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The infrared spectra of mixtures of HC1 and the following have been recorded in the gas phase and low temperature matrices: argon, ethene, ethyne, de-benzene, fluorobenzene, CO, CO 2 , SOz, CC1*, CHCls, de-acetone, ethanal, HCN and acrylonitrile. The features which have been measured are: firstly the changes in the integrated intensity of lines in the rotation-vibration spectrum of the fundamental HC1 band as a function of interactions with other components of the mixture, and secondly bands associated with specific interactions forming hydrogen-bonded complexes. The enhancement of HC1 is generally found to vary linearly with the pressure of added gas over a limited pressure range. Assuming that line enhancement is caused by collisionally-induced rotation-translation energy exchange to or from the HC1 molecule, a combination of expressions derived from Ehrenfest's Adiabatic Principle and the "rigid rotor" approximation leads to a model which qualitatively predicts the enhancements observed. The model also rationalises the enhancement of HCN and SOa absorptions by HC1. Examination of the experimentally determined data leads to the conclusion that the total intermolecular force between the monomer base and HC1 controls the degree of enhancement but it is concluded that there is no general connection between the degree of HC1 enhancement and hydrogen-bond strength. Hydrogen-bonded complexes were examined in the gas and argon matrix phases and the shifts in the modified hydrogen chloride stretch compared for various bases. The spectra of pi-complexes formed between HC1 and ethene, ethyne and benzene were found to be detectable by low-resolution infrared spectroscopy at room temperature. Complexation of HCN, he-acetone and de-acetone with HC1 caused CN and C=O band shifts. The Chem-X molecular modelling program was evaluated by using it to predict the geometry of simple complexes for which experimental data is already available. It is concluded that the program requires more development before it can be confidently used as a theoretical aid with which to study hydrogen-bonded dimers.

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of the thesis entitled: Computational studies on supramolecular hydrogen-bonded structures: from nanocapsules to proteins.In this thesis different methods were used to study several systems in which the hydrogen bond has a key role. The validity of the theoretical methods applied was always contrasted with the experimental evidences available from the group of Prof. Javier de Mendoza in the context of an intense collaboration in the Institute of Chemical Research of Catalonia (ICIQ). In certain cases the theoretical results provided an explanation to experimental observations and in other cases they had the prediction as main objective. In Chapter II the general concepts of the Density Functional Theory (DFT) and of the Molecular Mechanics (MM) are described, emphasizing the specific methods used in the thesis.In Chapter III a DFT study is presented on the dimerization of the 2-ureidopyrimidone (UPy), and also on the tautomeric equilibrium established from this molecule. The influence of the substituent in position 6 of the pyrimidinone ring and the solvent effects were explained.Chapter IV deals with systems also based in dimers of ureidopyrimidone, but much larger. A molecule is described, composed of 3 UPy moieties bound to a cyclotriveratrylene unit, which self-assembles leading to the formation of a nanocapsule able to trap fullerenes inside. The nanocapsule shows higher affinity for certain fullerenes. The viability of the complexes (CTV-3UPy)2Cn(n=60,70,76,78,84,90) was studied as well as the preferences of the host. The aim was giving an explanation to experimental results obtained with C60 and C70 and predicting selectivity for higher fullerenes.Chapter V presents a Molecular Dynamics study on the effect of the punctual mutation R337H in the stability of the tetramerization domain of the protein p53 (p53TD). It has been experimentally demonstrated that this mutation prevents the protein from carrying out its normal function as a tumour suppressor. The simulations allowed explaining the disruption process suffered by the mutant protein.Using the same methods as in the previous chapter, chapter VI presents a study on the interaction of several ligands with the surface of the wild type protein (p53TD) and the mutant protein (R337H p53TD). The ligands tested were of the oligoguanidinium type and tetraguanidilated calix[4]arenes. The calixarenes proved to stabilize the structure of the mutant protein, maintaining it in a conformation similar to that of the wild type protein. Chapter VII describes the study, by means of Molecular Dynamics, of the unspecific interaction between a DNA molecule and undecaguanidinium ligands. The simulations proved that the ligands have high affinity for the DNA. In Chapter VIII the conclusions of the overall thesis are summarized.Resumen de la tesis doctoral titulada: Computational studies on supramolecular hydrogen-bonded structures: from nanocapsules to proteins. / En esta Tesis se han utilizado diferentes métodos computacionales para estudiar diversos sistemas en los cuales los enlaces de hidrógeno juegan un papel crucial. La validez de los métodos teóricos aplicados se ha contrastado siempre con las evidencias experimentales disponibles, procuradas por el grupo del Prof. Javier de Mendoza en el contexto de una estrecha colaboración en el Instituto Catalán de Investigación Química (ICIQ). En determinados casos los resultados teóricos han proporcionado una explicación a fenómenos observados experimentalmente y en otros casos han tenido como objetivo la predicción.En el Capítulo II se exponen los conceptos generales de la Teoría del Funcional de la Densidad (DFT) y de la Mecánica Molecular, poniendo mayor énfasis en los métodos concretos que se han utilizado en la Tesis. En el Capítulo III se presenta un estudio mediante métodos DFT sobre la dimerización y el equilibrio tautomérico establecido a partir de la 2-ureidopirimidona (UPy). Se estudió la influencia del sustituyente en posición 6 del anillo de pirimidona y del disolvente CHCl3. En el Capítulo IV se presenta un estudio sobre sistemas también basados en el dímero de UPy, pero mucho más grandes. Se describe una molécula compuesta por 3 UPys unidas a una unidad de ciclotriveratrileno (CTV) que dimeriza por auto-ensamblaje dando lugar a una nanocápsula capaz de atrapar fulerenos, mostrando mayor afinidad por algunos de ellos. Se estudió la viabilidad de los complejos (CTV-3UPy)2Cn(n=60,70,76,78,84,90) y las preferencias de la cápsula con ánimo explicativo y predictivo.En el Capítulo V se presenta un estudio de Dinámica Molecular sobre el efecto de la mutación puntual R337H en la estabilidad del dominio de tetramerización de la proteína p53 (p53TD). Se ha demostrado experimentalmente que tal mutación impide que la proteína lleve a cabo su función como supresor tumoral y por tanto favorece el desarrollo de tumores. Las simulaciones permitieron explicar el proceso de disrupción de la proteína mutada.Usando los mismos métodos que en el capítulo anterior, el Capítulo VI presenta un estudio sobre la interacción de ligandos tipo oligoguanidinas y calix[4]arenos tetraguanidilados con la superficie de la proteína de tipo salvaje p53TD y de la proteína mutada R337H p53TD. Los calixarenos demostraron estabilizar la estructura de la proteína mutada, manteniéndola en una conformación parecida a la de la proteína de tipo salvaje. En el Capítulo VII se describe el estudio, también mediante Dinámica Molecular, de la interacción inespecífica entre una molécula de ADN y ligandos undecaguanidina. Las simulaciones demostraron que los ligandos tienen una alta afinidad por el ADN.En el Capítulo VIII se presenta un resumen de las conclusiones de la Tesis.

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Hydrogen bonding is seen extensively in Nature. It is manifest in DNA/RNA nucleic acid (nucleobase) pairing, the defining feature of the double helix, as well as in secondary structures in protein folding such as hairpin loops. This importance, thus coupled with the aesthetic appeal of nucleobase hydrogen-bonding interactions, has inspired us to design and synthesize new hydrogen-bonded assemblies that make use of Watson-Crick and Hoogsteen interactions. Currently, novel supramolecular architectures are being developed for the formation of supramolecular polymers via Watson-Crick hydrogen bonding of guanosine and cytidine. Supramolecular polymer formation occurs through hydrogen bonding, electronic interactions, and metal chelation, and allows for a highly thermodynamic system that can easily be broken and reformed through external stimuli. By synthesizing linear, metal-nucleobase, and functionalized guanosine entities, a variety of new “monomers” have been obtained. Their use in construction of main chain and side chain polymers, and G-quartet hydrogels are now being explored. The hydrogen bonding motifs used to develop supramolecular polymers are also attractive for developing through bond electron transfer systems. One inspiration for developing artificial donor-acceptor systems (i.e., linked through non-covalent interactions) comes from the light harvesting systems found in Nature. Triggered by a pulse of UV light, electron transfer across bridges, including charge separation and charge recombination processes can occur and the rates can be determined. As one part of this study, collaborators Igor Rubtsov and David Beratan studied how perturbing the vibrational modes of the bridge via IR pulse excitation, affected electron transfer. Mid-IR excitation of the donor-acceptor systems slowed the rate of electron transfer, likely because the molecular vibrations either disrupted the bridging hydrogen bonds or distorted the electronic interactions of the bridge. This observance could lend itself to the possibility of designing IR-controlled molecular switches and other devices Another mode of hydrogen bonding, Hoogsteen interactions, was explored in the context of developing a guanosine-quadruplex binder. Specifically, a pyrrole-based inosine was designed to direct hydrogen bonding via an extended Hoogsteen interaction in order to bind to quadruplex DNA. Quadruplex DNA has been studied as a folded form of DNA and, if stabilized, can inhibit gene replication especially amongst cancer strands. In summary, the candidate’s research efforts have focused on exploiting hydrogen bonding in nucleobases to construct novel supramolecular assemblies that could see eventual applications in materials chemistry, nanotechnology, and gene therapy. / text

The conformational energy differences have been determined for ethylene glycol, 2- chloroethanol, and 2,2- dichloroethanol in the neat liquid, DMSO, and H20 with Raman spectroscopy. Spectra in the 0-H valence region were utilized to determine the energy difference between interand intramolecularly hydrogen bonded species. It was found that the solvent effect on the relative stabilities of the gauche and trans rotamers of the alcohols differ significantly. The results also indicate that, unlike ethylene glycol, there is significant intramolecular hydrogen bond formation in the halogenated alcohols in the neat liquid phase. Stronger intramolecular hydrogen bond formation was observed in dichloroethanol than in 2-chloroethanol.

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