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Pesquisa

Curriculum Vitae
Investigação
Publicações
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Manual de Docência
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Pessoal Docente

Pedro Jorge Araújo Alves da Silva

Curriculum Vitae

  • Out. 2010-presente: Professor Associado. Universidade Fernando Pessoa
  • 2001-Set. 2010: Professor Auxiliar. Universidade Fernando Pessoa
  • Mar-2001: Doutoramento em Química. Faculdade de Ciências da Universidade do Porto. Aprovado por unanimidade.
  • 1997-2000: Realização de trabalho experimental conducente à elaboração da dissertação de doutoramento. O trabalho foi realizado nos Departamentos de Bioquímica da Universidade Agrícola de Wageningen , Holanda, e de Biotecnologia, Universidade Técnica de Delft, Holanda e de Química da Faculdade de Ciências da Universidade do Porto
  • 1992-1996: Licenciatura em Bioquímica. Faculdade de Ciências da Universidade do Porto. (16/20)

    Investigação

  • Estudo de mecanismos de reacções enzimáticas
  • Aplicação de métodos quânticos a sistemas de interesse biológico
  • Aplicação de técnicas bioquímicas, espectroscópicas e electroquímicas (U.V./Vis, EPR, voltametria cíclica, electrocatálise, enzimologia, bioinformática) na elucidação da relação estrutura/função de metaloproteínas.
  • O papel das hidrogenases no metabolismo do Pyrococcus furiosus
  • Tese de Doutoramento
  • Publicações

    [31] Pedro J. Silva and Carlos E. P. Bernardo (2018), Influence of Alkyne and Azide Substituents on the Choice of the Reaction Mechanism of the Cu+-Catalyzed Addition of Azides to Iodoalkynes J. Phys. Chem. A, 122, 7497-7507    [free reprint upon registration]

    [30] Pedro J. Silva (2016), Refining the reaction mechanism of O2 towards its substrate in cofactor-free dioxygenases PeerJ 4:e2805   [PDF]

    [29] Pedro J. Silva (2016), Will 1,2-dihydro-1,2-azaborine-based drugs resist metabolism by cytochrome P450 compound I? PeerJ 4:e2299   [PDF]

    [28] Carlos E. P. Bernardo and Pedro J. Silva (2016), Computational exploration of the reaction mechanism of the Cu+-catalysed synthesis of indoles from N-aryl enaminones Royal Society Open Science 3:150582  [PDF]

    [27] Pedro J. Silva and Viviana Rodrigues (2015), Mechanistic pathways of mercury removal from the organomercurial lyase active site. PeerJ 3:e1127   [PDF]

    [26] Pedro J. Silva (2014) With or without light: comparing the reaction mechanism of dark-operative protochlorophyllide oxidoreductase with the energetic requirements of the light-dependent protochlorophyllide oxidoreductase PeerJ, 2, e551 [PDF]

    [25] Carlos E. P. Bernardo and Pedro J. Silva (2014) Computational development of rubromycin-based lead compounds for HIV-1 reverse transcriptase inhibition PeerJ, 2, e470 [PDF]

    [24] Carlos E. P. Bernardo, Nicholas P. Baumann, Piotr Piecuch and Pedro J. Silva (2013) Evaluation of density functional methods on the geometric and energetic descriptions of species involved in Cu+-promoted catalysis. J. Mol. Model., 19, 5457-5467

    [23] Carla Sousa and Pedro J. Silva (2013) BBr3-Assisted Cleavage of Most Ethers Does Not Follow the Commonly Assumed Mechanism. Eur. J. Org. Chem., 2013, 5195-5199. Correction in Eur. J. Org. Chem., 2013, 8048

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

    [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. Erratum in Theoretical Chemistry Accounts, 132, 1307.

    [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 upon registration]

    [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 upon registration]

    [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 upon registration]

    [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 [free reprint upon registration]

    [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 [free reprint upon registration]

    [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 [free reprint upon registration]

    [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.

    Disciplinas

  • Bioquímica Fisiológica (2018/19)
  • Bioquímica Aplicada
  • Química Analítica I
  • Química Analítica II
  • Química Geral
  • Química Orgânica (2018/19)
  • Bioquímica
  • Bioquímica I
  • Bioquímica II
  • Química Fisiológica
  • Biomatemática
  • Google
    Web Nas minhas páginas
  • Manual de Docência

    Horário de Atendimento

    Sexta-feira das 10h às 12h.

    Mensagens aos alunos

    Hobbies

    Links


    Resumos das aulas teóricas de Química Fisiológica
    Uma panorâmica geral das vias metabólicas
    A general overview of the major metabolic pathways
  • TCA cycle
  • Glycolysis
  • Gluconeogenesis
  • Pentose-phosphate pathway
  • Aminoacid degradation and urea cycle
  • Fatty acids metabolism
  • Glycogen metabolism



  • Input files for basis set superposition error (BSSE) computation using Gamess(US) or PcGamess / Firefly
    How to set up a procgrp file to run parallel computations with PCGamess / Firefly

    General and Organic Chemistry -  Prof. Steve Harding, UCLA. Um site muito completo: inclui exercícios, exames (e respectivas correcções) e algumas aulas...
    Farmácias de serviço, páginas amarelas, e outras informações uteis

    Interesting scientific blogs:
  • (Bio)Chemical Matters
    - my personal scientific blog
  • In the Pipeline - Medicinal and Organic Chemistry

                               
  • Página mantida por Pedro Silva.