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

Journal Article · 04 November 2019 · Journal of Chemical Physics

DOI: https://doi.org/10.1063/1.5126216 · OSTI ID:1604454

^[1]

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

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.

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

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

Grant/Contract Number:: SC0008850; SC0008550

OSTI ID:: 1604454

Alternate ID(s):: OSTI ID: 1573087

Journal Information:: Journal of Chemical Physics, Vol. 151, Issue 17; ISSN 0021-9606

Publisher:: American Institute of Physics (AIP)Copyright Statement

Country of Publication:: United States

Language:: English

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Energy benchmarks for water clusters and ice structures from an embedded many-body expansion Gillan, M. J.; Alfè, D.; Bygrave, P. J. The Journal of Chemical Physics, Vol. 139, Issue 11 https://doi.org/10.1063/1.4820906	journal	September 2013
Theoretical Study of Protein–Ligand Interactions Using the Molecules-in-Molecules Fragmentation-Based Method Thapa, Bishnu; Beckett, Daniel; Erickson, Jon Journal of Chemical Theory and Computation, Vol. 14, Issue 10 https://doi.org/10.1021/acs.jctc.8b00531	journal	August 2018
Combining Quantum Mechanics Methods with Molecular Mechanics Methods in ONIOM Vreven, Thom; Byun, K. Suzie; Komáromi, István Journal of Chemical Theory and Computation, Vol. 2, Issue 3 https://doi.org/10.1021/ct050289g	journal	May 2006
Understanding the many-body expansion for large systems. I. Precision considerations Richard, Ryan M.; Lao, Ka Un; Herbert, John M. The Journal of Chemical Physics, Vol. 141, Issue 1 https://doi.org/10.1063/1.4885846	journal	July 2014
Assessment of the Performance of the M05−2X and M06−2X Exchange-Correlation Functionals for Noncovalent Interactions in Biomolecules Hohenstein, Edward G.; Chill, Samuel T.; Sherrill, C. David Journal of Chemical Theory and Computation, Vol. 4, Issue 12 https://doi.org/10.1021/ct800308k	journal	November 2008
Accuracy of finite-difference harmonic frequencies in density functional theory Liu, Kuan-Yu; Liu, Jie; Herbert, John M. Journal of Computational Chemistry, Vol. 38, Issue 19 https://doi.org/10.1002/jcc.24811	journal	May 2017
The Fragment Molecular Orbital Method for Geometry Optimizations of Polypeptides and Proteins Fedorov, Dmitri G.; Ishida, Toyokazu; Uebayasi, Masami The Journal of Physical Chemistry A, Vol. 111, Issue 14 https://doi.org/10.1021/jp0671042	journal	April 2007
Density-Functional Tight-Binding Combined with the Fragment Molecular Orbital Method Nishimoto, Yoshio; Fedorov, Dmitri G.; Irle, Stephan Journal of Chemical Theory and Computation, Vol. 10, Issue 11 https://doi.org/10.1021/ct500489d	journal	October 2014
Efficient and Accurate Fragmentation Methods Pruitt, Spencer R.; Bertoni, Colleen; Brorsen, Kurt R. Accounts of Chemical Research, Vol. 47, Issue 9 https://doi.org/10.1021/ar500097m	journal	May 2014
An efficient implementation of the “cluster-in-molecule” approach for local electron correlation calculations Li, Shuhua; Shen, Jun; Li, Wei The Journal of Chemical Physics, Vol. 125, Issue 7 https://doi.org/10.1063/1.2244566	journal	August 2006
Accurate Prediction of Lattice Energies and Structures of Molecular Crystals with Molecular Quantum Chemistry Methods Fang, Tao; Li, Wei; Gu, Fangwei Journal of Chemical Theory and Computation, Vol. 11, Issue 1 https://doi.org/10.1021/ct500833k	journal	December 2014
Many-Body Energy Decomposition with Basis Set Superposition Error Corrections Mayer, István; Bakó, Imre Journal of Chemical Theory and Computation, Vol. 13, Issue 5 https://doi.org/10.1021/acs.jctc.7b00303	journal	April 2017
Periodic boundary conditions for QM/MM calculations: Ewald summation for extended Gaussian basis sets Holden, Zachary C.; Richard, Ryan M.; Herbert, John M. The Journal of Chemical Physics, Vol. 139, Issue 24 https://doi.org/10.1063/1.4850655	journal	December 2013
Assessment of Fragmentation Strategies for Large Proteins Using the Multilayer Molecules-in-Molecules Approach Thapa, Bishnu; Beckett, Daniel; Jovan Jose, K. V. Journal of Chemical Theory and Computation, Vol. 14, Issue 3 https://doi.org/10.1021/acs.jctc.7b01198	journal	February 2018
The variational explicit polarization potential and analytical first derivative of energy: Towards a next generation force field Xie, Wangshen; Song, Lingchun; Truhlar, Donald G. The Journal of Chemical Physics, Vol. 128, Issue 23 https://doi.org/10.1063/1.2936122	journal	June 2008
2-body:Many-body QM:QM study of structures, energetics, and vibrational frequencies for microhydrated halide ions Sexton, Thomas More; Tschumper, Gregory S. Taylor & Francis https://doi.org/10.6084/m9.figshare.7445942.v1	text	January 2018
Calculating excited states of molecular aggregates by the renormalized excitonic method Ma, Yingjin; Ma, Haibo arXiv https://doi.org/10.48550/arxiv.1303.0617	text	January 2013

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