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Improving the study of proton transfers between amino acid sidechains in soluti...
Silva, Pedro J.; Perez, Marta A. S.; Brás, Natércia F.; Fernandes, Pedro A.; Ramos, Maria JoãoWe have studied the influence of implicit solvent models, inclusion of explicit water molecules, inclusion of vibrational effects, and density functionals on the quality of the predicted pK a of small amino acid side chain models. We found that the inclusion of vibrational effects and explicit water molecules is crucial to improve the correlation between the computed and the experimental values. In these micro-...
Successes and failures of DFT functionals in acid/base and redox reactions of o...
Silva, Pedro J.; Ramos, Maria JoãoThe performance of 18 different DFT functionals in the prediction of absolute and relative energies of organic and biochemical acid/base and redox reactions was evaluated, using MP2 extrapolated to the complete basis set limit and CCSD(T)/aug-cc-pVTZ energies as benchmark. Absolute reduction energies were predicted with relatively large average errors (2–4 kcal mol−1) except for the best functional, PBE0 (1.3 ±...
Computational Characterization of the Substrate-Binding Mode in Coproporphyrino...
Silva, Pedro J.; Ramos, Maria JoãoOxygen-dependent coproporphyrinogen III oxidase catalyzes the sequential decarboxylation of the propionate substituents present on the A and B rings of coproporphyrinogen III in the heme biosynthetic pathway. Although extensive experimental investigation of this enzyme has already afforded many insights into its reaction mechanism, several key features (such as the substrate binding mode, the characterization o...
Computational insights into the photochemical step of the reaction catalyzed by...
Silva, Pedro J.; Ramos, Maria JoãoThe light-dependent enzyme protochlorophyllide oxidoreductase (EC:1.3.1.33) catalyzes the conversion of protochlorophyllide (PChlide) into chlorophyllide during chlorophyll synthesis. The reaction has been proposed to proceed through light-induced weakening of the C17–C18 double bond in PChlide, which then facilitates hydride transfer from a NADPH cosubstrate molecule. We have performed DFT and TDDFT computatio...
Computational Studies on the Reactivity of Substituted 1,2-Dihydro-1,2-azaborines
Silva, Pedro J.; Ramos, Maria JoãoWe have investigated important intermediates of electrophilic aromatic substitution reactions and one-electron oxidation of substituted 1,2-dihydro-1,2-azaborines with density-functional theory. The results show that electrophilic substitution reactions and one-electron oxidation of substituted 1,2-azaborines are generally much more favorable than those of the corresponding benzene derivatives. Both chlorinatio...
Studies of inclusion complexes between cyclodextrins and polyazamacrocyclic che...
Henriques, Elsa S.; Bastos, Margarida; Geraldes, Carlos F. G. C.; Ramos, Maria JoãoThe complexes between [gamma]-cyclodextrin and lanthanide (III) chelates of the polyazamacrocycles DOTA (DOTA [reverse not equivalent] 1,4,7,10-tertraazacyclododecane-1,4,7,10-tetraacetate) and DOTP (DOTP [reverse not equivalent] 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetramethylenephosphonate) have been thought out to enhance the potential of such chelates as contrast agents for MRI. Given the actual demand f...
Representação gráfica de quantidades em crianças de 5 anos: Berlindes e livros
Ramos, Maria JoãoDissertação de Mestrado em Psicologia Educacional ; Neste trabalho aborda-se o tema da representação gráfica de quantidades associadas a referentes em crianças de 5 anos que frequentam o Jardim de Infância. Do quadro teórico de referência destacam-se as contribuições da teoria dos campos conceptuais de Vergnaud (1988), os estudos sobre a representação gráfica das quantidades de F.Siegrist e H.Sinclair (1983) e...
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