Elementos transponíveis (TEs) são sequências de DNA que possuem a capacidade de transposição no genoma hospedeiro. O principal objetivo deste trabalho reside na investigação em torno de possíveis contribuições de TEs nos genomas das algas C. reinhardtii e V. carteri, mais especificamente, na arquitetura dos genes ortólogos nestas espécies. Neste contexto, análises em sílico em larga escala foram realizadas, buscando-se identificar associações entre TEs e os genes ortólogos. Os resultados indicaram que os genes em C. reinhardtii tendem a acumular mais cópias de TEs em relação aos seus ortólogos em V. carteri. C. reinhardtii apresentou maior densidade de cópias de TEs para as regiões flanqueadora 5´ , flanqueadora 3´ e intrônica quando comparada a V. carteri; o inverso foi verificado quando analisada a densidade de TEs nas regiões codificantes. Análises para apurar a distribuição dos elementos em regiões intergênicas e intragênicas foram estabelecidas, nas quais a frequência observada dos elementos foi comparada à frequência esperada segundo a distribuição randômica de TEs no genoma, simulada computacionalmente. Foram constatadas regiões em que a presença dos elementos encontra-se significativamente abaixo do esperado, a exemplo de intervalos adjacentes ao início e ao término dos genes, o que provavelmente reflete a seleção negativa de eventos de integração nestas delimitações, em virtude dos efeitos deletérios associados à disrupção de estruturas de regulação da expressão gênica. De forma geral, nas regiões flanqueadoras 5´ e 3´, foi identificada a tendência de elevação da frequência padronizada de TEs à medida que a classe de distância avaliada se distancia do início e do término do gene, respectivamente. A baixa representatividade dos elementos também foi constatada em regiões intragênicas. O estudo da distribuição de TEs nos íntrons dos genes ortólogos indicou a preservação destas regiões quanto à fixação de TEs, sendo a representatividade abaixo do esperado mais evidente em intervalos adjacentes ao éxon, o que minimiza a chance de ruptura no padrão de splicing dos genes. Em sequências codificantes, a escassez de TEs - esperada devido ao provável efeito deletério destes eventos para a função do gene - foi constatada nos ortólogos das duas espécies. No entanto, inovações decorrentes da integração dos elementos em regiões codificantes podem resultar em efeitos evolutivos positivos, embora estes eventos sejam raros. Nas espécies analisadas foram identificados dois casos, de especial interesse, em que um domínio da sequência peptídica encontra-se localizado em região derivada de TE: o primeiro refere-se ao gene Cre06.g262800, em C. reinhardtii, no qual foi identificado o domínio PHD-finger associadao ao elemento Gypsy-5-LTR_CR; o segundo remete ao gene Vocar20001092m.g, em V. carteri, no qual o domínio zinc knuckle foi reconhecido em região derivada do elemento Gypsy3-LTR_VC. Estes genes constituem exemplos da contribuição de TEs na evolução de sequências codificadoras nas espécies C. reinhardtii e V. carteri, corroborando a hipótese de que os TEs podem contribuir na evolução da arquitetura dos genes, apesar do efeito disruptivo inerente à integração dos mesmos em regiões gênicas. / Transposable elements (TEs) are DNA sequences able to transpose in the host genome. The aim of this study resides in the investigation of TEs contributions in the algae C. reinhardtii and V. carteri genomes, more specifically in the architecture of orthologous genes in these species. In this context, large scale in silico analysis were performed to identify associations between TEs and orthologous genes. The results indicated that genes in the C. reinhardtii specie tend to accumulate more TEs copies than orthologous genes in V. carteri. C. reinhardtii showed higher density of TEs copies in the 5´ flanking, 3´ flanking and intronic regions when compared to V. carteri; the opposite was observed in coding regions. Investigation of the elements distribution in the intergenic and intragenic regions was performed, in which the observed TE frequency was compared to expected TE frequency from the simulated random distribution of the elements in the genome. It was verified regions where TE frequency was significantly lower than expected, as in gene boundaries adjacencies, probably reflecting a negative selection of the TE integration events in these delimitations due to deleterious effects associated with disruption of gene regulatory structures. In general terms, it was observed an increasing standardized frequency in the 5´ and 3´ flanking regions as the distance from gene start and gene end, respectively, increases. TEs underrepresentation was also verified in the intragenic regions. The study of TEs distribution in the introns of orthologous genes revealed the preservation of these structures in relation to TEs fixation, with a stronger underrepresentation near exon, which minimizes the chance of gene splicing pattern disruption. In the coding sequences, the TEs scarcity - expected due the likely deleterious effects to gene function - was verified in the orthologous of both species. However, in rare instances, innovations mediated by TEs integration in the coding regions can lead to positive evolutionary effects. In the species analyzed two instances of particular interest were observed, in which the domain of peptide sequence is located in the region derived from TE. The first one refers to the Cre06.g262800 gene, in the C. reinhardtii specie, which has a PHD-finger domain associated with Gypsy-5-LTR_CR element. The second one refers to the Vocar20001092m.g gene, in V. carteri, in which the zinc knuckle was recognized in region derived from Gypsy3-LTR_VC element. These genes are examples of TEs contributions in the evolution of coding sequences in the C. reinhardtii and V. carteri species, corroborating the hypothesis that TEs can contribute to the evolution of gene architecture, despite the inherent disruptive effect in their integration in the gene regions.

Elementos transponíveis (TEs) são sequências de DNA que possuem a capacidade de transposição no genoma hospedeiro. O principal objetivo deste trabalho reside na investigação em torno de possíveis contribuições de TEs nos genomas das algas C. reinhardtii e V. carteri, mais especificamente, na arquitetura dos genes ortólogos nestas espécies. Neste contexto, análises em sílico em larga escala foram realizadas, buscando-se identificar associações entre TEs e os genes ortólogos. Os resultados indicaram que os genes em C. reinhardtii tendem a acumular mais cópias de TEs em relação aos seus ortólogos em V. carteri. C. reinhardtii apresentou maior densidade de cópias de TEs para as regiões flanqueadora 5´ , flanqueadora 3´ e intrônica quando comparada a V. carteri; o inverso foi verificado quando analisada a densidade de TEs nas regiões codificantes. Análises para apurar a distribuição dos elementos em regiões intergênicas e intragênicas foram estabelecidas, nas quais a frequência observada dos elementos foi comparada à frequência esperada segundo a distribuição randômica de TEs no genoma, simulada computacionalmente. Foram constatadas regiões em que a presença dos elementos encontra-se significativamente abaixo do esperado, a exemplo de intervalos adjacentes ao início e ao término dos genes, o que provavelmente reflete a seleção negativa de eventos de integração nestas delimitações, em virtude dos efeitos deletérios associados à disrupção de estruturas de regulação da expressão gênica. De forma geral, nas regiões flanqueadoras 5´ e 3´, foi identificada a tendência de elevação da frequência padronizada de TEs à medida que a classe de distância avaliada se distancia do início e do término do gene, respectivamente. A baixa representatividade dos elementos também foi constatada em regiões intragênicas. O estudo da distribuição de TEs nos íntrons dos genes ortólogos indicou a preservação destas regiões quanto à fixação de TEs, sendo a representatividade abaixo do esperado mais evidente em intervalos adjacentes ao éxon, o que minimiza a chance de ruptura no padrão de splicing dos genes. Em sequências codificantes, a escassez de TEs - esperada devido ao provável efeito deletério destes eventos para a função do gene - foi constatada nos ortólogos das duas espécies. No entanto, inovações decorrentes da integração dos elementos em regiões codificantes podem resultar em efeitos evolutivos positivos, embora estes eventos sejam raros. Nas espécies analisadas foram identificados dois casos, de especial interesse, em que um domínio da sequência peptídica encontra-se localizado em região derivada de TE: o primeiro refere-se ao gene Cre06.g262800, em C. reinhardtii, no qual foi identificado o domínio PHD-finger associadao ao elemento Gypsy-5-LTR_CR; o segundo remete ao gene Vocar20001092m.g, em V. carteri, no qual o domínio zinc knuckle foi reconhecido em região derivada do elemento Gypsy3-LTR_VC. Estes genes constituem exemplos da contribuição de TEs na evolução de sequências codificadoras nas espécies C. reinhardtii e V. carteri, corroborando a hipótese de que os TEs podem contribuir na evolução da arquitetura dos genes, apesar do efeito disruptivo inerente à integração dos mesmos em regiões gênicas. / Transposable elements (TEs) are DNA sequences able to transpose in the host genome. The aim of this study resides in the investigation of TEs contributions in the algae C. reinhardtii and V. carteri genomes, more specifically in the architecture of orthologous genes in these species. In this context, large scale in silico analysis were performed to identify associations between TEs and orthologous genes. The results indicated that genes in the C. reinhardtii specie tend to accumulate more TEs copies than orthologous genes in V. carteri. C. reinhardtii showed higher density of TEs copies in the 5´ flanking, 3´ flanking and intronic regions when compared to V. carteri; the opposite was observed in coding regions. Investigation of the elements distribution in the intergenic and intragenic regions was performed, in which the observed TE frequency was compared to expected TE frequency from the simulated random distribution of the elements in the genome. It was verified regions where TE frequency was significantly lower than expected, as in gene boundaries adjacencies, probably reflecting a negative selection of the TE integration events in these delimitations due to deleterious effects associated with disruption of gene regulatory structures. In general terms, it was observed an increasing standardized frequency in the 5´ and 3´ flanking regions as the distance from gene start and gene end, respectively, increases. TEs underrepresentation was also verified in the intragenic regions. The study of TEs distribution in the introns of orthologous genes revealed the preservation of these structures in relation to TEs fixation, with a stronger underrepresentation near exon, which minimizes the chance of gene splicing pattern disruption. In the coding sequences, the TEs scarcity - expected due the likely deleterious effects to gene function - was verified in the orthologous of both species. However, in rare instances, innovations mediated by TEs integration in the coding regions can lead to positive evolutionary effects. In the species analyzed two instances of particular interest were observed, in which the domain of peptide sequence is located in the region derived from TE. The first one refers to the Cre06.g262800 gene, in the C. reinhardtii specie, which has a PHD-finger domain associated with Gypsy-5-LTR_CR element. The second one refers to the Vocar20001092m.g gene, in V. carteri, in which the zinc knuckle was recognized in region derived from Gypsy3-LTR_VC element. These genes are examples of TEs contributions in the evolution of coding sequences in the C. reinhardtii and V. carteri species, corroborating the hypothesis that TEs can contribute to the evolution of gene architecture, despite the inherent disruptive effect in their integration in the gene regions.

Inositol phosphates (IPs) have important cellular functions from teleomere maintenance (IP7 and IP8) to Ca2+ signaling pathways (1, 4, 5-IP3). Yet there is no robust, quantitative method to separate all the inositol phosphate isomers from IP1 to IP8. Four findings contributed heavily towards the development of a robust, quantitative IP isomer separation and identification method on the EskpertTM MicroLC 200+ QTrap 6500 system with a SelexIonTM DMS attachment. 1) TCA from inositol phosphate algal extractions was removed by elution with 100 mM ammonium carbonate, ammonium formate, or ammonium bicarbonate or by immobilized metal affinity chromatography (Fe-NTA columns). 2) A 250 mM ammonium carbonate and 25% methanol gradient was run on a weak anion exchange column to separate all the inositol phosphates from each other (IP1 through IP8. 3) Using ten different inositol phosphate isomer standards and fluoro- IP3 as an internal standard for future quantitation and recovery studies, isomer separation was obtained using SelexIonTM DMS with a 2- propanol modifier. 4) Ion suppression of inositol phosphate signals caused by 250 mM ammonium carbonate can be alleviated with a post-column dilution. The final assembled EskpertTM MicroLC 200+ QTrap 6500 system with a SelexIonTM DMS attachment and post-column dilution method was able to separate out IP isomers from IP1 to IP6 and detect IP7 and IP8. Once further optimized using the full compensation voltage range and a more polar modifier such as methanol, this method will allow the lipid biosynthesis pathways of C. reinhardtii, a promising candidate for algal biofuels, to be better studied.

Diacylglycerol acyltransferase (DGAT) is a key for the synthesis of triacylglycerol (TAG) from diacylglycerol in the unicellular green alga Chlamydomonas reinhardtii.Acetyl-CoA carboxylase (ACCase) and fatty acid synthase (FAS) are responsible for the synthesis of fatty acids. We found the TAG and fatty acid synthesis related genes in C. reinhardtii, including five DGAT (DGAT1 (JGI 184281), DGAT2 (JGI 400751), DGAT3 (JGI 285889), DGAT4 (JGI 141301), and DGAT5 (JGI 190539)), three £] ketoacyl-ACP reductase isoforms ( (JGI 153976), (JGI 153976), and (JGI 194728)) and two £] ketoacyl-ACP synthase isofroms ( (JGI 139619) and (JGI 205887)) for FAS, and ACC £\ (NCBI XP_001696945.1), ACC £] (NCBI XP_001703187.1) and ACC biotin carboxylase ( NCBI XP_001702319.1)) for ACCase in C. reinhardtii. This investigation designed the primers of the above genes to determine whether acetate influences their mRNA expression levels in cell-wall less strain CC400 in the nitrogen starvation condition. The results showed that the absence of nitrogen in the medium triggered the lipid accumulation for the strains of CC400 in the condition of 50 £gE light. DGAT3 mRNA levels were increased by nitrogen starvation. For the FAS genes, in the strain of CC400 showed no increased mRNA levels upon exposure to nitrogen starvation. The mRNA levels of ACC£\, ACC £] and ACC biotin carboxylase were more or less decreased by nitrogen starvation in CC400 strains. Thus, the responses of DGAT gene expression to acetate supplement were checked. The absence of acetate from the medium partly inhibited the nitrogen starvation induced increases in lipid and DGAT3 mRNA levels, and the mRNA levels of DGAT1 and DGAT2 in the nitrogen starvation condition. However, DGAT4 mRNA levels were significantly induced by the absence of acetate from the medium. In conclusion, the present study demonstrate that acetate is required for the nitrogen starvation induced DGAT3 gene expression (mRNA levels) and lipid accumulation in C. reinhardtii.

This study was to determine the effects of several selected environmental factors (temperature, salinity, light intensity, and acetate) on the nitrogen starvation induced lipid accumulation in Chlamydomonas reinhardtii CC 400 by the Nile Red staining of lipid in the cells. Nitrogen starvation induced lipid accumulation, the extent of lipid accumulation increased as nitrogen concentrations in the medium decreased. For the 9.4 mM NH4Cl of HS medium as 100% N, the absence of NH4Cl from the medium will show the maximum induction in the lipid accumulation. This was also observed in the treatment of algal cells in mid-log phase by the absence of NH4Cl in the medium. A decrease in temperature down to 15oC depressed the nitrogen starvation induction in lipid accumulation for the algal cells from the mid-log phase, while the elevation in the light intensity up to 300 £gmol photons • m-2 • s-1 also showed an inhibitory effect. However, the transfer to darkness for the nitrogen starvation also inhibited the lipid increase. The addition of 100 mM NaCl enhanced the nitrogen starvation induced lipid accumulation but the NaCl level up to 200 mM inhibited the increment. The nitrogen starvation induction of lipid increase was partly inhibited due to the absence of acetate, whereas the increase in acetate concentrations in the medium did not have effect on lipid accumulation as compared to normal acetate addition in the medium. Overall, the results of the present study show that light and acetate are essential factors for the maximum lipid accumulation in C. reinhardtii by nitrogen starvation.

Several expression systems for recombinant protein production, essentially cells or whole organisms are currently in use today. Recently, research into recombinant protein production revealed a more attractive expression system based on the microalgae, C. reinhardtii, for significant savings in cost and production of correctly folded recombinant proteins. However, protein yield in the microalgae remain very low, non-predictable and whether this was due to limitations in the system was unclear. Using the expression of E. coli β-glucuronidase (gus) in C. reinhardtii chloroplast, the overall aim of the project was to address if the low recombinant gus yield in C. reinhardtii was due to limitations that affect growth and protein production, and if the fluxes for recombinant gus production were suboptimal (limiting). The finding was used to implement a strategy for a more predictable recombinant protein yield in C. reinhardtii. The research involved a range of experiments, analysis, and Flux Balance Analysis (FBA) modelling. The growth of C. reinhardtii cultures were characterized in autotrophic, heterotrophic and mixotrophic conditions to identify factors that limit growth and recombinant gus yields. These factors were availability of light, carbon and nitrogen substrates, pH changes, protein burden and energetic limitation (ATP). The highest biomass was obtained in autotrophic and mixotrophic cultures (>1 g/litre), the lowest biomass was in heterotrophic cultures (~0.4 g/litre). The recombinant gus yields on the basis of dry cell weight were: mixotrophic cultures (0.038%), autotrophic cultures (0.032%), heterotrophic cultures (0.026%). No detectable protein burden was observed for expression of recombinant gus in autotrophic and mixotrophic conditions, but protein burden was significant in heterotrophic condition (15 – 18% reduction in growth rate). A strategy that significantly increased growth and cell productivity (>3 fold) in heterotrophic condition was identified. FBA was used to identify suboptimal amino acid steady state fluxes (bottlenecks) that limited the gus yield. Using FBA modelling, model verifications and corrections, a strategy that significantly increased the yield of recombinant gus in each cell (~2 fold) was identified. Put together, the total increase represents a 6 fold increase in recombinant gus yield. Furthermore, this research presented a framework for identifying, analysing and understanding the effect of the uptake of individual amino acid towards recombinant protein yield.

Les phytochélatines (PC) sont des polypeptides ayant la structure générale, (alpha-Glu-Cys)n-Gly, où n = 2 à 11. Leur synthèse est induite par un grand nombre de végétaux en réponse à une élévation de la concentration du milieu en métaux, en particulier le cadmium (ci-après, Cd). Le but de cette étude a été de développer un outil pour évaluer la biodisponibilité du Cd dans les eaux douces. Pour ce faire, une méthode analytique a été réalisée afin de déterminer les phytochélatines induites dans les algues C. reinhardtii. Celle-ci consiste à utiliser la chromatographie liquide couplée à la spectrométrie de masse en tandem (LCHP-SM/SM) "on-line". L’ionisation des molécules est celle faite par électronébulisation (IEN) (traduction de electrospray ionisation). L’objectif principal de ce mémoire est la validation de cette méthode : la détermination des courbes de calibration et des limites de détection et l'identification d'interférences potentielles. L’utilisation de dithiothreitol (DTT) à une concentration de 25 mM a été nécessaire à la conservation de la forme réduite des phytochélatines. En effet, suite à la validation de la méthode d’analyse des phytochélatines il a été démontré qu’elle représente un potentiel d’application. Ceci dans la mesure où l’induction des phytochélatines (PC2, PC3 et PC4) dans les algues C. reinhardtii a été possible à deux concentrations de Cd (1 x 10-7 M et 1 x 10 6 M) et ce, après plusieurs temps d'induction (1, 2, 4, et 6 h). Ainsi, l’étude de la stabilité des phytochélatines a été réalisée et toutes les températures examinées ont démontré une diminution des phytochélatines analysées par HPLC-ESI-MS/MS. Il se pourrait que la cause de la dégradation des phytochélatines soit physique ou chimique plutôt que bactérienne. Toutefois, un approfondissement au niveau de la purification de la solution d’extraction serait nécessaire à la mise au point de la dite méthode analytique afin de quantifier les phytochélatines dans l’algue C. reinhardtii. / Phytochelatins (PC) are polypeptides having the general structure, (alpha-Glu-Cys)n-Gly, where n = 2 to 11. Many plants respond to an elevated concentration of metals in environment, particularly Cd, by synthesizing PC. The purpose of this study was to develop a tool to assess the bioavailability of the Cd in fresh water by determining phytochelatins in algae, C. reinhardtii, by online HPLC-ESI-MS/MS. The gold of this work was the validation of the analytical method i.e. the determination of the calibration curves and the limits of detection. The addition of dithiothreitol (DTT), 25 mM, was found to be necessary to maintain the PC in their reduced form for analysis. It was shown that the liquid chromatography coupled to tandem mass spectrometry (HPLC-ESI-MS/MS) technique has excellent potential for PC analysis, however, it will still requires some more work with respect to sample purification. Furthermore, the stability of the PC was evaluated for different sample storage temperatures. At all temperatures studied, some degradation of PC was observed possibly due to physical rather than chemical or bacterial reasons. Finally, the induction of phytochelatins (PC2, PC3 and PC4) was observed in C. reinhardtii for two Cd concentrations (10-7 M and 10-6 M) and for several induction times (1, 2, 4, and 6 h).

Les phytochélatines (PC) sont des polypeptides ayant la structure générale, (alpha-Glu-Cys)n-Gly, où n = 2 à 11. Leur synthèse est induite par un grand nombre de végétaux en réponse à une élévation de la concentration du milieu en métaux, en particulier le cadmium (ci-après, Cd). Le but de cette étude a été de développer un outil pour évaluer la biodisponibilité du Cd dans les eaux douces. Pour ce faire, une méthode analytique a été réalisée afin de déterminer les phytochélatines induites dans les algues C. reinhardtii. Celle-ci consiste à utiliser la chromatographie liquide couplée à la spectrométrie de masse en tandem (LCHP-SM/SM) "on-line". L’ionisation des molécules est celle faite par électronébulisation (IEN) (traduction de electrospray ionisation). L’objectif principal de ce mémoire est la validation de cette méthode : la détermination des courbes de calibration et des limites de détection et l'identification d'interférences potentielles. L’utilisation de dithiothreitol (DTT) à une concentration de 25 mM a été nécessaire à la conservation de la forme réduite des phytochélatines. En effet, suite à la validation de la méthode d’analyse des phytochélatines il a été démontré qu’elle représente un potentiel d’application. Ceci dans la mesure où l’induction des phytochélatines (PC2, PC3 et PC4) dans les algues C. reinhardtii a été possible à deux concentrations de Cd (1 x 10-7 M et 1 x 10 6 M) et ce, après plusieurs temps d'induction (1, 2, 4, et 6 h). Ainsi, l’étude de la stabilité des phytochélatines a été réalisée et toutes les températures examinées ont démontré une diminution des phytochélatines analysées par HPLC-ESI-MS/MS. Il se pourrait que la cause de la dégradation des phytochélatines soit physique ou chimique plutôt que bactérienne. Toutefois, un approfondissement au niveau de la purification de la solution d’extraction serait nécessaire à la mise au point de la dite méthode analytique afin de quantifier les phytochélatines dans l’algue C. reinhardtii. / Phytochelatins (PC) are polypeptides having the general structure, (alpha-Glu-Cys)n-Gly, where n = 2 to 11. Many plants respond to an elevated concentration of metals in environment, particularly Cd, by synthesizing PC. The purpose of this study was to develop a tool to assess the bioavailability of the Cd in fresh water by determining phytochelatins in algae, C. reinhardtii, by online HPLC-ESI-MS/MS. The gold of this work was the validation of the analytical method i.e. the determination of the calibration curves and the limits of detection. The addition of dithiothreitol (DTT), 25 mM, was found to be necessary to maintain the PC in their reduced form for analysis. It was shown that the liquid chromatography coupled to tandem mass spectrometry (HPLC-ESI-MS/MS) technique has excellent potential for PC analysis, however, it will still requires some more work with respect to sample purification. Furthermore, the stability of the PC was evaluated for different sample storage temperatures. At all temperatures studied, some degradation of PC was observed possibly due to physical rather than chemical or bacterial reasons. Finally, the induction of phytochelatins (PC2, PC3 and PC4) was observed in C. reinhardtii for two Cd concentrations (10-7 M and 10-6 M) and for several induction times (1, 2, 4, and 6 h).

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.