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      Discovering chemistry with an ab initio nanoreactor

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          Abstract

          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. 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.

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          Advances in methods and algorithms in a modern quantum chemistry program package.

          Advances in theory and algorithms for electronic structure calculations must be incorporated into program packages to enable them to become routinely used by the broader chemical community. This work reviews advances made over the past five years or so that constitute the major improvements contained in a new release of the Q-Chem quantum chemistry package, together with illustrative timings and applications. Specific developments discussed include fast methods for density functional theory calculations, linear scaling evaluation of energies, NMR chemical shifts and electric properties, fast auxiliary basis function methods for correlated energies and gradients, equation-of-motion coupled cluster methods for ground and excited states, geminal wavefunctions, embedding methods and techniques for exploring potential energy surfaces.
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            Earth's early atmosphere.

            J. Kasting (1993)
            Ideas about atmospheric composition and climate on the early Earth have evolved considerably over the last 30 years, but many uncertainties still remain. It is generally agreed that the atmosphere contained little or no free oxygen initially and that oxygen concentrations increased markedly near 2.0 billion years ago, but the precise timing of and reasons for its rise remain unexplained. Likewise, it is usually conceded that the atmospheric greenhouse effect must have been higher in the past to offset reduced solar luminosity, but the levels of atmospheric carbon dioxide and other greenhouse gases required remain speculative. A better understanding of past atmospheric evolution is important to understanding the evolution of life and to predicting whether Earth-like planets might exist elsewhere in the galaxy.
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              Quantum Chemistry on Graphical Processing Units. 3. Analytical Energy Gradients, Geometry Optimization, and First Principles Molecular Dynamics.

              We demonstrate that a video gaming machine containing two consumer graphical cards can outpace a state-of-the-art quad-core processor workstation by a factor of more than 180× in Hartree-Fock energy + gradient calculations. Such performance makes it possible to run large scale Hartree-Fock and Density Functional Theory calculations, which typically require hundreds of traditional processor cores, on a single workstation. Benchmark Born-Oppenheimer molecular dynamics simulations are performed on two molecular systems using the 3-21G basis set - a hydronium ion solvated by 30 waters (94 atoms, 405 basis functions) and an aspartic acid molecule solvated by 147 waters (457 atoms, 2014 basis functions). Our GPU implementation can perform 27 ps/day and 0.7 ps/day of ab initio molecular dynamics simulation on a single desktop computer for these systems.
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                Author and article information

                Journal
                101499734
                35773
                Nat Chem
                Nat Chem
                Nature chemistry
                1755-4330
                1755-4349
                30 September 2014
                02 November 2014
                December 2014
                01 June 2015
                : 6
                : 12
                : 1044-1048
                Affiliations
                [1 ]Department of Chemistry, Stanford University, Stanford, CA 94305
                [2 ]Advanced Micro Devices, Sunnyvale, CA 94088
                Author notes
                [* ]To whom correspondence should be addressed: toddjmartinez@ 123456gmail.com
                Article
                NIHMS631486
                10.1038/nchem.2099
                4239668
                25411881
                3efece0e-430c-44f2-b8c5-6dc82d0d59a0
                History
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                Chemistry
                Chemistry

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