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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:
ORCiD logo [1]
  1. The Ohio State Univ., Columbus, OH (United States)
Publication Date:
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

Citation Formats

Herbert, John M. Fantasy versus reality in fragment-based quantum chemistry. United States: N. p., 2019. Web. doi:10.1063/1.5126216.
Herbert, John M. Fantasy versus reality in fragment-based quantum chemistry. United States. doi:https://doi.org/10.1063/1.5126216
Herbert, John M. Mon . "Fantasy versus reality in fragment-based quantum chemistry". United States. doi:https://doi.org/10.1063/1.5126216. https://www.osti.gov/servlets/purl/1604454.
@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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Ab initio molecular dynamics with intramolecular noncovalent interactions for unsolvated polypeptides
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Analytic gradient for the embedding potential with approximations in the fragment molecular orbital method
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Efficient vibrational analysis for unrestricted Hartree–Fock based on the fragment molecular orbital method
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Analytic second derivatives for the efficient electrostatic embedding in the fragment molecular orbital method
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Ab initio NMR chemical shift calculations on proteins using fragment molecular orbitals with electrostatic environment
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Simulations of Raman Spectra Using the Fragment Molecular Orbital Method
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Fragment molecular orbital method: analytical energy gradients
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The Fragment Molecular Orbital Method for Geometry Optimizations of Polypeptides and Proteins
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Derivatives of the approximated electrostatic potentials in the fragment molecular orbital method
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Importance of the hybrid orbital operator derivative term for the energy gradient in the fragment molecular orbital method
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Fragment molecular orbital-based molecular dynamics (FMO-MD) method with MP2 gradient
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Energy gradients in combined fragment molecular orbital and polarizable continuum model (FMO/PCM) calculation
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Efficient Geometry Optimization of Large Molecular Systems in Solution Using the Fragment Molecular Orbital Method
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Simulations of infrared and Raman spectra in solution using the fragment molecular orbital method
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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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Explicit Polarization: A Quantum Mechanical Framework for Developing Next Generation Force Fields
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Fragment Molecular Orbital Molecular Dynamics with the Fully Analytic Energy Gradient
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Effective Fragment Molecular Orbital Method: A Merger of the Effective Fragment Potential and Fragment Molecular Orbital Methods
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The Effective Fragment Molecular Orbital Method for Fragments Connected by Covalent Bonds
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Analytic Gradients for the Effective Fragment Molecular Orbital Method
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The Effective Fragment Potential Method:  A QM-Based MM Approach to Modeling Environmental Effects in Chemistry
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Noncovalent Interactions in Extended Systems Described by the Effective Fragment Potential Method: Theory and Application to Nucleobase Oligomers
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When are Many-Body Effects Significant?
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Water nanodroplets: Predictions of five model potentials
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Density-Functional Tight-Binding Combined with the Fragment Molecular Orbital Method
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The fragment molecular orbital method combined with density-functional tight-binding and the polarizable continuum model
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The Fragment Molecular Orbital Method Based on Long-Range Corrected Density-Functional Tight-Binding
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A Fragment Quantum Mechanical Method for Metalloproteins
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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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Assessment and acceleration of binding energy calculations for protein-ligand complexes by the fragment molecular orbital method
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Geometry Optimization of the Active Site of a Large System with the Fragment Molecular Orbital Method
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Molecules-in-molecules fragment-based method for the evaluation of Raman spectra of large molecules
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Vibrational Circular Dichroism Spectra for Large Molecules through Molecules-in-Molecules Fragment-Based Approach
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Surface-enhanced Raman scattering from polystyrene on gold clusters
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Infrared spectroscopy of proteins
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Local Amide I Mode Frequencies and Coupling Constants in Polypeptides
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Accuracy of finite-difference harmonic frequencies in density functional theory
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Ab Initio NMR Chemical Shift Calculations Using Fragment Molecular Orbitals and Locally Dense Basis Sets
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Application of the Systematic Molecular Fragmentation by Annihilation Method to ab Initio NMR Chemical Shift Calculations
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Approximating CCSD(T) Nuclear Magnetic Shielding Calculations Using Composite Methods
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Locally dense basis sets for chemical shift calculations
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Segmented Contracted Basis Sets Optimized for Nuclear Magnetic Shielding
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Calculating nuclear magnetic resonance shieldings using systematic molecular fragmentation by annihilation
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Protein NMR Chemical Shift Calculations Based on the Automated Fragmentation QM/MM Approach
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Fragment density functional theory calculation of NMR chemical shifts for proteins with implicit solvation
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Automated Fragmentation QM/MM Calculation of Amide Proton Chemical Shifts in Proteins with Explicit Solvent Model
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Fragment-Based Approach for the Evaluation of NMR Chemical Shifts for Large Biomolecules Incorporating the Effects of the Solvent Environment
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A new hierarchical parallelization scheme: Generalized distributed data interface (GDDI), and an application to the fragment molecular orbital method (FMO)
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Large-Scale MP2 Calculations on the Blue Gene Architecture Using the Fragment Molecular Orbital Method
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Hybrid Distributed/Shared Memory Model for the RI-MP2 Method in the Fragment Molecular Orbital Framework
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