The Experts below are selected from a list of 84 Experts worldwide ranked by ideXlab platform
Kazuhiro Ishida - One of the best experts on this subject based on the ideXlab platform.
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Molecular Integrals over the gauge-including atomic orbitals. II. The Breit-Pauli interaction.
Journal of computational chemistry, 2003Co-Authors: Kazuhiro IshidaAbstract:Each accompanying coordinate expansion (ACE) formula is derived for each of the orbit-orbit interaction, the spin-orbit coupling, the spin-spin coupling, and the contact interaction Integrals over the gauge-including atomic orbitals (GIAOs) by the use of the solid harmonic gradient (SHG) operator. Each ACE formula is the general formula derived at the first time for each of the above Molecular Integrals over GIAOs. These Molecular Integrals are arising in the Breit-Pauli two-electron interaction for a relativistic calculation. We may conclude that we can derive a certain ACE formula for any kind of Molecular Integral over solid harmonic Gaussian-type orbitals by using the SHG operator. The present ACE formulas will be useful, for example, for a calculation of a molecule in a uniform magnetic field, for a relativistic calculation, and so on, with the GIAO as a basis function.
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Molecular Integrals over the gauge-including atomic orbitals
The Journal of Chemical Physics, 2003Co-Authors: Kazuhiro IshidaAbstract:Each general formula can be derived by the use of the solid harmonic gradient operator [K. Ishida, Recent Res. Dev. Quantum Chem. 2, 147 (2001)] for each of the ten kinds of Molecular Integral over the gauge-including atomic orbitals (GIAOs). Each is obtained with the accompanying coordinate expansion (ACE) formula. These ten kinds are the overlap, the kinetic energy, the nuclear attraction, the electron repulsion, the angular momentum, the quadrupole moment, the field, the first kind field gradient, the second kind field gradient, and the “dipole-field” Integrals. Except for the overlap and angular momentum Integrals, we derive the general formula of these eight Molecular Integrals at the first level. These ACE formulas will be useful, for example, for a calculation of a molecule in a uniform magnetic field, for a relativistic calculation, and so on, using GIAO as a basis function.
Maxim V. Fedorov - One of the best experts on this subject based on the ideXlab platform.
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solvation thermodynamics of organic molecules by the Molecular Integral equation theory approaching chemical accuracy
Chemical Reviews, 2015Co-Authors: Ekaterina L Ratkova, David S. Palmer, Maxim V. FedorovAbstract:The Integral equation theory (IET) of Molecular liquids has been an active area of academic research in theoretical and computational physical chemistry for over 40 years because it provides a consistent theoretical framework to describe the structural and thermodynamic properties of liquid-phase solutions. The theory can describe pure and mixed solvent systems (including anisotropic and nonequilibrium systems) and has already been used for theoretical studies of a vast range of problems in chemical physics / physical chemistry, Molecular biology, colloids, soft matter, and electrochemistry. A consider- able advantage of IET is that it can be used to study speci fi c solute − solvent interactions, unlike continuum solvent models, but yet it requires considerably less computational expense than explicit solvent simulations.
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Solvent Binding Analysis and Computational Alanine Scanning of the Bovine Chymosin–Bovine κ-Casein Complex Using Molecular Integral Equation Theory
Journal of chemical theory and computation, 2013Co-Authors: David S. Palmer, Jesper Sørensen, Birgit Schiøtt, Maxim V. FedorovAbstract:We demonstrate that the relative binding thermodynamics of single-point mutants of a model protein-peptide complex (the bovine chymosin-bovine κ-casein complex) can be calculated accurately and efficiently using Molecular Integral equation theory. The results are shown to be in good overall agreement with those obtained using implicit continuum solvation models. Unlike the implicit continuum models, however, Molecular Integral equation theory provides useful information about the distribution of solvent density. We find that experimentally observed water-binding sites on the surface of bovine chymosin can be identified quickly and accurately from the density distribution functions computed by Molecular Integral equation theory. The bovine chymosin-bovine κ-casein complex is of industrial interest because bovine chymosin is widely used to cleave bovine κ-casein and to initiate milk clotting in the manufacturing of processed dairy products. The results are interpreted in light of the recent discovery that camel chymosin is a more efficient clotting agent than bovine chymosin for bovine milk.
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an accurate prediction of hydration free energies by combination of Molecular Integral equations theory with structural descriptors
Journal of Physical Chemistry B, 2010Co-Authors: Ekaterina L Ratkova, Gennady N Chuev, Volodymyr P Sergiievskyi, Maxim V. FedorovAbstract:In this work, we report a novel method for the estimation of the hydration free energy of organic molecules, the structural descriptors correction (SDC) model. The method is based on a combination of the reference interaction site model (RISM) with several empirical corrections. The model requires only a small number of chemical descriptors associated with the main features of the chemical structure of solutes: excluded volume, branch, double bond, benzene ring, hydroxyl group, halogen atom, aldehyde group, ketone group, ether group, and phenol fragment. The optimum model was selected after testing of different RISM free energy expressions on a training set of 65 molecules. We show that the correction parameters of the SDC model are transferable between different chemical classes, which allows one to cover a wide range of organic solutes. The new model substantially increases the accuracy of calculated HFEs by RISM giving the standard deviation of the error for a test set of 120 organic molecules around 1.2 kcal/mol.
Bin Gao - One of the best experts on this subject based on the ideXlab platform.
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General recurrence-relation generation scheme for Molecular Integral evaluation.
Journal of computational chemistry, 2020Co-Authors: Bin GaoAbstract:We develop a new scheme for evaluating different Molecular Integrals using Gaussian type orbitals. In this new scheme, the evaluation of Integrals is performed in two steps during runtime. The first step is a top-down procedure that maps each recurrence relation into a jagged array (array of arrays), where each element of a member array represents either the final results or some intermediate Integrals that are stored in our developed data structure "coarse-grained circular buffer". This step is the same for all different one- and two-electron operators so that the same algorithm and source codes can be used. In the second step, a bottom-up procedure is carried out that computes all the intermediate and the final Molecular Integrals by backtracking elements from the last member array of each jagged array. Different source codes should in principle be used for different electron operators in the second step, but which can be generated automatically by our developed recurrence-relation compiler. The currently proposed general recurrence-relation generation scheme provides a new, generic and automatic programming way for various one- and two-electron Integrals needed in computational chemistry. Users can even introduce new electron operators and evaluate their Integrals during runtime by combining the implementation of the proposed new scheme and the just-in-time compilation technique.
Walter Rocchia - One of the best experts on this subject based on the ideXlab platform.
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including diverging electrostatic potential in 3d rism theory the charged wall case
Journal of Chemical Physics, 2018Co-Authors: Ivan Vyalov, Walter RocchiaAbstract:Although three-dimensional site-site Molecular Integral equations of liquids are a powerful tool of the modern theoretical chemistry, their applications to the problem of characterizing the electrical double layer originating at the solid-liquid interface with a macroscopic substrate are severely limited by the fact that an infinitely extended charged plane generates a divergent electrostatic potential. Such potentials cannot be treated within the standard 3D-Reference Interaction Site Model equation solution framework since it leads to functions that are not Fourier transformable. In this paper, we apply a renormalization procedure to overcome this obstacle. We then check the validity and numerical accuracy of the proposed computational scheme on the prototypical gold (111) surface in contact with water/alkali chloride solution. We observe that despite the proposed method requires, to achieve converged charge densities, a higher spatial resolution than that suited to the estimation of bioMolecular solvat...
S. Wilson - One of the best experts on this subject based on the ideXlab platform.
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Literate programming in quantum chemistry: a collaborative approach to the development of theory and computer code
Molecular Physics, 2005Co-Authors: Harry M. Quiney, S. WilsonAbstract:Literate programming has not so far found widespread application in quantum chemistry. Here we suggest that literate programming would do much to enhance the communication of the methods and algorithms of computational quantum chemistry. We argue that literate programming can foster a collaborative approach to the development of theory and code in quantum chemistry. We consider a collaborative approach to computational quantum chemistry via a collaborative virtual environment involving literate programming methods and contrast this with the more traditional approaches, such as the UK's Collaborative Computational Project 1. A sample literate program for the evaluation of the incomplete gamma function is presented using C and the literate programming conventions introduced by Knuth. This demonstrates the application of literate programming methodology to the heart of the Molecular Integral problem when Gaussian basis sets are employed. We briefly indicate how literate programming techniques may prove usefu...
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Practical AB Initio Methods for Molecular Electronic Structure Studies. III. Molecular Integrals Over Gaussian-Type Functions
Problem Solving in Computational Molecular Science, 1997Co-Authors: S. WilsonAbstract:The evaluation of Molecular Integrals over Gaussian-type functions lies at the heart of practical realization of contemporary quantum chemical theories. The aims of the present article are two-fold. First, to provide an introduction to the problem of Molecular Integral evaluation for the quantum chemistry package user; to give a elementary, yet fairly thorough, introduction to the steps, both analytical and computational, involved in the evaluation of the simplest of Integrals. Second, to provide a brief overview of developments that have taken place in the field of Molecular Integral evaluation since the 1983 review by Saunders.