Pedro J. Silva (2023) The reaction mechanism of the Cu(I) catalyzed alkylation of hetero-substituted alkynes. Catalysts, 13:17   [PDF]
 Pedro J. Silva , Maria Osswald-Claro e Rosário Castro Mendonça (2022) How to tune the absorption spectrum of chlorophylls to enable better use of the available solar spectrum PeerJ Physical Chemistry, 4:e26   [PDF]
 Pedro J. Silva (2022) Computational development of inhibitors of plasmid-borne bacterial dihydrofolate reductase Antibiotics, 11: 779   [PDF]
 Pedro J. Silva and Qi Cheng (2022) An Alternative Proposal for the Reaction Mechanism of Light-Dependent Protochlorophyllide Oxidoreductase ACS Catalysis ,12:2589-2605  [PDF]
 Pedro J. Silva and Carlos E. P. Bernardo (2021) Unveiling the reaction mechanism of the Das/Chechik/Marek synthesis of stereodefined quaternary carbon centers. Applied Sciences, 11: 5002 [PDF]
 Pedro J. Silva (2020) Response to "Molecular-level understanding of biological energy coupling and transduction" Biophys. Chem 264, 106512
 Pedro J. Silva (2020) New insights into the mechanism of Schiff base synthesis from aromatic amines in the absence of acid catalyst or polar solvents PeerJ Organic Chemistry, 2, e4   [PDF]
 Sandra V.R.L. Silva and Pedro J. Silva (2020) Computational improvement of small-molecule inhibitors of Bacillus anthracis protective antigen activation through isostere-based substitutions. Journal of Biomolecular Structure and Dynamics DOI:10.1080/07391102.2020.1792987       FREE reprint >
 Pedro J. Silva (2020), Chemiosmotic misundertandings Biophys. Chem 264, 106424
 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]
 Pedro J. Silva (2016), Refining the reaction mechanism of O2 towards its substrate in cofactor-free dioxygenases PeerJ 4:e2805   [PDF]
 Pedro J. Silva (2016), Will 1,2-dihydro-1,2-azaborine-based drugs resist metabolism by cytochrome P450 compound I? PeerJ 4:e2299   [PDF]
 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]
 Pedro J. Silva and Viviana Rodrigues (2015), Mechanistic pathways of mercury removal from the organomercurial lyase active site. PeerJ 3:e1127   [PDF]
 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]
 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]
 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
 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
 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]
 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.
 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
 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
 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]
 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]
 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
 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]
 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]
 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.
 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.
 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
 Pedro J. Silva (2008) Assessing the reliability of sequence similarities detected through hydrophobic sequence analysis. Proteins: Structure, Function and Bioinformatics, 70, 1588-1594
 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]
 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]
 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.
 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.
 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 .
 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.
 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.
 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.
 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.