations Using Density-Functional Tight-Binding Combined with the Fragment Molecular Orbital Method
journal, December 2015

  • Nishimoto, Yoshio; Nakata, Hiroya; Fedorov, Dmitri G.
  • The Journal of Physical Chemistry Letters, Vol. 6, Issue 24
  • DOI: 10.1021/acs.jpclett.5b02490

Third-order density-functional tight-binding combined with the fragment molecular orbital method
journal, September 2015


Three-body expansion of the fragment molecular orbital method combined with density-functional tight-binding
journal, January 2017

  • Nishimoto, Yoshio; Fedorov, Dmitri G.
  • Journal of Computational Chemistry, Vol. 38, Issue 7
  • DOI: 10.1002/jcc.24693

Adaptive frozen orbital treatment for the fragment molecular orbital method combined with density-functional tight-binding
journal, February 2018

  • Nishimoto, Yoshio; Fedorov, Dmitri G.
  • The Journal of Chemical Physics, Vol. 148, Issue 6
  • DOI: 10.1063/1.5012935

Simulating Water with the Self-Consistent-Charge Density Functional Tight Binding Method:  From Molecular Clusters to the Liquid State
journal, July 2007

  • Hu, Hao; Lu, Zhenyu; Elstner, Marcus
  • The Journal of Physical Chemistry A, Vol. 111, Issue 26
  • DOI: 10.1021/jp070308d

Three pillars for achieving quantum mechanical molecular dynamics simulations of huge systems: Divide-and-conquer, density-functional tight-binding, and massively parallel computation
journal, June 2016

  • Nishizawa, Hiroaki; Nishimura, Yoshifumi; Kobayashi, Masato
  • Journal of Computational Chemistry, Vol. 37, Issue 21
  • DOI: 10.1002/jcc.24419

Parallel implementation of efficient charge-charge interaction evaluation scheme in periodic divide-and-conquer density-functional tight-binding calculations
journal, October 2017

  • Nishimura, Yoshifumi; Nakai, Hiromi
  • Journal of Computational Chemistry, Vol. 39, Issue 2
  • DOI: 10.1002/jcc.25086

A Variational Linear-Scaling Framework to Build Practical, Efficient Next-Generation Orbital-Based Quantum Force Fields
journal, February 2013

  • Giese, Timothy J.; Chen, Haoyuan; Dissanayake, Thakshila
  • Journal of Chemical Theory and Computation, Vol. 9, Issue 3
  • DOI: 10.1021/ct3010134

Challenges for Density Functional Theory
journal, December 2011

  • Cohen, Aron J.; Mori-Sánchez, Paula; Yang, Weitao
  • Chemical Reviews, Vol. 112, Issue 1
  • DOI: 10.1021/cr200107z

Self-Interaction and Strong Correlation in DFTB
journal, July 2007

  • Hourahine, B.; Sanna, S.; Aradi, B.
  • The Journal of Physical Chemistry A, Vol. 111, Issue 26
  • DOI: 10.1021/jp070173b

Delocalization errors in a hubbard-like model: Consequences for density-functional tight-binding calculations of molecular systems
journal, July 2011

  • Lundberg, Marcus; Nishimoto, Yoshio; Irle, Stephan
  • International Journal of Quantum Chemistry, Vol. 112, Issue 6
  • DOI: 10.1002/qua.23178

Influence of the self-interaction error on the structure of the DFT exchange hole
journal, February 2002


The impact of the self-interaction error on the density functional theory description of dissociating radical cations: Ionic and covalent dissociation limits
journal, January 2004

  • Gräfenstein, Jürgen; Kraka, Elfi; Cremer, Dieter
  • The Journal of Chemical Physics, Vol. 120, Issue 2
  • DOI: 10.1063/1.1630017

Insights into Current Limitations of Density Functional Theory
journal, August 2008


On the relationship between bond-length alternation and many-electron self-interaction error
journal, September 2012

  • Körzdörfer, Thomas; Parrish, Robert M.; Sears, John S.
  • The Journal of Chemical Physics, Vol. 137, Issue 12
  • DOI: 10.1063/1.4752431

Perspective: Fifty years of density-functional theory in chemical physics
journal, May 2014

  • Becke, Axel D.
  • The Journal of Chemical Physics, Vol. 140, Issue 18
  • DOI: 10.1063/1.4869598

Self-Interaction Error in Density Functional Theory: An Appraisal
journal, April 2018

  • Bao, Junwei Lucas; Gagliardi, Laura; Truhlar, Donald G.
  • The Journal of Physical Chemistry Letters, Vol. 9, Issue 9
  • DOI: 10.1021/acs.jpclett.8b00242

Improving self-consistent field convergence by varying occupation numbers
journal, January 1999

  • Rabuck, Angela D.; Scuseria, Gustavo E.
  • The Journal of Chemical Physics, Vol. 110, Issue 2
  • DOI: 10.1063/1.478177

Implementation and benchmark of a long-range corrected functional in the density functional based tight-binding method
journal, November 2015

  • Lutsker, V.; Aradi, B.; Niehaus, T. A.
  • The Journal of Chemical Physics, Vol. 143, Issue 18
  • DOI: 10.1063/1.4935095

Charges in the hydrophobic interior of proteins
journal, August 2010

  • Isom, D. G.; Castaneda, C. A.; Cannon, B. R.
  • Proceedings of the National Academy of Sciences, Vol. 107, Issue 37
  • DOI: 10.1073/pnas.1004213107

Density functionals for the Yukawa electron-electron interaction
journal, November 1995

  • Savin, Andreas; Flad, Heinz-J�rgen
  • International Journal of Quantum Chemistry, Vol. 56, Issue 4
  • DOI: 10.1002/qua.560560417

A well-tempered density functional theory of electrons in molecules
journal, January 2007

  • Livshits, Ester; Baer, Roi
  • Physical Chemistry Chemical Physics, Vol. 9, Issue 23
  • DOI: 10.1039/b617919c

Range-Separated Exchange Functionals with Slater-Type Functions
journal, February 2012

  • Seth, Michael; Ziegler, Tom
  • Journal of Chemical Theory and Computation, Vol. 8, Issue 3
  • DOI: 10.1021/ct300006h

Range separated functionals in the density functional based tight-binding method: Formalism
journal, December 2011

  • Niehaus, Thomas A.; Della Sala, Fabio
  • physica status solidi (b), Vol. 249, Issue 2
  • DOI: 10.1002/pssb.201100694

Parametrization and Benchmark of Long-Range Corrected DFTB2 for Organic Molecules
journal, December 2017

  • Vuong, Van Quan; Akkarapattiakal Kuriappan, Jissy; Kubillus, Maximilian
  • Journal of Chemical Theory and Computation, Vol. 14, Issue 1
  • DOI: 10.1021/acs.jctc.7b00947

Tight-binding approach to time-dependent density-functional response theory
journal, February 2001


Time-Dependent Extension of the Long-Range Corrected Density Functional Based Tight-Binding Method
journal, March 2017

  • Kranz, Julian J.; Elstner, Marcus; Aradi, Bálint
  • Journal of Chemical Theory and Computation, Vol. 13, Issue 4
  • DOI: 10.1021/acs.jctc.6b01243

Long-range correction for tight-binding TD-DFT
journal, October 2015

  • Humeniuk, Alexander; Mitrić, Roland
  • The Journal of Chemical Physics, Vol. 143, Issue 13
  • DOI: 10.1063/1.4931179

DFTBaby: A software package for non-adiabatic molecular dynamics simulations based on long-range corrected tight-binding TD-DFT(B)
journal, December 2017


General atomic and molecular electronic structure system
journal, November 1993

  • Schmidt, Michael W.; Baldridge, Kim K.; Boatz, Jerry A.
  • Journal of Computational Chemistry, Vol. 14, Issue 11, p. 1347-1363
  • DOI: 10.1002/jcc.540141112

Fragmentation Methods: A Route to Accurate Calculations on Large Systems
journal, August 2011

  • Gordon, Mark S.; Fedorov, Dmitri G.; Pruitt, Spencer R.
  • Chemical Reviews, Vol. 112, Issue 1
  • DOI: 10.1021/cr200093j

Investigation of the interaction between molecules at medium distances
journal, April 1975


Toward a Molecular Orbital Derived Empirical Potential for Liquid Simulations
journal, January 1997

  • Gao, Jiali
  • The Journal of Physical Chemistry B, Vol. 101, Issue 4
  • DOI: 10.1021/jp962833a

Theoretical Study of Protein–Ligand Interactions Using the Molecules-in-Molecules Fragmentation-Based Method
journal, August 2018

  • Thapa, Bishnu; Beckett, Daniel; Erickson, Jon
  • Journal of Chemical Theory and Computation, Vol. 14, Issue 10
  • DOI: 10.1021/acs.jctc.8b00531

Automated error control in divide-and-conquer self-consistent field calculations: Automated Error Control
journal, February 2018

  • Kobayashi, Masato; Fujimori, Toshikazu; Taketsugu, Tetsuya
  • Journal of Computational Chemistry, Vol. 39, Issue 15
  • DOI: 10.1002/jcc.25174

Extending the Power of Quantum Chemistry to Large Systems with the Fragment Molecular Orbital Method
journal, August 2007

  • Fedorov, Dmitri G.; Kitaura, Kazuo
  • The Journal of Physical Chemistry A, Vol. 111, Issue 30
  • DOI: 10.1021/jp0716740

Exploring chemistry with the fragment molecular orbital method
journal, January 2012

  • Fedorov, Dmitri G.; Nagata, Takeshi; Kitaura, Kazuo
  • Physical Chemistry Chemical Physics, Vol. 14, Issue 21
  • DOI: 10.1039/c2cp23784a

Effective Fragment Molecular Orbital Method: A Merger of the Effective Fragment Potential and Fragment Molecular Orbital Methods
journal, August 2010

  • Steinmann, Casper; Fedorov, Dmitri G.; Jensen, Jan H.
  • The Journal of Physical Chemistry A, Vol. 114, Issue 33
  • DOI: 10.1021/jp101498m

The Fragment Molecular Orbital Method for Geometry Optimizations of Polypeptides and Proteins
journal, April 2007

  • Fedorov, Dmitri G.; Ishida, Toyokazu; Uebayasi, Masami
  • The Journal of Physical Chemistry A, Vol. 111, Issue 14
  • DOI: 10.1021/jp0671042

On the accuracy of the 3-body fragment molecular orbital method (FMO) applied to density functional theory
journal, May 2004


The three-body fragment molecular orbital method for accurate calculations of large systems
journal, December 2006


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

Fully analytic energy gradient in the fragment molecular orbital method
journal, March 2011

  • Brorsen, Kurt; Fedorov, Dmitri G.
  • The Journal of Chemical Physics, Vol. 134, Issue 12
  • DOI: 10.1063/1.3568010

Subsystem Analysis for the Fragment Molecular Orbital Method and Its Application to Protein–Ligand Binding in Solution
journal, March 2016

  • Fedorov, Dmitri G.; Kitaura, Kazuo
  • The Journal of Physical Chemistry A, Vol. 120, Issue 14
  • DOI: 10.1021/acs.jpca.6b00163

10 Residue Folded Peptide Designed by Segment Statistics
journal, August 2004


Designing a 20-residue protein
journal, April 2002

  • Neidigh, Jonathan W.; Fesinmeyer, R. Matthew; Andersen, Niels H.
  • Nature Structural Biology, Vol. 9, Issue 6
  • DOI: 10.1038/nsb798

Analytic gradient for second order Møller-Plesset perturbation theory with the polarizable continuum model based on the fragment molecular orbital method
journal, May 2012

  • Nagata, Takeshi; Fedorov, Dmitri G.; Li, Hui
  • The Journal of Chemical Physics, Vol. 136, Issue 20
  • DOI: 10.1063/1.4714601

A long-range correction scheme for generalized-gradient-approximation exchange functionals
journal, August 2001

  • Iikura, Hisayoshi; Tsuneda, Takao; Yanai, Takeshi
  • The Journal of Chemical Physics, Vol. 115, Issue 8
  • DOI: 10.1063/1.1383587

A new hybrid exchange–correlation functional using the Coulomb-attenuating method (CAM-B3LYP)
journal, July 2004

  • Yanai, Takeshi; Tew, David P.; Handy, Nicholas C.
  • Chemical Physics Letters, Vol. 393, Issue 1-3, p. 51-57
  • DOI: 10.1016/j.cplett.2004.06.011

A Direct Comparison of Protein Structure in the Gas and Solution Phase:  The Trp-cage
journal, November 2007

  • Patriksson, Alexandra; Adams, Christopher M.; Kjeldsen, Frank
  • The Journal of Physical Chemistry B, Vol. 111, Issue 46
  • DOI: 10.1021/jp709901t

Rattle: A “velocity” version of the shake algorithm for molecular dynamics calculations
journal, October 1983


Kick: Constraining a stochastic search procedure with molecular fragments
journal, January 2009

  • Addicoat, Matthew A.; Metha, Gregory F.
  • Journal of Computational Chemistry, Vol. 30, Issue 1
  • DOI: 10.1002/jcc.21026

Stochastic structure determination for conformationally flexible heterogenous molecular clusters: Application to ionic liquids
journal, August 2013

  • Addicoat, Matthew A.; Fukuoka, Syou; Page, Alister J.
  • Journal of Computational Chemistry, Vol. 34, Issue 30
  • DOI: 10.1002/jcc.23420

A fast intrinsic localization procedure applicable for a b i n i t i o and semiempirical linear combination of atomic orbital wave functions
journal, May 1989

  • Pipek, János; Mezey, Paul G.
  • The Journal of Chemical Physics, Vol. 90, Issue 9
  • DOI: 10.1063/1.456588

Tinker 8: Software Tools for Molecular Design
journal, August 2018

  • Rackers, Joshua A.; Wang, Zhi; Lu, Chao
  • Journal of Chemical Theory and Computation, Vol. 14, Issue 10
  • DOI: 10.1021/acs.jctc.8b00529

A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu
journal, April 2010

  • Grimme, Stefan; Antony, Jens; Ehrlich, Stephan
  • The Journal of Chemical Physics, Vol. 132, Issue 15
  • DOI: 10.1063/1.3382344

Effective Ion Mobility Calculations for Macromolecules by Scattering on Electron Clouds
journal, August 2014

  • Alexeev, Yuri; Fedorov, Dmitri G.; Shvartsburg, Alexandre A.
  • The Journal of Physical Chemistry A, Vol. 118, Issue 34
  • DOI: 10.1021/jp505012c

Rapid and accurate assessment of GPCR-ligand interactions Using the fragment molecular orbital-based density-functional tight-binding method
journal, July 2017

  • Morao, Inaki; Fedorov, Dmitri G.; Robinson, Roger
  • Journal of Computational Chemistry, Vol. 38, Issue 23
  • DOI: 10.1002/jcc.24850

GAMESS As a Free Quantum-Mechanical Platform for Drug Research
journal, September 2012

  • Alexeev, Yuri; P. Mazanetz, Michael; Ichihara, Osamu
  • Current Topics in Medicinal Chemistry, Vol. 12, Issue 18
  • DOI: 10.2174/156802612804910269

Zwitterionic States in Gas-Phase Polypeptide Ions Revealed by 157-nm Ultra-Violet Photodissociation
journal, October 2006

  • Kjeldsen, Frank; Silivra, Oleg A.; Zubarev, Roman A.
  • Chemistry - A European Journal, Vol. 12, Issue 30
  • DOI: 10.1002/chem.200600248

Gas-phase protein salt bridge stabilities from collisional activation and electron transfer dissociation
journal, September 2017


Room-Temperature Infrared Spectroscopy Combined with Mass Spectrometry Distinguishes Gas-Phase Protein Isomers
journal, September 2009

  • Fung, Y. M. Eva; Besson, Thierry; Lemaire, Joël
  • Angewandte Chemie International Edition, Vol. 48, Issue 44
  • DOI: 10.1002/anie.200901516

Proteins in the gas phase: Proteins in the gas phase
journal, November 2012

  • Meyer, Tim; Gabelica, Valérie; Grubmüller, Helmut
  • Wiley Interdisciplinary Reviews: Computational Molecular Science, Vol. 3, Issue 4
  • DOI: 10.1002/wcms.1130

On the Zwitterionic Nature of Gas-Phase Peptides and Protein Ions
journal, May 2010


Quantum Chemical Methods for the Prediction of Energetic, Physical, and Spectroscopic Properties of Ionic Liquids
journal, January 2017

  • Izgorodina, Ekaterina I.; Seeger, Zoe L.; Scarborough, David L. A.
  • Chemical Reviews, Vol. 117, Issue 10
  • DOI: 10.1021/acs.chemrev.6b00528

Implementation of replica-exchange umbrella sampling in GAMESS
journal, July 2018


Works referencing / citing this record:

Fantasy versus reality in fragment-based quantum chemistry
journal, November 2019

  • Herbert, John M.
  • The Journal of Chemical Physics, Vol. 151, Issue 17
  • DOI: 10.1063/1.5126216