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

Title: Ab Initio Reactive Computer Aided Molecular Design

Abstract

Few would dispute that theoretical chemistry tools can now provide keen insights into chemical phenomena. Yet the holy grail of efficient and reliable prediction of complex reactivity has remained elusive. Fortunately, recent advances in electronic structure theory based on the concepts of both element- and rank-sparsity, coupled with the emergence of new highly parallel computer architectures, have led to a significant increase in the time and length scales which can be simulated using first principles molecular dynamics. This then opens the possibility of new discovery-based approaches to chemical reactivity, such as the recently proposed ab initio nanoreactor. Here, we argue that due to these and other recent advances, the holy grail of computational discovery for complex chemical reactivity is rapidly coming within our reach.

Authors:
ORCiD logo [1]
  1. Stanford Univ., CA (United States). Dept. of Chemistry and PULSE Inst.; SLAC National Accelerator Lab., Menlo Park, CA (United States)
Publication Date:
Research Org.:
SLAC National Accelerator Lab., Menlo Park, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES); National Science Foundation (NSF)
OSTI Identifier:
1390717
Grant/Contract Number:  
AC02-76SF00515; N00014-14-1-0590; ACI-1450179
Resource Type:
Accepted Manuscript
Journal Name:
Accounts of Chemical Research
Additional Journal Information:
Journal Volume: 50; Journal Issue: 3; Journal ID: ISSN 0001-4842
Publisher:
American Chemical Society
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY

Citation Formats

Martínez, Todd J. Ab Initio Reactive Computer Aided Molecular Design. United States: N. p., 2017. Web. doi:10.1021/acs.accounts.7b00010.
Martínez, Todd J. Ab Initio Reactive Computer Aided Molecular Design. United States. https://doi.org/10.1021/acs.accounts.7b00010
Martínez, Todd J. Tue . "Ab Initio Reactive Computer Aided Molecular Design". United States. https://doi.org/10.1021/acs.accounts.7b00010. https://www.osti.gov/servlets/purl/1390717.
@article{osti_1390717,
title = {Ab Initio Reactive Computer Aided Molecular Design},
author = {Martínez, Todd J.},
abstractNote = {Few would dispute that theoretical chemistry tools can now provide keen insights into chemical phenomena. Yet the holy grail of efficient and reliable prediction of complex reactivity has remained elusive. Fortunately, recent advances in electronic structure theory based on the concepts of both element- and rank-sparsity, coupled with the emergence of new highly parallel computer architectures, have led to a significant increase in the time and length scales which can be simulated using first principles molecular dynamics. This then opens the possibility of new discovery-based approaches to chemical reactivity, such as the recently proposed ab initio nanoreactor. Here, we argue that due to these and other recent advances, the holy grail of computational discovery for complex chemical reactivity is rapidly coming within our reach.},
doi = {10.1021/acs.accounts.7b00010},
journal = {Accounts of Chemical Research},
number = 3,
volume = 50,
place = {United States},
year = {2017},
month = {3}
}

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

Citation Metrics:
Cited by: 14 works
Citation information provided by
Web of Science

Save / Share:

Works referenced in this record:

Computer-aided molecular design
journal, October 1987


Application of the PM6 method to modeling proteins
journal, December 2008


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

Coupled-cluster theory in quantum chemistry
journal, February 2007


Tuned Range-Separated Hybrids in Density Functional Theory
journal, March 2010


Principles for a direct SCF approach to LICAO - MO ab - initio calculations : Direct
journal, September 1982

  • Almlöf, J.; Faegri, K.; Korsell, K.
  • Journal of Computational Chemistry, Vol. 3, Issue 3
  • DOI: 10.1002/jcc.540030314

Tensor hypercontraction density fitting. I. Quartic scaling second- and third-order Møller-Plesset perturbation theory
journal, July 2012

  • Hohenstein, Edward G.; Parrish, Robert M.; Martínez, Todd J.
  • The Journal of Chemical Physics, Vol. 137, Issue 4
  • DOI: 10.1063/1.4732310

Quantum Chemistry on Graphical Processing Units. 1. Strategies for Two-Electron Integral Evaluation
journal, January 2008

  • Ufimtsev, Ivan S.; Martínez, Todd J.
  • Journal of Chemical Theory and Computation, Vol. 4, Issue 2
  • DOI: 10.1021/ct700268q

Efficient implementation of effective core potential integrals and gradients on graphical processing units
journal, July 2015

  • Song, Chenchen; Wang, Lee-Ping; Sachse, Torsten
  • The Journal of Chemical Physics, Vol. 143, Issue 1
  • DOI: 10.1063/1.4922844

Atomic orbital-based SOS-MP2 with tensor hypercontraction. I. GPU-based tensor construction and exploiting sparsity
journal, May 2016

  • Song, Chenchen; Martínez, Todd J.
  • The Journal of Chemical Physics, Vol. 144, Issue 17
  • DOI: 10.1063/1.4948438

Microscopic pressure-cooker model for studying molecules in confinement
journal, September 2014


Copper Coordination Features of Human Islet Amyloid Polypeptide: The Type 2 Diabetes Peptide
journal, September 2016


Charge Transfer and Polarization in Solvated Proteins from Ab Initio Molecular Dynamics
journal, June 2011

  • Ufimtsev, Ivan S.; Luehr, Nathan; Martinez, Todd J.
  • The Journal of Physical Chemistry Letters, Vol. 2, Issue 14
  • DOI: 10.1021/jz200697c

Ab Initio Quantum Chemistry for Protein Structures
journal, October 2012

  • Kulik, Heather J.; Luehr, Nathan; Ufimtsev, Ivan S.
  • The Journal of Physical Chemistry B, Vol. 116, Issue 41
  • DOI: 10.1021/jp307741u

Current Status of Transition-State Theory
journal, January 1996

  • Truhlar, Donald G.; Garrett, Bruce C.; Klippenstein, Stephen J.
  • The Journal of Physical Chemistry, Vol. 100, Issue 31
  • DOI: 10.1021/jp953748q

Ab Initio Molecular Dynamics with Explicit Solvent Reveals a Two-Step Pathway in the Frustrated Lewis Pair Reaction
journal, November 2015

  • Pu, Maoping; Privalov, Timofei
  • Chemistry - A European Journal, Vol. 21, Issue 49
  • DOI: 10.1002/chem.201502926

Rich Athermal Ground-State Chemistry Triggered by Dynamics through a Conical Intersection
journal, October 2016

  • Mignolet, Benoit; Curchod, Basile F. E.; Martínez, Todd J.
  • Angewandte Chemie International Edition, Vol. 55, Issue 48
  • DOI: 10.1002/anie.201607633

Computational Catalysis Using the Artificial Force Induced Reaction Method
journal, March 2016


Navigating molecular space for reaction mechanisms: an efficient, automated procedure
journal, March 2014


Complex Chemical Reaction Networks from Heuristics-Aided Quantum Chemistry
journal, February 2014

  • Rappoport, Dmitrij; Galvin, Cooper J.; Zubarev, Dmitry Yu.
  • Journal of Chemical Theory and Computation, Vol. 10, Issue 3
  • DOI: 10.1021/ct401004r

Discovering chemistry with an ab initio nanoreactor
journal, November 2014

  • Wang, Lee-Ping; Titov, Alexey; McGibbon, Robert
  • Nature Chemistry, Vol. 6, Issue 12
  • DOI: 10.1038/nchem.2099

Automated Discovery and Refinement of Reactive Molecular Dynamics Pathways
journal, January 2016

  • Wang, Lee-Ping; McGibbon, Robert T.; Pande, Vijay S.
  • Journal of Chemical Theory and Computation, Vol. 12, Issue 2
  • DOI: 10.1021/acs.jctc.5b00830

Escaping free-energy minima
journal, September 2002

  • Laio, A.; Parrinello, M.
  • Proceedings of the National Academy of Sciences, Vol. 99, Issue 20
  • DOI: 10.1073/pnas.202427399

Graph Theory Meets Ab Initio Molecular Dynamics: Atomic Structures and Transformations at the Nanoscale
journal, August 2011


Computing with feeling
journal, January 1977


A system for interactive molecular dynamics simulation
conference, January 2001

  • Stone, John E.; Gullingsrud, Justin; Schulten, Klaus
  • Proceedings of the 2001 symposium on Interactive 3D graphics - SI3D '01
  • DOI: 10.1145/364338.364398

Interactive Chemical Reactivity Exploration
journal, September 2014

  • Haag, Moritz P.; Vaucher, Alain C.; Bosson, Maël
  • ChemPhysChem, Vol. 15, Issue 15
  • DOI: 10.1002/cphc.201402342

Crystal Structure Determination of the Pentagonal-Pyramidal Hexamethylbenzene Dication C 6 (CH 3 ) 6 2+
journal, November 2016

  • Malischewski, Moritz; Seppelt, K.
  • Angewandte Chemie International Edition, Vol. 56, Issue 1
  • DOI: 10.1002/anie.201608795

Ab Initio Interactive Molecular Dynamics on Graphical Processing Units (GPUs)
journal, September 2015

  • Luehr, Nathan; Jin, Alex G. B.; Martínez, Todd J.
  • Journal of Chemical Theory and Computation, Vol. 11, Issue 10
  • DOI: 10.1021/acs.jctc.5b00419

Inverse design of molecules with optimal reactivity properties: acidity of 2-naphthol derivatives
journal, January 2012

  • De Vleeschouwer, Freija; Yang, Weitao; Beratan, David N.
  • Physical Chemistry Chemical Physics, Vol. 14, Issue 46
  • DOI: 10.1039/c2cp42623d

Computer-Assisted Synthetic Planning: The End of the Beginning
journal, April 2016

  • Szymkuć, Sara; Gajewska, Ewa P.; Klucznik, Tomasz
  • Angewandte Chemie International Edition, Vol. 55, Issue 20
  • DOI: 10.1002/anie.201506101

Computer-Assisted Design of Complex Organic Syntheses
journal, October 1969


Computer-assisted mechanistic evaluation of organic reactions. 1. Overview
journal, May 1980

  • Salatin, Timothy D.; Jorgensen, William L.
  • The Journal of Organic Chemistry, Vol. 45, Issue 11
  • DOI: 10.1021/jo01299a001

Computer-aided molecular design of solvents for accelerated reaction kinetics
journal, September 2013

  • Struebing, Heiko; Ganase, Zara; Karamertzanis, Panagiotis G.
  • Nature Chemistry, Vol. 5, Issue 11
  • DOI: 10.1038/nchem.1755

Works referencing / citing this record:

Water models for biomolecular simulations: Water models for biomolecular simulations
journal, November 2017

  • Onufriev, Alexey V.; Izadi, Saeed
  • Wiley Interdisciplinary Reviews: Computational Molecular Science, Vol. 8, Issue 2
  • DOI: 10.1002/wcms.1347

Computational Chemistry: The Fate of Current Methods and Future Challenges
journal, December 2017

  • Grimme, Stefan; Schreiner, Peter R.
  • Angewandte Chemie International Edition, Vol. 57, Issue 16
  • DOI: 10.1002/anie.201709943

Semiempirical molecular orbital models based on the neglect of diatomic differential overlap approximation
journal, October 2018

  • Husch, Tamara; Vaucher, Alain C.; Reiher, Markus
  • International Journal of Quantum Chemistry, Vol. 118, Issue 24
  • DOI: 10.1002/qua.25799

A quantitative uncertainty metric controls error in neural network-driven chemical discovery
journal, January 2019

  • Janet, Jon Paul; Duan, Chenru; Yang, Tzuhsiung
  • Chemical Science, Vol. 10, Issue 34
  • DOI: 10.1039/c9sc02298h

Making machine learning a useful tool in the accelerated discovery of transition metal complexes
journal, July 2019

  • Kulik, Heather J.
  • WIREs Computational Molecular Science, Vol. 10, Issue 1
  • DOI: 10.1002/wcms.1439

Enumeration of de novo inorganic complexes for chemical discovery and machine learning
journal, January 2020

  • Gugler, Stefan; Janet, Jon Paul; Kulik, Heather J.
  • Molecular Systems Design & Engineering, Vol. 5, Issue 1
  • DOI: 10.1039/c9me00069k