Journal ArticleDOI
The IEF version of the PCM solvation method: an overview of a new method addressed to study molecular solutes at the QM ab initio level
TLDR
The integral equation formalism (IEF) as mentioned in this paper is a recent method addressed to solve the electrostatic solvation problem at the QM level with the aid of apparent surface charges (ASC).Abstract:
The integral equation formalism (IEF) is a recent method (the grounds have been elaborated at the beginning of 1997) addressed to solve the electrostatic solvation problem at the QM level with the aid of apparent surface charges (ASC). IEF uses a new formalism of this problem, based on integral operators never used before in the chemical community and it manages to treat on the same footing linear isotropic solvent models, as well as anisotropic liquid crystals and ionic solutions. In this overview we emphasize the good performances of IEF at the lowest level of its potentialities, i.e. for isotropic solvents, as a new approach to compute solvation free energies and properties (dipole hyperpolarizabilities) of molecular solutes, as well as energy gradients for geometry optimization procedures. Finally we present a new IEF implementation of the nonequilibrium problem for electronic spectra which appears to be decidedly competitive with the previous more standard ASC formulations.read more
Citations
More filters
Journal ArticleDOI
Universal solvation model based on solute electron density and on a continuum model of the solvent defined by the bulk dielectric constant and atomic surface tensions.
TL;DR: The SMD model may be employed with other algorithms for solving the nonhomogeneous Poisson equation for continuum solvation calculations in which the solute is represented by its electron density in real space, including, for example, the conductor-like screening algorithm.
Journal ArticleDOI
A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations.
Yong Duan,Chun Wu,Shibasish Chowdhury,Mathew C. Lee,Guoming Xiong,Wei Zhang,Rong Yang,Piotr Cieplak,Piotr Cieplak,Ray Luo,Tai-Sung Lee,Tai-Sung Lee,James W. Caldwell,Junmei Wang,Peter A. Kollman +14 more
TL;DR: A third‐generation point‐charge all‐atom force field for proteins is developed and initial tests on peptides demonstrated a high‐degree of similarity between the calculated and the statistically measured Ramanchandran maps for both Ace‐Gly‐nme and Ace‐Ala‐Nme di‐peptides.
Journal ArticleDOI
Advances in molecular quantum chemistry contained in the Q-Chem 4 program package
Yihan Shao,Zhengting Gan,Evgeny Epifanovsky,Andrew T. B. Gilbert,Michael Wormit,Joerg Kussmann,Adrian W. Lange,Andrew Behn,Jia Deng,Xintian Feng,Debashree Ghosh,Matthew Goldey,Paul R. Horn,Leif D. Jacobson,Ilya Kaliman,Rustam Z. Khaliullin,Tomasz Kuś,Arie Landau,Jie Liu,Emil Proynov,Young Min Rhee,Ryan M. Richard,Mary A. Rohrdanz,Ryan P. Steele,Eric J. Sundstrom,H. Lee Woodcock,Paul M. Zimmerman,Dmitry Zuev,Ben Albrecht,Ethan Alguire,Brian J. Austin,Gregory J. O. Beran,Yves A. Bernard,Eric J. Berquist,Kai Brandhorst,Ksenia B. Bravaya,Shawn T. Brown,David Casanova,Chun-Min Chang,Yunqing Chen,Siu Hung Chien,Kristina D. Closser,Deborah L. Crittenden,Michael Diedenhofen,Robert A. DiStasio,Hainam Do,Anthony D. Dutoi,Richard G. Edgar,Shervin Fatehi,Laszlo Fusti-Molnar,An Ghysels,Anna Golubeva-Zadorozhnaya,Joseph Gomes,Magnus W. D. Hanson-Heine,Philipp H. P. Harbach,Andreas W. Hauser,Edward G. Hohenstein,Zachary C. Holden,Thomas-C. Jagau,Hyunjun Ji,Benjamin Kaduk,Kirill Khistyaev,Jae-Hoon Kim,Jihan Kim,Rollin A. King,Phil Klunzinger,Dmytro Kosenkov,Tim Kowalczyk,Caroline M. Krauter,Ka Un Lao,Adèle D. Laurent,Keith V. Lawler,Sergey V. Levchenko,Ching Yeh Lin,Fenglai Liu,Ester Livshits,Rohini C. Lochan,Arne Luenser,Prashant Uday Manohar,Samuel F. Manzer,Shan-Ping Mao,Narbe Mardirossian,Aleksandr V. Marenich,Simon A. Maurer,Nicholas J. Mayhall,Eric Neuscamman,C. Melania Oana,Roberto Olivares-Amaya,Darragh P. O’Neill,John Parkhill,Trilisa M. Perrine,Roberto Peverati,Alexander Prociuk,Dirk R. Rehn,Edina Rosta,Nicholas J. Russ,Shaama Mallikarjun Sharada,Sandeep Sharma,David W. Small,Alexander J. Sodt,Tamar Stein,David Stück,Yu-Chuan Su,Alex J. W. Thom,Takashi Tsuchimochi,Vitalii Vanovschi,Leslie Vogt,Oleg A. Vydrov,Tao Wang,Mark A. Watson,Jan Wenzel,Alec F. White,Christopher F. Williams,Jun Yang,Sina Yeganeh,Shane R. Yost,Zhi-Qiang You,Igor Ying Zhang,Xing Zhang,Yan Zhao,Bernard R. Brooks,Garnet Kin-Lic Chan,Daniel M. Chipman,Christopher J. Cramer,William A. Goddard,Mark S. Gordon,Warren J. Hehre,Andreas Klamt,Henry F. Schaefer,Michael W. Schmidt,C. David Sherrill,Donald G. Truhlar,Arieh Warshel,Xin Xu,Alán Aspuru-Guzik,Roi Baer,Alexis T. Bell,Nicholas A. Besley,Jeng-Da Chai,Andreas Dreuw,Barry D. Dunietz,Thomas R. Furlani,Steven R. Gwaltney,Chao-Ping Hsu,Yousung Jung,Jing Kong,Daniel S. Lambrecht,WanZhen Liang,Christian Ochsenfeld,Vitaly A. Rassolov,Lyudmila V. Slipchenko,Joseph E. Subotnik,Troy Van Voorhis,John M. Herbert,Anna I. Krylov,Peter Gill,Martin Head-Gordon +156 more
TL;DR: A summary of the technical advances that are incorporated in the fourth major release of the Q-Chem quantum chemistry program is provided in this paper, covering approximately the last seven years, including developments in density functional theory and algorithms, nuclear magnetic resonance (NMR) property evaluation, coupled cluster and perturbation theories, methods for electronically excited and open-shell species, tools for treating extended environments, algorithms for walking on potential surfaces, analysis tools, energy and electron transfer modelling, parallel computing capabilities, and graphical user interfaces.
RESEARCH ARTICLE Advances in molecular quantum chemistry contained in the Q-Chem 4 program package
Yihan Shao,Zhengting Gan,Evgeny Epifanovsky,Michael Wormit,Joerg Kussmann,Adrian W. Lange,Andrew Behn,Jia Deng,Xintian Feng,Debashree Ghosh,Matthew Goldey,Paul R. Horn,L eif,J ie Liu,I. Proynov,Ryan M. Richard,Mary A. Rohrdanz,Ryan P. Steele,Eric J. Sundstrom,H. Lee Woodcock,Dmitry Zuev,Ben Albrecht,Ethan Alguire,Brian Austin,Gregory J. O. Beran,Yves A. Bernard,Eric Berquist,Kai Brandhorst,Ksenia B. Bravaya,Shawn T. Brown,David Casanova,Chun-Min Chang,Yunqing Chen,Siu Hung Chien,Kristina D. Closser,Deborah L. Crittenden,Hainam Do,Anthony D. Dutoi,Richard G. Edgar r,Laszlo Fusti-Molnar,Anna Golubeva-Zadorozhnaya,Joseph Gomes,Andreas W. Hauser,Edward G. Hohenstein,Zachary C. Holden +44 more
TL;DR: Detailed benchmarks of the comparative accuracy of modern density functionals for bonded and non-bonded interactions, tests of attenuated second order Møller–Plesset methods for intermolecular interactions, and tests of the accuracy of implicit solvation models are provided.
Journal ArticleDOI
The ONIOM Method and Its Applications
Lung Wa Chung,W. M. C. Sameera,Romain Ramozzi,Alister J. Page,Miho Hatanaka,Galina P. Petrova,Travis V. Harris,Travis V. Harris,Xin Li,Zhuofeng Ke,Fengyi Liu,Hai Bei Li,Lina Ding,Keiji Morokuma +13 more
TL;DR: This paper presents a meta-analyses of the proton-probes of Na6(CO3)(SO4)2, Na2SO4, and Na2CO3 of the response of the H2O/O2 “spatially aggregating substance,” which has the potential to alter the structure of the molecule and provide clues to the “building blocks” of DNA.
References
More filters
Journal ArticleDOI
COSMO : a new approach to dielectric screening in solvents with explicit expressions for the screening energy and its gradient
Andreas Klamt,Gerrit Schüürmann +1 more
TL;DR: In this paper, an algorithm for the accurate calculation of dielectric screening effects in solvents is presented, which leads to rather simple expressions for the screening energy and its analytic gradient with respect to the solute coordinates.
Journal ArticleDOI
Electrostatic interaction of a solute with a continuum. A direct utilizaion of AB initio molecular potentials for the prevision of solvent effects
TL;DR: In this article, a method is presented which utilizes the calculation of the molecular electrostatic potential or the electric field at a discrete number of preselected points to evaluate the environmental effects of a solvent on the properties of a molecular system.
Journal ArticleDOI
Quantum Calculation of Molecular Energies and Energy Gradients in Solution by a Conductor Solvent Model
Vincenzo Barone,Maurizio Cossi +1 more
TL;DR: In this paper, a new implementation of the conductor-like screening solvation model (COSMO) in the GAUSSIAN94 package is presented, which allows Hartree−Fock (HF), density functional (DF) and post-HF energy, and HF and DF gradient calculations: the cavities are modeled on the molecular shape, using recently optimized parameters, and both electrostatic and nonelectrostatic contributions to energies and gradients are considered.
Journal ArticleDOI
A new integral equation formalism for the polarizable continuum model: Theoretical background and applications to isotropic and anisotropic dielectrics
TL;DR: In this paper, a new integral equation formulation of the polarizable continuum model (PCM) is presented, which allows one to treat in a single approach dielectrics of different nature: standard isotropic liquids, intrinsically anisotropic medialike liquid crystals and solid matrices, or ionic solutions.