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Adamovic, Ivana. "Solvation!" Washington, D.C. : Oak Ridge, Tenn. : United States. Dept. of Energy. Office of Science ; distributed by the Office of Scientific and Technical Information, U.S. Dept. of Energy, 2004. http://www.osti.gov/servlets/purl/835373-NLtQXD/webviewable/.
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19 Dec 2004.Published through the Information Bridge: DOE Scientific and Technical Information. "IS-T 2009" Ivana Adamovic. 12/19/2004. Report is also available in paper and microfiche from NTIS.
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Yokogawa, Daisuke. "Development of solvation theories focused on solvation structure and electronic structure". 京都大学 (Kyoto University), 2008. http://hdl.handle.net/2433/66209.
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Amman, Nahom. "The Solvation Chemistry of Polyoxometalates". Thesis, Umeå universitet, Kemiska institutionen, 2020. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-173088.
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Doyle, Carrie C. "Interfacial Potentials in Ion Solvation". University of Cincinnati / OhioLINK, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1595499330707637.
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Carlotto, Silvia. "Modeling of dynamic solvation effects". Doctoral thesis, Università degli studi di Padova, 2008. http://hdl.handle.net/11577/3426266.
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Reactivity of molecular and supramolecular systems is greatly modified by the surrounding environment, often a fluid medium, and an active area of research is nowadays the study of the influence of a solvent structure on the static and dynamic properties of photo-active and paramagnetic probes, varying solvent properties, sample geometry and external perturbations.
Standard continuum solvent theories are based on crude representations of the probe. Solvation processes depend in a specific way upon the structure of the solute, and in particular on molecular features as shape, flexibility, distribution of charges and anisotropy of the polarizability. Augmented solvent continuum approaches have been developed to interpret chromophore dynamics to account for persistent solvent local structures. Description of collective solvent modes is also necessary to understand relaxation processes affecting dynamics at longer times, in complex fluid environments: phase transitions in supercooled liquids, rheological properties of emulsions and colloids, confinement effects and finally micro and nano-probes dynamics. The inclusion of solvent effects is of great importance, in order to understand the physical mechanisms responsible of the tuning of the optical properties and therefore to the ultimate possibility to design nanomaterials with specific optical response. Theoretical methodologies based on stochastic and hydrodynamic modeling have proven over the years to be a powerful approach, especially when coupled with advanced quantum mechanical treatments, to describe effectively the dynamical aspects of solvation. The relationship between spectroscopic measurements and molecular properties can be gathered only indirectly, that is, structural and dynamic molecular characteristics can be inferred by the systematic application of modelling and numerical simulations to interpret experimental observables. A straightforward way to achieve this goal is the employment of spectroscopic evidence as the "target" of a fitting procedure of molecular, mesoscopic and macroscopic parameters entering the model. A more refined methodology is based on the combination of quantum mechanical calculations of structural parameters possibly including environmental and fast vibrational and librational averaging, and direct feeding of calculated molecular parameters into dynamic models based on molecular dynamics, coarse grain dynamics, and above all stochastic modeling or a combination of the three.
Our main objective in this PhD work has been to discuss the degree of progress of advanced theoretical models are explored, aimed at clarifying the influence of solvent-driven relaxation processes on optic, magnetic and rheological observables. In particular we have developed integrated computational approaches to the interpretation of fluorescence emission of organic molecules in solvated environments, CW-ESR spectroscopy and rheological properties of ordered systems via combination of advanced quantum mechanical approaches, stochastic modeling of relaxation processes, and, in the last case, macroscopic models.
In the first period we have shown that the model proposed is able to reproduce the spectral position and shape of the emission spectra. In particular the model reproduces the red shift expected for TICT excited states when the dielectric constant of the solvent increases. We developed a stochastic approach to the interpretation of the emission fluorescence of 4-(N,N-dimethylamino) benzonitrile (DMABN). Than we proceed by extending the modeling approach, in which internal degrees of freedom are coupled with an effective solvent relaxation variable. The extension of the model is applied to the simulation of the emission spectra of DMABN-Crown5, a DMABN derivative. Evaluation of potential energy surfaces using advanced QM approach and estimates of dissipative parameters based on hydrodynamic arguments are discussed. Emission fluorescence is calculated by solving a diffusion/sink/source equation for the stationary population of excited state, and compared to experimentally measured emission fluorescence of DMABN and DMABN-Crown5. Next we developed the complete a priori simulation of the ESR spectra of complex systems in solution. The usefulness and reliability of the method are demonstrated on the very demanding playground represented by the tuning of the equilibrium between 310- and ?-helices of polypeptides by different solvents. The starting point is good agreement between computed and X-ray diffraction structures for the 310-helix adopted by the double spin-labelled heptapeptide Fmoc-(Aib-Aib-TOAC)2-Aib-OMe. Next, density functional computations, including dispersion interactions and bulk solvent effects, suggest another energy minimum corresponding to an ?-helix in polar solvents, which, eventually, becomes the most stable structure. Computation of magnetic and diffusion tensors provides the basic ingredients for the building of complete spectra by methods rooted in the Stochastic Liouville Equation (SLE). The remarkable agreement between computed and experimental spectra at different temperatures allowed us to identify helical structures in the various solvents. The generality of the computational strategy and its implementation in effective and user-friendly computer codes pave the route toward systematic applications in the field of biomolecules and other complex systems. Finally, the purpose of the last part of the PhD period has been to analyze the dynamical behavior of a low viscosity nematic liquid crystals in presence of micro-size probe. We present a study of the translational friction coefficients of spherical and ellipsoidal probes moving in nematic liquid crystalline fluids, by solving numerically the constitutive hydrodynamic equations of nematic. The evaluation of the translational friction coefficients is based on a numerical solution of Leslie-Ericksen constitutive equations for the case of incompressible nematic fluids. The nematic medium is described by a vector field which specifies the director orientation in each point and by the velocity vector field. Simulation of director dynamics surrounding the moving probe are presented, and the dependence of translational diffusion upon liquid crystal viscoelastic parameters is discussed. The time evolution of director field, described by Leslie-Ericksen equations, is studied in the presence of an orienting magnetic field in two characteristic situations: director of motion parallel and perpendicular to field.
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Archer, Geoffrey Philip. "Spectroscopic studies of solvation : Part 1, Solvation of thiols; Part 2, Hydration of deoxyribonucleic acid". Thesis, University of Leicester, 1989. http://hdl.handle.net/2381/35412.
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The extent of hydrogen bonding in ethanethiol is determined using a correlation between the chemical shift of the sulphydryl proton and the stretching frequencies of the component bands of the vS-H infrared band The component bands having stretching frequencies at 2585 cm-1 and 2570 cm-1 for non hydrogen bonded and mono-hydrogen bonded thiol groups respectively. It is calculated that the pure liquid at 22°C. contains ca. 49% free SH bonds. A dimerisation constant of 0.038 dm3 mol-1 is estimated at 22°C. 2-Hydroxyethanethiol is used to investigate the strength of hydrogen bonding to the thiol group in aqueous solutions. The results of the IR and NIR studies are consistent with the formation of hydrogen bonds of S-H O type between thiol and water molecules. Salt and solvent effects upon the phosphate and thiophosphate groups of Sodium Dimethyphosphate (NaDMP) and Sodium Dimethylthiophosphate (NaDMSP) are investigated. Infrared spectra in the and v3P-O of DMP and DMSP suggest that the order of strength of binding of metal ion to phosphate/thiophosphate group is Na+ < Mg2+ < Ca2f. The results indicate that solvent-separated ion pairs dominate in aqueous solutions, whereas, mono- and bi-dentate contact ion pairs are favoured in DMSO and methanol solutions. The thiophosphate group is solvated by methanol and water, primarily at the oxygen site. No evidence was found to support hydrogen bond formation to the anionic sulphur site. Infrared spectra were also consistent with Mg2+ and Ca2+ interacting with the Oxygen atom, but not the Sulphur atom. DNA hydration is investigated using high field NMR spectrometry. Frozen aqueous DNA solutions were found to have a broad NMR signal due to hydration water. From this signal it is estimated that, at -12°C., the DNA samples are hydrated by ca. 25 water molecules per base pair of DNA.
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Patel, Kirankumar B. "Studies of solvation by spectroscopic methods". Thesis, University of Leicester, 1985. http://hdl.handle.net/2381/33846.
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The work described in this thesis is concerned with the use of relatively simple compounds in dilute solution to study solvation phenonena. Spectroscopic techniques such as infrared and NMR have been used to follow the environment of the 'probe' throughout various mixed and pure solvent states. The potential of NMR spectroscopy to solvation has been explored. Solvent effects on the resonance show that the sensitivity decreases in the order phosphine oxides - phosphonates - phosphates. This trend is also seen amongst carbonyl ccmpounds where the NMR sensitivity decreases in the order ketones - acetates - carbonates. It is thought that the paramagnetic contribution to the chenical shift may be inportant in dictating these shifts. Based on the evidence of previous work, it was always accepted that water formed the hydrate with maximum solvation number. The results from the ester study are important since it may be a mistake to assume such fixed solvation. The fundamental infrared work incorporates a study that investigates the relevance of coupling in systems such as phosphate mono-anions, carboxylate anions and others. The results for the phosphate mono-anions shew that the coupling between the P-O modes is sensitive to solvent perturbations. This trend is also partly seen amongst the carboxylate anions. Finally, the validity of Gutmann's Acceptor Number is examined. It is concluded that this solvent scale is only applicable to solvated states that are identical with those for triethylphosphine oxide.
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Day, Tyler James Frederick. "Ion solvation dynamics in binary solvents". Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1999. http://www.collectionscanada.ca/obj/s4/f2/dsk1/tape7/PQDD_0021/NQ46338.pdf.
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Johansson, Anna CV. "Solvation properties of proteins in membranes". Doctoral thesis, Stockholms universitet, Institutionen för biokemi och biofysik, 2009. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-27437.
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Knowledge about the insertion and stabilization of membrane proteins is a key step towards understanding their function and enabling membrane protein design. Transmembrane helices are normally quite hydrophobic to insert efficiently, but there are many exceptions with unfavorable polar or titratable residues. Since evolutionary conserved these amino acids are likely of paramount functional importance, e.g. the four arginines in the S4 voltage sensor helix of voltage-gated ion channels. This has lead to vivid discussion about their conformation, protonation state and cost of insertion. To address such questions, the main focus of this thesis has been membrane protein solvation in lipid bilayers, evaluated using molecular dynamics simulations methods. A main result is that polar and charged amino acids tend to deform the bilayer by pulling water/head-groups into the hydrophobic core to keep their hydrogen bonds paired, thus demonstrating the adaptiveness of the membrane to allow specific and quite complex solvation. In addition, this retained hydration suggests that the solvation cost is mainly due to entropy, not enthalpy loss. To further quantify solvation properties, free energy profiles were calculated for all amino acids in pure bilayers, with shapes correlating well with experimental in vivo values but with higher magnitudes. Additional profiles were calculated for different protonation states of the titratable amino acids, varying lipid composition and with transmembrane helices present in the bilayer. While the two first both influence solvation properties, the latter seems to be a critical aspect. When the protein fraction in the models resemble biological membranes, the solvation cost drops significantly - even to values compatible with experiment. In conclusion, by using simulation based methods I have been able to provide atomic scale explanations to experimental results, and in particular present a hypothesis for how the solvation of charged groups occurs.
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Gosal, Nrinder Singh. "Solvation and reactivity of inorganic complexes". Thesis, University of Leicester, 1985. http://hdl.handle.net/2381/33692.
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A simplified description is given of the operation of a multiwire proportional chamber (MWPC) in the soft X-ray imaging application. Expressions are developed to allow the calculation of the distribution of induced charge on the cathodes of an MWPC. With extensions to permit direct comparison, the calculations are subjected to detailed experimental verification. A generalised, approximate formulation of the distribution with one independent parameter is described. The prediction of cathode system position response using the theoretical distributions is demonstrated. The available MWPC position readout methods are reviewed, and where possible their differential non-linearity is measured experimentally. A new position-sensitive cathode of good linearity and spatial resolution is presented. The effect of the wires of an MWPC on its imaging performance is briefly considered. An attempt is made to assess the contribution to MWPC spatial resolution of the range of the electrons produced initially by an X-ray absorption event in argon-methane mixtures. In conclusion, the important causes of MWPC imaging imperfection are noted and classified.
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Kile, Jennifer Lynn. "Solvation Energy Calculations of Homologous Trimethylammoniocarboxylates". Thesis, Virginia Tech, 2004. http://hdl.handle.net/10919/10127.
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Calculating the solvation energies of surfactants is a way to predict the cmc. The solvation energies were determined for a homologous series of betaines, (CH₃)₃N+(CH₂)nCOO- where n = 1 to 6. Their structure is composed of only the hydrophilic head group of a surfactant. The solvation energies were determined from both the gas phase energy and free energy of solution. Conformational analysis was performed on each molecule to locate the lowest energy structures and determine the Boltzmann population of each conformation for each molecule. The final solvation energies for each molecule are expectation values based on their energies and Boltzmann populations. The plotted solvation energies versus n form a parabolic curve that is similar to the literature cmc data where the betaine has a long hydrocarbon tail. However, the solvation energies peak at n = 3 and the cmc data peaks at n = 4. The dipole moments were also examined. The gas phase dipole moments were graphed and have a maximum at n = 3, similar to the solvation energy. The solution dipole moments have a linear graph, not comparable to the solvation energies. Therefore, the stability of the gas phase structures contributes more to the final solvation energy than the stability of the molecule in water.
The correlation between the plots of log cmc vs n and solvation energy vs n indicates that it is possible to computationally predict the cmc with this method. The hydrophobic contribution can be accounted for based on a known correlation between chain length and the cmc, and the hydrophilic contribution can be examined with this method. Therefore, it is possible to design a new surfactant molecule that has a cmc within the range of the biological activity to be sent for synthesis.Master of Science
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Álvarez, García Daniel. "Protein solvation preferences: applications to drug discovery". Doctoral thesis, Universitat de Barcelona, 2014. http://hdl.handle.net/10803/285451.
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Computer-aided drug design is a key player in current drug discovery projects. Structure-based computational approaches use the target structural information to suggest potentially active and safe drugs. However, the process is far from trivial and novel methodologies are continuously sought to address two main factors usually simplified and overlooked: Target flexibility and the effect and structure of water molecules at the binding site.
As demonstrated by different NMR and crystallography experiments, small organic solvents (e.g. ethanol, isopropanol, acetonitrile) are able to identify binding sites and provide clues for rational drug design. MDmix is a simulation-based method that exploits this natural behavior in silico. By using small organic molecules and water mixtures, each one with a distinct chemical nature, key interaction spots are identified on the protein surface allowing the identification and characterization of binding sites for hit discovery and lead optimization.
The work presented in this thesis is divided in two main publications: In the first one, the effect of target flexibility was investigated to establish some guidelines on how to treat this important factor during the simulations. We found that flexibility is essential for correctly identifying induced binding sites but might lead to uninterpretable results when large conformational changes occur. Soft restraints applied during the simulation are suggested as a way to obtain reproducible results and still characterize high affinity interaction sites (hot spots) with mild errors on the energy estimates.
In the second publication, the use of solvent mixtures for the identification of experimentally known pharmacophores was evaluated in two test systems for which many inhibitors are known (e.g. heat shock protein 90 and HIV protease 1). The explicit treatment of water molecules provides interaction maps which identify the most favorable interactions in the binding site with unprecedented accuracy when compared to classical molecular interaction potentials. Moreover, we demonstrate how the interaction maps obtained for the water molecules accompanying the small organic solvents are useful to identify non-displaceable waters. Both the solvent interaction maps and the water interaction maps are extremely useful information for the identification of novel active molecules and for the optimization of potency for already active ones.
Finally, a software package is presented that aims at facilitating the use of the methodology and at helping in adopting it to everyday drug design projects. A final chapter treats ongoing and future research where method improvements and practical uses in real examples are discussed.
MDmix being a simulation-based method, the target flexibility and the explicit treatment of the solvent provide significant advantages over traditional approaches for binding site finding and characterization. This novel approach, which is applicable to previously unmet targets and binding sites, offers a new alternative in the challenging process of drug design.El diseño de fármacos asistido por ordenador es actualmente un actor fundamental en el proceso de descubrimiento de nuevos fármacos. Las aproximaciones basadas en estructura usan la información estructural de la Diana terapéutica para proponer moléculas activas y seguras. Sin embargo, el proceso dista de ser sencillo y nuevas metodologías están continuamente siendo investigadas para solventar las limitaciones actuales, siendo la flexibilidad de la diana y el tratamiento y la estructura del agua en la cavidad, dos factores usualmente obviados o simplificados. Como ha sido demostrado por varios experimentos de NMR y cristalografía, moléculas pequeñas de solventes orgánicos (p.e. etanol, acetamida o acetonitrilo), son capaces de identificar sitios de unión y proporcionan pistas para el diseño racional de nuevas moléculas bioactivas. MDmix es un método basado en simulación molecular que explota dicho fenómeno in silico. Usando mezclas de moléculas orgánicas pequeñas y agua, cada una con propiedades químicas diferentes, se identifican mapas energéticos de interacción sobre la superficie de la diana. Esta información nos permite identificar sitios de unión para ligandos y caracterizar dicha interacción para guiar el proceso de identificación de hits y la optimización de cabezas de serie. El trabajo presentado en esta tesis se puede dividir en dos publicaciones principales: En la primera, el efecto de la flexibilidad de la diana es estudiado para establecer unas guías de actuación a la hora de simular el sistema. Encontramos que la flexibilidad es fundamental a la hora de identificar cavidades inducidas o con alto grado de flexibilidad pero, a la vez, la interpretación de los resultados es mucho más compleja cuando hay cambios conformacionales. Por otra banda, aplicando restricciones suaves a la movilidad de los átomos, se gana reproducibilidad en los resultados y los errores en la estimación energética son mínimos. En la segunda publicación, se estudió el uso de diferentes mezclas de solventes para la identificación de farmacóforos experimentales en dos sistemas test (heat shock protein 90 y HIV proteasa 1). El tratamiento explícito del agua proporciona mapas energéticos capaces de identificar correctamente los puntos de interacción más favorables con una precisión sin precedentes cuando se compara con otros métodos. Además, demostramos como los mapas energéticos obtenidos para las moléculas de agua son capaces de discernir entre aguas desplazables y no desplazables por un potencial ligando. La información extraída de dichos mapas puede ser de alta utilidad para guiar la identificación de nuevas moléculas activas y para la optimización de la potencia de ligandos ya identificados. Finalmente, se presenta un programa de código abierto escrito en python cuyo objetivo es facilitar el uso de la metodología así como su adopción en cualquier proyecto de diseño de fármacos. En el capítulo final se discuten posibles mejoras y aplicaciones prácticas del método en proyectos actualmente en investigación y direcciones futuras a seguir. MDmix, siendo un método basado en simulación molecular, permite incorporar la flexibilidad de la diana y tratar explícitamente el efecto del solvente. Por ello, ofrece ventajas significativas sobre aproximaciones tradicionales en la identificación de sitios de unión y su caracterización. Siendo aplicable sobre cualquier diana, aún sin conocimiento previo, ofrece una nueva alternativa en el siempre desafiante proceso del diseño de fármacos.
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Murdock, Stuart Erwin. "Atomistic simulation of solvation thermodynamics and structure". Thesis, Queen's University Belfast, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.368478.
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Chacko, Blesson. "Hydrophobicity, solvation and structure formation in liquids". Thesis, Loughborough University, 2017. https://dspace.lboro.ac.uk/2134/27536.
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In this thesis we use density functional theory (DFT) to study the solvent mediated interactions between solvophobic, solvophilic and patchy nanostructures namely rectangular cross section blocks. We calculate both the density profiles and local compressibility around the blocks and the results obtained for our model system provide a means to understanding the basic physics of solvent mediated interactions between nanostructures, and between objects such as proteins in water, that possess hydrophobic and hydrophilic patches. Our results give an improved understanding of the behaviour of liquids around solvophobic objects and solvophobicity (hydrophobicity) in general. Secondly, we look into the physics incorporated in standard mean-field DFT. This is normally derived by making what appears to be a rather drastic approximation for the two body density distribution function: ρ(2)(r,r′) ≈ ρ(r)ρ(r′), where ρ(r) is the one-body density distribution function. We provide a rationale for why the DFT often does better than this approximation would make you expect. Finally, we develop a lattice model to understand the nature of the pattern formation exhibited by certain systems of particles deposited on liquid-air interfaces and in particular the nature of the transitions between the different patterned structures that are observed. This is done using Monte Carlo computer simulations and DFT and links the observed microphase ordering with the micellisation process seen e.g. in surfactant systems.
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Basa, Ma Leah Terencia Navarro. "Ionic Liquids: Solvation Characteristics and Cellulose Dissolution". University of Toledo / OhioLINK, 2010. http://rave.ohiolink.edu/etdc/view?acc_num=toledo1273730112.
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Pang, Teck Siong. "Thermodynamics of ion-solvation in nonaqueous solutions". Thesis, Pang, Teck Siong (1995) Thermodynamics of ion-solvation in nonaqueous solutions. PhD thesis, Murdoch University, 1995. https://researchrepository.murdoch.edu.au/id/eprint/51562/.
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This thesis is concerned with the study of the thermodynamics of ion-solvation in pure organic solvents and in aqueous organic solvent mixtures. The thermodynamic quantities studied are enthalpy, entropy, partial molal volume and partial molal heat capacity.
As the partial molal volumes and heat capacities of electrolytes in organic solvents are relatively unexplored, a review is deemed to be useful and is treated as a major part of the thesis. The review includes a survey of reported data together with summaries of methods for determining partial molal quantities of electrolytes and ions.
Heats of solution of electrolytes were measured calorimetrically in acetonitrilewater, ethanol-water and ethylene glycol-water mixtures and standard enthalpies and entropies of transfer calculated. In addition, densities and heat capacities of electrolytes in ethanol-water mixtures were also measured and apparent molal volumes and heat capacities of transfer calculated. A reference electrolyte method based on tetraphenylphosphonium tetraphenylborate (TPTB) was used to obtain the ionic values. The dependence of the thermodynamic transfer quantities on solvent composition is discussed in terms of sol vent-solvent interactions.
Densities and heat capacities of electrolytes were also measured in pure ethanol, N,N-dimethylformamide, N-methylfomamide, dimethylsidphoxide and nitromethane and ionic partial molal volumes and heat capacities determined again using the TPTB assumption. Except for N, N-dimethylformamide and dimethylsulphoxide, the Hepler equation is (mostly) in agreement with the ionic volumes. The depart ure of the ionic volumes from the Hepler model for these two solvents is attributed to steric hindrance. A statistical analysis was carried out to relate ionic mo!a! volumes to ion and solvent properties. For large ions such as RX. Ph4P and BPhf, ionic radius (as r3) and solvent molar volume were found to be the dominating factors while ionic radius (also as r3), ion hydrogen bonding ability and the solvent solubility parameter are significant for the small ions.
Ionic partial molal heat capacities are discussed in terms of the theory of Frank and Wen. Cp° (str) (solution structure contribution) were obtained by subtracting Cp° (int) (intrinsic heat capacity) from Cp° and were explained in terms of solvent properties.
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Spadina, Mario. "Solvation and Ion Specificity in Complex Media". Thesis, Montpellier, 2019. http://www.theses.fr/2019MONTS020/document.
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Le but de cette thèse était de créer des modèles pour deux applications qui apparaissent couramment en chimie séparative, à savoir la séparation solide-liquide et la séparation liquide-liquide. L'avantage de la modélisation est manifeste dans les deux cas. L'étude fondamentale des propriétés des ions et de leur solvatation dans les milieux complexes, en tenant compte de façon simplifié des différents effets mis en jeu, nous a permis de construire un cadre qui utile aussi bien aux chimistes en laboratoire qu’aux ingénieurs lors de la conception des procédés. Nous avons adapté cette stratégie sur deux systèmes différents, qui peuvent tous deux être considérés comme complexes. Le premier système modèle pour étudier la séparation solide-liquide était des nanotubes de TiO2 dispersés dans une solution aqueuse. Ce système a été étudié au moyen de la Théorie de la Fonctionnelle de la Densité Classique couplée à une méthode de régulation de charge, au sein de l'ensemble Grand-Canonique. La méthode s'est avérée efficace pour établir la description complète des propriétés de charge des nanotubes de TiO2. Dans ce cas, nous nous sommes intéressés à obtenir la description de l'ion à l'intérieur des nanotubes chargés sous l'influence du champ électrique (créé par les nanotubes). Les calculs ont prédit des effets tels que la différence de charge de surface entre la surface externe et la surface interne, ou la violation de l'électroneutralité à l'intérieur des nanotubes. Il a été démontré que le modèle était en accord avec les données expérimentales. De plus, la méthode peut être utilisée directement pour prédire diverses techniques de titrage. Une simple généralisation de l'approche proposée permettra d'étudier l'efficacité d'adsorption réelle du procédé de séparation solide-liquide. Le second système modèle concerne l'étude du procédé d'extraction liquide-liquide et il comprend trois parties distinctes. Les trois parties ont été consacrées aux cas des extractants non ioniques, puis acides (échangeurs d'ions), et enfin aux mélanges synergiques d'extractants. Un modèle simple de thermodynamique statistique, dans lequel nous avons incorporé certains des concepts bien établis en chimie colloïdale, a fourni une approche de type matière molle pour calculer le processus à l'échelle de l'ingénieur. Nous avons développé une approche classique d'équilibres simples pour une compréhension plus large et plus intuitive de la formation des agrégats polydisperses dans l'extraction liquide-liquide. La principale conclusion présentée est que l’on doit proposer un nouveau paradigme pour la chimie : à l'équilibre, de nombreux agrégats de composition très différente mais similaires en énergie libre, coexistent. Avec la polydispersité obtenue, nous avons ainsi proposé un outil pour étudier un comportement plus "global" de l'extraction liquide-liquide. Cela nous a poussés à passer des considérations classiques d'isothermes d'extraction à celles plus précises des " cartes " d’extraction. Un grand soin a été apporté à l'étude de la synergie puisqu'il s'agit d'une important question depuis 60 ans dans la communauté scientifique et industrielle de la séparation. A notre connaissance, la première rationalisation quantitative de la synergie d’extraction a été proposée dans le cadre de cette thèse. Les effets sous-jacents des contrôles enthalpique et entropique sur la structuration des phases organiques ont été découplés et étudiés en détail. Nous espérons que cette thèse a démontré l'importance de la modélisation mésoscopique sur des exemples pratiques utilisés à la fois par les chimistes et les ingénieursThe object of this thesis was to create models for two applications which readily appear in separation chemistry, namely the solid-liquid and the liquid-liquid extractions. The benefit of modelling in both cases is twofold. Studying the fundamental properties of ions and their solvation properties in the complex media, and simplifying the expression for important effects, enables us to construct the framework which can be used by both chemists in the laboratory, as well as the chemical engineers in the process design. For two applications we adapted two different systems, both of which can be considered as complex. The model system to study the solid-liquid separation were TiO$_{mathrm{2}}$ nanotubes dispersed in the aqueous solution. This system was studied by the means of Classical Density Functional Theory coupled with the charge regulation method, within the Grand-canonical ensemble. Indeed, the method proved to be successful in establishing the full description of the charge properties of TiO$_{mathrm{2}}$ nanotubes. In this case, we were interested in obtaining the description of ion inside the charged nanotubes under influence by the electric field (exhibited by nanotubes). Calculations predicted effects such as the difference in surface charge between the outer and the inner surface, or the violation of electroneutrality inside the nanotubes. It was demonstrated that the model was in the agreement with the experimental data. Moreover, the method can be directly used to predict titration for various techniques. A simple generalization of the proposed approach can be used to study the actual adsorption efficiency of the solid-liquid separation process. The model system to study the liquid-liquid extraction process included three distinct parts. The three parts were devoted to the cases on non-ionic, acidic ion exchangers, and finally the synergistic mixtures of extractants. Simple bulk statistical thermodynamics model, in which we incorporated some of the well-established concepts in colloidal chemistry provided a soft-matter approach for the calculation of actual engineering-scale processes. Were have expanded a classical simple equilibria approach to broader, more intuitive polydisperse aggregates formation that underlines the liquid-liquid extraction. The key finding can be presented as a current opinion or newly-proposed paradigm: at equilibrium, many aggregates completely different in composition but similar in free energy coexist. With obtained polydispersity, we were equipped with a tool to study a more 'global' behavior of liquid-liquid extraction. This urged us to pass our considerations of historical extraction isotherms to extraction 'maps'. Great care was devoted to the study of synergy since it is a 60-year old ongoing question in the separation industrial and science community. To our best knowledge, the first quantitative rationalization total synergistic extraction was proposed within this thesis. Underlying effects of enthalpy and entropy control on the organic phase structuring were decoupled and studied in detail. Hopefully, this thesis demonstrated the importance of mesoscopic modelling to assist both chemists and chemical engineers in practical examples
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Hart, Erin F. "Using the Abraham Solvation Parameter Model to Predict Solute Transfer into Various Mono- and Multi-Functional Organic Solvents". Thesis, University of North Texas, 2018. https://digital.library.unt.edu/ark:/67531/metadc1157615/.
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The Abraham Solvation Parameter Model (ASPM) is a linear, free-energy relationship that can be used to predict various solute properties based on solute-solvent interactions. The ASPM has been used to predict log (K or Cs,organic/Cs,gas) values, as well as log (P or Cs,organic/Cs,water) values for solute transfer into the following organic solvents: 2-methoxyethanol, 2-ethoxyethanol, 2-propoxyethanol, 2-isopropoxyethanol and 2-butoxyethanol. The derived log (K or Cs,organic/Cs,gas) correlations describe the experimental data to within 0.14 log units (or less). The derived log (P or Cs,organic/Cs,water) correlations describe the experimental data to within 0.16 log units (or less). The ASPM has also been used to predict the enthalpies of solvation of organic solutes dissolved in the following solvents: acetic acid, dimethyl carbonate, diethyl carbonate, 1-butanol, 1-pentanol, 1-hexanol. The derived enthalpy of solvation correlations, using the L solute descriptor, describe the experimental data to within 2.50 log units (or less). The derived enthalpy of solvation correlations, using the V solute descriptor, describe the experimental data to within 3.10 log units (or less). Validation analyses have been performed on several of the correlations; and, as long as the solute descriptors fall within the given ranges as reported, the original correlations show good predictive ability for determining 1) solute transfer into, and 2) enthalpy of solvation for the aforementioned solvents.
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Mintz, Christina. "Predicting Chemical and Biochemical Properties Using the Abraham General Solvation Model". Thesis, University of North Texas, 2009. https://digital.library.unt.edu/ark:/67531/metadc28373/.
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Several studies were done to illustrate the versatillity of the Abraham model in mathematically describing the various solute-solvent interactions found in a wide range of different chemical and biological systems. The first study focused on using the solvation model to construct mathematical correlations describing the minimum inhibitory concentration of organic compounds for growth inhibition towards the three bacterial strains Porphyromonas gingivalis, Selenomonas artemidis, and Streptococcus sobrinus. The next several studies expand the practicallity of the Abraham model by predicting free energies of partition in chemical systems. The free energy studies expand the use of the Abraham model to other temperatures and properties by developing correlations for the enthalpies of solvation of gaseous solutes of various compounds dissolved in water, 1-octanol, hexane, heptane, hexadecane, cyclohexane, benzene, toluene, carbon tetrachloride, chloroform, methanol, ethanol, 1-butanol, propylene carbonate, dimethyl sulfoxide, 1,2-dichloroethane, N,N-dimethylformamide, tert-butanol, dibutyl ether, ethyl acetate, acetonitrile, and acetone. Also, a generic equation for linear alkanes is created for use when individual datasets are small. The prediction of enthalpies of solvation is furthered by modifying the Abraham model so that experimental data measured at different temperatures can be included into a single correlation expression. The temperature dependence is directly included in the model by separating each coefficient into an enthalpic and entropic component. Specifically, the final study describes the effects of temperature on the sorption coefficients of organic gases onto humic acid. The derived predicted values for each research study show a good correlation with experimental values.
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Wang, Shu. "Thermodynamic properties predictions using the COSMO-SAC solvation method". Access to citation, abstract and download form provided by ProQuest Information and Learning Company; downloadable PDF file, 366 p, 2007. http://proquest.umi.com/pqdweb?did=1362532041&sid=24&Fmt=2&clientId=8331&RQT=309&VName=PQD.
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Carlsson, Jens. "Challenges in Computational Biochemistry: Solvation and Ligand Binding". Doctoral thesis, Uppsala University, Department of Cell and Molecular Biology, 2008. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-8738.
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Accurate calculations of free energies for molecular association and solvation are important for the understanding of biochemical processes, and are useful in many pharmaceutical applications. In this thesis, molecular dynamics (MD) simulations are used to calculate thermodynamic properties for solvation and ligand binding.
The thermodynamic integration technique is used to calculate pKa values for three aspartic acid residues in two different proteins. MD simulations are carried out in explicit and Generalized-Born continuum solvent. The calculated pKa values are in qualitative agreement with experiment in both cases. A combination of MD simulations and a continuum electrostatics method is applied to examine pKa shifts in wild-type and mutant epoxide hydrolase. The calculated pKa values support a model that can explain some of the pH dependent properties of this enzyme.
Development of the linear interaction energy (LIE) method for calculating solvation and binding free energies is presented. A new model for estimating the electrostatic term in the LIE method is derived and is shown to reproduce experimental free energies of hydration. An LIE method based on a continuum solvent representation is also developed and it is shown to reproduce binding free energies for inhibitors of a malaria enzyme. The possibility of using a combination of docking, MD and the LIE method to predict binding affinities for large datasets of ligands is also investigated. Good agreement with experiment is found for a set of non-nucleoside inhibitors of HIV-1 reverse transcriptase.
Approaches for decomposing solvation and binding free energies into enthalpic and entropic components are also examined. Methods for calculating the translational and rotational binding entropies for a ligand are presented. The possibility to calculate ion hydration free energies and entropies for alkali metal ions by using rigorous free energy techniques is also investigated and the results agree well with experimental data.
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Arslanargin, Ayse. "Ion solvation in aqueous and non-aqueous solvents". University of Cincinnati / OhioLINK, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1439281594.
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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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Lui, Matthew Yuk Yu. "Special solvation behaviour of salts in ionic liquid". Thesis, Imperial College London, 2012. http://hdl.handle.net/10044/1/9250.
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In a previous study1 from the Welton Group, the reactivity resulting from mixing two different and reactive salts together was observed to be highly dependent on the type of solvent, with molecular and ionic liquids exhibiting fundamentally different reaction pathways. Ionic liquids were shown to be extremely dissociating solvents and the salts behaved as discrete reactive species. Conversely, in molecular solvents neutral ion pairs or clusters were formed. In this thesis, further evidence of the charge screening behaviour of ionic liquids will be presented. The investigation was carried out by using Kosower's charge-transfer complex, 1-ethyl-4-(methoxycarbonyl)pyridinium iodide,2 which is only spectroscopically active when its ions are in direct contact, hence allowing charge transfer to occur. The behaviour of this salt is therefore a good indicator of the number of pyridinium iodide contact ion pairs in solution and can be used as a probe for the amount of ion-pairing in both ionic and molecular liquids. In the second part of the investigation, the SN2 reaction of two reactive salts (1-butyl-1-methylpyrrolidinium bromide and dimethyl-4-nitrophenylsulfonium bis(trifluoromethanesulfonyl)imide) in ionic liquid/molecular liquid mixtures was studied. The aim was to examine whether complete charge screening behaviour could be achieved in ionic liquid/molecular liquid mixtures of different compositions. This research also provided some insights of general behaviour of salts in ionic liquid/molecular solvent mixtures.
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Shah, Prateek Pinakin. "Thermodynamics of apolar solvation in mixed aqueous solvents". Access to citation, abstract and download form provided by ProQuest Information and Learning Company; downloadable PDF file, 227 p, 2008. http://proquest.umi.com/pqdweb?did=1601517501&sid=3&Fmt=2&clientId=8331&RQT=309&VName=PQD.
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Jones, Justin A. "Aqueous Solvation Method for Recombinant Spider Silk Proteins". DigitalCommons@USU, 2015. https://digitalcommons.usu.edu/etd/4267.
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Two major hurdles face the production of recombinant spider silk protein (rSSp) based materials. First, the production of sufficient quantities of rSSp has proven difficult due to their highly repetitive nature and protein size (>250kDa). Secondly, rSSp and native silks are practically insoluble in water based solutions, necessitating the use of harsh organic solvents that can remain in the material after production. While others are working on solving production problems, this dissertation demonstrates a novel aqueous solubilization method that is rapid (<1 minute) and results in near 100% solubilization of the rSSp. From this new solubilization method films, foams, gels (hydrogels and lyogels), adhesives, coatings and fibers have been produced as well as the previously unreported sponge. All of these novel materials were derived from entirely aqueous solutions with and without minor additives to influence the final physical state of the rSSp.
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Spångberg, Daniel. "Cation Solvation in Water and Acetonitrile from Theoretical Calculations". Doctoral thesis, Uppsala University, Department of Materials Chemistry, 2003. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-3598.
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Metal ions solvated in aqueous, non-aqueous, and mixtures of solvents occur in many chemical contexts, for example in electrochemical applications and solvent separation. Solvated ions appear in high concentration in the living organisms, where their presence or absence can fundamentally alter the functions of life. In many of these cases, understanding the selective solvation and the dynamics of the ions is essential for the understanding of the processes involved.
Computer simulation provides a molecular level of detail of the solvation process usually not available from experiments. The quality of the interaction models employed in the theoretical description is of particular importance, since even rather small changes in the interaction can lead to substantial and qualitative differences.
This thesis describes the development of a sequence of increasingly refined analytical ion-solvent potentials from ab initio calculations for the systems Li+(aq), Na+(aq), Mg2+(aq), Al3+(aq), Li+(MeCN), Na+(MeCN), Li+(aq, MeCN), and Na+(aq, MeCN). Molecular dynamics simulations using these potentials were subsequently performed, and some key-properties computed. The reliability of the computed thermodynamical, structural and dynamical properties was scrutinized.
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Moakes, Greg. "Study of Lithium Solvation Environments in Water-saturated Nitrobenzene". Diss., Georgia Institute of Technology, 2006. http://hdl.handle.net/1853/14105.
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It was found that there exist three major water environments when water is dissolved in nitrobenzene. 2H NMR has proved that these solvatomers exist irrespective of whether lithium salt is added to the system. 7Li NMR experiments suggested that the first solvatomer is majority nitrobenzene, the second a mixed solvation shell consisting of nitrobenzene and water and the third solvatomer is a large water aggregated at the glass surface. The mixed solvation state is short lived and is promoted by addition of water of by supersaturating the system upon cooling. This is a high energy state and decays either into the homogenous bulk NB state or to the surface of the glass wall, depending on if glass surface is present. In the 7Li NMR experiments, the hydrophobicity of the salt, determined by the anion, affects the relative intensity of the three 7Li resonances.
Addition of lithium serves to promote hydrogen bonding in the majority nitrobenzene solvatomer, as confirmed by FTIR and neutron diffraction studies. There is no evidence that it has an effect on the size of the mixed solvatomer or the water aggregate immobilized on the glass surface. A reasonable hypothesis is that lithium exchanges between the water species which are formed independent of lithium involvement. The system is summarized as follows:
Below critical water concentration (~200mM) nitrobenzene/water is a homogeneous distribution of water molecules in nitrobenzene. Addition of lithium salt to such a system has two main affects. First, the lithium promotes hydrogen bonding between the dissolved water molecules, as confirmed by FTIR and neutron scattering. Second, the hydrogen bonded water may precipitate causing microheterogeneity of the system, leading to a second resonance observed in both the 2H and 7Li NMR spectra (LiNB/W). In the presence of glass, a third solvation state can nucleate at the glass surface; this solvation state has character even closer to that of bulk water (LiW). These two supplementary solvation states can be artificially induced by either adding aliquots of water or cooling.
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Bizjak, Tanja. "Ultrafast photoinduced intra- und intermolecular charge transfer and solvation". Diss., lmu, 2004. http://nbn-resolving.de/urn:nbn:de:bvb:19-29695.
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Mitsui, Masaaki. "Solvation structure and nonradiative dynamics of hydrated aromatic clusters". 京都大学 (Kyoto University), 2000. http://hdl.handle.net/2433/151657.
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Spångberg, Daniel. "Cation solvation in water and acetonitrile from theoretical calculations /". Uppsala : Acta Universitatis Upsaliensis : Univ.-bibl. [distributör], 2003. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-3598.
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Alexandersson, Kristján Friðrik. "The hydrated torsions method : incremental solvation of amino acids". Thesis, University of Oxford, 2013. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.639817.
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In this thesis, the development and applications of the Hydrated Torsions (HT) method are discussed. The method is designed to study the incremental solvation of biomolecules and thus is ideal for the study of zwitterion formation. A reduced dimensionality approach, torsional path integral Monte Carlo, is used to explicitly treat the torsional motion of the biomolecules to provide anharmonic and quantum corrections of the torsional free energy. Four amino acids are treated with the HT method in this work; glycine, alanine, proline and serine. The initial development was performed using glycine. Microsolvated amino acid clusters were studied, with the number of solvent molecules ranging from one to six. The low energy structures identified in the work using density functional theory are in good agreement with structures found in the literature. The hydrogen bond networks formed in the structures were found to resemble hydrogen bond networks found in analogous water clusters. The incremental addition of water molecules to glycine and alanine reduced the electronic ,energy difference between the zwitterionic and neutral systems by a linear amount, up until the fourth water molecule due to stabilization of the more polar zwitterion. After four water molecules the stabilization is diminished and the make-up of the hydrogen bond network becomes more important. This change in electronic energy difference after four water molecules was not observed for proline and serine. Water molecules added to the systems beyond four water molecules do not affect the free energy difference as much as when one to four water molecules are added. Calculations indicate that the zwitterionic systems are not been fully stabilized at four, five or six water molecules, so this change in free energy behaviour must be due to the vibrational characteristics of the systems. Frequency analysis of the systems reveals that the difference in frequency of the torsional vibrational modes is not enough to cause this, so other low frequency modes are likely to be affecting the free energy.
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Hanf, Karl J. M. (Karl John Mortley) 1969. "Protein design with hierarchical treatment of solvation and electrostatics". Thesis, Massachusetts Institute of Technology, 2002. http://hdl.handle.net/1721.1/29223.
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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Physics, 2002.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.
Includes bibliographical references (p. 249-258).
A detailed treatment of the electrostatic energy of biomolecules in solution is used for two applications that require consideration of large numbers of states: multiple-site titration and protein design. The continuum electrostatic model is combined with covalent, van der Waals, and non-polar energy terms, and the statistical mechanical basis for this model is reviewed. Multiple-site titration is modeled with four titratable residues of the protein barstar. A full enumeration of the titration states is used to predict pH-dependent properties of the system, and the effects of several simplifying assumptions are evaluated. The analytical continuum electrostatics (ACE) method, a computationally inexpensive approximation of the electrostatic free energy, is evaluated in the context of predicting group terms of the binding free energy. A primary source of error in the ACE prediction of atomic solvation energies is identified and ameliorated. A procedure is developed which optimizes the parameters of the ACE method in order to minimize its errors as compared to finite-difference solution of the linearized Poisson-Boltzmann equation. Parameter sets optimized on a "testing" biomolecular binding system yield reduced average errors for related biomolecular systems. Finally, a protein design method is developed which uses the dead-end elimination and A* discrete search algorithms to systematically search large numbers (10²⁴) of structures, varying the proteinsequence and the side chain conformation at all selected residues.
(cont.) The method is novel in its co-optimization of binding and folding free energies, its use of three levels of increasingly detailed discrete search (sequence, fleximers, and rotamers), and its use of three hierarchical energy functions to successively screen candidate structures identified by the discrete search. Redesigning sets of three and seven residues of the protein barstar, the wild-type sequence, which is experimentally known to bind very tightly to barnase, is ranked very highly by this method (#5 out of 8000, or #89 out of 1.3 x 10⁹), unlike that of previous protein design studies. The present method chooses a structure for the wild-type sequence that is very similar to the crystal structure. Several novel sequences predicted to bind more tightly than wild-type barstar are promising candidates for synthesis.
by Karl J.M. Hanf.
Ph.D.
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Liu, Mimi. "Single-Ion Solvation in Water and in Molten Salts". University of Cincinnati / OhioLINK, 2021. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1627664846799413.
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Misin, Maksim. "Can approximate integral equation theories accurately predict solvation thermodynamics". Thesis, University of Strathclyde, 2016. http://digitool.lib.strath.ac.uk:80/R/?func=dbin-jump-full&object_id=27856.
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The thesis focuses on the prediction of solvation thermodynamics using integral equation theories. Our main goal is to improve the approach using a rational correction. We achieve it by extending recently introduced pressure correction, and rationalizing it in the context of solvation entropy. The improved model (to which we refer as advanced pressure correction) is rather universal. It can accurately predict solvation free energies in water at both ambient and non-ambient temperatures, is capable of addressing ionic solutes and salt solutions, and can be extended to non-aqueous systems. The developed approach can be used to model processes in biological systems, as well as to extend related theoretical models further.
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Ishida, Tateki. "Electronic Structure and Statistical Mechanical Approach to Solvation Processes". 京都大学 (Kyoto University), 1999. http://hdl.handle.net/2433/157185.
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本文データは平成22年度国立国会図書館の学位論文(博士)のデジタル化実施により作成された画像ファイルを基にpdf変換したものであるKyoto University (京都大学)
0048
新制・課程博士
博士(理学)
甲第7938号
理博第2104号
新制||理||1122(附属図書館)
UT51-99-M243
京都大学大学院理学研究科化学専攻
(主査)教授 加藤 重樹, 教授 廣田 襄, 教授 木寺 詔紀
学位規則第4条第1項該当
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Konda, Sai Sriharsha Manoj. "Computational Investigation of Spin Traps Using Hybrid Solvation Models". Digital Commons @ East Tennessee State University, 2009. https://dc.etsu.edu/etd/1801.
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The cyclic nitrone 5,5-dimethyl-1-pyrroline-N-oxide (DMPO), and the lesser known linear phenyl-N-tert-butylnitrone (PBN) and its phosphorylated analogues have been used as spin traps for the investigation of free radicals in biological systems. Theoretical work on these molecules suggests that there are important differences in their properties between biological systems and isolated molecules in the gas phase, most likely resulting from intra and intermolecular hydrogen bonding. Most dielectric solvation models such as the polarized continuum model and COSMO are incapable of direct determination of solvent-spin trap chemical interactions. To examine this, hybrid models incorporating COSMO for long range effects and discrete solvent molecules for short range effects, at the DFT/B3LYP/6-31G* level of theory, have been used to study the stabilization and alteration of the spin trap molecules properties in protic and aprotic polar solvents. The hybrid models have been successfully implemented to support the prominent role played by hydrogen bonding interactions in the stabilization of spin traps.
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Quan, Chaoyu. "Mathematical methods for implicit solvation models in quantum chemistry". Thesis, Paris 6, 2017. http://www.theses.fr/2017PA066587/document.
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Cette thèse est consacrée à étudier et à améliorer les modèles mathématiques et les méthodes utilisées pour les modèles de solvatation implicite en chimie quantique. Ce manuscrit est composée de deux parties. Dans la première partie où nous analysons l'interface soluté-solvant, nous donnons, pour la première fois, une caractérisation complète de la surface moléculaire lisse, c'est-à-dire la surface exclue du solvant (SES). À partie de cette caractérisation, nous développons un algorithme de maillage par morceaux pour les surfaces moléculaires différentes, en particulier pour la SES, en utilisant la triangulation à front avançant. De plus, la cavité de la SES (la région entourée par la SES) est une description plus précise de la cavité de soluté. Dans la deuxième partie, nous construisons donc un modèle de continuum polarisable basé (PCM) sur la SES, dans lequel le paramètre de permittivité diélectrique est continu. Le problème électrostatique de ce modèle consiste à résoudre une équation de Poisson définie sur R3. Nous développons ensuite une méthode de Schwarz particulière, où seules les équations locales restreintes à des boules doivent être résolues. Enfin, nous étudions le modèle de solvatation de Poisson-Boltzmann, un autre modèle de solvatation implicite, qui tient compte à la fois de la permittivité diélectrique et de la force ionique du solvant. Une méthode de Schwarz similaire est proposée pour résoudre l'équation de Poisson-Boltzmann associée en résolvant des équations locales restreintes aux boules comme pour le PCM basé sur la SESThis thesis is devoted to study and improve the mathematical models and methods used in implicit solvation models in quantum chemistry. The manuscript is composed of two parts. In the first part where we analyze the solute-solvent interface, we give, for the first time, a complete characterization of the so-called “smooth” molecular surface, i.e., the solvent excluded surface (SES). Based on this characterization, we develop a piecewise meshing algorithm for different molecular surfaces, especially the SES, using the advancing-front triangulation. Further, it has been pointed out in the literature that the SES-cavity (the region enclosed by the SES) is a more accurate description of the solute cavity. In the second part, we therefore construct an SES-based polarizable continuum model (PCM), in which the dielectric permittivity parameter is continuous. The electrostatic problem of this model involves solving a Poisson equation defined in R3. We then develop a particular Schwarz domain decomposition method where only local equations restricted to balls need to be solved. Finally, the Poisson-Boltzmann solvation model, another implicit solvation model, is also investigated, which takes into account both the dielectric permittivity and the ionic strength of the solvent. A similar Schwarz domain decomposition method is proposed to solve the associated Poisson-Boltzmann equation by solving local equations restricted to balls as it is for the SES-based PCM
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BOTTARI, CETTINA. "Solvation effects of ionic liquid/water mixtures on biomolecules". Doctoral thesis, Università degli Studi di Trieste, 2020. http://hdl.handle.net/11368/2960827.
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onic liquids (ILs) belong to a broad class of ionic compounds that, differently from conventional salts, are usually liquid at T < 100°C. They are
characterized by vanishing vapour pressure, good thermal stability, high ion density and ionic conductivity. Thanks to the large variety of available ions,
the physico-chemical properties of ILs can be modulated by careful selection of both cation and anion with specic characteristics for tailored applications.
A more convenient strategy for an ecient tuning of the performances of ILs consists in mixing ILs with other ionic or molecular liquids, such as e.g. water.
It is observed that addition of water to ILs allows to improve some of their properties and performances, especially for applications in biological eld. For
instance, recent studies reported on the capability of IL/water solutions to enhance the structural stability of proteins, enzymes and deoxyribonucleic acid
(DNA) also at high temperatures. This PhD thesis aims to show the usefulness of synchrotron-based UV Resonance Raman (SR-UVRR) spectroscopy for investigating i) the structural dynamics of IL/water solutions and ii) the solvation effects of these IL-based solvents on bio-molecules, such as peptides and DNA. UVRR exhibits several advantages with respect to conventional spontaneous Raman spectroscopy, as the signicant increment of the detection limit that allows to study the samples in very high diluted conditions and the selective enhancement of the Raman cross section of vibrations associated to specic molecular groups of the same system. Thanks to the unique tunability of the synchrotron emission, the UVRR spectra of aqueous solutions of imidazolium-based ILs have been excited at different wavelengths nely matching with the resonance transitions occurring in the system. These spectra showed to have good sensitivity to the modications induced on the local structure of solutions of ILs by i) the change of the anion and ii) the substitution on the imidazolium ring of progressively longer alkyl-chains. Additionally, some UVRR signals are specically informative on the effect induced by addition of water on the strength of hydrogen bonds (H-bonds) in IL-water solutions. The molecular view provided by SR-UVRR experiments has been further complemented by the structural parameters extracted by Small Angle Neutron Scattering (SANS) measurements performed on the same IL/water mixtures.
The investigation of the structure-dynamic relationship in IL/water solutions is the preliminary step for the deep comprehension of the effects of these
mixtures on the solvation dynamics of molecules of biological interest, such as peptides and DNA. This is an issue of special interest by considering that
the solute-solvent interactions are strongly related to the biological activity of bio-macromolecules. Some results will be presented in this thesis, concerning
the case of two dierent type of bio-systems:
i) small peptides dissolved in IL/water solutions: the UVRR spectra of peptides contain several spectroscopic markers of the structural rearrangement
induced by the hydration shell on peptides, such as the Amide bands that are usually not well detectable in spontaneous Raman spectra. The analysis of these spectral features can provide insights on the peculiar effect induced on the hydration dynamics of peptides by dfferent ILs;
ii) DNA dissolved in IL/water solutions: a suitable choice of the exciting radiation allows to collect UVRR spectra of DNA where the vibrational
signals associated to the different nitrogenous bases are selectively enhanced. This gives the unique opportunity to disentangle specic bands
in the Raman spectra of DNA that appear usually very complex. Such approach can be conveniently used to obtain insights on the molecular
mechanism responsible of the dierent thermal stability exhibited by DNA structure in the presence of different IL/water solutions.Ionic liquids (ILs) belong to a broad class of ionic compounds that, differently from conventional salts, are usually liquid at T < 100°C. They are characterized by vanishing vapour pressure, good thermal stability, high ion density and ionic conductivity. Thanks to the large variety of available ions, the physico-chemical properties of ILs can be modulated by careful selection of both cation and anion with specic characteristics for tailored applications. A more convenient strategy for an ecient tuning of the performances of ILs consists in mixing ILs with other ionic or molecular liquids, such as e.g. water. It is observed that addition of water to ILs allows to improve some of their properties and performances, especially for applications in biological eld. For instance, recent studies reported on the capability of IL/water solutions to enhance the structural stability of proteins, enzymes and deoxyribonucleic acid (DNA) also at high temperatures. This PhD thesis aims to show the usefulness of synchrotron-based UV Resonance Raman (SR-UVRR) spectroscopy for investigating i) the structural dynamics of IL/water solutions and ii) the solvation efects of these IL-based solvents on bio-molecules, such as peptides and DNA. UVRR exhibits several advantages with respect to conventional spontaneous Raman spectroscopy, as the signicant increment of the detection limit that allows to study the samples in very high diluted conditions and the selective enhancement of the Raman cross section of vibrations associated to specic molecular groups of the same system. Thanks to the unique tunability of the synchrotron emission, the UVRR spectra of aqueous solutions of imidazolium-based ILs have been excited at diferent wavelengths nely matching with the resonance transitions occurring in the system. These spectra showed to have good sensitivity to the modications induced on the local structure of solutions of ILs by i) the change of the anion and ii) the substitution on the imidazolium ring of progressively longer alkyl-chains. Additionally, some UVRR signals are specically informative on the effect induced by addition of water on the strength of hydrogen bonds (H-bonds) in IL-water solutions. The molecular view provided by SR-UVRR experiments has been further complemented by the structural parameters extracted by Small Angle Neutron Scattering (SANS) measurements performed on the same IL/water mixtures. The investigation of the structure-dynamic relationship in IL/water solutions is the preliminary step for the deep comprehension of the effects of these mixtures on the solvation dynamics of molecules of biological interest, such as peptides and DNA. This is an issue of special interest by considering that the solute-solvent interactions are strongly related to the biological activity of bio-macromolecules. Some results will be presented in this thesis, concerning the case of two different type of bio-systems: i) small peptides dissolved in IL/water solutions: the UVRR spectra of peptides contain several spectroscopic markers of the structural rearrangement induced by the hydration shell on peptides, such as the Amide bands that are usually not well detectable in spontaneous Raman spectra. The analysis of these spectral features can provide insights on the peculiar effect induced on the hydration dynamics of peptides by different ILs; ii) DNA dissolved in IL/water solutions: a suitable choice of the exciting radiation allows to collect UVRR spectra of DNA where the vibrational signals associated to the different nitrogenous bases are selectively enhanced. This gives the unique opportunity to disentangle specic bands in the Raman spectra of DNA that appear usually very complex. Such approach can be conveniently used to obtain insights on the molecular mechanism responsible of the different thermal stability exhibited by DNA structure in the presence of different IL/water solutions.
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Caricato, Marco. "Theoretical Models to describe Time-Dependent and Nonequilibrium Solvation". Doctoral thesis, Scuola Normale Superiore, 2005. http://hdl.handle.net/11384/85801.
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Mukhopadhyay, Abhishek. "Investigating the effect of charge hydration asymmetry and incorporating it in continuum solvation framework". Diss., Virginia Tech, 2015. http://hdl.handle.net/10919/72901.
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One of the essential requirements of biomolecular modeling is an accurate description of water as a solvent. The challenge is to make this description computationally facile -- reasonably fast, simple, robust and easy to incorporate into existing software packages, yet accurate. The most rigorous procedure to model the effect of aqueous solvent is to explicitly model every water molecule in the system. For many practical applications, this approach is computationally too intense, as the number of required water atoms is on an average at least one order of magnitude larger than the number of atoms of the molecule of interest. Implicit solvent models, in which solvent molecules are replaced by a continuous dielectric, have become a popular alternative to explicit solvent methods. However, implicit solvation models often lack various microscopic details which are crucial for accuracy. One such missing effect that is currently missing from popular implicit models is the so called effect of charge hydration asymmetry (CHA). The missing effect of charge hydration asymmetry -- the asymmetric response of water upon the sign of solute charge -- manifests a characteristic, strong dependence of solvation free energies on the sign of solute charge. Here, we incorporate this missing effect into the continuum solvation framework via the conceptually simplest Born equation and also in the generalized Born model. We identify the key electric multipole moments of model water molecules critical for the various degrees of CHA effect observed in studies based on molecular dynamics simulations using different rigid water models. We then use this gained insight to incorporate CHA first into the Born model, and then into the generalized Born model. The proposed framework significantly improves accuracy of the hydration free energy estimates tested on a comprehensive set of varied molecular solutes -- monovalent and divalent ions, small drug-like molecules, charged and uncharged amino acid dipeptides, and small proteins. We finally develop a methodology to resolve the issue with unacceptably large uncertainty that stems from a variety of fundamental and technical difficulties in experimental quantification of CHA from charged solutes. Using the proposed corrections in the continuum framework, we untangle the charge-asymmetric response of water from its symmetric response, and further circumvent the difficulties by extracting accurate estimate propensity of water to cause CHA from accurate experimental hydration free energies of neutral polar molecules. We show that the asymmetry in water's response is strong, about 50% of the symmetric response.Ph. D.
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Masia, Marco. "Solvation dynamics and ion transport in conventional solvents and plasticizers". Doctoral thesis, Universitat Politècnica de Catalunya, 2005. http://hdl.handle.net/10803/6607.
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El argumento fundamental de esta tesis es el estudio de la solvatación iónica por medio de cálculos con ordenador. Tres lineas de investigación han sido seguidas:(i) Solvatación y mobilidad ionica. Las características principales del processo de intercambio entre la primera y la segunda capa de hidratación iónica para Li+ en agua se ha encontrado ser independiente del estado termodinamico en gran medida. Ha sido demostrado que el desplazamiento cuadrático medio de moléculas pertenecientes a complejos inertes está caracterizado por un largo transitorio debido a la lenta relajación rotacional del complejo. El incremento del coeficiente de difusión iónico debido a los intecambios en la capa de solvatación ha sido calculado por primera vez en el caso de Li+ y Na+. Finalmente, se han derivado leyes de probabilidad que ponen en relación la estereoquímica y la velocidad iónica instantanea.
(ii) Plastificantes. Se propone un nuevo procedimiento para el desarrollo de campos de fuerza intramoleculares, que funciona satisfactoriamente en el caso de dos moleculas de interés en las Batterias a Iones de Litio: carbonato de etileno y -butirolactona. Respecto a la solvatación de Li+ en los dos solventes, el ión está coordenado por 4 moleculas a través del oxigeno del carbonilo con pequeñas distorsiones de la geometría molecular. La nueva asignación de los modos vibracionales hecha para las dos moléculas ha permitido calcular los cambios inducidos por el ión litio, explicando varias caracteristicas de los espectros esperimentales.
(iii) Polarización. Se ha estudiado la eficacia de los metodos de polarización más comunes para simulaciones de Dinámica Molecular en dímeros ión-molécula, usando calculos ab initio como referencia. En lugar de centrarnos en la superficie de energía potencial completa (procedimiento típico), se ha considerado solo la parte electrostática. Se han desarrollado nuevos modelos polarizables para agua y tetracloruro de carbono, que reproducen el comportamiento de sistemas carga-molécula. Ha sido encontrado que, en el caso de dímeros ión-molécula, se requiere una corrección de amortiguamento de la polarización a cortas distancias. El método de los dipolos puntuales junto al método de amortiguamento de Thole reproduce satisfactoriamente las características principales para cationes y aniones atómicos.
The underlying topic of this thesis is the study of ion solvation by means of computer calculations. Three lines of investigation have been followed:
(i) Solvation and Ionic Mobility. The main features of the exchange process between first and second ionic hydration shells for Li+ in water have been found to be largely independent of the thermodynamic state. It has been shown that the mean square displacement of molecules belonging to inert complexes is characterized by a long transient due to the slow rotational relaxation of the complex. The increase of the ionic diffusion coefficient due to solvation shell exchanges has been computed for the first time in the case of Li+ and Na+. Finally, probability laws have been derived which relate the stereochemistry and the instantaneous ionic velocity.
(ii) Plasticizers. A new approach for the development of intramolecular force fields is proposed, which performs satisfactorily in the case of two molecules of interest for Lithium Ion Batteries: ethylene carbonate and -butyrolactone. Concerning the solvation of Li+ in both solvents, it is coordinated by 4 molecules through the carbonyl oxygen with slight distorsions of the molecular geometry. The new vibrational mode assignment performed for both molecules has allowed to compute the vibrational shifts induced by the lithium ion, explaining a number of features present in the experimental spectra.
(iii) Polarization. The performance of the most commonly used polarization methods for Molecular Dynamics simulation is studied for ion-molecule dimers, using ab initio calculations as benchmark. Instead of focusing on the full potential energy surface (the standard approach), only the electrostatic part is considered. New polarizable models have been developed for water and carbon tetrachloride, which reproduce the behaviour of charge-molecule systems. In the case of ion-molecule dimers it has been found that a polarization damping correction is required at short distances. The point dipole method in conjunction with the Thole damping scheme reproduces rather satisfactorily the main features both for atomic cations and anions.
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Huffman, Carmen Louise. "The role of charge in solvation at liquid/liquid interfaces". College Park, Md. : University of Maryland, 2005. http://hdl.handle.net/1903/2663.
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Thesis (Ph. D.)--University of Maryland, College Park, 2005.Thesis research directed by: Chemistry. Title from t.p. of PDF. Includes bibliographical references. Published by UMI Dissertation Services, Ann Arbor, Mich. Also available in paper.
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Costa, Paolo [Verfasser], Wolfram [Gutachter] Sander e Patrick [Gutachter] Nürnberger. "Solvation of arylcarbenes / Paolo Costa. Gutachter: Wolfram Sander ; Patrick Nürnberger". Bochum : Ruhr-Universität Bochum, 2016. http://d-nb.info/1102525030/34.
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Kropman, Michel François. "Ion solvation in water femtosecond spectroscopy of hydrogen-bond dynamics /". [S.l. : Amsterdam : s.n.] ; Universiteit van Amsterdam [Host], 2004. http://dare.uva.nl/document/74586.
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Hubel, Hannes. "Solvation effects in real and simulated liquids and biological systems". Thesis, Queen Mary, University of London, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.408849.
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Skerratt, R. G. "Solvation and hydrolysis studies of phosphonium salts and their ylides". Thesis, Staffordshire University, 1988. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.380994.
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Roberts, K. "Further studies toward the development of an empirical solvation model". Thesis, Swansea University, 1986. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.638680.
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Solvolytic rate data are obtained (mainly by conductimetric technique) for reactions of 1-adamantyl iodide, trinitrophenolate (picrate), heptafluorobutyrate, trifluoroacetate, and 2-adamantyl trifluoromethanesulphonate (triflate) and perchlorate in binary aqueous mixtures of ethanol, methanol, acetone, trifluoroethanol and hexafluoroisopropanol, and also for the iodide substrate in acetic and formic acids. Additional data for iodine catalyzed solvolyses of 1-adamantyl iodide are reported. Rate data are also obtained for solvolyses of 1-adamantyl halides utilising a micro-cell and for solvolyses of t-butyl-heptafluorobutyrate in several of the binary aqueous mixtures highlighted above. Solvent ionizing power scales are calculated for each of the leaving groups and correlated with existing ionizing power scales based on other leaving groups, results are discussed in terms of the varying solvent and leaving group effects in operation. Direct comparison between the solvatochromically derived Z scale is made with that of the iodide ionizing power scale, and several alternative approaches to the analysis of solvent effects on rates are discussed. Kinetic data for solvolyses of several methyl and para-toluene sulphonate derivates are also obtained (via 1H nmr and uv spectrophotometric techniques, respectively) in a wide range of aqueous sulphuric and hydrochloric acid media. Solvent nucleophilicity and solvent ionizing power parameters for tosylates, are calculated utilising established information acquired through solvolytic study of these substrates in aqueous alcoholic and related media. These are compared with existing Hammett function and activity data, and utilised to calculate solvolytic rate constants allowing direct comparison with observed. Lastly, molecular mechanics calculations of solvolytic reactivity at bridgehead carbon spanning 22 orders of magnitude are correlated with a revised and uniform experimental data set based on the tosylate leaving group.
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Grahn, Hans. "Paramagnetic relaxation reagents : nuclear magnetic resonance studies of preferential solvation". Doctoral thesis, Umeå universitet, Kemiska institutionen, 1986. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-100714.
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The interactions between neutral paramagnetic relaxation reagents (PARR's) and certain aromatic compounds have been studied by 1H and 13 C spin-lattice relaxation time measurements. In media such as cyclohexane and carbon tetrachloride, Cr(acac)3 becomes preferentially solvated by aromatic solutes. The solvation is significantly suppressed in a more interacting solvent like dichloromethane. Paramagnetic induced chemical shifts of the aromatic outer sphere ligand indicate in addition to relaxation data, a preferential orientation caused by dipole-dipole interactions. For benzene or for several alkylated benzenes which have small or no permanent dipole moments, the interaction is electrostatic, i.e. of a dipole-dipole induced type and where the easily polarizable aromatic ring is preferred in the solvation sphere. Carbon tetrachloride is shewn to have a specific PARR interaction. If co-ordination number, solution structure etc., are to be determined using weakly interacting substrates, this solvent should be avoided. A multivariate statistical approach is also reported, where 13 C electron-nuclear relaxation data and induced shifts of monosubstituted arcmatics have been related to different physical descriptors. Most of the variance in relaxation and shift data is best described by the dipole moment. The results support a dipole-dipole interaction as the preferred solvation mechanism. The preferential solvation of several organic substrates with the diamagnetic Co(acac)3 is studied by varying the substrate concentration in cyclohexane. By the use of 59 Co shift, it is shown that proton donating solutes such as chloroform and methanol have a specific solvation. The order of preference is close to that obtained in Cr(acac)3 solutions.Diss. (sammanfattning) Umeå : Umeå universitet, 1986, härtill 5 uppsatser
digitalisering@umu
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Banham, S. F. "Ionisation and solvation as key processes in heterogeneous stratospheric chemistry". Thesis, University of East Anglia, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.296344.
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