Carlos Cunha

Ab initio ground state potential energy surfaces for Rg–Br2(Rg=He, Ne, Ar) complexes

High-level ab initio molecular electronic structure calculations are performed for Rg–Br2 (Rg=He, Ne, Ar) complexes at CCSD(T) (coupled cluster using single and double excitations with a noniterative perturbation treatment of triple excitations) level of theory. Specific augmented correlation consistent basis sets are used for each noble atom (Rg), supplemented with an additional set of bond functions. Effective-core potentials (ECPs), augmented with diffusion (sp) and polarization (3df ) functions, have been employed for the bromine atoms. For all complexes, the CCSD(T) potential energy surfaces (PESs) show double-minimum topology, with wells at both linear and T-shaped configurations; the linear minimum is found to be deeper than the T-shaped one. Vibrational corrections are taken into account for all the complexes and their effects in the stability of the linear and T-shaped conformers are examined. For each complex and each configuration (linear and T-shaped), Re equilibrium intermolecular distances, ...

The van der Waals potential energy surfaces and structures of He–ICl and Ne–ICl clusters

The potential energy surfaces of the ground electronic state of rare gas interhalogen van der Waals molecules, Rg–ICl (Rg=He, Ne), are calculated at CCSD(T) (coupled cluster using single and double excitations with a noniterative perturbation treatment of triple excitations) level of theory. Calculations have been performed with specific augmented correlation consistent basis sets for the noble atom (Rg), supplemented with an additional set of bond functions. For iodine atom a correlation consistent triple zeta valence basis set in conjunction with large-core Stuttgart–Dresden–Bonn relativistic pseudopotential has been employed. The CCSD(T) results predict the existence of three minima on the Rg–ICl potential energy surfaces at collinear (Rg–ICl), antilinear (Rg–ClI), and near T-shaped configurations, with the collinear structure to be the lowest one. Bound states calculated from the intermolecular potential surfaces show that zero-order vibrational corrections do not alter the stability of the three stru...

He79Br2 B,v=8←X,v″=0 excitation spectrum: Ab initio prediction and spectroscopic manifestation of a linear isomer

The B←X rovibronic excitation spectrum of the HeBr2 van der Waals complex is calculated using an ab initio potential energy surface for the ground electronic state. The coupled-cluster single double triple calculations predict double-minimum topology (linear and T-shaped wells) for the X-state potential with a low isomerization barrier. The two lowest vibrational levels, assigned to T-shaped and linear isomers using the localization patterns of the corresponding wave functions, are almost degenerated and lie slightly above the isomerization barrier. This indicates that T-shaped and linear isomers can coexist even at low temperatures and give rise to two separated bands in the excitation spectrum. The main band of the B←X excitation spectrum is assigned to transitions from the T-shaped isomer, whereas the very good agreement between the observed and calculated spectrum, using the ab initio X-state potential, demonstrates that the unassigned secondary band corresponds to excitation of the linear isomer of t...

CCSD(T) intermolecular potential between He atom and ClF molecule: Comparison with experiment

The potential energy surface of the He–ClF complex is calculated using for He atom an efficient basis set of aug-cc-pV5Z augmented with a set of 3s3p2d2 f1g set of midbond functions and aug-cc-pVTZ, aug-cc-pVQZ for Cl and F atoms, respectively, at coupled-cluster with single and double excitations and a noniterative perturbation treatment of triple excitations [CCSD(T)] level. Three local minima are found for the He–ClF that correspond to linear He–Cl–F (collinear) and He–F–Cl (antilinear) configurations and a asymmetric T-shaped structure. The well depths and the equilibrium distances are 63.53 cm−1 and 3.54 A (collinear), 41.09 cm−1 and 3.23 A (T-shaped) and 33.80 cm−1 and 3.93 A (antilinear). Bound states calculations are carried out for the CCSD(T) surface and the sensitivity of the rovibrational levels to the errors of the computed potential energy surface at different configuration regions is discussed. The computed energy levels up to a total angular momentum J=3 are in general accord with experime...

Vibrational predissociation of NeBr2 (X, v=1) using an ab initio potential energy surface

Quantum mechanical calculations on the vibrational predissociation dynamics of NeBr2 are performed using an ab initio (coupled cluster using single and double excitations with a noniterative perturbation treatment of triple excitations) potential energy surface. Energy positions, lifetimes, and final rotational state distributions are determined for vibrational predissociation from the two lowest linear (n=0) and T-shaped (n=1) van der Waals levels of NeBr2 (X, v=1). Comparison with the experimental assumption as regards the energy transfer to rotation provides information about the type of isomer involved in the experimental vibrational predissociation process, suggesting that it was the linear one.

Effects of protein-protein interactions on electron transfer: docking and electron transfer calculations for complexes between flavodoxin and c-type cytochromes

Abstract Theoretical studies of protein-protein association and electron transfer were performed on the binary systems formed by Desulfovibrio vulgaris Hildenborough (D. v. H.) flavodoxin and D. v. H. cytochrome c553 and by flavodoxin and horse heart cytochrome c. Initial structures for the complexes were obtained by rigid-body docking and were refined by MD to allow for molecular flexibility. The structures thus obtained were analysed in terms of their relative stability through the calculation of excess energies. Electrostatic, van der Waals and solvation energy terms showed all to have significant contributions to the stability of complexes. In the best association solutions found for both cytochromes, these bind to different zones of flavodoxin. The binding site of flavodoxin observed for cytochrome c is in accordance with earlier works [27]. The various association modes found were characterised in terms of electron transfer using the Pathways model. For complexes between flavodoxin and horse heart cytochrome c, some correlation was observed between electron tunnelling coupling factors and conformation energy; the best conformation found for electron transfer corresponded also to the best one in terms of energy. For complexes between flavodoxin and cytochrome c553 this was not the case and a lower correlation was observed between electron tunnelling coupling factors and excess energies. These results are in accordance with the differences in the experimental dependence of electron transfer rates with ionic strength observed between these two cases.

Theoretical prediction of a linear isomer for NeBr2(X1Γg + an ab initio approach

A supermolecular approach is used to predict the stationary structures of the NeBr2(X1Γg +) van der Waals cluster. The intermolecular potential is calculated using the single and double excitation coupled-cluster method with non-iterative perturbation treatment of triple excitations [CCSD(T)]. Relativistic effects are included for the Br atoms using effective core potentials (ECPs) and their efficiency is tested for Br2 and NeBr2 molecules. Our results for NeBr2 show minima for both linear and T-shaped configurations, in accord with previous ab initio calculations for rare gas-Br2 species. The dependence of the interaction potential, as a function of the Br-Br bond, is also presented. Finally, vibrational analysis is carried out to examine the stability of the two isomers including zero-point vibrational energy effects.

Crystallization and preliminary X-ray analysis of a membrane-bound nitrite reductase from Desulfovibrio desulfuricans ATCC 27774

Nitrite reductase from the sulfate-reducing bacterium Desulfovibrio desulfuricans ATCC 27774 is a multihaem (type c) membrane-bound enzyme that catalyzes the dissimilatory conversion of nitrite to ammonia. Crystals of the oxidized form of this enzyme were obtained using PEG and CaCl(2) as precipitants in the presence of 3--(decylmethylammonium)propane-1-sulfonate and belong to the space group P2(1)2(1)2(1), with unit-cell parameters a = 78.94, b = 104.59, c = 143.18 A. A complete data set to 2.30 A resolution was collected using synchrotron radiation at the ESRF. However, the crystals may diffract to beyond 1.7 A and high-resolution data will be collected in the near future.

Crystallization and preliminary X-ray diffraction analysis of the di-haem cytochrome c peroxidase from Pseudomonas stutzeri

Crystals of cytochrome c peroxidase from Pseudomonas stutzeri were obtained using sodium citrate and PEG 8000 as precipitants. A complete data set was collected to a resolution of 1.6 A under cryogenic conditions using synchrotron radiation at the ESRF. The crystals belong to space group P2(1), with unit-cell parameters a = 69.29, b = 143.31, c = 76.83 A, beta = 100.78 degrees. Four CCP molecules were found in the asymmetric unit, corresponding to a pair of dimers related by local dyads. The crystal packing in the structure shows that the functional dimers can dimerize, as suggested by previous biochemical studies.