This dissertation presents a detailed computational investigation into the vibrational properties of quinones involved in solar energy conversion processes in photosynthetic reaction centers. In particular, we focus on the vibrational properties of the ubiquinone molecule that occupies the QA binding site in purple bacterial photosynthetic reaction centers. To provide a foundation upon which to base computational studies of pigments in protein binding sites density functional theory based calculations of the vibrational properties of neutral ubiquinone in the gas phase and in solvent were undertaken. From single point energy calculations it was shown that at least eight ubiquinone conformers, each with slightly different FTIR spectra, could be present in solvent at room temperature. The calculated and experimental spectra for neutral ubiquinone in solution are very different from the spectra associated with ubiquinone in the QA binding in purple bacterial reaction centers. For this reason an ONIOM method was undertaken in which the pigment was treated using density functional theory based methods while the protein was treated using molecular mechanics. The ONIOM calculations not only modeled the experimental QA FTIR difference spectra but also resolved the long standing issue of whether a very strong hydrogen bond exists between the bound ubiquinone and the imidazole nitrogen of a histidine residue (HisM219). To further validate the usefulness of the ONIOM approach experimental isotope edited FTIR spectra obtained using purple bacterial reaction centers with a range of chainless symmetrical quinones incorporated were modeled. Again, the agreement between the calculated and experimental spectra is outstanding. We also modeled the vibrational properties of the ubisemiquinone anion radical both in solvent and in the QA binding site. Vibrational modes of ubisemiquinone display a greater degree of mixing of the various molecular groups of the molecule. Nonetheless the calculated FTIR spectra for ubisemiquinone in solution and in the QA site agree very well with that found experimentally. Vibrational frequencies of ubisemiquinone obtained from ONIOM calculated Raman spectra also agree very well with that found in experimental resonance Raman spectra associated with the ubisemiquinone anion radical in the QA binding site.

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O conjunto de funções de base gaussianas, o p-GCHF, foi gerado para os átomos Na, Al, Si, P, S e Cl pelo Método da Coordenada Geradora (MCG) através da expansão integral polinomial para discretizar (DIP) as equações de Griffin-Hill-Wheeler-Hartree-Fock (GHW-HF). A base p-GCHF, de qualidade 7Z, foi contraída por meio do programa Contract que opera segundo os preceitos de contração de Davidson. O processo de contração resultou em 9 funções do tipos e 7 funções p para os átomos de Na e Mg e de 9 funções s e 8 funções p para os átomos de Al, Si, P, S e Cl. Expoentes de polarização foram gerados através do programa Polarization em nível CISD para os átomos de H, B, C, N, O, F, Na, Mg, Al, Si, P, S e Cl. Foram necessários não mais do que 2p1d expoentes de polarização para compor a base p-GCHF para o átomo de H, 2d1f para os átomos da primeira fila e 3d2f, para os átomos da segunda fila da tabela periódica. Cálculos moleculares revelaram que a base p-GCHF é competitiva em energia com as bases cc-pVQZ e cc-pV5Z, entretanto apresentando custos computacionais bem menores que as mencionadas bases de Dunning. Análises das frequências vibracionais e das geometrias de otimização dos pontos estacionários, tanto mínimos quanto de estado de transição, também apontam similaridades entre o conjunto de base p-GCHF e a base cc-pVQZ, porém com diferenças de tempos de CPU que apontam a base gerada pelo MCG como computacionalmente vantajosa. Um conjunto de base capaz de descrever um dado sistema de maneira equivalente à célebres conjuntos de base da literatura, mas trazendo consigo o benefício da economia de tempo computacional é absolutamente oportuno principalmente àqueles que têm como objeto de estudo moléculas com um número considerável de átomos. / The gaussian basis sets p-GCHF was generated for a set of atoms from Na to Cl through the Generator Coordinate Method (GCM) based on a polynomial integral expansion to discretize the Griffin-Wheeler-Hartree-Fock equations. The p-GCHF is a 7z type basis sets and was contracted through the Contract program which works based on the Davidson\'s contraction model. The contraction process provided a set of 9s7p functions for Na and Mg atoms and 9s8p functions for Al, Si, P, S e Cl atoms. Polarizations exponents were acquired through the Polarization program at CISD level of theory for H, B, C, N, O, F, Na, Mg, Al, Si, P, S e Cl atoms. No more than 2p1d polarization exponents were necessary to compose the p-GCHF basis set for hydrogen atom, 2d1f for the first row of the periodic table and 3d2f for the second row one. Molecular calculations show that p-GCHF works like cc-pVQZ and cc-pV5Z basis sets but with less computational cost than the Dunning\'s ones. Vibrational frequency analysis and optimization geometry to the stationary points minimum as well as transition state, revealed similarities between p-GCHF and cc-pVQZ basis sets, but again with the GCM basis sets being computationally advantageous. A basis sets capable to describe a system like the main gaussian basis sets known in the literature but demanding less computational effort is very helpful above all for those who work with massive molecular systems.

O conjunto de funções de base gaussianas, o p-GCHF, foi gerado para os átomos Na, Al, Si, P, S e Cl pelo Método da Coordenada Geradora (MCG) através da expansão integral polinomial para discretizar (DIP) as equações de Griffin-Hill-Wheeler-Hartree-Fock (GHW-HF). A base p-GCHF, de qualidade 7Z, foi contraída por meio do programa Contract que opera segundo os preceitos de contração de Davidson. O processo de contração resultou em 9 funções do tipos e 7 funções p para os átomos de Na e Mg e de 9 funções s e 8 funções p para os átomos de Al, Si, P, S e Cl. Expoentes de polarização foram gerados através do programa Polarization em nível CISD para os átomos de H, B, C, N, O, F, Na, Mg, Al, Si, P, S e Cl. Foram necessários não mais do que 2p1d expoentes de polarização para compor a base p-GCHF para o átomo de H, 2d1f para os átomos da primeira fila e 3d2f, para os átomos da segunda fila da tabela periódica. Cálculos moleculares revelaram que a base p-GCHF é competitiva em energia com as bases cc-pVQZ e cc-pV5Z, entretanto apresentando custos computacionais bem menores que as mencionadas bases de Dunning. Análises das frequências vibracionais e das geometrias de otimização dos pontos estacionários, tanto mínimos quanto de estado de transição, também apontam similaridades entre o conjunto de base p-GCHF e a base cc-pVQZ, porém com diferenças de tempos de CPU que apontam a base gerada pelo MCG como computacionalmente vantajosa. Um conjunto de base capaz de descrever um dado sistema de maneira equivalente à célebres conjuntos de base da literatura, mas trazendo consigo o benefício da economia de tempo computacional é absolutamente oportuno principalmente àqueles que têm como objeto de estudo moléculas com um número considerável de átomos. / The gaussian basis sets p-GCHF was generated for a set of atoms from Na to Cl through the Generator Coordinate Method (GCM) based on a polynomial integral expansion to discretize the Griffin-Wheeler-Hartree-Fock equations. The p-GCHF is a 7z type basis sets and was contracted through the Contract program which works based on the Davidson\'s contraction model. The contraction process provided a set of 9s7p functions for Na and Mg atoms and 9s8p functions for Al, Si, P, S e Cl atoms. Polarizations exponents were acquired through the Polarization program at CISD level of theory for H, B, C, N, O, F, Na, Mg, Al, Si, P, S e Cl atoms. No more than 2p1d polarization exponents were necessary to compose the p-GCHF basis set for hydrogen atom, 2d1f for the first row of the periodic table and 3d2f for the second row one. Molecular calculations show that p-GCHF works like cc-pVQZ and cc-pV5Z basis sets but with less computational cost than the Dunning\'s ones. Vibrational frequency analysis and optimization geometry to the stationary points minimum as well as transition state, revealed similarities between p-GCHF and cc-pVQZ basis sets, but again with the GCM basis sets being computationally advantageous. A basis sets capable to describe a system like the main gaussian basis sets known in the literature but demanding less computational effort is very helpful above all for those who work with massive molecular systems.

Aqueous solutions of sodium acetate, NaCH₃CO₂, and acetic acid, CH₃COOH, were studied using Raman and infrared spectroscopy. The spectra were recorded over a large concentration range, in the terahertz region and up to 4000 cmˉ¹. In the isotropic Raman spectrum in R-format, a polarized band at 189 cmˉ¹ was assigned to the υ₁Na–O stretch of the hydrated Na⁺-ion and a shoulder at 245 cmˉ¹ to the restricted translation band, υsO–H⋯O* of the hydrated acetate ion, CH₃CO₂ˉ(aq). The CH₃CO₂ˉ(aq) and the hydrated acetic acid, CH₃COOH(aq), possess pseudo Cs symmetry. Geometrical parameters for the species in the gas phase and for CH₃CO₂ˉ(aq) and CH₃COOH(aq) are reported. Characteristic bands for CH₃CO2ˉ(aq) and CH₃COOH(aq) were assigned under the guidance of the DFT vibrational frequency calculations and discussed in detail. In aqueous NaCH₃CO₂ solutions, at high concentrations, no contact ion pairs could be detected, but instead solvent separated ion pairs were found. In LiCH₃CO₂(aq), however, contact ion pairs are formed which is indicated by the appearance of a shoulder at 939 cmˉ¹ and the shift of the symmetric stretching mode of the –CO₂ˉ group to higher wavenumbers.