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Discovering chemistry with an ab initio nanoreactor

Journal Article · · Nature Chemistry
DOI:https://doi.org/10.1038/nchem.2099· OSTI ID:1293892
 [1];  [1];  [2];  [1];  [2];  [3]
  1. Stanford Univ., CA (United States). PULSE Inst.; Stanford Univ., CA (United States). Dept. of Chemistry
  2. Stanford Univ., CA (United States). Dept. of Chemistry
  3. Stanford Univ., CA (United States). PULSE Inst.; Stanford Univ., CA (United States). Dept. of Chemistry; SLAC National Accelerator Lab., Menlo Park, CA (United States)
+ Show Author Affiliations
Chemical understanding is driven by the experimental discovery of new compounds and reactivity, and is supported by theory and computation that provides detailed physical insight. While theoretical and computational studies have generally focused on specific processes or mechanistic hypotheses, recent methodological and computational advances harken the advent of their principal role in discovery. Here we report the development and application of the ab initio nanoreactor – a highly accelerated, first-principles molecular dynamics simulation of chemical reactions that discovers new molecules and mechanisms without preordained reaction coordinates or elementary steps. Using the nanoreactor we show new pathways for glycine synthesis from primitive compounds proposed to exist on the early Earth, providing new insight into the classic Urey-Miller experiment. Ultimately, these results highlight the emergence of theoretical and computational chemistry as a tool for discovery in addition to its traditional role of interpreting experimental findings.
Research Organization:
SLAC National Accelerator Lab., Menlo Park, CA (United States)
Sponsoring Organization:
National Inst. of Health (NIH); National Science Foundation (NSF); USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22)
OSTI ID:
1293892
Journal Information:
Nature Chemistry, Journal Name: Nature Chemistry Journal Issue: 12 Vol. 6; ISSN 1755-4330
Publisher:
Nature Publishing GroupCopyright Statement
Country of Publication:
United States
Language:
English

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Prebiotic Chemistry of HCN Tetramerization by Automated Reaction Search journal March 2018
Performance of heterogeneous computing with graphics processing unit and many integrated core for hartree potential calculations on a numerical grid journal July 2016
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Automated reaction path searches for spin-forbidden reactions: Automated Reaction Path Searches journal March 2018
tsscds2018: A code for automated discovery of chemical reaction mechanisms and solving the kinetics journal June 2018
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Semiempirical molecular orbital models based on the neglect of diatomic differential overlap approximation journal October 2018
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An automated method to find reaction mechanisms and solve the kinetics in organometallic catalysis journal January 2017
Efficient prediction of reaction paths through molecular graph and reaction network analysis journal January 2018
Quantum chemical studies of redox properties and conformational changes of a four-center iron CO 2 reduction electrocatalyst journal January 2018
CBS extrapolation in electronic structure pushed to the end: a revival of minimal and sub-minimal basis sets journal January 2018
CBS extrapolation of Hartree–Fock energy: Pople and Dunning basis sets hand-to-hand on the endeavour journal January 2019
Detailed kinetic model for hexyl sulfide pyrolysis and its desulfurization by supercritical water journal January 2019
ReacNetGenerator: an automatic reaction network generator for reactive molecular dynamics simulations journal January 2020
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Deep learning for molecular design—a review of the state of the art journal January 2019
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Optimal basis sets for CBS extrapolation of the correlation energy: oV x Z and oV( x + d )Z journal April 2019
Geodesic interpolation for reaction pathways journal April 2019
Interactive molecular dynamics in virtual reality from quantum chemistry to drug binding: An open-source multi-person framework journal June 2019
Autocorrelation of electronic wave-functions: a new approach for describing the evolution of electronic structure in the course of dynamics journal May 2018
A roadmap for electronic grade 2D materials journal January 2019
Synthetic transitions: towards a new synthesis journal August 2016
Role of Mineral Surfaces in Prebiotic Chemical Evolution. In Silico Quantum Mechanical Studies journal January 2019
A Trajectory-Based Method to Explore Reaction Mechanisms journal November 2018
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Interactive molecular dynamics in virtual reality from quantum chemistry to drug binding: An open-source multi-person framework text January 2019
Reactive molecular dynamics: From small molecules to proteins text January 2018
Autocorrelation of electronic wave-functions: a new approach for describing the evolution of electronic structure in the course of dynamics text January 2018

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Related Subjects

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
97 MATHEMATICS AND COMPUTING
Chemical origin of life
Chemical physics
Reaction kinetics and dynamics
Reaction mechanisms