As cargas, dipolos, quadrupolos e multipolos atômicos de maior ordem, bem como suas derivadas, permitem um maior entendimento de diversas propriedades elétricas em sistemas moleculares, como momentos de dipolo, derivadas do momento dipolar, intensidades de infravermelho e potenciais eletrostáticos, além de forças eletrostáticas. Os multipolos aqui estudados foram aqueles advindos da Teoria Quântica de Átomos em Moléculas (QTAIM) e, em certos casos, foram comparados com resultados do formalismo CHELPG (CHarges from Electrostatic Potentials using a Grid based method). As investigações desse projeto foram divididas em duas etapas distintas, sendo que a primeira focou no desempenho dos multipolos atômicos na descrição dos potenciais eletrostáticos quando da interação de uma carga pontual carregada positivamente com uma molécula. Algumas simples moléculas diatômicas (F2, Cl2, BF, AlF, BeO, MgO, LiH e NaCl) e outras mais complexas (H2O, H2CO, NH3, PH3, BF3 e CO2) foram consideradas nesta etapa, sendo que os cálculos foram feitos com B3LYP/6-311G(3d,3p). Já, na segunda etapa, estudou-se o modelo carga - fluxo de carga - fluxo de dipolo (CCFDF, do inglês \"charge - charge flux - dipole flux\") na investigação e interpretação das intensidades fundamentais de infravermelho em modos de vibração molecular. Nessa etapa optou-se pelo estudo de sistemas que apresentavam ligações de hidrogênio, como homodímeros (H2O-H2O, HF-HF, HCl-HCl, HCN-HCN, HNC-HNC e NH3-NH3) e heterodímeros (HF-HCN, HCl-HF e HF-H2O). Os cálculos destes sistemas foram realizados com CCSD/cc-pVQZ-mod. Os resultados sugerem que os multipolos QTAIM são melhores que as cargas CHELPG, na maioria dos casos, para descrição dos potenciais eletrostáticos em sistemas próton - molécula. Por sua vez, o modelo CCFDF/QTAIM consegue reproduzir as intensidades de infravermelho em dímeros que apresentam ligações de hidrogênio. Finalmente, o aumento de intensidade do estiramento X-H do monômero doador, em dímeros lineares, é explicado pela variação da contribuição de fluxo de carga durante a dimerização. / The charges, dipoles, quadrupoles and high order terms, along with their derivatives, allow a better understanding of electric properties. We can cite dipole moments, dipole moment derivatives, infrared intensities, electrostatic potentials and electrostatic forces. The multipoles treated here are obtained from the Quantum Theory of Atoms in molecules (QTAIM) and they are compared with CHELPG (CHarges from Electrostatic Potentials using a Grid based method) results. The investigations of this project can be divided in two distinct parts and the first one focuses in the performance of atomic multipoles in the description of electrostatic potentials when one positive particle interacts with molecules. Some simple diatomic (F2 , Cl2 , BF, AlF, BeO, MgO, LiH and NaCl) and polyatomic molecules (H2O, H2CO, NH3 ,PH3 ,BF3 and CO2) were considered in this investigation and the calculations were carried out at the B3LYP/6-311G(3d,3p) level. The second part of this dissertation was a study of infrared intensities in vibrational modes by means of the charge-charge flux -dipole flux model. The systems treated now are dimers with hydrogen bonds such as homodimers (H2O-H2O, HF-HF, HCl-HCl, HCN-HCN, HNC-HNC and NH3-NH3) and heterodimers (HF-HCN, HCl-HF and HF-H2O). The calculations of these systems were carried out at the CCSD/cc-pVQZ-mod level. The results suggest that QTAIM multipoles are better in describing electrostatic potentials in almost all proton-molecule arrangements than CHELPG charges. The charge-charge flux -dipole flux model can reproduce infrared intensities of dimer with hydrogen bonds. Finally, the increase in intensities of X-H stretching modes associated to the donor monomer in linear dimers is explained by changes in charge flux contributions during dimerization.

Calcium regulates many biological processes through interaction with proteins with different conformational, dynamic, and metal binding properties. Previous studies have shown that the electrostatic environment plays a key role in calcium binding affinity. In this research, we aim to dissect the contribution of the electrostatic environment to calcium binding affinity using protein design. Many natural calcium binding proteins undergo large conformational changes upon calcium binding which hampers the study of these proteins. In addition, cooperativity between multiple calcium binding sites makes it difficult to study site-specific binding affinity. The design of a single calcium binding site into a host system eliminates the difficulties that occur in the study of calcium binding affinity. Using a computer algorithm we have rationally designed several calcium binding sites with a pentagonal bipyramidal geometry in the non-calcium dependent cell adhesion protein CD2 (CD2-D1) to better investigate the key factors that affect calcium binding affinity. The first generation proteins are all in varying electrostatic environments. The conformational and metal binding properties of each of these designed proteins were analyzed. The second generation designed protein, CD2.6D79, was designed based on criteria learned from the first generation proteins. This protein contains a novel calcium binding site with ligands all from the â-strands of the non-calcium dependent cell adhesion protein CD2. The resulting protein maintains native secondary and tertiary packing and folding properties. In addition to its selectivity for calcium over other mono and divalent metal ions, it displays strong metal binding affinities for calcium and its analogues terbium and lanthanum. Furthermore, our designed protein binds CD48, the ligand binding partner of CD2, with an affinity three-fold stronger than CD2. The electrostatic potential of the calcium binding site was modified through mutation to facilitate the study of the effect of electrostatic interactions on calcium binding affinity. Several charge distribution mutants display varying metal binding affinities based on their charge, distance to the calcium binding site, and protein stability. This study will provide insight into the key site factors that control calcium binding affinity and calcium dependent biological function.

As cargas, dipolos, quadrupolos e multipolos atômicos de maior ordem, bem como suas derivadas, permitem um maior entendimento de diversas propriedades elétricas em sistemas moleculares, como momentos de dipolo, derivadas do momento dipolar, intensidades de infravermelho e potenciais eletrostáticos, além de forças eletrostáticas. Os multipolos aqui estudados foram aqueles advindos da Teoria Quântica de Átomos em Moléculas (QTAIM) e, em certos casos, foram comparados com resultados do formalismo CHELPG (CHarges from Electrostatic Potentials using a Grid based method). As investigações desse projeto foram divididas em duas etapas distintas, sendo que a primeira focou no desempenho dos multipolos atômicos na descrição dos potenciais eletrostáticos quando da interação de uma carga pontual carregada positivamente com uma molécula. Algumas simples moléculas diatômicas (F2, Cl2, BF, AlF, BeO, MgO, LiH e NaCl) e outras mais complexas (H2O, H2CO, NH3, PH3, BF3 e CO2) foram consideradas nesta etapa, sendo que os cálculos foram feitos com B3LYP/6-311G(3d,3p). Já, na segunda etapa, estudou-se o modelo carga - fluxo de carga - fluxo de dipolo (CCFDF, do inglês \"charge - charge flux - dipole flux\") na investigação e interpretação das intensidades fundamentais de infravermelho em modos de vibração molecular. Nessa etapa optou-se pelo estudo de sistemas que apresentavam ligações de hidrogênio, como homodímeros (H2O-H2O, HF-HF, HCl-HCl, HCN-HCN, HNC-HNC e NH3-NH3) e heterodímeros (HF-HCN, HCl-HF e HF-H2O). Os cálculos destes sistemas foram realizados com CCSD/cc-pVQZ-mod. Os resultados sugerem que os multipolos QTAIM são melhores que as cargas CHELPG, na maioria dos casos, para descrição dos potenciais eletrostáticos em sistemas próton - molécula. Por sua vez, o modelo CCFDF/QTAIM consegue reproduzir as intensidades de infravermelho em dímeros que apresentam ligações de hidrogênio. Finalmente, o aumento de intensidade do estiramento X-H do monômero doador, em dímeros lineares, é explicado pela variação da contribuição de fluxo de carga durante a dimerização. / The charges, dipoles, quadrupoles and high order terms, along with their derivatives, allow a better understanding of electric properties. We can cite dipole moments, dipole moment derivatives, infrared intensities, electrostatic potentials and electrostatic forces. The multipoles treated here are obtained from the Quantum Theory of Atoms in molecules (QTAIM) and they are compared with CHELPG (CHarges from Electrostatic Potentials using a Grid based method) results. The investigations of this project can be divided in two distinct parts and the first one focuses in the performance of atomic multipoles in the description of electrostatic potentials when one positive particle interacts with molecules. Some simple diatomic (F2 , Cl2 , BF, AlF, BeO, MgO, LiH and NaCl) and polyatomic molecules (H2O, H2CO, NH3 ,PH3 ,BF3 and CO2) were considered in this investigation and the calculations were carried out at the B3LYP/6-311G(3d,3p) level. The second part of this dissertation was a study of infrared intensities in vibrational modes by means of the charge-charge flux -dipole flux model. The systems treated now are dimers with hydrogen bonds such as homodimers (H2O-H2O, HF-HF, HCl-HCl, HCN-HCN, HNC-HNC and NH3-NH3) and heterodimers (HF-HCN, HCl-HF and HF-H2O). The calculations of these systems were carried out at the CCSD/cc-pVQZ-mod level. The results suggest that QTAIM multipoles are better in describing electrostatic potentials in almost all proton-molecule arrangements than CHELPG charges. The charge-charge flux -dipole flux model can reproduce infrared intensities of dimer with hydrogen bonds. Finally, the increase in intensities of X-H stretching modes associated to the donor monomer in linear dimers is explained by changes in charge flux contributions during dimerization.

Interaction preferences in protein - DNA complexes Dávid Jakubec Abstract Interactions of proteins with DNA lie at the basis of many fundamental bio- logical processes. Despite ongoing efforts, the rules governing the recognition of specific nucleic acid sequences have still not been universally elucidated. In this work, I attempt to explore the recognition process by splitting the intricate network of contacts at the protein - DNA interface into contribu- tions of individual amino acid - nucleotide pairs. These pairs are extracted from existing high-resolution structures of protein - DNA complexes and in- vestigated by bioinformatics and computational-chemistry based methods. Criteria of specificity based on the coupling of observed geometrical prefer- ences and the respective interaction energies are introduced. The application of these criteria is used to expand the library of amino acid - nucleotide pairs potentially significant for direct sequence recognition. Electrostatic poten- tial maps are calculated for individual nucleotides as well as for selected complexes to investigate the physical basis of the observed specificity. 1

Una de les àrees més prometedores en recerca biomèdica i farmacèutica és el disseny molecular computacional, que intenta establir relacions entre propietats físico-químiques i activitat biològica. L'èxit d'aquestes tècniques depen críticament de la qualitat de la descripció molecular. En aquest sentit, metodologies basades en potencials d'interacció molecular (MIP) són eines útils per la comparació de compostos que presenten comportaments biològics semblants. Aquest projecte desenvolupa eines per comparar molècules basades en la caracterització de llurs MIPs. El programa de similaritat molecular MIPsim ha estat desenvolupat i aplicat a diferents problemes biològics. Aquesta tesi consisteix en quatre estudis científics que mostren l'ús del MIPSim en aliniament molecular, catalisi enzimàtica, en acoratge de molècules dins el lligand i en estudis 3D-QSAR. / One of the most promising areas in biomedical and pharmaceutical research is computer assisted molecular design, which tries to stablish relationships between physicochemical properties and biological activity. The success of these techniques depends critically on the quality of the molecular description. In this sense, methodologies based on molecular interaction potentials (MIP) are useful tools for the comparison of compounds displaying related biological behaviours. This project aims to develop tools to compare 'molecules based on the characterization 'of their MIPs. To this end, the molecular similarity program MIPSim has been further developed and applied to different biological problems. This thesis consists on four scientific studies showing the use of MIPSim for molecular alignment, enzymatic catalysis, ligand-protein docking and 3D-QSAR analyses.