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Submitted by Jorge Silva (jorgelmsilva@ufrrj.br) on 2017-07-12T18:05:35Z No. of bitstreams: 1 2016 - Felipe Augusto da Silva.pdf: 12688361 bytes, checksum: 9f1ec0867eb071ebf8dbb7f89606cf25 (MD5) / Made available in DSpace on 2017-07-12T18:05:35Z (GMT). No. of bitstreams: 1 2016 - Felipe Augusto da Silva.pdf: 12688361 bytes, checksum: 9f1ec0867eb071ebf8dbb7f89606cf25 (MD5) Previous issue date: 2016-09-29 / To understand the behavior of molecules in liquid fase is fundamental for comprihend many chemical and physical process, became reference to severa! areas of scientific and tecnologic knowledge. Methods using polarizable continuum model (PCM) have been proposed and revised to achieve more acurated results and the aplicability of the method. MultiPatch is a analitic and eficient molecular smface tesselation method. This smface is necessary to calcule the eletrostatic component of the interaction energy between solute and solvent Delta G s. The method was tested by comparing the results for the smface area and the energy Delta G s obtained using internai methods of the software GAMESS. / Entender o comportamento de mol?culas em fase l?quida ? fundamental para o compreender diversos processos qu?micos e f?sicos, sendo assim refer?ncia para diversas ?reas do conhecimento cient?fico e tecnol?gico. M?todos usando o modelo de cont?nuo polariz?vel (PCM) tem sido propostos e revisados com o objetivo de melhorar a acur?cia dos resultados e a aplicabilidade desse modelo. MultiPatch ? um m?todo anal?tico e eficiente para se obter uma tessela??o da superf?cie molecular necess?ria para o computo de uma das componentes, de origem eletrost?tica, da energia de intera??o entre soluto e solvente Delta G s:. O m?todo foi testado comparando seus resultados para ?rea da superf?cie e a energia Delta G s com o m?todos internos do software GAMESS.

This dissertation presents a study of the molecular mechanism underlying the highly efficient solar energy conversion processes that occur in the Photosystem I (PS I) reaction centers in plants and bacteria. The primary electron donor P700 is at the heart of solar energy conversion process in PS I and the aim is to obtain a better understanding of the electronic and structural organization of P700 in the ground and excited states. Static Fourier Transform Infra-Red (FTIR) difference spectroscopy (DS) in combination with site directed mutagenesis and Density Functional Theory (DFT) based vibrational frequency simulations were used to investigate how protein interactions such as histidine ligation and hydrogen bonding modulate this organization. (P700+-P700) FTIR DS at 77K were obtained from a series of mutants from the cyanobacterium Synechocystis sp. 6803 (S. 6803) where the amino acid residues near the C=O groups of the two chlorophylls of P700 where specifically changed. (P700+-P700) FTIR DS was also obtained for a set of mutants from C. reinhardtii where the axial ligand to A0-, the primary electron acceptor in PS I was modified. The FTIR DS obtained from these mutants provides information on the axial ligands, the hydrogen bonding status as well as the polarity of the environment of specific functional groups that are part of the chlorophyll molecules that constitute P700. Assignment of the FTIR bands to vibrational modes in specific types of environment is very difficult. In order to assist the assignment of the difference bands in experimental spectra DFT based vibrational mode frequency calculations were undertaken for Chl-a and Chl-a+ model molecular systems under different set of conditions; in the gas phase, in solvents using the Polarizable Continuum Model (PCM), in the presence of explicit solvent molecules using QM/MM methods, and in the presence of axial ligands and hydrogen bonds. DFT methods were also used to calculate the charge, spin and redox properties of Chl-a/Chl-a’ dimer models that are representative of P700, the primary electron donor in PS I.

MSc (Chemistry) / Department of Chemistry