The Journal of Physical Chemistry B 2010, 114 Revisiting the Salt-Induced Conformational Change of DNA with 3D-RISM Theory. Yutaka Maruyama, Norio Yoshida and Fumio Hirata.The Journal of Physical Chemistry A 2010, 114 Modeling Solvatochromic Shifts Using the Orbital-Free Embedding Potential at Statistically Mechanically Averaged Solvent Density. An MM/3D-RISM Approach for Ligand Binding Affinities. Samuel Genheden, Tyler Luchko, Sergey Gusarov, Andriy Kovalenko and Ulf Ryde.The Journal of Physical Chemistry B 2011, 115 Solvent and Salt Effects on Structural Stability of Human Telomere. Yutaka Maruyama, Taku Matsushita, Ryuichi Ueoka, and Fumio Hirata.Journal of Chemical Theory and Computation 2012, 8 Integral Equation Theory of Molecular Solvation Coupled with Quantum Mechanical/Molecular Mechanics Method in NWChem Package. Modified Anderson Method for Accelerating 3D-RISM Calculations Using Graphics Processing Unit. The Journal of Physical Chemistry A 2013, 117 Three-Dimensional Reference Interaction Site Model Self-Consistent Field Study of the Electronic Structure of 3+ in Aqueous Solution. Shinya Fujishige, Yukio Kawashima, Norio Yoshida, and Haruyuki Nakano.Journal of Chemical Theory and Computation 2015, 11 MTS-MD of Biomolecules Steered with 3D-RISM-KH Mean Solvation Forces Accelerated with Generalized Solvation Force Extrapolation. The Journal of Physical Chemistry B 2015, 119 Octanol–Water Partition Coefficient from 3D-RISM-KH Molecular Theory of Solvation with Partial Molar Volume Correction. WenJuan Huang, Nikolay Blinov, and Andriy Kovalenko.Solvation Thermodynamics of Organic Molecules by the Molecular Integral Equation Theory: Approaching Chemical Accuracy. The Journal of Physical Chemistry A 2015, 119 Uranyl Solvation by a Three-Dimensional Reference Interaction Site Model. Alexei Matveev, Bo Li, and Notker Rösch.Journal of Chemical Theory and Computation 2016, 12 3D-RISM-MP2 Approach to Hydration Structure of Pt(II) and Pd(II) Complexes: Unusual H-Ahead Mode vs Usual O-Ahead One. Shinji Aono, Toshifumi Mori, and Shigeyoshi Sakaki.Implementation of the SM12 Solvation Model into ADF and Comparison with COSMO. Journal of Chemical Theory and Computation 2017, 13 Averaged Condensed Phase Model for Simulating Molecules in Complex Environments. The Journal of Physical Chemistry B 2017, 121
#Amsterdam density functional package free#
Predicting Accurate Solvation Free Energy in n-Octanol Using 3D-RISM-KH Molecular Theory of Solvation: Making Right Choices. Dipankar Roy, Nikolay Blinov, and Andriy Kovalenko.The Journal of Physical Chemistry C 2019, 123 Dependence of Absorption and Emission Spectra on Polymorphs of Gold(I) Isocyanide Complexes: Theoretical Study with QM/MM Approach. Shinji Aono, Tomohiro Seki, Hajime Ito, Shigeyoshi Sakaki.The Journal of Physical Chemistry A 2019, 123 Performance of 3D-RISM-KH in Predicting Hydration Free Energy: Effect of Solute Parameters. The Journal of Physical Chemistry A 2020, 124 Evaluation of an Efficient 3D-RISM-SCF Implementation as a Tool for Computational Spectroscopy in Solution. Journal of Chemical Theory and Computation 2020, 16 Tackling Solvent Effects by Coupling Electronic and Molecular Density Functional Theory. Guillaume Jeanmairet, Maximilien Levesque, Daniel Borgis.This article is cited by 66 publications. This new development makes it possible to calculate at modest computational cost the electronic properties and molecular solvation structure of a solute molecule in a given molecular liquid or mixture from the first principles. Our predictions for the solvation free energy agree well with other approaches as well as experiment. To evaluate the accuracy of the present method, test calculations have been carried out for a number of small molecules, including four glycine conformers, a set of small organic compounds, and carbon nanotubes of various lengths in aqueous solution. The method yields all of the features available by using other solvation approaches, for instance infrared spectra of solvated molecules. This enables study of chemical reactions, including reaction coordinates and transition state search, with the molecular solvation described from the first principles. The analytical first derivatives of the free energy with respect to displacements of the solute nuclear coordinates have also been developed.
#Amsterdam density functional package software#
The three-dimensional reference interaction site model with the closure relation by Kovalenko and Hirata (3D-RISM-KH) in combination with the density functional theory (DFT) method has been implemented in the Amsterdam density functional (ADF) software package.
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