Morrison, J. C., S. Boyd, L. Marsano, B. Bialecki, T. Ericsson, and J. P. Santos. "
Numerical methods for solving the Hartree-Fock equations of diatomic molecules I."
Communications in Computational Physics. 5 (2008): 959-985.
AbstractThe theory of domain decomposition is described and used to divide the variable domain of a diatomic molecule into separate regions which are solved independently. This approach makes it possible to use fast Krylov methods in the broad interior of the region while using explicit methods such as Gaussian elimination on the boundaries. As is demonstrated by solving a number of model problems, these methods enable one to obtain solutions of the relevant partial differential equations and eigenvalue equations accurate to six significant figures with a small amount of computational time. Since the numerical approach described in this article decomposes the variable space into separate regions where the equations are solved independently, our approach is very well-suited to parallel computing and offers the long term possibility of studying complex molecules by dividing them into smaller fragments that are calculated separately.
Palma, M. L., and J. P. Santos. "
Spin-rotation and nuclear shielding constants of sulfur hexafluoride."
Molecular Physics. 106 (2008): 1241-1247.
AbstractWe present a first theoretical determination of the hyperfine coupling constants of a spherical top molecule using ab initio methods. The scalar and tensorial contributions to the spin-rotation constants and the diamagnetic and paramagnetic contributions to the nuclear shielding constant are calculated for the 32SF6 molecule. The corrections to the spin-rotation constants due to nuclear Thomas precession are evaluated and discussed. Our results are compared with previously reported experimental values.
Santos, J. P., M. C. Martins, A. M. Costa, P. Indelicato, and F. Parente. "
X-ray spectra emitted by Cl14+ ions in ECRIS plasmas."
Vacuum. 82 (2008): 1522-1524.
AbstractWe study the contribution of the most important processes leading to the creation of excited states of Cl14+ ions from the ground configurations of Cl ions in an Electron Cyclotron Resonance Ion Source (ECRIS), which lead to the emission of K X-ray lines. Theoretical values for inner-shell excitation, K and KL ionization cross-sections, and energies and transition probabilities for the de-excitation processes are calculated in the framework of the Multi-Configuration Dirac-Fock (MCDF) method. With reasonable assumptions about the electron energy distribution, a theoretical K[alpha] X-ray spectrum is obtained, which reproduces closely a recent experimental result.
Gavel, Olga Yu, Sergey A. Bursakov, Giulia Di Rocco, Jose Trincao, Ingrid J. Pickering, Graham N. George, Juan J. Calvete, Valery L. Shnyrov, Carlos D. Brondino, Alice S. Pereira, Jorge Lampreia, Pedro Tavares, Jose J. G. Moura, and Isabel Moura. "
{A new type of metal-binding site in cobalt- and zinc-containing adenylate kinases isolated from sulfate-reducers Desulfovibrio gigas and Desulfovibrio desulfuricans ATCC 27774}."
Journal Of Inorganic Biochemistry. 102 (2008): 1380-1395.
AbstractAdenylate kinase (AK) mediates the reversible transfer of phosphate groups between the adenylate nucleotides and contributes to the maintenance of their constant cellular level, necessary for energy metabolism and nucleic acid synthesis. The AK were purified from crude extracts of two sulfate-reducing bacteria (SRB), Desulfovibrio (D.) gigas NCIB 9332 and Desulfovibrio desulfuricans ATCC 27774, and biochemically and spectroscopically characterised in the native and fully cobalt- or zinc-substituted forms. These are the first reported adenylate kinases that bind either zinc or cobalt and are related to the subgroup of metal-containing AK found, in most cases, in Gram-positive bacteria. The electronic absorption spectrum is consistent with tetrahedral coordinated cobalt, predominantly via sulfur ligands, and is supported by EPR. The involvement of three cysteines in cobalt or zinc coordination was confirmed by chemical methods. Extended X-ray absorption fine structure (EXAFS) indicate that cobalt or zinc are bound by three cysteine residues and one histidine in the metal-binding site of the "LID" domain. The sequence (129)Cys-X-5-His-X-15-Cys-X-2-Cys of the AK from D. gigas is involved in metal coordination and represents a new type of binding motif that differs from other known zinc-binding sites of AK. Cobalt and zinc play a structural role in stabilizing the LID domain. (C) 2008 Elsevier Inc. All rights reserved.