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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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
Multiwfn: a multifunctional wavefunction analyzer.
Tian Lu,Feiwu Chen +1 more
TL;DR: Five practical examples involving a wide variety of systems and analysis methods are given to illustrate the usefulness of Multiwfn, a multifunctional program for wavefunction analysis.
Journal ArticleDOI
Long-range corrected hybrid density functionals with damped atom–atom dispersion corrections
Jeng-Da Chai,Martin Head-Gordon +1 more
TL;DR: The re-optimization of a recently proposed long-range corrected hybrid density functional, omegaB97X-D, to include empirical atom-atom dispersion corrections yields satisfactory accuracy for thermochemistry, kinetics, and non-covalent interactions.
Journal ArticleDOI
CHARMM: the biomolecular simulation program.
Bernard R. Brooks,Charles L. Brooks,Alexander D. MacKerell,Lennart Nilsson,Robert J. Petrella,Benoît Roux,Youngdo Won,Georgios Archontis,Christian Bartels,Stefan Boresch,Amedeo Caflisch,Leo S. D. Caves,Qiang Cui,Aaron R. Dinner,Michael Feig,Stefan Fischer,Jiali Gao,Milan Hodošček,Wonpil Im,K. Kuczera,Themis Lazaridis,Jianpeng Ma,V. Ovchinnikov,Emanuele Paci,Richard W. Pastor,Carol Beth Post,Jingzhi Pu,M. Schaefer,Bruce Tidor,Richard M. Venable,H. L. Woodcock,Xiongwu Wu,Wei Yang,Darrin M. York,Martin Karplus,Martin Karplus +35 more
TL;DR: An overview of the CHARMM program as it exists today is provided with an emphasis on developments since the publication of the original CHARMM article in 1983.
Journal Article
Long-Range Corrected Hybrid Density Functionals with Damped Atom-Atom Dispersion Corrections
TL;DR: Chai and Head-Gordon as discussed by the authors proposed a long-range corrected (LC) hybrid density functional with Damped Atom-Atom Dispersion corrections, which is called ωB97X-D.
References
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Journal ArticleDOI
Improved tangent estimate in the nudged elastic band method for finding minimum energy paths and saddle points
Graeme Henkelman,Hannes Jónsson +1 more
TL;DR: An improved way of estimating the local tangent in the nudged elastic band method for finding minimum energy paths is presented, and examples given where a complementary method, the dimer method, is used to efficiently converge to the saddle point.
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Efficient implementation of the gauge-independent atomic orbital method for NMR chemical shift calculations
Journal ArticleDOI
A full coupled‐cluster singles and doubles model: The inclusion of disconnected triples
TL;DR: The coupled cluster singles and doubles model (CCSD) as discussed by the authors is derived algebraically, presenting the full set of equations for a general reference function explicitly in spin-orbital form, and the computational implementation of the CCSD model, which involves cubic and quartic terms, is discussed and results are compared with full CI calculations for H2O and BeH2.
Journal ArticleDOI
Molecular Interactions in Solution: An Overview of Methods Based on Continuous Distributions of the Solvent
Jacopo Tomasi,Maurizio Persico +1 more
Journal ArticleDOI
Theoretical studies of enzymic reactions: Dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme
TL;DR: Electrostatic stabilization is an important factor in increasing the rate of the reaction step that leads to the formation of the carbonium ion intermediate, found in the cleavage of a glycosidic bond by lysozyme.