Journal ArticleDOI
Advances in methods and algorithms in a modern quantum chemistry program package
Yihan Shao,Laszlo Fusti Molnar,Yousung Jung,Jörg Kussmann,Christian Ochsenfeld,Shawn T. Brown,Andrew T. B. Gilbert,Lyudmila V. Slipchenko,Sergey V. Levchenko,Darragh P. O’Neill,Robert A. DiStasio,Rohini C. Lochan,Tao Wang,Gregory J. O. Beran,Nicholas A. Besley,John M. Herbert,Ching Yeh Lin,Troy Van Voorhis,Siu Hung Chien,Alexander J. Sodt,Ryan P. Steele,Vitaly A. Rassolov,Paul E. Maslen,Prakashan P. Korambath,Ross D. Adamson,Brian Austin,Jon Baker,Edward F. C. Byrd,Holger Dachsel,Robert J. Doerksen,Andreas Dreuw,Barry D. Dunietz,Anthony D. Dutoi,Thomas R. Furlani,Steven R. Gwaltney,Andreas Heyden,So Hirata,Chao-Ping Hsu,Gary S. Kedziora,Rustam Z. Khalliulin,Phil Klunzinger,Aaron M. Lee,Michael S. Lee,WanZhen Liang,Itay Lotan,Nikhil Nair,Baron Peters,Emil Proynov,Piotr A. Pieniazek,Young Min Rhee,Jim Ritchie,Edina Rosta,C. David Sherrill,Andrew C. Simmonett,Joseph E. Subotnik,H. Lee Woodcock,Weimin Zhang,Alexis T. Bell,Arup K. Chakraborty,Daniel M. Chipman,Frerich J. Keil,Arieh Warshel,Warren J. Hehre,Henry F. Schaefer,Jing Kong,Anna I. Krylov,Peter Gill,Martin Head-Gordon,Martin Head-Gordon +68 more
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TLDR
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.Abstract:
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.read more
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Accurate Molecular Crystal Lattice Energies from a Fragment QM/MM Approach with On-the-Fly Ab Initio Force Field Parametrization.
Shuhao Wen,Gregory J. O. Beran +1 more
TL;DR: This QM/MM fragment model reproduces full periodic MP2 lattice energies to within a couple kJ/mol at substantially reduced cost and Axilrod-Teller-Muto three-body dispersion energy plays a nontrivial role in several of the molecular crystals studied here.
Journal ArticleDOI
Heuristics-Guided Exploration of Reaction Mechanisms
TL;DR: A computational protocol is presented that constructs chemical reaction networks in a parallelized and automated manner and applies it to the Schrock dinitrogen-fixation catalyst to study alternative pathways of catalytic ammonia production.
Journal ArticleDOI
molSimplify: A toolkit for automating discovery in inorganic chemistry
TL;DR: An automated, open source toolkit for the first‐principles screening and discovery of new inorganic molecules and intermolecular complexes is presented through a divide‐and‐conquer tactic that flexibly combines force‐field preoptimization of organic fragments with alignment to first‐ Prussian trained metal‐ligand distances.
Journal ArticleDOI
Divide and conquer hartree-fock calculations on proteins
Xiao He,Kenneth M. Merz +1 more
TL;DR: The implementation of the divide-and-conquer (DC) algorithm, an algorithm with the potential to aid the achievement of true linear scaling within Hartree-Fock (HF) theory is revisited and a fragment-based initial guess using molecular fractionation with conjugated caps (MFCC) method significantly reduces the number of SCF cycles.
Journal ArticleDOI
Quantum Chemistry Behind Bioimaging: Insights from Ab Initio Studies of Fluorescent Proteins and Their Chromophores
Ksenia B. Bravaya,Bella L. Grigorenko,Alexander V. Nemukhin,Alexander V. Nemukhin,Anna I. Krylov +4 more
TL;DR: It is demonstrated that a three-center Hückel-like model provides a useful framework for understanding properties of FPs, and can explain changes in absorption wavelength upon protonation or other structural modifications of the chromophore, the magnitude of transition dipole moment, barriers to isomerization, and even non-Condon effects in one- and two-photon absorption.
References
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Journal ArticleDOI
Density‐functional thermochemistry. III. The role of exact exchange
TL;DR: In this article, a semi-empirical exchange correlation functional with local spin density, gradient, and exact exchange terms was proposed. But this functional performed significantly better than previous functionals with gradient corrections only, and fits experimental atomization energies with an impressively small average absolute deviation of 2.4 kcal/mol.
Journal ArticleDOI
Gaussian basis sets for use in correlated molecular calculations. I. The atoms boron through neon and hydrogen
TL;DR: In this paper, a detailed study of correlation effects in the oxygen atom was conducted, and it was shown that primitive basis sets of primitive Gaussian functions effectively and efficiently describe correlation effects.
疟原虫var基因转换速率变化导致抗原变异[英]/Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A
TL;DR: PfPMP1)与感染红细胞、树突状组胞以及胎盘的单个或多个受体作用,在黏附及免疫逃避中起关键的作�ly.
Journal ArticleDOI
General atomic and molecular electronic structure system
Michael W. Schmidt,Kim K. Baldridge,Jerry A. Boatz,Steven T. Elbert,Mark S. Gordon,Jan H. Jensen,Shiro Koseki,Nikita Matsunaga,Kiet A. Nguyen,Shujun Su,Theresa L. Windus,Michel Dupuis,John A. Montgomery +12 more
TL;DR: A description of the ab initio quantum chemistry package GAMESS, which can be treated with wave functions ranging from the simplest closed‐shell case up to a general MCSCF case, permitting calculations at the necessary level of sophistication.