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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The encapsulation of β-lapachone in 2-hydroxypropyl-β-cyclodextrin inclusion complex into liposomes: a physicochemical evaluation and molecular modeling approach.
Isabella Macário Ferro Cavalcanti,Elisângela A. M. Mendonça,Elisângela A. M. Mendonça,Mariane C. B. Lira,Sara B. Honrato,Celso A. Camara,Rosa Valéria da Silva Amorim,Josué Mendes Filho,Marcelo M. Rabello,Marcelo Zaldini Hernandes,Alejandro Ayala,Nereide S. Santos-Magalhães +11 more
TL;DR: Molecular modeling elucidates the formation of the inclusion complex, stabilized through hydrogen bonds, and the encapsulation ofβ-lap and β-lap:HPβ-CD into liposomes could provide an alternative means leading eventually to its use in cancer research.
Journal ArticleDOI
Dynamics on the Electronically Excited State Surface of the Bioluminescent Firefly Luciferase–Oxyluciferin System
Chang-ik Song,Young Min Rhee +1 more
TL;DR: It is revealed that the local chromophore-surrounding interaction patterns differ rather severely in the two states, and the importance of considering the time scales of the luminescence and the dynamics of the interaction is discussed.
Journal ArticleDOI
Engineering a nicotinamide mononucleotide redox cofactor system for biocatalysis.
William B. Black,Linyue Zhang,Wai Shun Mak,Sarah Maxel,Youtian Cui,Edward King,Bonnie Fong,Alicia Sanchez Martinez,Justin B. Siegel,Han Li +9 more
TL;DR: Redesign of a glucose dehydrogenase to use nicotinamide mononucleotide (NMN + ) instead of NAD(P) + enables the development of a noncanonical cofactor system that can be used to support redox chemistries both in vitro and in Escherichia coli.
Journal ArticleDOI
Characterization of the Reaction Path and Transition States for RNA Transphosphorylation Models from Theory and Experiment
TL;DR: Experimental and computational results are presented to characterize the mechanism of model phosphoryl transfer reactions that mimic RNA cleavage transesterification catalyzed by enzymes such as RNase A as well as endonucleolytic ribozymes such as the hammerhead, hairpin, hepatitis delta virus, VS and glmS RNAozymes.
Journal ArticleDOI
Ionization of cytosine monomer and dimer studied by VUV photoionization and electronic structure calculations.
TL;DR: A combined theoretical and experimental study of ionization of cytosine monomers and dimers suggests that multiple isomer are present in the molecular beam and the dominant role of this channel is supported by the computed energy thresholds for the CH(+) appearance and the barrierless or nearly barrierless ionization-induced proton transfer observed for five isomers of the dimer.
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.