Solvation Research Papers - Academia.edu (original) (raw)

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- Chemistry, Inorganic Chemistry, Solution Chemistry, Solvation

Ultrasonic velocity, density, viscosity, and electrical conductivity have been measured for an aqueous solution of KCl at different concentrations and temperatures, the frequency is maintained at a constant value. Using the above experimental data, parameters such as Rao's constant, Wada's constant, solvation number, and surface tension were calculated and the molecular interactions between molecules of KCl and water at different temperatures was studied. Using Walden's plot, the ionicity of the solution was also studied.

- by Dr. Manoj K U M A R Praharaj
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- Materials Science, Thermodynamics, Chemistry, Solvation
- by Dr. Manoj K U M A R Praharaj
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- Materials Science, Thermodynamics, Chemistry, Solvation
- by Shoichi Katsuta
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- Chemistry, Inorganic Chemistry, Capillary electrophoresis, Solvation
- by Shoichi Katsuta
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- Chemistry, Inorganic Chemistry, Solvation, Macrocycle
- by Patrick Hare
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- Chemistry, Kinetics, Photochemistry, Quantum Theory

Quantum-chemical approaches that have been used lately for computing Franck–Condon barriers for electron transfer reactions are analyzed. Attention is focused on the processes whose description goes beyond the linear response approximation, including redox reactions with the cleavage of chemical bonds. Various approaches that take into account the solvation effects are discussed. The role played by the cluster models of the electrode in the description of specific interaction of reactants and products with the electrode surface is emphasized. The influence the dynamics of the nearest coordination sphere of metal aquacomplexes has on the electron transfer rate are interpreted anew. Examples of calculation of the electron penetration probability are considered, and important qualitative effects associated with the dependence of this parameter on the reactant orientation and the electrode charge are analyzed. Urgent problems the quantum electrochemistry faces in the near future are rev...

- by Renat Nazmutdinov
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- Chemistry, Quantum Chemistry, Electrochemistry, Chemical Physics

In this work, we assess a previously advanced hypothesis that predicts the existence of ion channels in the capsid of small and non-enveloped icosahedral viruses. With this purpose we examine Triatoma Virus (TrV) as a case study. This virus has a stable capsid under highly acidic conditions but disassembles and releases the genome in alkaline environments. Our calculations range from a subtle sub-atomic proton interchange to the dismantling of a large-scale system representing several million of atoms. Our results provide structure-based explanations for the three roles played by the capsid to enable genome release. First, we observe, for the first time, the formation of a hydrophobic gate in the cavity along the five-fold axis of the wild-type virus capsid, which can be disrupted by an ion located in the pore. Second, the channel enables protons to permeate the capsid through a unidirectional Grotthuss-like mechanism, which is the most likely process through which the capsid senses...

- by María Marta Branda
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- Computer Science, Biophysics, Chemistry, Molecular Dynamics Simulation
- by kiyull yang
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- Chemistry, Organic Chemistry, Physical Organic Chemistry, Solvation
- by Justin Jones
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- Materials Science, Chemistry, Biology, Solvation

Atomistic molecular dynamics simulations have been performed to investigate effective interactions of isolated water molecules dispersed in trihexyltetradecylphosphonium-orthoborate ionic liquids (ILs). The intrinsic free energy changes in solvating one water molecule from gas phase into bulk IL matrices were estimated as a function of temperature, and thereafter, the calculations of potential of mean force between two dispersed water molecules within different IL matrices were performed using umbrella sampling simulations. The systematic analyses of local ionic microstructures, orientational preferences, probability and spatial distributions of dispersed water molecules around neighboring ionic species indicate their preferential coordinations to central polar segments in orthoborate anions. The effective interactions between two dispersed water molecules are partially or totally screened as their separation distance increases due to interference of ionic species in between. These ...

- by Aatto Laaksonen
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- Engineering, Chemistry, Ionic Liquid, Chemical Physics
- by James T. Hynes
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- Engineering, Physics, Chemistry, Computational Chemistry
- by maxim totrov
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- Computer Science, Algorithms, Thermodynamics, Chemistry

This thesis describes the development and refinement of a number of techniques for molecular docking and ligand database screening, as well as the application of these techniques to predict the structures of several protein-ligand complexes and to discover novel ligands of an important receptor protein. Global energy optimisation by Monte-Carlo minimisation in internal co-ordinates was used to predict bound conformations of eight protein-ligand complexes. Experimental X-ray crystallography structures became available after the predictions were made. Comparison with the X-ray structures showed that the docking procedure placed 30 to 70% of the ligand molecule correctly within 1.5A from the native structure. The discrimination potential for identification of high-affinity ligands was derived and optimised using a large set of available protein-ligand complex structures. A fast boundary-element solvation electrostatic calculation algorithm was implemented to evaluate the solvation comp...

- by maxim totrov
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- Computer Science, Chemistry, Drug Discovery, Solvation

- by Sten Sarman
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- Engineering, Chemistry, Ionic Liquid, Chemical Physics
- by Peter Lee
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- Engineering, Computer Science, Chemistry, Polymer Chemistry

According to the Bronsted definition, any compound which has a hydrogen atom is an acid, since it may be lost as a proton. A thermodynamical cycle is proposed to calculate absolute pKa values for Bronsted acids in aqueous solution. The equilibrium of dissociation of a Bronsted acid depends on the interaction of the acid and its conjugate base with solvent molecules. There fore the pKa value depends on the solvent medium. The polarizable continuum model (PCM) was used to describe the solvent, and absolute pKa values were computed for different compounds: HCOOH, CH3COOH, C6H5COOH, FCH2COOH and CH3CH2COOH. The model of furnishes pKa values was in good agreement with the experimental results for some classes of compounds. The quantum Mechanics (QM) calculations were carried out with the GAUSSIAN 98 program based on HF/6-31+G** level.

- by M. Khaleghian
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- Chemistry, Theoretical Physical Chemistry, Aqueous Solution, Dissociation Constant
- by Asiri Asiri
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- Chemistry, Solvation, CHEMICAL SCIENCES, M. S. Chinese Chemical Letters 2009
- by anjum rehman khan
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- Engineering, Chemistry, Physical Chemistry, Quantum Theory
- by Dr. TUHIN PRADHAN Pradhan
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- Chemistry, Fluorescence, Solution Chemistry, Solvation
- by Vera Bohomoletz Henriques
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- Engineering, Physics, Materials Science, Thermodynamics
- by Hector Martinez-Seara
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- Chemistry, Molecular Dynamics, Solvation, Sodium
- by Yüksel ALTUN
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- Chemistry, Solution Chemistry, Solvation, Factor analysis
- by Yüksel ALTUN
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- Chemistry, Solvation, Factor analysis, CHEMICAL SCIENCES
- by Taisung Lee
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- Thermodynamics, Chemistry, RNA, Protein Folding
- by Issarly Rivas
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- Engineering, Materials Science, Thermodynamics, Chemistry
- by Issarly Rivas
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- Engineering, Materials Science, Thermodynamics, Chemistry
- by Jan Zielkiewicz
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- Engineering, Chemistry, Chemical Physics, Medicine
- by Jan Zielkiewicz
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- Chemistry, Social Media, Solvation, Alcohol

The dynamical properties of solvation water of hyperactive antifreeze protein from Choristoneura fumiferana (CfAFP) are analyzed and discussed in context of its antifreeze activity. The protein comprises of three well-defined planes and one of them binds to the surface of ice. The dynamical properties of solvation water around each of these planes were analyzed separately; the results are compared with the dynamical properties of solvation water of ice around its two crystallographic planes: basal and prism. Three main conclusions are inferred from our investigations. The first one is that the solvation shell of CfAFP does not seem to be particularly far-ranged, at least not beyond what is usually observed for proteins that do not interact with ice. Therefore, it does not appear to us that the antifreeze activity is enhanced by a long-ranged retardation of water mobility. Also the correlation between the collective mobility of water and the collective mobility of protein atoms highl...

- by Jan Zielkiewicz
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- Engineering, Chemistry, Chemical Physics, Medicine

It is generally acknowledged that the mobility of protein atoms and the mobility of water molecules in the solvation layer are connected. In this article, we answer the question whether a similar interdependence exists between the motions of atoms of proteins separated by the hydration layers of variable thickness. The system consisted of a kinesin catalytic domain and a tubulin dimer. It was studied using molecular dynamics simulations. The analyzed atoms were located at the two distant protein surfaces that were facing each other. We demonstrated that the low-frequency (ca. 2 THz and less) collective movements of these two separate sets of atoms are to some extent interdependent. Based on this finding, it can be inferred that the low frequency large-scale internal motions of these proteins are also partially interdependent. The water-mediated protein-protein interactions, which are responsible for this interdependence, have a relatively long range of at least 2 nm at room temperat...

- by Jan Zielkiewicz
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- Chemistry, Chemical Physics, Vibration, Medicine
- by Jan Zielkiewicz
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- Chemistry, Water, Chemical Physics, Medicine
- by Shigenori Tanaka
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- Chemistry, Solvation, Chem/Bio-informatics, Computational Method
- by Shigenori Tanaka
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- Chemistry, Technology, Estrogen Receptor, Solvation
- by Mamadou Diallo
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- Engineering, Thermodynamics, Chemistry, Medicine
- by Mamadou Diallo
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- Thermodynamics, Chemistry, Water, Quantum Theory

The solvation structure and ionic conductivity of Ca(TFSI)2/tetraglyme solutions were studied using a combination of experimental and theoretical approaches. A higher fraction of free ions was detected in solutions with higher molar... more

- by Cristina Iojoiu
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- Thermodynamics, Chemistry, Solvation, DIELECTRIC

We seek to answer the question posed in the title by simulation of the tri-iodide ion in water, modeling the intermolecular interactions by classical potentials. The decrease in solvation free energy as a function of the dipole moment of the ion is calculated using an extended dynamics simulation method. This decrease is approximately quadratic in the ion dipole. Symmetry breaking occurs if this decrease is greater than the energy required to polarize the ion. We use ab initio calculations on an isolated ion to find the electronic and vibrational contributions to the polarizability, from which the polarization energy can be calculated. The solvated ion is found to be more stable when displaced along the asymmetric stretching coordinate, due to contributions of this deformation to the molecular dipole. As a test of the model’s reliability, it is used to derive solvation force autocorrelation functions from which time scales for vibrational energy and phase relaxation are estimated. T...

- by Ronnie Kosloff
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- Engineering, Chemistry, Chemical Physics, Ab initio calculations
- by Dmitry Matyushov
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- Materials Engineering, Physics, Condensed Matter Physics, Materials Science
- by Dmitry Matyushov
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- Engineering, Chemistry, Chemical Physics, Medicine

A phenomenological model of electron transfer reactions in solvents undergoing glass transition is discussed. The reaction constant cuts off slow polarization modes from the spectrum of nuclear thermal motions active on the observation time scale. The arrest of nuclear solvation in turn affects the reaction activation barrier making it dependent on the rate. The resultant rate constant is sought from a self-consistent equation. The model describes well the sharp change in the solvent Stokes shift of optical lines in the glass-transition region. It is also applied to describe the temperature dependence of primary charge separation and reduction of primary pair in photosynthetic reaction centers. The model shows that a weak dependence of the primary charge separation rate on temperature can be explained by dynamical arrest of nuclear solvation on the picosecond time scale of electron transfer. For reduction of primary pair by cytochrome, the model yields a sharp turnover of the reacti...

- by Dmitry Matyushov
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- Engineering, Chemistry, Chemical Physics, Medicine

A microscopic model of the time-resolved Stokes shift is developed. The model calculates the solvation dynamics by combining the atomic resolution of the solute structure with dipolar dynamics from the polarization structure factors of the homogeneous solvent. Calculations are made for coumarin 153 and quinoxaline optical dyes with atomic geometries and charge distributions taken from quantum calculations. Stokes shift dynamics is calculated and compared to experiment in high-temperature acetonitrile and methanol and in low-temperature 2-methyl-tetrahydrofurane using dielectric relaxation data from experiment.

- by Dmitry Matyushov
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- Engineering, Chemistry, Optical Spectroscopy, Chemical Physics

We report Monte Carlo simulations of solvation of a point dipole in dipolar–quadrupolar solvents of varying dipole moment and axial quadrupole. The simulations are carried out to test the prediction of dielectric solvation models of a monotonic increase of the absolute value of the solvation chemical potential |μp| with the solvent dielectric constant ε. Dielectric constants are obtained from pure liquid simulations carried out for each solvent used in solvation simulations. A raising dependence of |μp| on ε, in qualitative agreement with dielectric solvation models, is seen when the solvent dipole moment is varied at constant solvent quadrupole. An increase in the axial quadrupole at constant solvent dipole reduces the dielectric constant at the same time leading to higher |μp| values. The simulations and dielectric models thus give the opposite dependence on the solvent quadrupole for any solvent dipole. We also show that for solvation in dipolar–quadrupolar solvents the saturatio...

- by Dmitry Matyushov
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- Engineering, Thermodynamics, Chemistry, Monte Carlo Simulation
- by Dmitry Matyushov
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- Engineering, Physics, Computational Physics, Chemistry
- by João Marcos Cordeiro
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- Biochemistry, Biophysics, Chemistry, Quantum Theory
- by Robert Balawender
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- Chemistry, Computational Chemistry, Solvation, Ammonia
- by Junjun Mao
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- Chemistry, Crystallography, Molecular Biology, Medicine
- by Barry Ninham
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- Chemistry, Inorganic Chemistry, Solution Chemistry, Solvation

tetracyanoquinodimethane (TCNQ) is widel y used as a π- acceptor for the preparation of organic charge transfer. In this paper the effect of ten solvents on the ground state of TCNQ has been reported. DFT calculations have been done on the Schrodinger software and the effect of solvents have been theoretically calculat ed with the help of Poisson-Boltzmann solver. The solvation en ergy, chemical potential, hardness, electrophilicit y, HOMO- LUMO gap and the picture of the HOMO and LUMO of TC NQ in the ground state in the solvents have been reported

- by KAUSHAL SRIVASTAVA
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- Chemistry, Computational Chemistry, Organic Chemistry, Molecular modeling