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2001
Ferreira, I., Braz F. Fernandes, P. Vilarinho, E. Fortunato, and R. Martins. "Properties of Nanocrystalline n-Type Silicon Films Produced by Hot Wire Plasma Assisted Technique." MATERIALS RESEARCH SOCIETY SYMPOSIUM PROCEEDINGS. 664 (2001): A7. 6-A7. 6. Abstract
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Baldwin, J., W. C. Voegtli, N. Khidekel, P. Moenne-Loccoz, C. Krebs, AS Pereira, B. A. Ley, BH HUYNH, T. M. Loehr, P. J. Riggs-Gelasco, A. C. Rosenzweig, and J. M. Bollinger. "Rational reprogramming of the R2 subunit of Escherichia coli ribonucleotide reductase into a self-hydroxylating monooxygenase." Journal of the American Chemical Society. 123 (2001): 7017-7030. AbstractWebsite

The outcome of O-2 activation at the diiron(II) cluster in the R2 subunit of Escherichia coli (class I) ribonucleotide reductase has been rationally altered from the normal tyrosyl radical (Y122)(1) production to self-hydroxylation of a phenylalanine side-chain by two amino acid substitutions that leave intact the (histidine)(2)-(carboxylate)(4) ligand set characteristic of the diiron-carboxylate family. Iron ligand Asp (D) 84 was replaced with Glu (E), the amino acid found in the cognate position of the structurally similar diiron-carboxylate protein, methane monooxygenase hydroxylase (MMOH). We previously showed that this substitution allows accumulation of a mu -1,2-peroxodiiron(III) intermediate,(2 3) which does not accumulate in the wild-type (wt) protein and is probably a structural homologue of intermediate P (H-peroxo) in O-2 activation by MMOH.(4) In addition, the near-surface residue Trp (W) 48 was replaced with Phe (F), blocking transfer of the "extra" electron that occurs in wt R2 during formation of the formally Fe(LII)Fe(IV) cluster X.(5-7) Decay of the mu1,2-peroxodiiron(III) complex in R2-W38F/D84E gives an initial brown product, which contains very little YI22(.) and which converts very slowly (t(1/2) similar to 7 h) upon incubation at 0 degreesC to an intensely purple final product. X-ray crystallographic analysis of the purple product indicates that F208 has undergone epsilon -hydroxylation and the resulting phenol has shifted significantly to become st ligand to Fe2 of the diiron cluster. Resonance Raman (RR) spectra of the purple product generated with O-16(2) or O-18(2) show appropriate isotopic sensitivity in bands assigned to O-phenyl and Fe-O-phenyl vibrational modes, confirming that the oxygen of the Fe(III)-phenolate species is derived from Or. Chemical analysis, experiments involving interception of the hydroxylating intermediate with exogenous reductant, and Mossbauer and EXAFS characterization of the brown and purple species establish that F208 hydroxylation occurs during decay of the peroxo complex and formation of the initial brown product. The slow transition to the purple Fe(LII)-phenolate species is ascribed to a ligand rearrangement in which mu -O2- is lost and the F208-derived phenolate coordinates. The reprogramming to F208 monooxygenase requires both amino acid substitutions, as very little epsilon -hydroxyphenylalanine is formed and pathways leading to Y122(.) formation predominate in both R2-D84E and R2-W48F(2-7).

Indelicato, P., E. Lindroth, T. Beier, J. Bieron, A. M. Costa, I. Lindgren, J. P. Marques, A. M. Martenson-Pendrill, M. C. Martins, M. A. Ourdane, F. Parente, P. Patté, G. C. Rodrigues, S. Salomonson, and J. P. Santos. "Relativistic Calculations for Trapped Ions." Hyperfine Interactions. 132 (2001): 347-361. AbstractWebsite

We present recent results in the field of total binding energy calculations, Landщ factors, quantum electrodynamics corrections and lifetime that are of interest for ion traps and ion sources. We describe in detail MCDF and RMBPT calculation of ionic binding energies, which are needed for the determination of atomic masses from highly charged ion measurements. We also show new results concerning Landщ factor in 3-electron ions. Finally we describe how relativistic calculations can help understand the physics of heavy ion production ion sources.

Martins, R., H. Aguas, I. Ferreira, V. Silva, A. Cabrita, and E. Fortunato. "Role of ion bombardment and plasma impedance on the performances presented by undoped a-Si: H films." Thin solid films. 383.1 (2001): 165-168. Abstract
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Martins, R., H. Aguas, I. Ferreira, V. Silva, A. Cabrita, and E. Fortunato. "Role of ion bombardment and plasma impedance on the performances presented by undoped a-Si: H films." Thin Solid Films. 383 (2001): 165-168. Abstract
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Martins, R., �?guas Ferreira Silva Cabrita Fortunato H. I. V. "Role of ion bombardment and plasma impedance on the performances presented by undoped a-Si:H films." Thin Solid Films. 383 (2001): 165-168. AbstractWebsite

The aim of this paper was to present results of the role of the d.c. grid bias on the silane plasma impedance and its I-V characteristics to grow undoped amorphous silicon (a-Si:H) films by plasma enhanced chemical vapour deposition (PECVD) in conditions where some nanoparticles can be formed in the growth region of the deposition process, under proper ion bombardment. The results achieved show that the performances of the films produced are dependent on the self bias voltage that can present photosensitivities of approximately 107 (two orders of magnitude larger than the one exhibited by films grown under conventional conditions) with density of states determined by the constant photocurrent method below 4×1015 cm-3. Apart from that, the films grown are less affected by light soaking than the conventional films.

Aguas, Hugo, R. Martins, and E. Fortunato. "Role of ion bombardment on the properties of a-Si: H films." Vacuum. 60 (2001): 247-254. Abstract
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Ferreira, I., A. Cabrita, F. Braz Fernandes, E. Fortunato, and R. Martins. "Role of the gas pressure and hydrogen dilution on the properties of large area nanocrystalline p-type silicon films produced by hot wire technique." Materials Science and Engineering: C. 15.1 (2001): 141-144. Abstract
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Ferreira, I., M. E. V. Costa, L. Pereira, E. Fortunato, R. Martins, A. R. Ramos, and M. F. Silva. "Silicon carbide alloys produced by hot wire, hot wire plasma-assisted and plasma-enhanced CVD techniques." Applied surface science. 184.1 (2001): 8-19. Abstract
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Cabrita, A., L. Pereira, D. Brida, A. Lopes, A. Marques, I. Ferreira, E. Fortunato, and R. Martins. "Silicon carbide photodiodes: Schottky and PINIP structures." Applied surface science. 184.1 (2001): 437-442. Abstract
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Ferreira, Isabel, Rodrigo Martins, A. Cabrita, Hugo Águas, V. Silva, and Elvira Fortunato. "Silicon Films Produced by PECVD Under Powder Formation Conditions." Materials Science Forum. 382 (2001): 21-30. Abstract
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Martins, R., Águas Silva Ferreira Cabrita Fortunato H. V. I. "Silicon films produced by PECVD under powder formation conditions." Materials Science Forum. 382 (2001): 21-28. AbstractWebsite

The process conditions of growing thin silicon films by plasma enhanced chemical vapour deposition (PECVD) were presented. The plasma impedance was found to monitor the powders in the PECVD systems and good quality silicon films were grown close to the plasma regime where the powders were formed. The silicon films exhibited properties which were interpreted based on a two-phase model where silicon nanostructures were embedded in a disordered network.

Martins, Rodrigo, Hugo Águas, V. Silva, Isabel Ferreira, A. Cabrita, and Elvira Fortunato. "Silicon Films Produced by PECVD under Powder Formation Conditions." Materials Science Forum. Vol. 382. Trans Tech Publications, 2001. 21-30. Abstract
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Alves, T., S. Besson, AS Pereira, G. W. Pettigrew, JJG Moura, and I. Moura. "Structure-function studies of cytochrome c peroxidase from ps. nautica." Journal of Inorganic Biochemistry. 86 (2001): 122. AbstractWebsite
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Franco, R., AS Pereira, P. Tavares, A. Mangravita, MJ Barber, I. Moura, and GC Ferreira. "Substitution of murine ferrochelatase glutamate-287 with glutamine or alanine leads to porphyrin substrate-bound variants." Biochemical Journal. 356 (2001): 217-222. AbstractWebsite

Ferrochelatase (EC 4.99.1.1) is the terminal enzyme of the haem biosynthetic pathway and catalyses iron chelation into the protoporphyrin IX ring. Glutamate-287 (E287) of murine mature ferrochelatase is a conserved residue in all known sequences of ferrochelatase, is present at the active site of the enzyme, as inferred from the Bacillus subtilis ferrochelatase three-dimensional structure, and is critical for enzyme activity. Substitution of E287 with either glutamine (Q) or alanine (A) yielded variants with lower enzymic activity than that of the wild-type ferrochelatase and with different absorption spectra from the wild-type enzyme. In contrast to the wild-type enzyme, the absorption spectra of the variants indicate that these enzymes, as purified, contain protoporphyrin IX. Identification and quantification of the porphyrin bound to the E287-directed variants indicate that approx. 80% of the total porphyrin corresponds to protoporphyrin IX. Significantly, rapid stopped-flow experiments of the E287A and E287Q Variants demonstrate that reaction with Zn2+ results in the formation of bound Zn-protoporphyrin IX, indicating that the endogenously bound protoporphyrin IX can be used as a substrate. Taken together, these findings suggest that the structural strain imposed by ferrochelatase on the porphyrin substrate as a critical step in the enzyme catalytic mechanism is also accomplished by the E287A and E287Q variants, but without the release of the product. Thus E287 in murine ferrochelatase appears to be critical For the catalytic process by controlling the release of the product.

Fortunato, Elvira, Patrícia Nunes, António Marques, Daniel Costa, Hugo Águas, Isabel Ferreira, Maria EV Costa, and Rodrigo Martins. "Thin Film Metal Oxide Semiconductors Deposited on Polymeric Substrates." MRS Proceedings. 685.1 (2001). Abstract
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Fortunato, Elvira, Patr{\'ıcia Nunes, António Marques, Daniel Costa, Hugo Águas, Isabel Ferreira, Maria EV Costa, and Rodrigo Martins. "Thin Film Metal Oxide Semiconductors Deposited on Polymeric Substrates." MRS Proceedings. Vol. 685. Cambridge University Press, 2001. D5-12. Abstract
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Cabrita, A., J. Figueiredo, L. Pereira, H. Aguas, V. Silva, D. Brida, I. Ferreira, E. Fortunato, and R. Martins. "Thin film position sensitive detectors based on pin amorphous silicon carbide structures." Applied surface science. 184.1 (2001): 443-447. Abstract
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Cabrita, A., J. Figueiredo, L. Pereira, H. Aguas, V. Silva, D. Brida, I. Ferreira, E. Fortunato, and R. Martins. "Thin film position sensitive detectors based on pin amorphous silicon carbide structures." Applied surface science. 184 (2001): 443-447. Abstract
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Martins, R., H. Águas, I. Ferreira, E. Fortunato, and L. Guimarães. "Towards the improvement of the stability of a-Si: H pin devices." Solar energy. 69 (2001): 257-262. Abstract
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Martins, R., H. Aguas, I. Ferreira, E. Fortunato, and L. Guimaraes. "Towards the improvement of the stability of a-Si: H pin devices." Solar energy. 69 (2001): 257-262. Abstract
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Fortunato, Elvira, Patrícia Nunes, António Marques, Daniel Costa, Hugo Águas, Isabel Ferreira, Maria EV Costa, and Rodrigo Martins. "Zinc oxide thin films deposited by rf magnetron sputtering on mylar substrates at room temperature." MRS Proceedings. 685 (2001). Abstract
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Fortunato, Elvira, Patr{\'ıcia Nunes, António Marques, Daniel Costa, Hugo Águas, Isabel Ferreira, Maria EV Costa, and Rodrigo Martins. "Zinc oxide thin films deposited by rf magnetron sputtering on mylar substrates at room temperature." MRS Proceedings. Vol. 685. Cambridge University Press, 2001. D5-10. Abstract
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Cabrito, I., AS Pereira, P. Tavares, S. Besson, C. Brondino, B. Hoffman, K. Brown, M. Tegoni, C. Cambillau, JJG Moura, and I. Moura. "{Nitrous oxide reductase (N2OR) from Pseudomonas nautica 617}." Journal Of Inorganic Biochemistry. 86 (2001): 165.