Готові списки джерел за темами / Solvation energies

Добірка наукової літератури з теми "Solvation energies"

Автор: Grafiati
Опубліковано: 10 грудня 2022
Оновлено: 28 січня 2023

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Статті в журналах з теми "Solvation energies"

1

Tanner, Dennis D., Natasha Deonarian, and Abdelmajid Kharrat. "Electron affinities and Marcus reorganization energies. A correlation between gas phase electron affinities and solution phase redox potentials." Canadian Journal of Chemistry 67, no. 1 (January 1, 1989): 171–75. http://dx.doi.org/10.1139/v89-028.

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Redox potentials determined by cyclic voltammetry were used in conjunction with published electron affinities to determine the solvation energies for series of three classes of compounds: substituted benzoquinones, substituted nitrobenzenes, and polynuclear aromatic hydrocarbons. Excellent linear correlations were obtained between the measured electron affinities and the E0 of the substrates. The calculated electron affinities, EA (E0), were computed using the average solvation energies for the three classes of compounds, and were found to be in excellent agreement with the measured values. The nitrobenzenes and quinones had one solvation energy, while the aromatic hydrocarbons were correlated with a significantly different value. The solvation energy of a variety of compounds could also be related to their Marcus reorganization energiesλ(0), by a linear plot with a high correlation coefficient. From simple electrochemical measurements of similar compounds, either electron affinities or Marcus λ(0) values can be estimated. Keywords: electron affinities, Marcus reorganization energies, cyclic voltammetry.
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2

Arnett, Edward M. "Solvation energies of organic ions." Journal of Chemical Education 62, no. 5 (May 1985): 385. http://dx.doi.org/10.1021/ed062p385.

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3

Nhan, Pham Le, and Nguyen Tien Trung. "THEORETICAL EVALUATION OF THE pKa VALUES OF 5-SUBSTITUED URACIL DERIVATIVES." Vietnam Journal of Science and Technology 55, no. 6A (April 23, 2018): 63. http://dx.doi.org/10.15625/2525-2518/55/6a/12365.

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Density functional theory (DFT) calculations using numerical basis sets were employed to predict the solvation energies, Gibbs free energies and pKa values of a series of 5-substituted uracil derivatives. Obtained results show that solvation energies are not significantly different between DFT methods using the numerical (DNP) and Gaussian basis set (aug-cc-pVTZ). It is noteworthy that the independent and suitable solvation energy of proton of -258.6 kcal/mol has been proposed for the evaluation of pKa values in conjunction with the numerical basis set. In addition, the calculated pKa values suggest that the anti-conformation of 5-formyluracil is the most stable form in the aqueous solution.
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4

Pola, Martina, Michal A. Kochman, Alessandra Picchiotti, Valentyn I. Prokhorenko, R. J. Dwayne Miller, and Michael Thorwart. "Linear photoabsorption spectra and vertical excitation energies of microsolvated DNA nucleobases in aqueous solution." Journal of Theoretical and Computational Chemistry 16, no. 04 (April 4, 2017): 1750028. http://dx.doi.org/10.1142/s0219633617500286.

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Employing density functional theory (DFT) and time-dependent density functional theory (TDDFT) calculations in combination with the semiclassical nuclear ensemble method, we have simulated the photoabsorption spectra of the four canonical DNA nucleobases in aqueous solution. In order to model the effects of solvation, for each nucleobase, a number of solvating water molecules were explicitly included in the simulations, and additionally, the bulk solvent was represented by a continuous polarizable medium. We find that the effect of the solvation shell in general is significant, and its inclusion improves the realism of the spectral simulations. The involvement of lone electron pairs in the hydrogen bonding with the solvating water molecules has the effect of systematically increasing the energies of vertical excitation into the [Formula: see text]-type states. Apart from a systematic blue shift of around [Formula: see text][Formula: see text]eV observed in the absorption peaks, the calculated photoabsorption spectra reproduce the measured ones with good accuracy. The photoabsorption spectra are dominated by excited states with [Formula: see text] and partial [Formula: see text] character. No low-energy charge transfer states are observed with the use of the CAM-B3LYP and M06-2X functionals.
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5

Huang, David M., Phillip L. Geissler, and David Chandler. "Scaling of Hydrophobic Solvation Free Energies†." Journal of Physical Chemistry B 105, no. 28 (July 2001): 6704–9. http://dx.doi.org/10.1021/jp0104029.

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6

Jalan, Amrit, Robert W. Ashcraft, Richard H. West, and William H. Green. "Predicting solvation energies for kinetic modeling." Annual Reports Section "C" (Physical Chemistry) 106 (2010): 211. http://dx.doi.org/10.1039/b811056p.

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7

Pathak, Yashaswi, Siddhartha Laghuvarapu, Sarvesh Mehta, and U. Deva Priyakumar. "Chemically Interpretable Graph Interaction Network for Prediction of Pharmacokinetic Properties of Drug-Like Molecules." Proceedings of the AAAI Conference on Artificial Intelligence 34, no. 01 (April 3, 2020): 873–80. http://dx.doi.org/10.1609/aaai.v34i01.5433.

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Solubility of drug molecules is related to pharmacokinetic properties such as absorption and distribution, which affects the amount of drug that is available in the body for its action. Computational or experimental evaluation of solvation free energies of drug-like molecules/solute that quantify solubilities is an arduous task and hence development of reliable computationally tractable models is sought after in drug discovery tasks in pharmaceutical industry. Here, we report a novel method based on graph neural network to predict solvation free energies. Previous studies considered only the solute for solvation free energy prediction and ignored the nature of the solvent, limiting their practical applicability. The proposed model is an end-to-end framework comprising three phases namely, message passing, interaction and prediction phases. In the first phase, message passing neural network was used to compute inter-atomic interaction within both solute and solvent molecules represented as molecular graphs. In the interaction phase, features from the preceding step is used to calculate a solute-solvent interaction map, since the solvation free energy depends on how (un)favorable the solute and solvent molecules interact with each other. The calculated interaction map that captures the solute-solvent interactions along with the features from the message passing phase is used to predict the solvation free energies in the final phase. The model predicts solvation free energies involving a large number of solvents with high accuracy. We also show that the interaction map captures the electronic and steric factors that govern the solubility of drug-like molecules and hence is chemically interpretable.
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8

Palmer, Bentley J., та Ross H. Hill. "The energetics of the oxidative addition of trisubstituted silanes to photochemically generated (η5-C5R5)Mn(CO)2". Canadian Journal of Chemistry 74, № 11 (1 листопада 1996): 1959–67. http://dx.doi.org/10.1139/v96-223.

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The rates for the oxidative addition reaction of trisubstituted silanes (Et3SiH, Et2MeSiH, EtMe2SiH, Et2SiH2) to photochemically generated (η5-C5R5)Mn(CO)2 (R5 = H5, Me5, H4Me) species have been measured for the temperature range 70–125 K. The reactions were carried out in either neat silane or a 50/50, by volume, mixture of methylcyclohexane and silane. The activation energies, determined using Arrhenius law, varied from 2 to 35 kj/mol. The kinetic data fit an isokinetic relationship with an isokinetic temperature of 102 ± 6 K. The results are interpreted in terms of a variation in the loss of solvation prior to the oxidative addition. When the solvating molecule is methylcyclohexane, then loss of the solvent molecule precedes oxidative addition. In cases where solvation is by the silane, the incomplete loss of this silane precedes the oxidative addition. Key words: mechanism, oxidative addition, solvation.
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9

Tachikawa, Hiroto, Anders Lund, and Masaaki Ogasawara. "A model calculation on structures and excitation energies of the hydrated electron." Canadian Journal of Chemistry 71, no. 1 (January 1, 1993): 118–24. http://dx.doi.org/10.1139/v93-017.

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Model calculations were made on the hydrated electron by using the ab initio MO method combined with the MR-SD-Cl method and the coupled cluster theory. The models used in the calculations were water clusters denoted by [e−(H2O)n(H2O)m], where n = 2,3,4, and 6 for the first solvation shell and m = 0–28 for the second and third solvation shells. In these model calculations, the interactions between the excess electron and the water molecules in the first solvation shell are explicitly calculated by ab initio MO methods and the water molecules in the second and third solvation shells were represented by the fractional charges obtained at the MP2/D95V** level. The stabilization energies and the solvation radius r(e−–O), in terms of the distance between the center of the cavity and an oxygen atom of the surrounding water molecules, increased monotonically with the number of water molecules in the first solvation shell. On the other hand, the first excitation energy was not dependent on the number of water molecules in solvation shells, but constant, with the value of ca. 2.0 eV. On the basis of the present calculations, we suggest that (1) the energetic stability of excess electrons depends on both short-range interaction and long-range interaction, (2) the first excitation energy is critically affected by only the short-range interactions, and the excitation is theoretically attributed to the1s→2p transition of the excess electron.
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10

Chan, Hue Sun, and Ken A. Dill. "SOLVATION: HOW TO OBTAIN MICROSCOPIC ENERGIES FROM PARTITIONING AND SOLVATION EXPERIMENTS." Annual Review of Biophysics and Biomolecular Structure 26, no. 1 (June 1997): 425–59. http://dx.doi.org/10.1146/annurev.biophys.26.1.425.

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Дисертації з теми "Solvation energies"

1

Kurusu, Tamaki. "Computer simulation of free energies to predict cis/trans equilibria of prolyl peptides and solvation free energies of phenylalanyl peptides." Thesis, Virginia Tech, 1996. http://hdl.handle.net/10919/45091.

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Two computer simulation studies were performed; one to help understand the structure-function relationships of prolyl peptides (Part I) and the other to help predict more efficient pharmaceutical drug delivery by molecular modification of small peptides (Part II).

In Part I, the free energy perturbation (FEP) method, using AMBER, was utilized to calculate the Gibbs free energy difference between cis and trans conformers of Ace-Tyr-Pro- NMe and Ace-Asn-Pro-NMe, from which the ratio of cis to trans conformers was obtained. Our simulation generated much lower %cis for both peptides as compared with experimental values and possible problems in our computational schemes are presented. However, our results were encouraging in that they predicted preference of trans conformers for both peptides and higher %cis for Ace-Tyr-Pro-NMe, compared to Ace-Asn-Pro-NMe, which agrees with experimental results.

Part II applied semi empirical (AMS0L) and microscopic simulation (POLARIS) methods to obtain the solvation free energies of a series of phenylalanyl peptides with various degrees of methylation on their backbone nitrogens. It was clearly predicted that as a peptide length increased, so solvation free energy decreased, indicating less favorable permeability through the cell membrane system, in agreement with data in the literature. AMSOL also showed that solvation free energy change upon methylation was variable depending on the position of the substituted backbone nitrogen, which disagrees with the literature. However, non-systematic solvation free energy change of small amines upon methylation was successfully predicted by AMSOL, in good accord with experimental data.


Master of Science
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2

Cumberworth, Alexander Michael. "Implicit solvent models and free energies of solvation in the context of protein folding." Thesis, University of British Columbia, 2015. http://hdl.handle.net/2429/52833.

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Given the wide and fundamental roles proteins play in cells, as well as their potential medical and industrial applications, a detailed understanding of the relationships between sequence, structure, dynamics, and function is of critical importance. Molecular models are required to solve this problem, as well as models of the associated conformational spaces. One of the most challenging aspects of modeling these vast ensembles is the computer power required to carry out the requisite simulations. Reduced solvent models, and particularly a class referred to as implicit solvent models, have been developed extensively; however, they make many assumptions and approximations that are likely to affect accuracy. Here, several implicit solvent models commonly used for protein modeling are evaluated by comparing the expected changes in free energies of solvation upon folding ΔGsolv derived from micro--ms simulations of fast folding proteins to those given by the implicit solvent models. In the majority of cases, there is a significant and substantial difference between the ΔGsolv values calculated from the two approaches, with the implicit solvent models excessively favouring the folded state over the unfolded state. This could only be remedied by selecting values for the model parameters -- the internal dielectric constant for the polar term and the surface tension coefficient for the apolar term -- that were system specific or physically unrealistic.
Science, Faculty of
Graduate
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3

Pollard, Travis P. "Local Structure and Interfacial Potentials in Ion Solvation." University of Cincinnati / OhioLINK, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1491562324303743.

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4

Gebhardt, Julia [Verfasser], and Niels [Akademischer Betreuer] Hansen. "Biomolecular force fields probed by free energies of binding and solvation / Julia Gebhardt ; Betreuer: Niels Hansen." Stuttgart : Universitätsbibliothek der Universität Stuttgart, 2021. http://nbn-resolving.de/urn:nbn:de:bsz:93-opus-ds-116887.

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5

Attah, Isaac Kwame. "BINDING ENERGIES AND SOLVATION OF ORGANIC MOLECULAR IONS, REACTIONS OF TRANSITION METAL IONS WITH, AND PLASMA DISCHARGE IONIZATION OF MOLECULAR CLUSTERS." VCU Scholars Compass, 2013. http://scholarscompass.vcu.edu/etd/525.

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In this dissertation, different approaches have been employed to address the quest of understanding the formation and growth mechanisms of carbon-containing molecular ions with relevance to astrochemistry. Ion mobility mass spectrometry and DFT computations were used to investigate how a second nitrogen in the pyrimidine ring will affect the formation of a covalent bond between the benzene radical cation and the neutral pyrimidine molecule, after it was shown that a stable covalent adduct can be formed between benzene radical cation and the neutral pyridine. Evidence for the formation of a more stable covalent adduct between the benzene radical cation and the pyrimidine is reported here. The effect of substituents on substituted-benzene cations on their solvation by an HCN solvent was also investigated using ion mobility mass spectrometry and DFT computations were also investigated. We looked at the effect of the presence of electron-withdrawing substituents in fluorobenzene, 1,4 di- fluorobenzene, and benzonitrile on their solvation by up to four HCN ligands, and compared it to previous work done to determine the solvation chemistry of benzene and phenylacetylene by HCN. We report here the observed increase in the binding of the HCN molecule to the aromatic ring as the electronegativity of the substituent increased. We also show in this dissertation, DFT calculations that reveal the formation of both hydrogen-bonded and electrostatic isomers, of similar energies for each addition to the ions respectively. The catalytic activity of the 1st and 2nd row TM ions towards the polymerization of acetylene done using the reflectron time of flight mass spectrometry and DFT calculations is also reported in this dissertation. We explain the variation in the observed trend in C-H/C-C activity of these ions. We also report the formation of carbide complexes by Zr+, Nb+, and Mo+, with the acetylene ligands, and show the thermodynamic considerations that influence the formation of these dehydrogenated ion-ligand complexes. Finally, we show in this dissertation, a novel ionization technique that we employed to generate ions that could be relevant to the interstellar and circumstellar media using the reflectron time of flight mass spectrometry.
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6

Moine, Edouard. "Estimation d’énergies de GIBBS de solvatation pour les modèles cinétiques d’auto-oxydation : développement d’une banque de données étendue et recherche d’équations d’état cubiques et SAFT adaptées à leur prédiction." Thesis, Université de Lorraine, 2018. http://www.theses.fr/2018LORR0295/document.

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Les réactions d’oxydation d’hydrocarbures en phase liquide (aussi appelées auto-oxydation) jouent un rôle essentiel dans un grand nombre de procédés de l’industrie pétrochimique car elles assurent la conversion du pétrole en composés chimiques organiques valorisables. Elles régissent également la stabilité à l’oxydation des carburants (vieillissement) et des produits chimiques dérivés du pétrole. Ces réactions d’oxydation en phase liquide relèvent de mécanismes radicalaires en chaîne impliquant des milliers d’espèces et de réactions élémentaires. La modélisation cinétique de tels systèmes reste actuellement un défi car elle nécessite de disposer de données thermodynamiques et cinétiques précises, qui sont rares dans la littérature. Le logiciel EXGAS, développé au LRGP, permet de générer automatiquement des modèles cinétiques détaillés pour des réactions d’oxydation d’hydrocarbures en phase gazeuse. Qu’il s’agisse d’une phase gazeuse ou liquide, les réactions élémentaires mises en jeu sont de même nature et la méthodologie de génération du mécanisme est la même. Pour passer d’un mécanisme en phase gaz à un mécanisme en phase liquide il convient d’adapter les valeurs des constantes d’équilibre et de vitesse (appelées constantes thermocinétiques) des réactions du mécanisme. L’objectif de cette thèse est de proposer une méthode pour corriger les constantes thermocinétiques de la phase gaz pour qu’elles deviennent applicables à la phase liquide. Cette correction fait intervenir une grandeur appelée énergie de GIBBS de solvatation molaire partielle. Une analyse de la définition précise de cette quantité nous a permis de montrer qu’elle s’exprime simplement en fonction d’un coefficient de fugacité et d’une densité molaire. Nous avons ensuite relié cette grandeur à des quantités thermodynamiques mesurables (coefficients d’activité, constantes de HENRY …) et nous nous sommes appuyés sur toutes les données qu’il nous a été possible de trouver dans la littérature pour créer la banque de données expérimentales d’énergies de GIBBS de solvatation molaires partielles la plus complète (intitulée CompSol). Cette banque de données a ensuite servi à valider l’utilisation de l’équation d’état UMR-PRU pour prédire ces énergies. Les bases d’une équation d’état de type SAFT, au paramétrage original, développé dans le cadre de cette thèse, ont été posées. Notre objectif était de simplifier l’estimation des paramètres corps purs de cette équation d’état en proposant une méthode de paramétrage ne nécessitant aucune procédure d’optimisation, claire et reproductible, à partir de données très facilement accessibles dans la littérature. Cette équation a été utilisée pour estimer les énergies de GIBBS de solvatation molaires des corps purs et les énergies de GIBBS de solvatation molaires partielles de systèmes {soluté+solvant}. Enfin, ces méthodes d’estimation des énergies de GIBBS de solvatation molaires partielles ont été combinées au logiciel EXGAS afin de modéliser l’oxydation du n-butane en phase liquide
Liquid phase oxidation of hydrocarbons (also called autoxidation) is central to a large number of processes in the petrochemical industry as it plays a key role in the conversion of petroleum feedstock into valuable organic chemicals. This phenomenon is also crucial in oxidation-stability studies of fuels and its derivatives (aging). These liquid-phase oxidation reactions entail radical mechanisms involving more than thousands of compounds and elementary reactions. Kinetic modelling of these kinds of reactions remains a significant challenge because it requires thermodynamic and kinetic parameters, which are not abundant in literature. The EXGAS software, developed at LRGP, is able to generate these kinds of models but only for oxidation reactions taking place in a gaseous phase. It is assumed that the nature of elementary reactions in the liquid and gaseous phases is the same. The unique need to transfer a kinetic mechanism from a gas phase to a liquid phase is to update kinetic rate constant values and equilibrium constant values (called thermokinetic constants) of mechanism reactions. Therefore, in the framework of this PhD thesis, a new method aimed at applying a correction term to thermokinetic constants of gaseous phases is proposed in order to obtain constants usable to describe liquid-phase mechanisms. This correction involves a quantity called partial molar solvation GIBBS energy. An analysis of the precise definition of this property led us to conclude that it can be simply expressed as a function of fugacity coefficients and liquid molar density. As a result, this property could also be expressed with respect to measurable thermodynamic quantities as activity coefficients or HENRY’s law constants. By combining all the experimental data related to these measurable properties that can be found in the literature, it was possible to develop a comprehensive databank of partial molar solvation GIBBS energies (called the CompSol database). This database was used to validate the use of the UMR-PRU equation of state to predict solvation quantities. Moreover, the bases of a new parameterization for SAFT-type equations of state were laid. It consists in estimating pure-component parameters of SAFT-like equation using a very simple, reproducible and transparent path for non-associating pure components. This equation was used to calculate partial molar GIBBS energy of solvation of pure and mixed solutes. Last, equations of state were combined with EXGAS software to model the oxidation of n-butane in the liquid phase
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7

Opoku-Agyeman, Bernice. "Complexities in Nonadiabatic Dynamics of Small Molecular Anions." The Ohio State University, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=osu1503094708588515.

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8

Jeanmairet, Guillaume. "Une théorie de la fonctionnelle de la densité moléculaire pour la solvatation dans l'eau." Phd thesis, Université Pierre et Marie Curie - Paris VI, 2014. http://tel.archives-ouvertes.fr/tel-01067993.

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La théorie de la fonctionnelle de la densité classique est utilisée pour étudier la solvatation de solutés quelconques dans le solvant eau. Une forme approchée de la fonctionnelle d'excès pour l'eau est proposée. Cette fonctionnelle nécessite l'utilisation de fonctions de corrélation du solvant pur. Celles-ci peuvent être calculées par simulations numériques, dynamique moléculaire ou Monte Carlo ou obtenues expérimentalement. La minimisation de cette fonctionnelle donne accès à l'énergie libre de solvatation ainsi qu'à la densité d'équilibre du solvant. Différentes corrections de cette fonctionnelle approchée sont proposées. Une correction permet de renforcer l'ordre tétraédrique du solvant eau autour des solutés chargés, une autre permet de reproduire le comportement hydrophobe à longue distance de solutés apolaires. Pour réaliser la minimisation numérique de la fonctionnelle, la théorie a été implémentée sur une double grille tridimensionnelle pour les coordonnées angulaires et spatiales, dans un code de minimisation fonctionnelle écrit en Fortran moderne, mdft. Ce programme a été utilisé pour étudier la solvatation en milieu aqueux de petits solutés atomiques neutres et chargés et de petites molécules polaires et apolaires ainsi que de solutés plus complexes, une argile hydrophobe et une petite protéine. Dans chacun des cas la théorie de la fonctionnelle de la densité classique permet d'obtenir des résultats similaires à ceux théoriquement exacts obtenus par dynamique moléculaire, avec des temps de calculs inférieurs d'au moins trois ordres de grandeurs.
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9

Basdevant, Nathalie. "Un Modèle de Solvatation Semi-Implicite pour la Simulation des Macromolécules Biologiques." Phd thesis, Université d'Evry-Val d'Essonne, 2003. http://tel.archives-ouvertes.fr/tel-00010619.

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Анотація:
Dans la cellule des organismes vivants, le solvant (l'eau) joue un rôle très important dans la stabilisation des structures tridimensionnelles des macromolécules biologiques et lors de leurs interactions. Les méthodes théoriques de simulations de modélisation moléculaire permettent de compléter les informations partielles sur l'hydratation des biomolécules obtenues par les méthodes expérimentales. Nous avons développé un nouveau modèle de solvatation semi-implicite pour représenter le solvant en modélisation moléculaire. Ce modèle décrit le solvant comme des particules microscopiques dont les propriétés diélectriques découlent des lois macroscopiques de l'électrostatique. Nous obtenons ainsi à l'équilibre électrostatique un fluide de particules de Lennard-Jones non polaires, polarisables par le champ électrique créé par le soluté. Ce modèle a l'intérêt de prendre en compte la structure moléculaire du solvant tout en calculant efficacement l'énergie libre électrostatique de solvatation du système. De plus, il est d'un faible coût numérique comparé aux méthodes explicites. Après avoir implémenté notre modèle dans un programme de dynamique moléculaire et l'avoir paramétré de façon simple, nous l'avons appliqué à plusieurs peptides, protéines et acides nucléiques (ADN et ARN de transfert). Les trajectoires de ces simulations sont stables sur une à deux nanosecondes, et les structures obtenues sont tout à fait en accord avec les méthodes expérimentales et les méthodes théoriques de solvatation explicites. Notre modèle permet également de retrouver les sites préférentiels d'hydratation des molécules étudiées identifiés expérimentalement ou théoriquement, malgré l'absence de liaisons hydrogène dans notre solvant. De plus, nous observons de bonnes corrélations entre les énergies libres électrostatiques de solvatation calculées avec notre modèle et celles calculées avec les méthodes de résolution de l'équation de Poisson-Boltzmann, et ces résultats paraissent très encourageants.
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10

Shimizu, Karina. "Estudo do método de equalização da eletronegatividade no cálculo de energias livres de solvatação GBEEM-ELR." Universidade de São Paulo, 2005. http://www.teses.usp.br/teses/disponiveis/46/46132/tde-14092006-174816/.

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Анотація:
O método de equalização da eletronegatividade (Electronegativity Equalization Method, EEM), fundamentado em teoria do funcional da densidade eletrônica, foi combinado à aproximação de Born generalizada para moléculas (Generalized Born, GB), e denominado GBEEM (Dias et al., 2002). Os momentos de dipolo permanente no vácuo e em meio condensado (constante dielétrica ~ 80), e distribuições de cargas atômicas, mostraram boa concordância com modelo SM5.4 baseado em cargas CM1 em nível PM3 (12 moléculas, correspondendo a 29 cargas atômicas). Este resultado é interessante devido à simplicidade inerente do GBEEM e seu baixo custo computacional. Uma nova parametrização das durezas e eletronegatividades foi feita com o objetivo de melhorar a distribuição de cargas atômicas em moléculas isoladas em relação ao modelo CM1. Um conjunto de 250 estruturas/cargas PM3/CM1 de moléculas neutras pertencentes a 13 funções orgânicas foi utilizado como alvo na parametrização, utilizando uma metodologia Algoritmo Genético/Simplex de pesquisa de mínimos (Menegon et al., 2002). Boa concordância entre os modelos foi obtida. A validação da parametrização e do EEM foi efetuada usando moléculas bifuncionais (tetrapeptídeo e trisacarídeo) mostrando também boa concordância e robustez. Entretanto, a análise do momento de dipolo permanente das 250 moléculas mostrou uma séria limitação do EEM, e portanto do GBEEM, apesar da boa concordância entre as cargas EEM e CM1. O EEM superestimou os momentos de dipolo. Tal fato pode decorrer de vários fatores, dentre os quais, o truncamento da expansão nas cargas atômicas e ausência de tratamento explícito de interação de troca (exchange). Foi sugerida uma aproximação que restringe a transferência de carga entre grupos na molécula que contornou a limitação do método na predição de momentos de dipolo no vácuo e meio condensado (Shimizu et al., 2004). Com base nos recentes resultados, foi desenvolvido um modelo de solvatação baseado no GBEEM e no modelo de Floris-Tomasi. A calibração foi feita com um conjunto de 62 moléculas neutras (13 grupos funcionais) tendo como alvo as energias livres de hidratação experimentais. Os resultados apresentaram um desvio médio absoluto de 0,71 kcal/mol em relação aos valores experimentais.
The electronegativity equalization method (EEM), founded on density functional theory (DFT), has been combined to the generalized Born approximation (GB) for molecules, and called GBEEM (Dias et al., 2002). The permanent dipole moment in vacuum and condensed phase (dieletric constant ~ 80), and atomic charges distributions, have shown good agreement with SM5.4 solvation model based on CM1 charges at PM3 level (12 molecules, corresponding to 29 atomic charges). This result is interesting due the simplicity of GBEEM and its low computational cost. A new parameterization of the hardness and electronegativities was done with the aim to improve the atomic charges distribution on isolated molecules in comparison to CM1 model. The training set with 250 PM3/CM1 structures/charges of neutral molecules in 13 different organic functions was employed as target in the parameterization. A new optimization approach composed of Genetic and Simplex algorithms was used to fit parameters (Menegon et al., 2002). Good agreement between the models was found. The validation of parameterization and EEM was done using bifunctional molecules (tri-glucose and tetra-peptide) showing good agreement and robustness. However, analysis of permanent dipole moments of 250 molecules shown a serious caveat of EEM and GBEEM, beside the good agreement between EEM and CM1 charges. EEM has overestimated the dipole moments. Such result may be due to the truncated expansion in atomic charges and lacking of explicit treatment of exchange interaction. A new approximation was proposed constraining the charge transfer between groups within the molecule. This approximation corrected the caveat of EEM in the prediction of dipole moments in vacuum and condensed phase (Shimizu et al., 2004). Based on these results, a new solvation model was developed founded in GBEEM and Floris-Tomasi model. The parameterization was done with a training set of 62 neutral molecules (13 functional groups) and experimental hydration free energies as target. This new solvation model has produced a mean absolute deviation, MAD, of 0.71 kcal/mol comparing to experimental data.
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Частини книг з теми "Solvation energies"

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Purisima, Enrico O. "Calculation of Solvation Free Energies." In High Performance Computing Systems and Applications, 299–307. Boston, MA: Springer US, 1998. http://dx.doi.org/10.1007/978-1-4615-5611-4_29.

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Giesen, David J., Candee C. Chambers, Gregory D. Hawkins, Christopher J. Cramer, and Donald G. Truhlar. "Modeling Free Energies of Solvation and Transfer." In ACS Symposium Series, 285–300. Washington, DC: American Chemical Society, 1998. http://dx.doi.org/10.1021/bk-1998-0677.ch015.

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Warshel, A., and Z. T. Chu. "Calculations of Solvation Free Energies in Chemistry and Biology." In Structure and Reactivity in Aqueous Solution, 71–94. Washington, DC: American Chemical Society, 1994. http://dx.doi.org/10.1021/bk-1994-0568.ch006.

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Lim, Carmay, Shek Ling Chan, and Philip Tole. "Solvation Free Energies from a Combined Quantum Mechanical and Continuum Dielectric Approach." In Structure and Reactivity in Aqueous Solution, 50–59. Washington, DC: American Chemical Society, 1994. http://dx.doi.org/10.1021/bk-1994-0568.ch004.

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Muñoz, J., X. Barril, F. J. Luque, J. L. Gelpí, and M. Orozco. "Partitioning of Free Energies of Solvation into Fragment Contributions: Applications in Drug Design." In Mathematical and Computational Chemistry, 143–68. Boston, MA: Springer US, 2001. http://dx.doi.org/10.1007/978-1-4757-3273-3_10.

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Marjolin, Aude, Christophe Gourlaouen, Carine Clavaguéra, Pengyu Y. Ren, Johnny C. Wu, Nohad Gresh, Jean-Pierre Dognon, and Jean-Philip Piquemal. "Toward accurate solvation dynamics of lanthanides and actinides in water using polarizable force fields: from gas-phase energetics to hydration free energies." In Highlights in Theoretical Chemistry, 115–28. Berlin, Heidelberg: Springer Berlin Heidelberg, 2012. http://dx.doi.org/10.1007/978-3-642-34450-3_10.

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7

Nitzan, Abraham. "Solvation Dynamics." In Chemical Dynamics in Condensed Phases. Oxford University Press, 2006. http://dx.doi.org/10.1093/oso/9780198529798.003.0022.

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Solvent dynamical effects on relaxation and reaction process were considered in Chapters 13 and 14. These effects are usually associated with small amplitude solvent motions that do not appreciably change its configuration. However, the most important solvent effect is often equilibrium in nature—modifying the free energies of the reactants, products, and transition states, thereby affecting the free energy of activation and sometime even the course of the chemical process. Solvation energies relevant to these modifications can be studied experimentally by calorimetric and spectroscopic methods, and theoretically by methods of equilibrium statistical mechanics. With advances of experimental techniques that made it possible to observe timescales down to the femtosecond regime, the dynamics of solvation itself became accessible and therefore an interesting subject of study. Moreover, we are now able to probe molecular processes that occur on the same timescale as solvation, making it necessary to address solvation as dynamic in addition to energetic phenomenon. This chapter focuses on the important and most studied subclass of these phenomena—solvation dynamics involving charged and polar solutes in dielectric environments. In addition to their intrinsic importance, these phenomena play a central role in all processes involving molecular charge rearrangement, most profoundly in electron transfer processes that are discussed in the next chapter. Consider, as a particular example, a neutral (q = 0) atomic solute embedded in a dielectric solvent, that undergoes a sudden change of its charge to q = e, where e is the magnitude of the electron charge. This can be achieved, for example, by photoionization. The dipolar solvent molecules respond to this change in the local charge distribution by rotating in order to make their negative end point, on the average, to the just formed positive ion. Thus, the solvent configuration changes in response to the sudden change in a local charge distribution. The driving force for this change is the lowering of overall free energy that accompanies the buildup of solvent polarization.
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Mate, C. Mathew, and Robert W. Carpick. "Physical Origins of Surface Forces." In Tribology on the Small Scale, 181–233. Oxford University Press, 2019. http://dx.doi.org/10.1093/oso/9780199609802.003.0007.

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The energies and forces between contacting surfaces originate from the interaction forces between atoms and molecules. This chapter discusses how these atomic level forces lead to various types of force–separation relations as two surfaces are brought into contact. This chapter covers the interactions between atoms (repulsive atomic potentials and van der Waals interactions), the interactions within liquid and aqueous media (solvation forces, electrostatic double layer, hydration repulsion, hydrophobic attraction), and electrostatic interactions from contact electrification. Due to their ubiquitous effect on adhesion, van der Waals interactions are discussed at length, including examples for calculating adhesive forces in different geometries using Hamaker constants.
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Peschke, Michael, Arthur T. Blades, and Paul Kebarle. "3 Determination of sequential metal ion-ligand binding energies by gas phase equilibria and theoretical calculations: Application of results to biochemical pr." In Metal Ion Solvation and Metal-Ligand Interactions, 77–119. Elsevier, 2001. http://dx.doi.org/10.1016/s1075-1629(01)80005-1.

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Fawcett, W. Ronald. "Spectroscopic Studies of Liquid Structure and Solvation." In Liquids, Solutions, and Interfaces. Oxford University Press, 2004. http://dx.doi.org/10.1093/oso/9780195094329.003.0009.

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Spectroscopy involves the study of the interactions of electromagnetic radiation with matter. In the case of liquids, radiation of a wide range of frequencies, and thus energies, has been used, all the way from radio-frequency waves to X-rays. Experiments involving neutrons, which are associated with very short wavelengths, are also important. In the spectroscopic experiment the incident radiation may be either absorbed or scattered and the experimental information is obtained by examining the intensity and direction of the radiation after it has passed through the sample. Several spectroscopic techniques will be considered in this chapter. X-ray and neutron diffraction techniques are powerful tools for studying the structure of liquids and have been introduced in chapter 2. They may also be used to study the structure of solutions and determine distribution functions for both the solute and solvent. The feasibility of these experiments depends on the number of different nuclei involved in the system. UV-visible spectroscopy is mainly used to study electronic transitions in polyatomic species. These species are often complex ions formed between the electrolyte and the solvent, or between the cation and one or more anions. Vibrational spectroscopy involves electromagnetic radiation of lower energy, usually in the infrared region. It is used to study intramolecular vibrational modes and how they are altered by the environment in solution. It can also be used to study the bonds formed between solute and solvent in the solvation process. Finally, nuclear magnetic resonance spectroscopy and its application to the study of solvation will be discussed. This is a particularly powerful technique because it provides information about the environment of a given nucleus, and experiments specific to a given nucleus can be carried out provided the nucleus has a non-zero magnetic moment. Several other spectroscopic techniques are commonly used [G1] but those considered here provide a representative picture of what can be learnt from those experiments. One should remember that the atoms and molecules in liquids are not motionless but in a state of flux determined by the intermolecular interactions and temperature. From the study of microwave spectroscopy discussed in chapter 4, it was found that rotational diffusion processes in liquids are characterized by relaxation times the order of a few picoseconds.
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Тези доповідей конференцій з теми "Solvation energies"

1

Maréchal, M., and J. L. Souquet. "Accurate Conductivity Measurements to Solvation Energies in Nafion®." In Proceedings of the 10th Asian Conference. WORLD SCIENTIFIC, 2006. http://dx.doi.org/10.1142/9789812773104_0059.

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Queiroz, Nayhara B. D. F., and M. S. Amaral. "EFEITOS DE MICRO-HIDRATAÇÃO EM PROPRIEDADES CONFORMACIONAIS E ESPECTROSCÓPICAS DO ANTIBIÓTICO MARBOFLOXACINO." In VIII Simpósio de Estrutura Eletrônica e Dinâmica Molecular. Universidade de Brasília, 2020. http://dx.doi.org/10.21826/viiiseedmol2020177.

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Marbofloxacin (MRB) is a fluoroquinolone used as a veterinary antibiotic. Some analytical methods of optical absorption are used for their determination in pharmaceutical formulations. Thus, we decided to study the electronic absorption spectrum of MRB in the UV-Vis region. For this, we use the TD-DFT, COSMO methods - based on the solvation continuum model - and micro-hydration. The interactions of MRB in both water and vacuum were simulated using computational modeling techniques. Ab initio quantum calculations were used to optimize the geometry of the isolated molecule and in the optical transition energy calculations. The solute-solvent simulation was performed with the Molecular Dynamics technique in the NpT ensemble using a temperature of 300 K in the Amber computer package. The system balance was monitored by Root Mean Square Deviation. The analyzes of the absorption spectra were carried out using the micro-hydration method. This method involved the use of different numbers, from 2 to 8, of the water molecules of the first solvation layer to calculate transition energies. The transition energies were calculated using the TD-DFT method at the theory level B3LYP / 6-311G using together the Conductor-like Screening Model solvation model that assesses the effect of the solvent implicit in the system. For all micro-hydration systems, energy absorption decreases as the wavelength increases. Observing the values it is noticed that there was a deviation in the absorption spectrum 325.4 nm (in the isolated molecule) to 274.1 (with the addition of water). These values are within the experimental ones where we have the bands with maximum absorption at 268 nm and 335 nm.
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Hinde, Robert. "STEERING H-ATOM DIFFUSION THROUGH IMPURITY-DOPED SOLID PARAHYDROGEN: THE ROLE OF DIFFERENTIAL SOLVATION ENERGIES." In 69th International Symposium on Molecular Spectroscopy. Urbana, Illinois: University of Illinois at Urbana-Champaign, 2014. http://dx.doi.org/10.15278/isms.2014.ri06.

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4

Rodrigues, Allane C. C., Priscila Gomes, Ademir João Camargo, and Heibbe C. B. Oliveira. "Estudo da Energia Livre de Formação das Ligações de Hidrogênio da Dopamina em Solução Aquosa Usando CPMD." In VIII Simpósio de Estrutura Eletrônica e Dinâmica Molecular. Universidade de Brasília, 2020. http://dx.doi.org/10.21826/viiiseedmol2020105.

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Dopamine is an important neurotransmitter belonging to the catecholamine family, which acts on the central nervous system. This catecholamine plays a key role in regulating a variety of functions, such as motor and cognitive functions. This class of neurotransmitters is important for normal neurophysiology and is also the target of a broad spectrum of therapeutic and illicit agents. Evaluating the interaction of these neurotransmitters, in particular, dopamine with water molecules, is crucial for a better understanding of the conformational preferences of dopamine in solution, which consequently assists in the design of new drugs for the treatment of diseases associated with a malfunction of the system, and direct measurement, which is particularly essential for early warning of certain diseases. In this sense, the objective of this work is to examine the effects of aqueous solvation on the geometric and electronic parameters of dopamine using Car-Parrinelo Molecular Dynamics. The Car-Parrinello Molecular Dynamics simulation was performed using the CPMD program package (Version 4.1). The results indicate that dopamine interact swith several water molecules, with the formation of hydrogen bonds. In particular, there are two hydrogen bonds (H5···Owf and N3···Hwd) with an infinite residence time that strongly suggests the protonation of these groups.
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