Doctor of Philosophy / Department of Chemistry / Paul E. Smith / Kirkwood Buff (KB) theory is one of the most important theories of solutions. The theory can relate integrals over radial (pair) distribution functions (rdfs) in the grand canonical ensemble to common thermodynamic properties. An inversion of the KB theory has been proposed by Ben-Naim and this has led to the wide spread popularity of KB theory. The idea of the KB inversion procedure is to calculate KB integrals from available thermodynamic properties. The KB theory can be used to validate the force field (ff) parameters used in molecular dynamics simulations. We have tested a series of small molecule ff parameters using KB theory that consists of both atom centered partial atomic charges and extra charge sites. The results indicate that using extra charge sites, derived from QM calculations, does not necessarily provide a more accurate representation of condensed phase properties. A further study aimed at an ongoing project of deriving new biomolecular ff parameters based on KB theory, has developed ff parameters for esters in order to represent the ester conjugation of the phospholipid molecule. The models were further tested against experimental properties. Preferential solvation (PS) is an important concept of solution mixtures that can be described using KB theory. The difference between local composition and bulk composition in solution mixtures leads to the concept of PS. A generalized explanation based on local mole fractions was derived by Ben-Naim using KB theory. However, the original expressions have been modified over years. Here, we propose a new approach based on local volume fractions to explore PS in binary and ternary solution mixtures. Experimental and simulation data were used to examine different approaches to PS. A relationship between the rdf and the triplet distribution function can be obtained using the Kirkwood Superposition Approximation (KSA). A combination of Fluctuation Solution Theory and experimental rdfs are used to examine the KSA at a series of state points for pure water. The accuracy of several other approximate relationships between the pair and triplet correlation functions was also investigated and are in good agreement for regions of the phase diagram where the compressibility is small.

京都大学 / 0048 / 新制・課程博士 / 博士(工学) / 甲第20714号 / 工博第4411号 / 新制||工||1685(附属図書館) / 京都大学大学院工学研究科合成・生物化学専攻 / (主査)教授 杉野目 道紀, 教授 村上 正浩, 教授 松田 建児 / 学位規則第4条第1項該当 / Doctor of Philosophy (Engineering) / Kyoto University / DGAM

Neste trabalho, sondas solvatocrômicas foram empregadas no estudo de solventes puros, misturas aquosas de solventes próticos e apróticos, líquidos iônicos e suas misturas aquosas. As sondas estudadas foram agrupadas em duas séries, cujas mudanças relevantes foram: (i) série RPMBr2: R de metila a 1-octila permitiu a variação da hidrofobicidade da sonda enquanto o pKa se manteve constante; (ii) série de merocianinas derivadas de piridina, quinolina e acridina. Isso resultou em sondas de hidrofobicidades diferentes com valores parecidos de pKa. Desta forma foi possível isolar os efeitos sobre solvatação provocados pela hidrofobicidade das sondas. As duas séries de sondas mostraram comportamentos solvatocrômicos diferentes. Uma equação modificada de Taft-Kamlet-Abboud permitiu as quantificações individuais de cada propriedade do solvente, tais como acidez, dipolaridade/polarizabilidade e hidrofobicidade para a resposta de cada sonda. O modelo de solvatação preferencial que considera explicitamente a presença de três espécies na mistura binária de solvente foi aplicado, este considera que a água, o solvente orgânico e a espécie solvente orgânico-água competem pela camada de solvatação da sonda. Os resultados deste tratamento ajudaram no entendimento das forças atuantes na solvatação, especialmente com relação aos efeitos das propriedades de ambos a sonda e o solvente, e do aumento da temperatura. Estudos preliminares de misturas aquosas de líquidos iônicos mostraram as semelhanças e as diferenças entre a solvatação por estas misturas \"verdes\" e a por misturas aquosas de álcoois. Uma aplicação do solvatocromismo para o entendimento de un fenômeno físco-químico foi apresentada: os resultados da aplicação do modelo de solvatação preferencial de sondas em misturas aquosas de tetrametiluréia foram usados para explicar o fenômeno de gelificação de proteína neste mesmo sistema de solventes. / In the present work, solvatochromic probes were employed in the study of pure solvents, binary mixtures of water with protic and aprotic solvents, ionic liquids and their aqueous binary mixtures The probes studied are classified in two series: (i) RPMBr2; where R = methyl to 1-octyl allowed increasing the hydrophobicity while maintaining the pKa constant. (ii) The second series involved derivatives of pyridine, quinoline and acridine, this allowed increasing probe hydrophobicity, while maintaining similar pKa. The two series of probes showed different solvatochromic behaviors both in pure solvents and binary solvent mixtures. A modified equation of Taft-Kamlet-Abboud allowed quantification of each solvent property, including acidity, dipolarity/polarizability and hydrophobicity to the response of each probe. The preferential solvation model which explicitly considers the presence of three species was employed; it considers the competition of water, organic solvent and the complex water-organic solvent in the probe solvation shell. The results shed light on the interactions that affect solvation, including temperature-induced desolvation. Preliminary results on aqueous ionic liquids showed the similarities and difference between solvation by these \"green\" mixtures and those of aqueous alcohols. An application of solvatochromism for understanding a physical-chemical phenomenon was presented: the results of application of preferential solvation model of probes in aqueous tetramethylurea mixtures was used to explain the gelation of the protein lysozyme in this same solvent system.

Neste trabalho, sondas solvatocrômicas foram empregadas no estudo de solventes puros, misturas aquosas de solventes próticos e apróticos, líquidos iônicos e suas misturas aquosas. As sondas estudadas foram agrupadas em duas séries, cujas mudanças relevantes foram: (i) série RPMBr2: R de metila a 1-octila permitiu a variação da hidrofobicidade da sonda enquanto o pKa se manteve constante; (ii) série de merocianinas derivadas de piridina, quinolina e acridina. Isso resultou em sondas de hidrofobicidades diferentes com valores parecidos de pKa. Desta forma foi possível isolar os efeitos sobre solvatação provocados pela hidrofobicidade das sondas. As duas séries de sondas mostraram comportamentos solvatocrômicos diferentes. Uma equação modificada de Taft-Kamlet-Abboud permitiu as quantificações individuais de cada propriedade do solvente, tais como acidez, dipolaridade/polarizabilidade e hidrofobicidade para a resposta de cada sonda. O modelo de solvatação preferencial que considera explicitamente a presença de três espécies na mistura binária de solvente foi aplicado, este considera que a água, o solvente orgânico e a espécie solvente orgânico-água competem pela camada de solvatação da sonda. Os resultados deste tratamento ajudaram no entendimento das forças atuantes na solvatação, especialmente com relação aos efeitos das propriedades de ambos a sonda e o solvente, e do aumento da temperatura. Estudos preliminares de misturas aquosas de líquidos iônicos mostraram as semelhanças e as diferenças entre a solvatação por estas misturas \"verdes\" e a por misturas aquosas de álcoois. Uma aplicação do solvatocromismo para o entendimento de un fenômeno físco-químico foi apresentada: os resultados da aplicação do modelo de solvatação preferencial de sondas em misturas aquosas de tetrametiluréia foram usados para explicar o fenômeno de gelificação de proteína neste mesmo sistema de solventes. / In the present work, solvatochromic probes were employed in the study of pure solvents, binary mixtures of water with protic and aprotic solvents, ionic liquids and their aqueous binary mixtures The probes studied are classified in two series: (i) RPMBr2; where R = methyl to 1-octyl allowed increasing the hydrophobicity while maintaining the pKa constant. (ii) The second series involved derivatives of pyridine, quinoline and acridine, this allowed increasing probe hydrophobicity, while maintaining similar pKa. The two series of probes showed different solvatochromic behaviors both in pure solvents and binary solvent mixtures. A modified equation of Taft-Kamlet-Abboud allowed quantification of each solvent property, including acidity, dipolarity/polarizability and hydrophobicity to the response of each probe. The preferential solvation model which explicitly considers the presence of three species was employed; it considers the competition of water, organic solvent and the complex water-organic solvent in the probe solvation shell. The results shed light on the interactions that affect solvation, including temperature-induced desolvation. Preliminary results on aqueous ionic liquids showed the similarities and difference between solvation by these \"green\" mixtures and those of aqueous alcohols. An application of solvatochromism for understanding a physical-chemical phenomenon was presented: the results of application of preferential solvation model of probes in aqueous tetramethylurea mixtures was used to explain the gelation of the protein lysozyme in this same solvent system.

Diese Arbeit ist Teil eines Weges, der die Polarisationsdynamik von Polynukleinsäure-Helices (DNA) zum Ziel hat. Die Dynamik kann im Prinzip von innen beobachtet werden, über Femtosekunden-zeitaufgelöste optische Spektroskopie eines Farbstoff-Moleküls anstelle einer Nukleinbase. Der optische Chromophor soll als solvatochrome Sonde der DNA Umgebung funktionieren. Dafür wurde 2-Amino-7-Nitro-Fluoren (ANF) gewählt, welches ideale solvatochrome Eigenschaften hat. Bevor der Einbau des Sondenmoleküls erfolgt, müssen dessen photophysikalischen Eigenschaften in reinen Lösungsmitteln und in Lösungsmittel-Mischungen weitgehend verstanden sein. Dieses Thema bestimmt den größeren Teil der Arbeit. ANF, aliphatische Derivate, und das entsprechende Nukleosid wurden synthesitsiert. Ihre thermodynamischen Eigenschaften, optischen Spektren, und ps Fluoreszenzlebensdauern werden für eine Reihe von Lösungsmitteln beschrieben. Präferentielle Solvatation in wässrigen Mischungen wird mit optischer Absorptions- und 1H NMR-Spektroskopie untersucht. Inclusionskomplexe mit Cyclodextrinen werden ebenfalls charakterisiert. Auf diese "klassischen" Studien folgt die fs-transiente optische Absorptionsspektroskopie von ANF und Derivaten. Die transienten Spektren werden zeilegt und die Banden für stimulierte Emission als Funktion der Zeit in den meisten Fällen erhalten. Damit erhält man eine Solvatations-Relaxationsfunktionen C(t) für die meisten Lösungsmittel (50 fs Zeitauflösung). Unterschiede zu bekannten Relaxationsfunktionen für die vieluntersuchte Sonde Coumarin 153 werden diskutiert. Wichtig ist, daß derart C(t) für ein ANF Nukleosid in Wasser existiert. Dies kann mit einer simulierten Kurve für ANF in DNA-Helices verglichen werden. Es folgt, dass gestapelte Chromophore im Innern dynamisch von jenen unterschieden werden können, die in die wässrige Umgebung herausgedreht sind. Der Cyaninfarbstoff Thiazol Orange (TO) wird von anderen Gruppen verwendet, um die Hybridisierung von DNA-Strängen zu verfolgen. Die Fluoreszenz von TO wird durch schnelle Isomerisation im S1 Zustand stark gelöscht. In dieser Arbeit wird die entsprechende innermolekulare Verdrillung mit fs-transienter Absorptionsspektroskopie und mit fs-zeitaufgelöster Fluoreszenzspektroskopie (Summenfrequenz-Erzeugung) zum ersten Mal zusammenhängend untersucht. Transiente Spektren in Lösung werden mit stationären Spektren in verschiedenen PNA/DNA Duplex-Konstrukten verglichen. Eine hochfrequente Schwingungsmode ist bei der strukturellen Reorganisation von TO nach S0 to S1 Anregung beteiligt. Zunehmende Aktivität begleitet die Verdrillung. Deshalb sollte die Form der stationären Fluoreszenzbande dazu geeignet sein, das verfügbare freie Volumen in DNA-Konstrukten abzuschätzen. / This work is part of an effort to observe the polarization dynamics of duplex polynucleic acids from the inside, through femtosecond time-resolved optical spectroscopy of a dye molecule which has been stacked into the structure at a well-defined site. The dye chromophore should act as a solvatochromic probe of its DNA environment. For a probe, 2-amino-7-nitro fluorene (ANF) had been selected since it has ideal solvatochromic properties. Before being linked into DNA, its photophysical properties in liquids and liquid mixtures should be understood. The larger part of this thesis deals with this topic. ANF, aliphatic derivatives, and the nucleoside were synthesized. Their thermodynamic properties, optical spectra, and ps fluorescence decay are examined in a wide range of solvents. For preferential solvation in aqueous mixtures, absorption results are compared with 1H NMR spectra. Inclusion properties were also explored. Femtosecond transient absorption spectroscopy of ANF and derivatives follows after these "classical" studies. The transient spectra are analyzed and, in most cases, the stimulated-emission band can be obtained as function of time. Ultrafast solvation relaxation functions (50 fs resolution) for many solvents are constructed from these data and discussed by comparison with a well-studied probe, Coumarin 153. Most importantly, the solvation relaxation of the ANF nucleoside in water is obtained and compared with a simulated relaxation of the chromophore in a DNA duplex. It follows that chromophores stacked inside DNA can be distinguished from chromophores which extend into the aqueous boundary layer. The cyanine dye Thiazole Orange (TO) is used by other groups to monitor the hybridisation of DNA strands. Its fluorescence is strongly quenched by intramolecular twisting in the excited state S1. In this thesis the twisting process is characterized by femtosecond transient absorption and fluorescence upconversion spectroscopy, combined, for the first time. The transient spectra are compared to stationary spectra in a PNA/DNA duplex where the degree of twisting is restricted. A high-frequency mode is shown to play an important role in the structural reorganisation of TO following S0 to S1 excitation. Its vibrational activity is correlated with twisting. Therefore the shape of the emission band may be used to estimate the available volume in DNA constructs.