Electronic coarse graining is a technique improving the predictive power of molecular dynamics simulations by representing electrons via a quantum harmonic oscillator. This construction, known as a Quantum Drude Oscillator, provides all molecular long-range responses by uniting many-body dispersion, polarisation and cross interactions to all orders. To demonstrate the predictive power of electronic coarse graining and provide insights into the physics of water, a molecular model of water based on Quantum Drude Oscillators is developed. The model is parametrised to the properties of an isolated molecule and a single cut through the dimer energy surface. Such a parametrisation makes the condensed phase properties of the model a prediction rather than a fitting target. These properties are studied in four environments via two-temperature adiabatic path integral molecular dynamics: a proton ordered ice, the liquid{vapour interface, supercritical and supercooled water. In all these environments, the model predicts a condensed phase in excellent agreement with experiment, showing impressive transferability. It predicts correct densities and pressures in liquid water from 220 K to 647 K, and a correct temperature of maximum density. Furthermore, it predicts the surface tension, the liquid-vapour critical point, density of ice II, and radial distribution functions across all conditions studied. The model also provides insight into the relationship between the molecular structure of water and its condensed phase properties. An asymmetry between donor and acceptor hydrogen bonds is identified as the molecular scale mechanism responsible for the surface orientation of water molecules. The dipole moment is identified as a molecular scale signature of liquid-like and gas-like regions in supercritical water. Finally, a link between the coordination number and the anomalous thermal expansion of the second coordination shell is also presented.

LFQO / Ligações de hidrogênio intramoleculares (LHI) estão entre as interações estabilizantes mais importantes que uma molécula pode apresentar, sendo muitas vezes a interação responsável por determinar o arranjo molecular. A avaliação da importância de ligações de hidrogênio para a estabilização de confôrmeros de uma molécula é realizada através de análise conformacional, que é o ramo da química orgânica que se atém a determinação da geometria molecular e da energia dos confôrmeros de uma molécula e de estudos para determinar quais as interações estéricas e eletrônicas que são responsáveis pela estabilização de cada confôrmero. Para investigar esta influência em compostos acíclicos 1,3-dissubstituídos, as preferências conformacionais dos compostos 3-R-propanol [R = OH (1), OCH3 (2), OCH2CH3(3), OCH(CH3)2 (4) e OC(CH3)3(5)], 3-R-butanol [R = OH(6), OCH3(7)] e 3-metil-3-R-butanol [R = OH (8), OCH3 (9)] foram avaliadas através de cálculos teóricos utilizando o funcional LC- ωPBE/6-311+G(d,p) atrelados a técnicas experimentais de espectroscopia no infravermelho e ressonância magnética nuclear. Os compostos 1, 2, 6 e 7 foram obtidos comercialmente, os demais foram sintetizados. Para todos os compostos o confôrmero mais estável foi o que apresenta LHI O-H...O. Através do estudo de população térmica observou-se que a somatória da população dos confôrmeros que fazem LHI sempre foi muito superior a população dos que não fazem LHI. A população térmica dos confôrmeros que fazem LHI foi de 65, 66, 73, 69, 97, 92, 79, 99 e 99 % para os compostos de 1 a 9, respectivamente. As análises de infravermelho mostraram que os valores de  aumentaram de 76, 87, 96, 100 e 112 cm-1 para os compostos de 1 a 5, respectivamente, indicando que a adição de grupos alquilas ao oxigênio aceptor de hidrogênio aumenta a força da LHI, apesar da repulsão estérica aumentar com o aumento do volume do substituinte. Os resultados de infravermelho mostram também que a força da LHI é maior para o composto 2 ( = 87 cm-1) do que para o composto 6 ( = 77 cm-1) indicando que a adição de grupos alquilas diretamente ao oxigênio aceptor de hidrogênio aumenta mais a força da LHI do que quando adicionados ao carbono α a este oxigênio. Os resultados de 3JHH obtidos pelo RMN de 1H mostraram que os valores de 3JHH são alterados com a mudança da basicidade do solvente. Os valores de 3JHH são menores em CCl4 e maiores em DMSO-d6 para todos os compostos. Uma equação foi proposta para mensurar a fração molar de confôrmeros com ligação de hidrogênio intramolecular através de constantes de acoplamento vicinais baseado em observações teóricas e experimentais. Os valores de fração molar dos confôrmeros que fazem LHI foram de 59, 53, 56, 57, 78, 88 e 74 % em CCl4 para 22, 13, 15, 12, 16, 44 e 13 % em piridina-d5, para os compostos de 1, 2, 3, 4, 5, 8 e 9, respectivamente. Estes resultados mostram que em solventes mais básicos, os confôrmeros que não fazem LHI são mais estáveis, consequentemente as rotações entre as ligações carbono-carbono são facilitadas e os valores de 3JHH são próximos ou maiores que 7,0 Hz, que é um valor médio para livre rotação. / Intramolecular hydrogen bonding is one of the most important intramolecular interactions, which is a critical element in deciding the molecular arrangement. Conformational analysis is the most powerful tool to evaluate the hydrogen bonding importance for a conformational preference. The term conformational analysis covers two aspects: determining molecular geometry and conformer energies, followed by studies to determine which steric and electronic interactions are responsible for the conformational stability. To investigate this influence in acyclic compound, the conformational preferences of 3-R-propanol [R = OH (1), OCH3 (2), OCH2CH3(3), OCH(CH3)2 (4) e OC(CH3)3(5)], 3-R-butanol [R = OH(6), OCH3(7)] e 3-metil- 3-R-butanol [R = OH (8), OCH3 (9)] are evaluated by means of theoretical calculations along with experimental infrared and nuclear magnetic resonance spectroscopies. Compounds 1, 2, 6, and 7 were purchased and the rest of remaining compound were synthesized. In fact, the most stable conformation of these compounds exhibit IAHB. Thermal population of hydrogenbonded conformers are 65, 66, 73, 69, 97, 92, 79, 99, and 99% for compound 1-9, respectively. Experimental infrared data show the red-shift value increase of 76, 87, 96, 100 to 112 cm-1 for compound 1-5, respectively, suggesting that the addition of alkyl groups to the IAHB proton acceptor atom increases the strength of this interaction and, although the steric repulsion increases along with increasing substituent volume, the increase in the IAHB strength is higher than the increase in the steric repulsion. Infrared data also show that the IAHB strength is greater for compound 2 ( = 87 cm-1) than for compound 6 ( = 77 cm-1), indicating that the increase in the IAHB strength is greater when alkyl groups are bonded directly to the oxygen proton acceptor than to the α-carbon. Experimental 3JH1H2 increases with the increase in solvent basicity for all compounds, indicating a change in the conformacional preference along with the increase in solvent basicity. An equation based on vicinal coupling constant is proposed to analyze 1,3-disubstituted acyclic compounds, allowing measurement of the experimental molar fraction (XHB) of conformers hydrogen-bonded in any solvent. The XHB values changed of 59, 53, 56, 57, 78, 88, and 74% in the CCl4 solvent to 22, 13, 15, 12, 16, 44, and 13% in pyridined5 as solvent. These results indicate that conformers hydrogen-bonded are predominant in nonbasic solvents, while the population of conformers non-hydrogen-bonded increases as solvent basicity increases.

LFQO / Ligações de hidrogênio intramoleculares (LHI) estão entre as interações estabilizantes mais importantes que uma molécula pode apresentar, sendo muitas vezes a interação responsável por determinar o arranjo molecular. A avaliação da importância de ligações de hidrogênio para a estabilização de confôrmeros de uma molécula é realizada através de análise conformacional, que é o ramo da química orgânica que se atém a determinação da geometria molecular e da energia dos confôrmeros de uma molécula e de estudos para determinar quais as interações estéricas e eletrônicas que são responsáveis pela estabilização de cada confôrmero. Para investigar esta influência em compostos acíclicos 1,3-dissubstituídos, as preferências conformacionais dos compostos 3-R-propanol [R = OH (1), OCH3 (2), OCH2CH3(3), OCH(CH3)2 (4) e OC(CH3)3(5)], 3-R-butanol [R = OH(6), OCH3(7)] e 3-metil-3-R-butanol [R = OH (8), OCH3 (9)] foram avaliadas através de cálculos teóricos utilizando o funcional LC- ωPBE/6-311+G(d,p) atrelados a técnicas experimentais de espectroscopia no infravermelho e ressonância magnética nuclear. Os compostos 1, 2, 6 e 7 foram obtidos comercialmente, os demais foram sintetizados. Para todos os compostos o confôrmero mais estável foi o que apresenta LHI O-H...O. Através do estudo de população térmica observou-se que a somatória da população dos confôrmeros que fazem LHI sempre foi muito superior a população dos que não fazem LHI. A população térmica dos confôrmeros que fazem LHI foi de 65, 66, 73, 69, 97, 92, 79, 99 e 99 % para os compostos de 1 a 9, respectivamente. As análises de infravermelho mostraram que os valores de  aumentaram de 76, 87, 96, 100 e 112 cm-1 para os compostos de 1 a 5, respectivamente, indicando que a adição de grupos alquilas ao oxigênio aceptor de hidrogênio aumenta a força da LHI, apesar da repulsão estérica aumentar com o aumento do volume do substituinte. Os resultados de infravermelho mostram também que a força da LHI é maior para o composto 2 ( = 87 cm-1) do que para o composto 6 ( = 77 cm-1) indicando que a adição de grupos alquilas diretamente ao oxigênio aceptor de hidrogênio aumenta mais a força da LHI do que quando adicionados ao carbono α a este oxigênio. Os resultados de 3JHH obtidos pelo RMN de 1H mostraram que os valores de 3JHH são alterados com a mudança da basicidade do solvente. Os valores de 3JHH são menores em CCl4 e maiores em DMSO-d6 para todos os compostos. Uma equação foi proposta para mensurar a fração molar de confôrmeros com ligação de hidrogênio intramolecular através de constantes de acoplamento vicinais baseado em observações teóricas e experimentais. Os valores de fração molar dos confôrmeros que fazem LHI foram de 59, 53, 56, 57, 78, 88 e 74 % em CCl4 para 22, 13, 15, 12, 16, 44 e 13 % em piridina-d5, para os compostos de 1, 2, 3, 4, 5, 8 e 9, respectivamente. Estes resultados mostram que em solventes mais básicos, os confôrmeros que não fazem LHI são mais estáveis, consequentemente as rotações entre as ligações carbono-carbono são facilitadas e os valores de 3JHH são próximos ou maiores que 7,0 Hz, que é um valor médio para livre rotação. / Intramolecular hydrogen bonding is one of the most important intramolecular interactions, which is a critical element in deciding the molecular arrangement. Conformational analysis is the most powerful tool to evaluate the hydrogen bonding importance for a conformational preference. The term conformational analysis covers two aspects: determining molecular geometry and conformer energies, followed by studies to determine which steric and electronic interactions are responsible for the conformational stability. To investigate this influence in acyclic compound, the conformational preferences of 3-R-propanol [R = OH (1), OCH3 (2), OCH2CH3(3), OCH(CH3)2 (4) e OC(CH3)3(5)], 3-R-butanol [R = OH(6), OCH3(7)] e 3-metil- 3-R-butanol [R = OH (8), OCH3 (9)] are evaluated by means of theoretical calculations along with experimental infrared and nuclear magnetic resonance spectroscopies. Compounds 1, 2, 6, and 7 were purchased and the rest of remaining compound were synthesized. In fact, the most stable conformation of these compounds exhibit IAHB. Thermal population of hydrogenbonded conformers are 65, 66, 73, 69, 97, 92, 79, 99, and 99% for compound 1-9, respectively. Experimental infrared data show the red-shift value increase of 76, 87, 96, 100 to 112 cm-1 for compound 1-5, respectively, suggesting that the addition of alkyl groups to the IAHB proton acceptor atom increases the strength of this interaction and, although the steric repulsion increases along with increasing substituent volume, the increase in the IAHB strength is higher than the increase in the steric repulsion. Infrared data also show that the IAHB strength is greater for compound 2 ( = 87 cm-1) than for compound 6 ( = 77 cm-1), indicating that the increase in the IAHB strength is greater when alkyl groups are bonded directly to the oxygen proton acceptor than to the α-carbon. Experimental 3JH1H2 increases with the increase in solvent basicity for all compounds, indicating a change in the conformacional preference along with the increase in solvent basicity. An equation based on vicinal coupling constant is proposed to analyze 1,3-disubstituted acyclic compounds, allowing measurement of the experimental molar fraction (XHB) of conformers hydrogen-bonded in any solvent. The XHB values changed of 59, 53, 56, 57, 78, 88, and 74% in the CCl4 solvent to 22, 13, 15, 12, 16, 44, and 13% in pyridined5 as solvent. These results indicate that conformers hydrogen-bonded are predominant in nonbasic solvents, while the population of conformers non-hydrogen-bonded increases as solvent basicity increases.

Controlling conformation of macromolecules, both in solution and solid state, has remained an exciting challenge till date as it confronts the entropy driven random coil conformation. Folded forms of biomacromolecules, like proteins and nucleic acids, have served as role-models to the scientists in terms of designing synthetic foldamers. The folded functional forms of proteins and nucleic acids have been shown to rely heavily on various factors, like directional hydrogen bonding, intrinsic conformational preferences of the backbone, solvation (e.g. hydrophobic effects), coulombic interactions, charge-transfer interactions, metal-ion complexation, etc. Chapter-1 discusses various designs of synthetic polymers explored by research groups world-over to emulate the exquisite conformational control exercised by biomacromolecular systems. Our laboratory has been extensively involved since 2004 in designing charge-transfer complexation induced folding of flexible donor-acceptor (DA) polymeric systems, such as those shown in Scheme 1. It was observed that such polymers adopt a folded conformation in polar solvents, like methanol, in the presence of an excess of an appropriate alkali metal ion. To explore folding in the solid state, Jonas and co-workers recently showed that a polyethylene-like polyester with long alkylene segments containing periodically located pendant propyl group forms a semicrystalline morphology with alternating crystalline and amorphous regions primarily because of the periodic folding of the backbone due to the steric exclusion of the propyl branches from the crystalline domains. In order to explore immiscibility-driven folding of polyethylene-like polyesters, Roy et al. designed a periodically grafted amphiphilic copolymer (PGAC) containing long alkylene segments (mimicking polyethylene) and pendant oligoethyleneglycol chains at periodic intervals (Scheme 2). Scheme 2: Proposed folding of a periodically grafted amphiphilic copolymer It was demonstrated that immiscibility between the hydrocarbon backbone and pendant PEG segments drives the polymer to adopt a folded zigzag conformation as shown in Scheme 2. The above synthetic strategy, however, does not permit easy structural variation of the side chain segments because the side-chain segment is covalently linked to the malonate monomer. In Chapter-2, a more general strategy to prepare periodically grafted copolymers has been described. In an effort to do so, we designed a series of clickable polyesters carrying propargyl/allyl functionality at regular intervals along the polymer backbone, as shown in Scheme 3. Scheme 3: Periodically clickable polyesters for the preparation of periodically grafted copolymers The polyesters were prepared by reacting either 2-propargyl-1,3-propanediol, 2,2-dipropargyl-1,3-propanediol or 2-allyl-2-propargyl-1,3-propanediol with an alkylene diacid chloride, namely 1,20-eicosanedioic acid chloride, under solution polycondensation conditions. Since these polyesters carry either, one propargyl, two propargyls or one propargyl and one allyl group on every repeat unit, it provides us an opportunity to synthesise exact graft copolymers with one side chain, two side chains or even two dissimilar side chains per repeat unit. In Chapter-3, the periodically clickable polyesters were reacted with MPEG-350 (PEG 350 monomethyl ether) azides using Cu(I) catalyzed azide-yne click reaction to generate periodically grafted amphiphilic copolymers (PGAC) carrying crystallizable hydrophobic backbone and pendant hydrophilic MPEG-350 side-chains (Scheme 4). Since the PGACs carry either one or two pendant MPEG-350 chains on every repeat unit, it allowed us to examine the effect of steric crowding on the crystallization propensity of the central alkylene segment. Scheme 4: Functionalization of periodically clickable polyesters with MPEG 350 azide by azide-yne click reaction From DSC studies, it was observed that increase in steric crowding at junctions resulting from increased side-chain volume hinders effective packing of the hydrocarbon backbone. As a result, both transition temperatures and the enthalpies associated with these transitions decreases. SAXS and AFM studies revealed the formation of lamellar morphology with alternate domains of PEG and hydrocarbon. Based on these observations, we proposed that self-segregation between hydrophobic backbone and hydrophilic side-chains induce the backbone to adopt a folded zigzag conformation (Scheme 5). Scheme 5: Schematic depiction of self-segregation induced folding of PGAC and their assembly on mica surface (AFM image) In order to study the effect of solvent polarity on conformational evolution of the periodically grafted amphiphilic copolymers, we randomly incorporated pyrene in the backbone of the polymer by reacting a small fraction (~ 5 mole %) of the propargyl groups with pyrene azide. Fluorescence study of the pyrene labelled polymer showed that increase in solvent polarity increases the intensity of the excimer band dramatically; this suggests the possible collapse of the polymer chain to the folded zigzag form. In an extension of this work, the PGAC was further used as template to synthesise layered silicates that appears to replicate the lamellar periodicity seen in the polymer. In order to study the effect of reversing the amphiphilicity on self-segregation, in Chapter-4, we synthesised a series of clickable polyesters carrying PEG segments of varying lengths, namely PEG 300, PEG 600 and PEG 1000, along the polymer backbone. The polymers were prepared by trans-esterification of 2-propargyl dihexylmalonate with different PEG-diols. These polyesters were then clicked with docosyl (C22) azide using Cu(I) catalyzed azide-yne click reaction to generate the desired periodically grafted amphiphilic polymers carrying crystallizable hydrophobic pendant chains at periodic intervals; the periodicity in this case was governed by the length of the PEG diols (Scheme 6). Scheme 6: PGACs carrying hydrophilic PEG backbone and crystallizable hydrophobic pendant docosyl chains Varying the average periodicity of grafting provided an opportunity to examine its consequences on the self-segregation behavior. Given the strong tendency of the pendant docosyl segments to crystallize, DSC studies proved useful to analyse the self-segregation; DOCOPEG 300 clearly exhibited the most effective self-segregation, whereas both DOCOPEG 600 and DOCOPEG 1000 showed weaker segregation. Based on the observations from DSC studies, we proposed that the PEG backbone adopts a hairpin like conformation (Scheme 7). Scheme 7: Proposed self-segregation through hairpin like conformation of backbone PEG segments In order to confirm the bulk morphology, we carried out small angle X-ray scattering (SAXS) and atomic force microscopic (AFM) studies. The SAXS profiles confirmed the observations from DSC studies, and only DOCOPEG 300 exhibited well-defined lamellar ordering. Thus, it is clear that the length of the backbone PEG segment (volume-fraction) strongly influences the morphology of the PGACs. Based on the inter-lamellar spacing from SAXS and the height measurements from AFM studies (Scheme 8), we proposed that these polymers form lamellar morphology through inter-digitation of the pendant docosyl side-chains. The observations from Chapters 3 and 4 suggested that the crystallization of the backbone has a dramatic effect on the conformation of the polymer backbone. In order to explore the possibility of independent crystallization of both backbone and pendant side-chains, the periodically clickable polyesters, described in Chapter-2, were quantitatively reacted with a fluoroalkyl azide, namely CF3(CF2)7CH2CH2N3 using Cu(I) catalyzed azide-yne click reaction; Chapter-5 describes these polyesters carrying long chain alkylene segments along the backbone and either one or two perfluoroalkyl segments located at periodic intervals along the polymer chain (Scheme 9). DSC thermograms of two of the samples showed two distinct endotherms associated with the melting of the individual domains, while the WAXS patterns confirm the existence of two separate peaks corresponding to the inter-chain distances within the crystalline lattices of the hydrocarbon (HC) and fluorocarbon (FC) domains; this confirmed the occurrence of independent crystallization of both the backbone and side chains. Scheme 10: Left-variation of SAXS profile of all three polymers as a function of temperature, Right- molecular modelling of representative FC-HC-FC triblock structures. Interestingly, a smectic-type liquid crystalline phase was observed at temperatures between the two melting transitions. SAXS data, on the other hand, revealed the formation of an extended lamellar morphology with alternating domains of HC and FC (Scheme 10). The inter-lamellar spacing calculated from SAXS matches reasonably well with those estimated from TEM images. Based on these observations, we proposed that the FC modified polymers adopt a folded zigzag conformation whereby the backbone alkylene (HC) segment becomes colocated at the center and is flanked by the perfluoroalkyl (FC) groups on either side, as depicted in Scheme 11. Melting of alternate HC domains first leads to the formation of a smectic-type liquid crystalline mesophase, wherein the crystalline FC domains retain the smectic ordering; this was confirmed by polarizing light microscopic observations. Scheme 11: Schematic presentation of self-segregation induced folding of polymer chains; and hence crystallization assisted assembly of these singly folded chains to form lamellar structure One interesting challenge would be to create unsymmetrical folded structures, wherein the top and bottom segments of the zigzag folded form would be occupied by two different segments, such as PEG and FC, whereas the backbone alkylene segment would form the central domain; this would lead to the possible formation of consecutive domains of PEG, HC and FC through immiscibility driven self-segregation process. In Chapter-6, several approaches to access such systems have been described; one such design that could have resulted in the successful synthesis of a periodically clickable polymer carrying orthogonally clickable propargyl and allyl groups along the backbone in an alternating fashion is depicted in (Scheme 12). The parent polyester was successfully synthesized and the propargyl group was first clicked with the FC-azide to yield the FC-clicked polyester; however, several attempts to click MPEG-SH onto the allyl groups using thiol-ene click reaction failed. Scheme 12: Scheme for the synthesis of alternating orthogonally clickable polymer In order to accomplish our final objective, we chose to first prepare the FC-clicked diacid chloride and polymerize it with an azide-alkyne clickable macro-diol, as depicted in Scheme 13; this approach was successful and yielded the desired clickable polyester bearing the FC segments at every alternate location. This polymer was then clicked with PEG-750 azide to yield the final targeted polymer that carries mutually immiscible FC and PEG-750 segments at alternating positions along the polymer backbone. The occurrence of self-segregation of FC, PEG-750 and the alkylene backbone (HC) was first examined by DSC studies, which appeared to suggest the presence of three peaks, although these were not very well-resolved. Scheme 13: Schematic for the synthesis of the polymer carrying FC and PEG 750 alternatingly along the backbone A schematic depiction of the anticipated organization of such unsymmetric folded macromolecules is shown in Scheme 15; it is evident that because of mutual immiscibility, the layers will be organized such that the FC domains of adjacent layers will be together and similarly the PEG domains of adjacent layers will also be together. Such an organization would lead to an estimated spacing that would correspond to a bilayer of the folded structures. Interestingly, SAXS study (Scheme 14) reveals the formation of lamellar morphology with a d-spacing of 14.6 nm. Scheme 14: Figure 6.10: SAXS profile of the polymer PE-FC-PEG 750 In order to gain an estimate of the expected inter-lamellar spacing, the end-to-end distance of a model repeat-unit was computed to be ~ 9.4 nm. It is, therefore, evident that the inter-lamellar spacing of 14.6 nm seen in the SAXS is significantly larger and must represent a bilayer type organization (Scheme 15). In this regard it is important to say that the organization of these alternatingly functionalized folded chains should give a variety of d-spacings. Because of highest electron density contrast of FC among PEG, HC and FC, we proposed that the d-spacing calculated from the SAXS profile corresponds to ‘d4’ in Scheme 15. This first demonstration of the formation of zigzag folded unsymmetric entities bearing dissimilar segments on either side of the folded chain holds exciting potential for a variety of different applications and beckons further investigations. Scheme 15: Schematic for the proposed self-assembly of the singly folded polymer chains

Le champ de force CLAYFF est largement employé pour modéliser les interfaces de minéraux argileux – et minéraux apparentés – avec une phase aqueuse. Dans les simulations, les particules d’argile sont typiquement représentées par des feuillets semi-infinis, ainsi seules les surfaces parallèles au plan du feuillet (surfaces basales) sont considérées. Cette simplification est valable dans la mesure où ces surfaces sont majoritaires, mais les feuillets d’argile sont en réalité de taille nanométrique et terminés par des surfaces latérales, ou bordures. Ces surfaces peuvent non seulement adsorber les espèces en solution mais sont aussi sujettes aux transferts de proton, et tous les processus physico-chimiques liés à l’acidité de la phase aqueuse se produisent de façon prédominante au niveau des bordures. En ajoutant au champ de force CLAYFF un terme angulaire métal-O‑H dont les paramètres ont été correctement ajustés, les simulations réalistes des interfaces de bordure deviennent possibles.Les paramètres des termes Al-O‑H et Mg-O‑H ont été obtenus à partir de calculs DFT sur des modèles structuraux du bulk, de la surface basale et de la bordure de la gibbsite Al(OH)3 et de la brucite Mg(OH)2, dont les feuillets peuvent être considérés comme le squelette des minéraux argileux et apparentés. De plus, le terme Si-O‑H a été paramétré à partir d’un modèle de bordure de la kaolinite Al2Si2O5(OH)4. Les propriétés structurales et dynamiques issues de simulations de dynamique moléculaire DFT et classiques basées sur CLAYFF avec et sans terme métal-O‑H ont été comparées. Le champ de force modifié améliore nettement la description des surfaces hydroxylées : l'orientation et la dynamique librationnelle des groupes hydroxyles, les liaisons hydrogène dans lesquelles ils sont impliqués, et la coordination des atomes de métal appartenant aux bordures sont tous plus proches de la réalité. / The CLAYFF force field is widely used to model the interfaces of clay minerals – and related layered materials – with an aqueous phase. In the simulations, clay particles are typically represented by semi-infinite layers, i.e. only surfaces parallel to the layer plane (basal surfaces) are considered. This simplification is acceptable to a certain extent, but clay layers are really nanosized and terminated by lateral surfaces or edges. These surfaces can not only adsorb solvated species but are also subject to proton transfers, and all physico-chemical processes related to the aqueous phase acidity predominantly occur at the edges. By adding to the CLAYFF force field a Metal-O‑H angle bending term whose parameters are correctly adjusted, the simulations of edge interfaces become possible.The parameters of Al-O‑H and Mg-O‑H terms were obtained from DFT calculations on bulk, basal surface and edge structural models of gibbsite Al(OH)3 and brucite Mg(OH)2, whose layers can be considered as the backbones of clay minerals and related materials. In addition, the Si-O‑H term was parametrized from an edge model of kaolinite Al2Si2O5(OH)4 . Molecular dynamics simulations based on DFT and on CLAYFF with and without Metal-O‑H term were performed. The modified force field clearly improves the description of hydroxylated surfaces : the orientation and the librational dynamics of the hydroxyl groups, the hydrogen bonding, and the coordination of metal atoms belonging to the edge are all closer to reality.

(FOR FIGURES REFER THE MAIN PDF FILE) Supramoleculr chemistry, aptly termed by Lehn as the study of molecular sociology, is the chemistry of the intermolecular bond, focusing on the structures and functions of “supermolecules” –chemical system formed by the association between two or more molecular components. While interrelated, this discipline forges beyond the domain of traditional molecular chemistry, which seeks to master the manipulation of the covalent bond between atoms and uncover the principle that governs the structures and properties of molecular species. Supramolecular chemistry assayas to blend the comprehensive resources of molecular chemistry with designed control of the intermolecular interactions to engineers supramolecular with features as well defined as those of the constituent molecular themselves. Not surprisingly, it has been stated that supramoleculars are to molecules and the intermolecular bond what molecules are to atoms and the covalent bond. In the realm of molecular crystals, the focus of supramolecular chemistry and indeed, the scope of the present thesis coverings with that of a rather recent, but rapidly emerging scientific discipline, namely crystal engineering. Coined nearly four decades ago in connection with photodimerization reaction in crystalline cinnamic acids, the term” crystal engineering” has since then broadened its expanse considerably and is, at present, most appropriately defined as“the understanding of intermolecular interactions in the context of crystal packing and the utilization of such understanding in the design of new solids with desired physical and chemical properties”. It would be befitting to remark that it is very pursuit (and more often than not, the elusive target) of being able to make functional solids by design that has allowed crystal engineering to evolve from an object of mere Scientific curiosity to a subject of tremendous utilization value. No proof for this assertion might be greater than that which lies in the fervent efforts put forth by pharmaceutical companies in understanding and controlling drug polymorphism, especially in the wake of the contemporary legal implications attendant with observing such a phenomenon. Polymorphism in molecular crystals results from the possibility of at least two different arrangements of the molecular of a given compound in the solid state and has therefore often been regarded as the” dark side” of crystal engineering. On one hand, polymorphism presents itself as an important probe in the study of structure-property relationship and allows elucidation of the varied macroscopic properties of the same molecule self-assembled in different crystalline environments. On the other hand, the phenomenon poses an implicit complication when predicating the product of a crystallization process forms the goal of a crystal engineering project. This is particularly true in case of crystal structure prediction (CSP) from the molecular structure of a given compound, where the experimentally obtained polymorphic modification may be a kinetic form and therefore, need not correspond to the one ranked lowest in energy from the computational studies. Indeed, this dichotomy between a thermodynamically and a kinetically controlled crystallization process reflects the underlying uncertainty associated with judging the outcome of a crystallization event. In this concept of a supramolecular synthon has been postulated to assimilate both thermodynamic and kinetic alternative, and therefore provide a working model for heuristic crystal design. By analogy with corey’s definition of a molecular synthon, a supramolecular synhon has been described” a structural unit within a supramolecule which can be formed and/or assembled by known or conceivable synthetic operations involving intermolecular interactions”. Being entirely probabilistic in nature, the robutness and thus, the transferability of a particular synthon to a designed crystal is assessed from a systermatic evolution of its recurrence in crystal structures of representative molecules. The Cambridge Structural Database (CSD), which announced the inclusion of the 500000th crystal structures in its archives last year, provides an invaluable cache of experimentally determined structures and the foundation for crystal design in this regard. The practically of the supramolecular synthon approach, now almost synthymous with crystal engineering, has been demonstrated not only in the successful design of a number of functional solids, but also in its possible application in CSP as a knowledge-based alternative. Irrespective of the approach, a basic paradigm can however be constructed from any crystal engineering strategy, viz. construct the molecular building blocks and assemble these, with a prior knowledge of the possible non-covalent interactions, in a manner that leads to the desired crystal structure. This premise will form the central theme of the present thesis, entitled “From molecular to supramolecular: Probing solid state self –assemblies of conformatonally locked polycyclitos and structural siblings”. The dissertation will deal with the nuances of the self-assemblies of four classes of structurally related crystalline polycyclie compounds, all fashioned from a prototypical rigid trans-decalin backbone derived from commonly available aromatic precursors like naphthalene and anthracene. The thesis will be presented in four chapters, each based on one of the four functional make-ups present in the molecular under study. • Chapter 1.Relating intramolecular O-H…Ohydrogen bondigs to conformational locking: Design and self-assemblies of crystalline polyclitols. • Chapter 2.Preferences of supramolecular assemblies towards competing inter- and intramolecular O-H…O hydrogen bonds: A case study in crystalline acyldervaeives of conformarionally locked polyclitols. •Chapter 3.Synthesis of novel polyhydroxylated flustrates: Probing fluorine interactions in a conformatonally constructed environment. • Chapter 4. Strength vs.accessiblity: Universe the patterns of self-recognition in designer conformationally locked aminoacohols. A brief overview of each chapter is presented below. The first chapter of the thesis investigates the supramolecular chemistry of an O-H…O Hydrogen Bond formed between hydroxyl groups that have been constrained to occupy spatiality invariant position in the crystal structure of a polycyclitol (a portmanteau word derived from polycyclic cyclitol). Having been constructed on a grid trans-decalin carbocyclic backbone, the polycyclitols under study 1-6 are conformatonally locked and destined to exhibit an axial rich disposition of the hydroxyl groups, so that the OH functionalities in 1,3-relationship are automatically brought into a favorable geometry for the formation of intramolecular O-H…O hydrogen bonds. Working within this paradigm, which was formulated both logically and on the basis of the observed H-bonding patterns in the crystal structures of several conformationally locked polyols, we were able to demonstrate that intramolecular H-bonding between 1,3-syndisxial OH groups can be used as a tool to preordain the position of the intermolecular O-H…O-bond donors and accepts in the specially crafted polycyclitols 1-3. this observation not only simplified a qualitative visualization of the various packing patterns in 1-3, but also allowed us to propose, based on previously reported CSD analysis, the packing motifs mostlikely to converge with the experimental results. Despite its qualitative nature, the O-H…O hydrogen bonding patters, proposed for 1-3 were found to conform well with those observed experimentally for the tetrols 1 and 3, and even for the two polymorphic modifications of the hexol 2[Figure 1] The determination role played by intramolecular O-H…O bonding in the supramolecular assembly of 2, a novel bicycle C2h symmetric hexol having an all axial disposition of the six hydroxyl functionalities, prompted us to study the crystal packing of the three diastereomeric perhydro-2,3,4q,6,6,8a-naphthalenehexols 4-6. the end-to-end co-operative intramolecular O-H…O-H hydrogen bonding chain on both faces of the molecule, as observed in case of 2, through an axial-equatorial. Figure 1. (left) one of the packing modes proposed for the hexol 2. Note that the H-bonding pattern involves all donor/acceptor oxygen and incorporates infinite chains of O-H…O bonds of O-H….O bonds; (right) Molecular packing observed experimentally in the polymorph of the hexol 2 Transposition of one or more of the peripheral yhdroyl groups. With increased freedom now allowed to the OH groups in the choice of their H-bonding partners, as a compared to 2 crystal packing in the polycyclitols 4-6 evolved from the simplistic model of hydrogen bonding proposed and observed for 2,to ivoke more complex patterns of self assembly mediated through O-H…O-bonds In the second chapter, the crystal structures of four conformationally locked esters, namely tetraaccetate 7/tetrabenzoate 8 of hexol 2 and the diacetate9/dibenzoate 10 of tetrol1,have been analyzed in order to examine the preference of their supramolecular assemblies towards competing inter and intramolecular O-H…O hydrogen bonds. To this end, all the four esters under study were specially crafted on a trans-decalin backbone with the objective of relegating the O-H…O H-bond donors( in form of the 30 OH groups) to the molecular interior and having the peripheral H-bond accepters (in form of the 20 acyl groups) in 1,3-syndiaxial relationship. It was anticipated that this common design element would allow the supramolecular assembly of the easters to evolve along two possible pathway, namely one which employs intermoleculars O-H…O H-bonds (pathway 1) and the other that sacrifises those for intramolecular O-H…O H-bonds and settles for a crystal packing dictated by weak intermolecular interactions alone (pathway 2) A pure sample of 7 crystallized along pathway 1 in two enantiotropic modifications, one obtained at room temperature (form) and the other at 20 C0 (form) [Figure 2]. Behaving much like a temperature guided molecular switch, the tetraacetate 7 could be shifted reversibly between the forms response to changes in the ambient temperature. Thus, the form converted at -4 OC to the denser form, which displayed an unusual kinetic stability till 67 OC and transformed back to the form beyond this temperature. Subsequently, the close similarity between the self-assemble of the two dimonrphs of 7 and the diastereomer 11 was exploited in order to stimulated 7 to fallow the pathway 2 through preferential inhibition of pathway 1[Figure 3]. Interstingly, the nucleation inhibition 11 was obtained serendipitously a route 7 via an apparent breakdownof furst-platter rule. Unlike the tetraceatate 7, crystal packing in the tetrabenzoate 8 preferred to fallow exclusively pathway 2. The individualistic nature of the self-assemblies of 7 and 8 found to be in contrast commonalities noted in the mode of molecular assembly in 9 and 10 both of which conformed to a combination of pathway 1 and 2. A rationale for the preferred crystallization pathway of the four estes 7-10 as well as probable mechanism for the observed reversible transformation between the forms the tetracetate 7 will be put forth in this chapter. Figure 2. (Model for pathway 1) Molecular packing in the forms of the tetraacetate 7. The non-interacting hydrogen atoms have been omitted for clarity. Figure 3. (Model for pathway 2) The nucleation inhibitor 11 and form of the tetraacetate 7. The non-interacting hydrogen atoms have been omitted in the molecular packing diagram for clarity. In light of the wide ranging application of organofluorine compounds and the ambiguity that resides over the disposition of fluorine as a H-bond accepter, the third chapter utilizes three specially designed fluorinated polycyclitols 12-14 investigate the role of covalently bonded flurine in crystal structures of lesser studied aliphatic fluorous substracts and probe its capacity to engage itself in C(sp3)-F…H-X(sp3)(X=O and/or C) H-bounding, in presence of its isostere, the hydrozyl group. Conformatonality locked with well defined spatial disposition of functional groups, all the fluorinated polycyclitols 12-14 bear a fluorohydrin moiety, embedded in a rigid trans-decalin framework. In 12 and 14, it was conceived that the presence of a hydroxyl donor in a favorable 1, 3-syndiaxial relationship to a fluoro group on one side and a hydroxyl group on the other would allow an unambiguous comparison between the two isoteric functionalities (C-OH and C-F) to serve as acceptors for intramolecular hydrogen bonds (O-H…O and purported O-H…F respectively) The difluorodiol 13 was sought to serve as a control to assess the change in the C-F…H-X interactions (if any) which might be observed upon incorporating the peripheral secondary hydroxyl groups in 14. The result presented in this chapter will revel, in particular, that C(sp3) –F…H-C(sp3) hydrogen bonds, though weak and lesser investigated, can indeed be observed and supramolecular recognition motifs, involving such interactions, can be conserved even in crystal structures laden with stronger O-H…O hydrogen bonds [Figure 4}. Figure 4. (Left) Molecular packing in the difluorodiol 13, showing how four intermolecular C-H…F hydrogen bonds forms a part of a R22 H-bonding motif (encircled). This centrosymmentic supramolecular recognition unit is observed even in the molecular packing in the difluorohexol 14 (right). Non-interacting H atoms have been omitted in both diagrams for the sake of clarity. The forth chapter details an in-depth study carried out on the self-assembly of a conformationally locked aminoalchohol 15, in which the amino protons serve as mere spectators, the molecular packing in the crystal being realized through the co-operativity between O-H…N H-bonds and weak π-π stacking interaction (Figure 5b). The crystal structure of 15 was quite intriguing on three sailent grounds (a) previous studies on the supramolecular assemblies in the aminols have shown that both amino and hydroxyl protons participate in H-bonding in the crystal structures of such compounds; (b) the fact that the hydrogen atoms of the NH2 group Figure 5. (Left) Laplacian distribution map in the planes defined by (a) the double bonds, (c) O-H…N-H-bond, and (d) π-π stacking interactions in the aminoalclhol 15. Contours havse been drawn at logarithmic intervals in ▼2 ρb, eÅ-5. Solid lines indicate positive contours and dotted lines negative contours. (b) Molecular packing in 15. Non-interacting H atoms have been omitted for the sake of clarity.remain as mere bystanders in anomalous if one were to abide by the Etter’s rule; (c) the rather well-difined π-π stacking interactions in crystal structure of the aminoalcohol occurs between isolated olefinic bonds-a rarely encountered form of non-covalent interaction. Charge destiny analysis was carried out on the aminoalcoholf 15 not only to catheterize the non-covalent interactions existing in the supramolecular assembly in terms of topological features of electrol destiny at their bond critical points, but also to confirm the non-involvement of the amino H-atoms in any form of either intra- or intermoalecular hydrogen bonds beyond the criteria of mere geometry (Figure a,c,d). The maverick nature of the self-assembly of 15 was elucidated as resulting from the preference of the molecules to assemble with O-H…N H-bonds. This automatically relegated the hydrogen atoms of the tertiary amine to the interior of the conformationally locked cabocycclic scaffold, thereby making them far less accessible than the peripheral C=C bonds.

Solvent effects play diverse roles in myriads of chemical, physical and biological processes. The solvent interacts with the solute by: i) non-specific (Coulombic, van der Waals interactions) and ii) specific interactions (hydrogen bonding, etc.). These interactions are responsible for solvation of the solute and are collectively termed as “solvent polarity”. Differential solvation of ground and excited electronic states is manifested in the absorption spectrum as a change in the band position, intensity or shape, which is termed as “solvatochromism”. Intermolecular hydrogen bonding (IHB) is a kind of specific solute-solvent interaction, which plays a key role in molecular or supramolecular photochemistry, as well as in photobiology. Solvation and its influence on various physico-chemical and biological processes can be understood by i) top-down; and ii) bottom-up approaches. In the top-down approach, the macroscopic properties like dielectric constant, refractive index are used to understand the microscopic solvation. This approach fails when specific interactions like hydrogen bonding interactions come into play, and furthermore it can reproduce only the macroscopic polarization of the solvent but fails miserably at the cybotactic region of solvation. With the recent advancements in the computational field, the molecular level description of solvation has been within reach for chemical physicists and experimentalists to corroborate their experimental results and in turn to visualize processes of fundamental or technologically relevant problems. The energy levels of the nπ* and ππ* singlet and triplet excited states of aromatic ketones are close-lying and therefore their energy levels can be altered by the substituents. The solvent polarity can be used as a surrogate to tune their energy levels. In certain cases, the lowest triplet or singlet excited states can switch their electronic character with increasing solvent polarity known as “electronic state switching” and thus modulate their photochemical or photophysical properties. Therefore, aromatic ketones were used as solvatochromic probes in this work. Comprehensive analyses of the solvent effects on xanthone (XT), 9,10-phenanthrenequinone (PQ) and benzophenone (Bzp) were carried out using steady-state and nanosecond time-resolved absorption, and resonance Raman spectroscopy in conjunction with ad hoc and classical-molecular dynamics and simulations generated supermolecule-continuum solvent model quantum mechanical calculations to corroborate the experimental outcomes and in turn to visualize the solvation process at the molecular level. The present thesis is divided into eight chapters and the summary of each chapter is described below: Chapter 1 provides a brief literature review of solvation effects and their influence on various physico-chemical and biological processes. Furthermore, the importance of understanding solvation at the molecular level and key concepts are discussed, which forms the heart of this thesis. Chapter 2 discusses the experimental and computational approaches used to study the solvation processes at the molecular level. A detailed explanation of spectroscopic techniques like resonance Raman (RR) and nanosecond-time resolved resonance Raman (ns-TR3) spectroscopy and their experimental and theoretical aspects are discussed, followed by a discussion on the fundamental concepts of computational methods like ab initio calculations density functional theory (DFT), and classical molecular dynamics and simulations (c-MDS) utilized in this study. Chapter 3 focuses on microscopic understanding of solvatochromic shifts observed for 9,10-phenanthrenequinone in protic solvents using UV-Vis and RR spectroscopy in conjunction with an ad hoc explicit solvation model and time-dependent density functional theory (TDDFT) calculations. The hypsochromic shift and bathochromic shift of the singlet nπ* and ππ* electronic transitions in protic solvents are due to hydrogen bond weakening and strengthening in the excited state for the corresponding electronic transitions, respectively as indicated by TD-DFT calculations and Kamlet-Taft linear solvation energy relationships. The hydrogen bond strengthening in the singlet ππ* excited state is further confirmed by Raman excitation profile (REP) analysis of PQ in different solvents. Furthermore, with increasing solvent polarity the two lowest singlet excited states undergo different hydrogen bonding mechanisms, leading to a decreasing energy gap between them. Therefore, hyperchromism of the nπ* transition has been hypothesized to be due to an increasing vibronic coupling between the lowest singlet nπ* and ππ* excited states. In Chapter 4, a real time observation of the thermal equilibrium between the lowest triplet excited states of PQ in acetonitrile solvent was carried out using ns-TR3 spectroscopy and this can explain its high reactivity towards H-atom abstraction, despite the fact that the lowest triplet excited state has ππ* character. Furthermore, extending the concept of hydrogen bonding mechanisms of the lowest singlet to the triplet excited states, the different hydrogen bonding mechanisms exhibited by them can lead to alteration of the intersystem crossing mechanisms in PQ. Chapter 5 highlights the very different role of intermolecular hydrogen bonding in the reduced reactivity of the xanthone (XT) triplet towards H-atom abstraction in protic solvents. The different hydrogen bonding mechanisms exhibited by the two lowest triplet excited states in protic solvents are derived from an ad hoc explicit solvation model, TD-DFT calculations and ns-time resolved absorption (ns-TRA): they separate them further in energy and thereby the nearest T2(nπ*) triplet state to the T1(ππ*) excited state plays an insignificant role in the reactivity towards H-atom abstraction, in contrast to the PQ triplet discussed in Chapter 4. Chapter 6 discusses the structure of XT triplet states using TR3 spectroscopy in combination with TD-DFT studies. The TR3 spectrum of the XT in acetonitrile identified a vibronic coupling mode responsible for the reactivity of XT towards H-atom abstraction, despite the fact that the lowest triplet excited state (T1) has ππ* character. This vibronic active mode is absent in the TR3 spectra of XT in protic solvents (methanol and ethanol). Furthermore, the REP analysis suggests that the nanosecond triplet-triplet absorption spectrum of XT in acetonitrile involves two different species, while in methanol it involves only one species. This observation is in agreement with the previous chapter (Chapter 5) which proposes a different hydrogen bonding mechanisms for the two lowest triplet excited states and their influence on the reduced reactivity towards H-atom abstraction. Chapters 3-6 emphasize the need for a proper solvation model at the molecular level to describe the various photophysical and photochemical processes of aromatic ketones. Therefore, Chapter 7 includes discussions on the bottom-up solvation methodology applied to benzophenone (Bzp) to understand its vibrational and electronic solvatochromic behaviour at the molecular level. Raman and UV-Vis spectroscopic techniques were used in conjunction with a c-MDS-generated supermolecule continuum solvation model DFT calculation to corroborate and to visualize the experimental outcome. The carbonyl stretching frequency of Bzp in protic solvents has two bands, corresponding to free carbonyl and hydrogen bonded carbonyl. Despite the fact that the macroscopic polarity of acetonitrile and methanol solvents are similar, the free carbonyl stretching of Bzp in methanol solvent was blue-shifted by 4 cm-1 with respect to the carbonyl stretching in acetonitrile solvent. The Gutmann’s acceptor number plot for carbonyl stretching frequencies indicates that the free carbonyl group is neighboured by a hydrophobic environment. The c-MDS-generated supermolecule-continuum solvation model DFT calculations suggest that the extended hydrogen bonding network of methanol solvent is responsible for the hydrophobic solvation around the free carbonyl. Furthermore, a linear correlation was obtained for the vibrational and electronic solvatochromism of the carbonyl frequency and energy of the singlet nπ* transition, respectively, which indicates that a variation in excitation wavelength for the singlet nπ* transition can arise from different solvation states. This can have implications for ultrafast processes associated with electron transfer, charge-transfer and also the photophysical aspects of excited states.Finally, Chapter 8 contains overall conclusions of the thesis and future directions for the present research area.

Orientador: Roberto Rittner Neto / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Química / Made available in DSpace on 2018-08-27T15:26:13Z (GMT). No. of bitstreams: 1 Cormanich_RodrigoAntonio_D.pdf: 10639408 bytes, checksum: 8d9f49120e3075dd18419db2187ca981 (MD5) Previous issue date: 2015 / Resumo: É reportado na presente tese de doutorado o estudo físico-químico de diferentes compostos orgânicos. Em específico, foram estudadas as preferências conformacionais e as interações intramoleculares de modelos de dipeptídios, como a Ac-Gli-NHMe e seus derivados fluorado CF3-C(O)-Gli-NHMe e metilado Ac-Gli-N(Me)2.... Observação: O resumo, na íntegra, poderá ser visualizado no texto completo da tese digital. / Abstract: The present PhD thesis reports physicochemical studies of several organic compounds. In particular, the conformational preferences and the intramolecular interactions of dipeptide models, as the Ac-Gly-NHMe and its fluorinated and Nmethyl derivatives CF3-C(O)-Gly-NHMe and Ac-Gly-N(Me)2, were investigated....Note: The complete abstract is available with the full electronic document / Doutorado / Quimica Organica / Doutor em Quimica

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