Curriculum Vitae

Investigação

Publicações

[22] Pedro J. Silva (2012) Unravelling the reaction mechanism of the reductive ring contraction of 1,2-pyridazines. J. Org. Chem., 77, 4653-4659

[21] Pedro J. Silva, Marta A. S. Perez, Natércia F. Brás, Pedro A. Fernandes and Maria J. Ramos (2012) Improving the study of proton transfers between amino acid sidechains in solution: choosing appropriate DFT functionals and avoiding hidden pitfalls. Theoretical Chemistry Accounts, 131, 1179-1185

[20] Natércia F. Brás, Marta A. S. Perez, Pedro A. Fernandes,Pedro J. Silva and Maria J. Ramos (2011) Accuracy of Density Functionals in the Prediction of Electronic Proton Affinities of Amino Acid Side Chains Journal of Chemical Theory and Computation, 7, 3898-3908

[19] Pedro J. Silva and Maria J. Ramos (2011) Successes and Failures of DFT Functionals in acid/base and redox reactions of organic and biochemical interest. Computational and Theoretical Chemistry, 966, 120-126

[18] Pedro J. Silva and Maria J. Ramos (2011) Computational Characterization of the Substrate-Binding Mode in Coproporphyrinogen III Oxidase J. Phys. Chem. B, 115, 1903-1910 [free reprint]

[17] Pedro J. Silva, Claudia Schulz, Martina Jahn, Dieter Jahn and Maria J. Ramos (2010) A Tale Of Two Acids: When Arginine Is A More Appropriate Acid Than H₃O⁺. J. Phys. Chem. B, 114, 8994–9001 [free reprint]

[16] Pedro J. Silva and Maria J. Ramos (2011) Computational insights into the photochemical step of the reaction catalyzed by protochlorophylide oxidoreductase. Int. J. Quantum Chem.,111, 1472-1479

[15] Pedro J. Silva and Maria J. Ramos (2009) Computational studies on the reactivity of substituted 1,2-dihydro-1,2-azaborines. J. Org. Chem, 74, 6120-6129 [free reprint]

[14] Pedro J. Silva (2009) Inductive and Resonance Effects on the Acidities of Phenol, Enols, and Carbonyl α-Hydrogens. J. Org. Chem, 74, 914-916

[13] Pedro J. Silva and Maria J. Ramos (2008) A comparative density-functional study of the reaction mechanism of the O₂-dependent coproporphyrinogen III oxidase. Bioorg. Med. Chem., 16, 2726-2733.

[12] Pedro J. Silva and Maria J. Ramos (2008) A comparative density-functional study of models for the reaction mechanism of uroporphyrinogen III synthase. J. Phys. Chem. B, 112, 3144-3148.

[11] van Haaster DJ, Silva PJ, Hagedoorn PL, Jongejan JA, Hagen WR. (2008) A re-investigation of the steady-state kinetics and the physiological function of the soluble NiFe-hydrogenase-I of Pyrococcus furiosus. J. Bacteriol., 190, 1584-1587

[10] Pedro J. Silva (2008) Assessing the reliability of sequence similarities detected through hydrophobic sequence analysis. Proteins: Structure, Function and Bioinformatics, 70, 1588-1594

[9] Pedro J. Silva and Maria J. Ramos (2007) Reaction Mechanism of the Vitamin K-Dependent Glutamate Carboxylase: A Computational Study. J. Phys. Chem. B, 111, 12883-12887

[8] Pedro J. Silva and Maria J. Ramos (2005) A Density-Functional Study of Mechanisms for the Cofactor-Free Decarboxylation Performed by Uroporphyrinogen III Decarboxylase. Journal of Physical Chemistry B, 109, 18195-18200

[7] Dora Pinho, Stéphane Besson, Pedro J. Silva, Baltazar de Castro e Isabel Moura (2005) Isolation and spectroscopic characterization of the membrane-bound nitrate reductase from Pseudomonas chlororaphis DSM 50135. Biochimica et Biophysica Acta – General Subjects, 1723, 151-162.

[6] Pedro J. Silva, Pedro A. Fernandes and Maria J. Ramos (2003) A theoretical study of radical-only and combined radical/carbocationic mechanisms of arachidonic acid cyclooxygenation by prostaglandin H synthase. Theoretical Chemistry Accounts, 110, 345-351.

[5] Frank A.M. de Bok, Peter-Leon Hagedoorn, Pedro J. Silva, Wilfred R. Hagen, Emile Schiltz, Kathrin Fritsche and Alfons J.M. Stams (2003) Two W-containing formate dehydrogenases (CO₂-reductases) involved in syntrophic propionate oxidation by Syntrophobacter fumaroxidans. European Journal of Biochemistry, 270, 2476-2485 .

[4] Pedro J. Silva, Eyke C. D. van den Ban, Hans Wassink, Huub Haaker, Baltazar de Castro, Frank T. Robb and Wilfred R. Hagen (2000) Enzymes of hydrogen metabolism in Pyrococcus furiosus. European Journal of Biochemistry, 267, 6541-6551.

[3] Wilfred R. Hagen, Pedro J. Silva, M.A. Amorim, Peter-Leon Hagedoorn, Hans Wassink, Huub Haaker and Frank T. Robb (2000) Novel structure and redox chemistry of the prosthetic groups of the iron-sulfur flavoprotein sulfide dehydrogenase from Pyrococcus furiosus; evidence for a [2Fe-2S] cluster with Asp(Cys) ₃ ligands. Journal of Biological Inorganic Chemistry, 5,  527-534.

[2] Pedro J. Silva, M. João Amorim, Peter-Leon Hagedoorn, Hans Wassink, Huub Haaker and Wilfred R. Hagen (1999) Effects of temperature on the electron transfer between Pyrococcus furiosus hydrogenase and its redox partners. Journal of Inorganic Biochemistry, 74, 297.

[1] Pedro J. Silva, Baltazar de Castro and Wilfred R. Hagen (1999) On the prosthetic groups of the NiFe sulfhydrogenase from Pyrococcus furiosus: topology, structure, and temperature-dependent redox chemistry. Journal of Biological Inorganic Chemistry, 4,  284-291.

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