Fantasy versus reality in fragment-based quantum chemistry

Herbert, John M.

doi:10.1063/1.5126216

Title: Fantasy versus reality in fragment-based quantum chemistry

Abstract

Since the introduction of the fragment molecular orbital method 20 years ago, fragment-based approaches have occupied a small but growing niche in quantum chemistry. These methods decompose a large molecular system into subsystems small enough to be amenable to electronic structure calculations, following which the subsystem information is reassembled in order to approximate an otherwise intractable supersystem calculation. Fragmentation sidesteps the steep rise (with respect to system size) in the cost of ab initio calculations, replacing it with a distributed cost across numerous computer processors. Such methods are attractive, in part, because they are easily parallelizable and therefore readily amenable to exascale computing. As such, there has been hope that distributed computing might offer the proverbial “free lunch” in quantum chemistry, with the entrée being high-level calculations on very large systems. While fragment-based quantum chemistry can count many success stories, there also exists a seedy underbelly of rarely acknowledged problems. As these methods begin to mature, it is time to have a serious conversation about what they can and cannot be expected to accomplish in the near future. Both successes and challenges are highlighted in this Perspective.

Authors:

^[1]

The Ohio State Univ., Columbus, OH (United States)

Publication Date:: 2019-11-04

Research Org.:: The Ohio State Univ., Columbus, OH (United States)

Sponsoring Org.:: USDOE Office of Science (SC), Basic Energy Sciences (BES). Chemical Sciences, Geosciences, and Biosciences Division

OSTI Identifier:: 1604454

Alternate Identifier(s):: OSTI ID: 1573087

Grant/Contract Number:: SC0008850; SC0008550

Resource Type:: Accepted Manuscript

Journal Name:: Journal of Chemical Physics

Additional Journal Information:: Journal Volume: 151; Journal Issue: 17; Journal ID: ISSN 0021-9606

Publisher:: American Institute of Physics (AIP)

Country of Publication:: United States

Language:: English

Subject:: 74 ATOMIC AND MOLECULAR PHYSICS

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                    Herbert, John M. Fantasy versus reality in fragment-based quantum chemistry.  United States: N. p., 2019. 
Web.  doi:10.1063/1.5126216.

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                    Herbert, John M. Fantasy versus reality in fragment-based quantum chemistry.  United States.  https://doi.org/10.1063/1.5126216

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                    Herbert, John M. Mon .  
"Fantasy versus reality in fragment-based quantum chemistry".  United States.  https://doi.org/10.1063/1.5126216.  https://www.osti.gov/servlets/purl/1604454.

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@article{osti_1604454,

  title        = {Fantasy versus reality in fragment-based quantum chemistry},

  author       = {Herbert, John M.},

  abstractNote = {Since the introduction of the fragment molecular orbital method 20 years ago, fragment-based approaches have occupied a small but growing niche in quantum chemistry. These methods decompose a large molecular system into subsystems small enough to be amenable to electronic structure calculations, following which the subsystem information is reassembled in order to approximate an otherwise intractable supersystem calculation. Fragmentation sidesteps the steep rise (with respect to system size) in the cost of ab initio calculations, replacing it with a distributed cost across numerous computer processors. Such methods are attractive, in part, because they are easily parallelizable and therefore readily amenable to exascale computing. As such, there has been hope that distributed computing might offer the proverbial “free lunch” in quantum chemistry, with the entrée being high-level calculations on very large systems. While fragment-based quantum chemistry can count many success stories, there also exists a seedy underbelly of rarely acknowledged problems. As these methods begin to mature, it is time to have a serious conversation about what they can and cannot be expected to accomplish in the near future. Both successes and challenges are highlighted in this Perspective.},

  doi          = {10.1063/1.5126216},

  journal      = {Journal of Chemical Physics},

  number       = 17,

  volume       = 151,

  place        = {United States},

  year         = {2019},

  month        = {11}

}

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Gordon, Mark S.; Freitag, Mark A.; Bandyopadhyay, Pradipta
The Journal of Physical Chemistry A, Vol. 105, Issue 2
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Perturbation theory of three-body exchange nonadditivity and application to helium trimer
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Lotrich, Victor F.; Szalewicz, Krzysztof
The Journal of Chemical Physics, Vol. 112, Issue 1
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Theoretical predictions suggest carbon dioxide phases III and VII are identical
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Sontising, Watit; Heit, Yonaton N.; McKinley, Jessica L.
Chem. Sci., Vol. 8, Issue 11
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Comparison of Intermolecular Interaction Energies from SAPT and DFT Including Empirical Dispersion Contributions
journal, October 2011

Hesselmann, Andreas
The Journal of Physical Chemistry A, Vol. 115, Issue 41
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Assessing Many-Body Effects of Water Self-Ions. II: H ₃ O ⁺ (H ₂ O) _n Clusters
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Egan, Colin K.; Paesani, Francesco
Journal of Chemical Theory and Computation, Vol. 15, Issue 9
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Natural population analysis
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Reed, Alan E.; Weinstock, Robert B.; Weinhold, Frank
The Journal of Chemical Physics, Vol. 83, Issue 2
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Fragment-Based Approaches for Supramolecular Interaction Energies: Applications to Foldamers and Their Complexes with Anions
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Debnath, Sibali; Sengupta, Arkajyoti; Jose, K. V. Jovan
Journal of Chemical Theory and Computation, Vol. 14, Issue 12
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Fermi resonance in solid CO ₂ under pressure
journal, February 2013

Sode, Olaseni; Keçeli, Murat; Yagi, Kiyoshi
The Journal of Chemical Physics, Vol. 138, Issue 7
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Determination of the absolute configuration of chiral molecules via density functional theory calculations of vibrational circular dichroism and optical rotation: The chiral alkane D3-anti-trans-anti-trans-anti-trans-perhydrotriphenylene
journal, February 2007

Stephens, P. J.; Devlin, F. J.; Schürch, S.
Theoretical Chemistry Accounts, Vol. 119, Issue 1-3
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Analytic gradient for the QM/MM-Ewald method using charges derived from the electrostatic potential: Theory, implementation, and application to ab initio molecular dynamics simulation of the aqueous electron
journal, April 2019

Holden, Zachary C.; Rana, Bhaskar; Herbert, John M.
The Journal of Chemical Physics, Vol. 150, Issue 14
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Crossover from melting to dissociation of CO2 under pressure: Implications for the lower mantle
journal, September 2011

Litasov, Konstantin D.; Goncharov, Alexander F.; Hemley, Russell J.
Earth and Planetary Science Letters, Vol. 309, Issue 3-4
DOI: 10.1016/j.epsl.2011.07.006

QM/MM: What Have We Learned, Where Are We, and Where Do We Go from Here?
journal, May 2007

Lin, Hai; Truhlar, Donald G.
ChemInform, Vol. 38, Issue 22
DOI: 10.1002/chin.200722224

A Simple Correction for Nonadditive Dispersion within Extended Symmetry-Adapted Perturbation Theory (XSAPT)
journal, August 2018

Lao, Ka Un; Herbert, John M.
Journal of Chemical Theory and Computation, Vol. 14, Issue 10
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The Use of Many-Body Expansions and Geometry Optimizations in Fragment-Based Methods
journal, July 2014

Fedorov, Dmitri G.; Asada, Naoya; Nakanishi, Isao
Accounts of Chemical Research, Vol. 47, Issue 9
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Fragment-Based Electronic Structure Approach for Computing Nuclear Magnetic Resonance Chemical Shifts in Molecular Crystals
journal, October 2014

Hartman, Joshua D.; Beran, Gregory J. O.
Journal of Chemical Theory and Computation, Vol. 10, Issue 11
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Scalable Electron Correlation Methods I.: PNO-LMP2 with Linear Scaling in the Molecular Size and Near-Inverse-Linear Scaling in the Number of Processors
journal, January 2015

Werner, Hans-Joachim; Knizia, Gerald; Krause, Christine
Journal of Chemical Theory and Computation, Vol. 11, Issue 2
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Ab initio molecular dynamics with intramolecular noncovalent interactions for unsolvated polypeptides
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Zhang, Lei; Li, Wei; Fang, Tao
Theoretical Chemistry Accounts, Vol. 135, Issue 2
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Fragment molecular orbital method: application to polypeptides
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Nakano, Tatsuya; Kaminuma, Tsuguchika; Sato, Toshiyuki
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Virtual Orbital Many-Body Expansions: A Possible Route towards the Full Configuration Interaction Limit
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Eriksen, Janus J.; Lipparini, Filippo; Gauss, Jürgen
The Journal of Physical Chemistry Letters, Vol. 8, Issue 18
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Harnessing desktop computers for ab initio calculation of vibrational IR/Raman spectra of large molecules
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Khire, Subodh S.; Sahu, Nityananda; Gadre, Shridhar R.
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Ab initio molecular dynamics of liquid water using embedded-fragment second-order many-body perturbation theory towards its accurate property prediction
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Willow, Soohaeng Yoo; Salim, Michael A.; Kim, Kwang S.
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Nakata, Hiroya; Fedorov, Dmitri G.
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Scalable Electron Correlation Methods. 3. Efficient and Accurate Parallel Local Coupled Cluster with Pair Natural Orbitals (PNO-LCCSD)
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Schwilk, Max; Ma, Qianli; Köppl, Christoph
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Hybrid Distributed/Shared Memory Model for the RI-MP2 Method in the Fragment Molecular Orbital Framework
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Pham, Buu Q.; Gordon, Mark S.
Journal of Chemical Theory and Computation, Vol. 15, Issue 10
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A generalized many-body expansion and a unified view of fragment-based methods in electronic structure theory
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Richard, Ryan M.; Herbert, John M.
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An Efficient Implementation of the Generalized Energy-Based Fragmentation Approach for General Large Molecules
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Hua, Shugui; Hua, Weijie; Li, Shuhua
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Gillan, M. J.; Alfè, D.; Bygrave, P. J.
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Theoretical Study of Protein–Ligand Interactions Using the Molecules-in-Molecules Fragmentation-Based Method
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Thapa, Bishnu; Beckett, Daniel; Erickson, Jon
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Richard, Ryan M.; Lao, Ka Un; Herbert, John M.
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Assessment of the Performance of the M05−2X and M06−2X Exchange-Correlation Functionals for Noncovalent Interactions in Biomolecules
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Hohenstein, Edward G.; Chill, Samuel T.; Sherrill, C. David
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Liu, Kuan-Yu; Liu, Jie; Herbert, John M.
Journal of Computational Chemistry, Vol. 38, Issue 19
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The Fragment Molecular Orbital Method for Geometry Optimizations of Polypeptides and Proteins
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Fedorov, Dmitri G.; Ishida, Toyokazu; Uebayasi, Masami
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Density-Functional Tight-Binding Combined with the Fragment Molecular Orbital Method
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Nishimoto, Yoshio; Fedorov, Dmitri G.; Irle, Stephan
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Efficient and Accurate Fragmentation Methods
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Pruitt, Spencer R.; Bertoni, Colleen; Brorsen, Kurt R.
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Kitaura, Kazuo; Ikeo, Eiji; Asada, Toshio
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Li, Shuhua; Shen, Jun; Li, Wei
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Fang, Tao; Li, Wei; Gu, Fangwei
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Many-Body Energy Decomposition with Basis Set Superposition Error Corrections
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Mayer, István; Bakó, Imre
Journal of Chemical Theory and Computation, Vol. 13, Issue 5
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Periodic boundary conditions for QM/MM calculations: Ewald summation for extended Gaussian basis sets
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Holden, Zachary C.; Richard, Ryan M.; Herbert, John M.
The Journal of Chemical Physics, Vol. 139, Issue 24
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Assessment of Fragmentation Strategies for Large Proteins Using the Multilayer Molecules-in-Molecules Approach
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Thapa, Bishnu; Beckett, Daniel; Jovan Jose, K. V.
Journal of Chemical Theory and Computation, Vol. 14, Issue 3
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The variational explicit polarization potential and analytical first derivative of energy: Towards a next generation force field
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Xie, Wangshen; Song, Lingchun; Truhlar, Donald G.
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Sexton, Thomas More; Tschumper, Gregory S.
Taylor & Francis
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Calculating excited states of molecular aggregates by the renormalized excitonic method
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Citation Formats

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Fast electron correlation methods for molecular clusters without basis set superposition errors journal, February 2008

Locally dense basis sets for chemical shift calculations journal, July 1989

Fragment molecular orbital method: use of approximate electrostatic potential journal, January 2002

Local correlation methods for solids: Comparison of incremental and periodic correlation calculations for the argon fcc crystal journal, June 2011

Second order Møller-Plesset perturbation theory based upon the fragment molecular orbital method journal, January 2004

Toward an Accurate and Inexpensive Estimation of CCSD(T)/CBS Binding Energies of Large Water Clusters journal, July 2016

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Ice Ih anomalies: Thermal contraction, anomalous volume isotope effect, and pressure-induced amorphization journal, May 2016

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Rapid computation of intermolecular interactions in molecular and ionic clusters: self-consistent polarization plus symmetry-adapted perturbation theory journal, January 2012

van der Waals interaction potentials: Many-body basis set superposition effects journal, October 1983

Evaluation of full valence correlation energies and gradients journal, June 2019

Structure of the gas-phase glycine tripeptide journal, January 2010

Fragment-Localized Kohn−Sham Orbitals via a Singles Configuration-Interaction Procedure and Application to Local Properties and Intermolecular Energy Decomposition Analysis journal, November 2008

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Correlation energy of diamond journal, September 1992

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Derivatives of the approximated electrostatic potentials in the fragment molecular orbital method journal, June 2009

Benchmark Relative Energies for Large Water Clusters with the Generalized Energy-Based Fragmentation Method journal, May 2017

Acetylene aggregates via cluster-building algorithm and molecular tailoring approach journal, February 2012

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Prediction of organic molecular crystal geometries from MP2-level fragment quantum mechanical/molecular mechanical calculations journal, November 2012

Large-Scale MP2 Calculations on the Blue Gene Architecture Using the Fragment Molecular Orbital Method journal, December 2011

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The fragment molecular orbital and systematic molecular fragmentation methods applied to water clusters journal, January 2012

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Improved Cluster-in-Molecule Local Correlation Approach for Electron Correlation Calculation of Large Systems journal, June 2014

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Scalable Electron Correlation Methods. 5. Parallel Perturbative Triples Correction for Explicitly Correlated Local Coupled Cluster with Pair Natural Orbitals
journal, December 2017

Fast electron correlation methods for molecular clusters without basis set superposition errors
journal, February 2008

Locally dense basis sets for chemical shift calculations
journal, July 1989

Fragment molecular orbital method: use of approximate electrostatic potential
journal, January 2002

Local correlation methods for solids: Comparison of incremental and periodic correlation calculations for the argon fcc crystal
journal, June 2011

Second order Møller-Plesset perturbation theory based upon the fragment molecular orbital method
journal, January 2004

Toward an Accurate and Inexpensive Estimation of CCSD(T)/CBS Binding Energies of Large Water Clusters
journal, July 2016

Two- and three-body, and relaxation energy terms in water clusters: Application of the hierarchical BSSE corrected decomposition scheme
journal, July 2019

Ice Ih anomalies: Thermal contraction, anomalous volume isotope effect, and pressure-induced amorphization
journal, May 2016

Accurate Composite and Fragment-Based Quantum Chemical Models for Large Molecules
journal, April 2015

Rapid computation of intermolecular interactions in molecular and ionic clusters: self-consistent polarization plus symmetry-adapted perturbation theory
journal, January 2012

van der Waals interaction potentials: Many-body basis set superposition effects
journal, October 1983

Evaluation of full valence correlation energies and gradients
journal, June 2019

Structure of the gas-phase glycine tripeptide
journal, January 2010

Fragment-Localized Kohn−Sham Orbitals via a Singles Configuration-Interaction Procedure and Application to Local Properties and Intermolecular Energy Decomposition Analysis
journal, November 2008

Approximating quantum many-body intermolecular interactions in molecular clusters using classical polarizable force fields
journal, April 2009

Correlation energy of diamond
journal, September 1992

Hydrogen-bond structure dynamics in bulk water: insights from ab initio simulations with coupled cluster theory
journal, January 2018

Derivatives of the approximated electrostatic potentials in the fragment molecular orbital method
journal, June 2009

Benchmark Relative Energies for Large Water Clusters with the Generalized Energy-Based Fragmentation Method
journal, May 2017

Acetylene aggregates via cluster-building algorithm and molecular tailoring approach
journal, February 2012

Anharmonic phonon quasiparticle theory of zero-point and thermal shifts in insulators: Heat capacity, bulk modulus, and thermal expansion
journal, August 2015

The Fragment Molecular Orbital Method Based on Long-Range Corrected Density-Functional Tight-Binding
journal, April 2019

Predicting finite-temperature properties of crystalline carbon dioxide from first principles with quantitative accuracy
journal, January 2016

Structures, energetics and vibrational spectra of (H ₂ O) ₃₂ clusters: a journey from model potentials to correlated theory
journal, July 2015

Energy-Based Molecular Fragmentation Methods
journal, April 2015

Incremental CCSD(T)(F12)|MP2-F12—A Method to Obtain Highly Accurate CCSD(T) Energies for Large Molecules
journal, December 2012

Achieving the CCSD(T) Basis-Set Limit in Sizable Molecular Clusters: Counterpoise Corrections for the Many-Body Expansion
journal, July 2013

Improved second-order Møller–Plesset perturbation theory by separate scaling of parallel- and antiparallel-spin pair correlation energies
journal, May 2003

Prediction of organic molecular crystal geometries from MP2-level fragment quantum mechanical/molecular mechanical calculations
journal, November 2012

Large-Scale MP2 Calculations on the Blue Gene Architecture Using the Fragment Molecular Orbital Method
journal, December 2011

Strong correlation in incremental full configuration interaction
journal, June 2017

Time-dependent density functional theory based upon the fragment molecular orbital method
journal, September 2007

N -body:Many-body QM:QM vibrational frequencies: Application to small hydrogen-bonded clusters
journal, November 2013

The fragment molecular orbital and systematic molecular fragmentation methods applied to water clusters
journal, January 2012

Approximating CCSD(T) Nuclear Magnetic Shielding Calculations Using Composite Methods
journal, October 2015

State of the Art in Counterpoise Theory
journal, November 1994

Density-based energy decomposition analysis for intermolecular interactions with variationally determined intermediate state energies
journal, October 2009

Improved Cluster-in-Molecule Local Correlation Approach for Electron Correlation Calculation of Large Systems
journal, June 2014

Low-Scaling Quantum Chemistry Approach to Excited-State Properties via an ab Initio Exciton Model: Application to Excitation Energy Transfer in a Self-Assembled Nanotube
journal, October 2015

A new near-linear scaling, efficient and accurate, open-shell domain-based local pair natural orbital coupled cluster singles and doubles theory
journal, April 2017

Linear-scaling self-consistent field methods for large molecules
journal, January 2013

Comments on “Further evidence for the existence of two kinds of H-bonds in ice Ih” by Li et al
journal, March 1995

Many-Body Expanded Full Configuration Interaction. II. Strongly Correlated Regime
journal, August 2019

Investigation of the hydrogen bonding in ice Ih by first-principles density function methods
journal, July 2012

Symmetry‐adapted perturbation theory based on density functional theory for noncovalent interactions
journal, August 2013

Counterpoise-corrected geometries and harmonic frequencies of N -body clusters: Application to (HF)n (n=3,4)
journal, January 2003

Ab Initio NMR Chemical Shift Calculations Using Fragment Molecular Orbitals and Locally Dense Basis Sets
journal, October 2016

A Fragment Quantum Mechanical Method for Metalloproteins
journal, November 2018

Local Amide I Mode Frequencies and Coupling Constants in Polypeptides
journal, August 2003

The individual and collective effects of exact exchange and dispersion interactions on the ab initio structure of liquid water
journal, August 2014

Vibrational studies on ${CO}_{2}$ up to 40 GPa by Raman spectroscopy at room temperature
journal, January 1998

Simulations of Raman Spectra Using the Fragment Molecular Orbital Method
journal, July 2014

Analytic energy gradient for second-order Møller-Plesset perturbation theory based on the fragment molecular orbital method
journal, July 2011

When are Many-Body Effects Significant?
journal, November 2016

Localizability of dynamic electron correlation
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