skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: 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 Laboratory (SLAC), Menlo Park, CA (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Basic Energy Sciences (BES); National Science Foundation (NSF); National Institutes of Health (NIH)
Grant/Contract Number:
OCI-1047577; U54 GM072970
OSTI ID:
1293892
Journal Information:
Nature Chemistry, Vol. 6, Issue 12; ISSN 1755-4330
Publisher:
Nature Publishing GroupCopyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 238 works
Citation information provided by
Web of Science

References (48)

Quantum Chemistry on Graphical Processing Units. 3. Analytical Energy Gradients, Geometry Optimization, and First Principles Molecular Dynamics journal August 2009
Charge Transfer and Polarization in Solvated Proteins from Ab Initio Molecular Dynamics journal June 2011
Dynamic Precision for Electron Repulsion Integral Evaluation on Graphical Processing Units (GPUs) journal March 2011
Ab Initio Quantum Chemistry for Protein Structures journal October 2012
Formation of Hollow Nanocrystals Through the Nanoscale Kirkendall Effect journal April 2004
Metadynamics as a Tool for Exploring Free Energy Landscapes of Chemical Reactions journal February 2006
Efficient Exploration of Reactive Potential Energy Surfaces Using Car-Parrinello Molecular Dynamics journal June 2003
Automated discovery of chemically reasonable elementary reaction steps journal March 2013
Complex Chemical Reaction Networks from Heuristics-Aided Quantum Chemistry journal February 2014
Stochastic Voyages into Uncharted Chemical Space Produce a Representative Library of All Possible Drug-Like Compounds journal May 2013
Toward Predicting Full Catalytic Cycle Using Automatic Reaction Path Search Method: A Case Study on HCo(CO) 3 -Catalyzed Hydroformylation journal January 2012
Archetypal energy landscapes journal August 1998
Synthesis of glycine-containing complexes in impacts of comets on early Earth journal September 2010
Ab initio simulation of the equation of state and kinetics of shocked water journal March 2009
Solid-State Polymerization of Acetylene under Pressure: Ab Initio Simulation journal March 1997
An examination of intrinsic errors in electronic structure methods using the Environmental Molecular Sciences Laboratory computational results database and the Gaussian-2 set journal January 1998
General Performance of Density Functionals journal October 2007
High-accuracy extrapolated ab initio thermochemistry. III. Additional improvements and overview journal March 2008
Organic Compound Synthes on the Primitive Eart: Several questions about the origin of life have been answered, but much remains to be studied journal July 1959
Solid State Polymerization of Acetylene at High Pressure and Low Temperature journal August 2000
FT-IR Study of the Solid State Polymerization of Acetylene under Pressure journal January 1996
Photodynamics in Complex Environments: Ab Initio Multiple Spawning Quantum Mechanical/Molecular Mechanical Dynamics † journal March 2009
Pathways for the formation and evolution of peptides in prebiotic environments journal January 2012
Molecules Detected in Interstellar Space book January 2011
Chemical evolution of biomolecule building blocks. Can thermodynamics explain the accumulation of glycine in the prebiotic ocean? journal January 2011
Gas-phase reaction of N 2 O 5 with water vapor: Importance of heterogeneous hydrolysis of N 2 O 5 and surface desorption of HNO 3 in a large Teflon chamber journal June 1998
Earth's early atmosphere journal February 1993
A Reassessment of Prebiotic Organic Synthesis in Neutral Planetary Atmospheres journal January 2008
Excited-State Electronic Structure with Configuration Interaction Singles and Tamm–Dancoff Time-Dependent Density Functional Theory on Graphical Processing Units journal May 2011
Generating Efficient Quantum Chemistry Codes for Novel Architectures journal November 2012
Quantum Chemistry on Graphical Processing Units. 1. Strategies for Two-Electron Integral Evaluation journal January 2008
Quantum Chemistry on Graphical Processing Units. 2. Direct Self-Consistent-Field Implementation journal March 2009
A ?Level-Shifting? method for converging closed shell Hartree-Fock wave functions journal July 1973
Accelerating self-consistent field convergence with the augmented Roothaan–Hall energy function journal February 2010
Convergence acceleration of iterative sequences. the case of scf iteration journal July 1980
Density‐functional thermochemistry. III. The role of exact exchange journal April 1993
A Standard Set of Pericyclic Reactions of Hydrocarbons for the Benchmarking of Computational Methods:  The Performance of ab Initio, Density Functional, CASSCF, CASPT2, and CBS-QB3 Methods for the Prediction of Activation Barriers, Reaction Energetics, and Transition State Geometries journal December 2003
Energy landscapes of nucleophilic substitution reactions: A comparison of density functional theory and coupled cluster methods: Energy Landscapes of S journal March 2007
Benchmark variational coupled cluster doubles results journal November 2000
Prediction of Reaction Barriers and Thermochemical Properties with Explicitly Correlated Coupled-Cluster Methods: A Basis Set Assessment journal August 2012
A growing string method for determining transition states: Comparison to the nudged elastic band and string methods journal May 2004
Advances in methods and algorithms in a modern quantum chemistry program package journal January 2006
Metadynamics as a Tool for Exploring Free Energy Landscapes of Chemical Reactions journal April 2006
Ion conformation and orientational order in a dicationic ionic liquid crystal studied by solid-state nuclear magnetic resonance spectroscopy journal March 2021
Earth's early atmosphere journal December 1984
Efficient Exploration of Reactive Potential Energy Surfaces Using Car-Parrinello Molecular Dynamics text January 2003
Earth's Early Atmosphere journal January 1987
Earth's Early Atmosphere journal January 1987

Cited By (38)

Computational Chemistry: The Fate of Current Methods and Future Challenges journal December 2017
Operando Modeling of Multicomponent Reactive Solutions in Homogeneous Catalysis: from Non‐standard Free Energies to Reaction Network Control journal December 2019
Theory-Based Extension of the Catalyst Scope in the Base-Catalyzed Hydrogenation of Ketones: RCOOH-Catalyzed Hydrogenation of Carbonyl Compounds with H 2 Involving a Proton Shuttle journal December 2017
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
Benchmarking density functional tight binding models for barrier heights and reaction energetics of organic molecules journal July 2017
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
Computational exploration of Pd-catalyzed C-H bond activation reactions journal September 2018
Semiempirical molecular orbital models based on the neglect of diatomic differential overlap approximation journal October 2018
Spin-inversion mechanisms in the reactions of transition metal cations (Sc + , Ti + , V + , Cr + , Mn + , Fe + , Co + , Ni + , and Cu + ) with OCS in the gas phase: A perspective from automated reaction path search calculations journal January 2019
vdW‐TSSCDS—An automated and global procedure for the computation of stationary points on intermolecular potential energy surfaces journal June 2019
Exploring the Chemistry of Low‐Temperature Ignition by Pressure‐Accelerated Dynamics journal January 2020
Theory and applications of surface micro‐kinetics in the rational design of catalysts using density functional theory calculations journal June 2017
Reactive molecular dynamics: From small molecules to proteins journal August 2018
Hemiaminal route for the formation of interstellar glycine: a computational study journal November 2019
Comparing quantitative prediction methods for the discovery of small-molecule chiral catalysts journal October 2018
A Novel Method for Calculation of Molecular Energies and Charge Distributions by Thermodynamic Formalization journal December 2019
A fast neural network approach for direct covariant forces prediction in complex multi-element extended systems journal September 2019
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
Fast screening of homogeneous catalysis mechanisms using graph-driven searches and approximate quantum chemistry journal January 2019
Simulated evolution of fluorophores for light emitting diodes journal March 2015
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
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
Semiempirical Molecular Orbital Models based on the Neglect of Diatomic Differential Overlap Approximation text January 2018
Interactive molecular dynamics in virtual reality from quantum chemistry to drug binding: An open-source multi-person framework text January 2019

Similar Records

Ab Initio Reactive Computer Aided Molecular Design
Journal Article · Tue Mar 21 00:00:00 EDT 2017 · Accounts of Chemical Research · OSTI ID:1293892
Ab initio study of phosphaalkenes
Miscellaneous · Wed Jan 01 00:00:00 EST 1992 · OSTI ID:1293892
Perspective on ab initio phonon thermal transport
Journal Article · Mon Aug 05 00:00:00 EDT 2019 · Journal of Applied Physics · OSTI ID:1293892
+1 more

Related Subjects

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