Showing papers by "Paolo Giannozzi published in 2003"

Oxygen adsorption on graphite and nanotubes

Abstract: We study the binding of molecular oxygen to a graphene sheet and to a (8,0) single walled carbon nanotube, by means of spin-unrestricted density-functional calculations. We find that triplet oxygen retains its spin-polarized state when interacting with graphene or the nanotube. This leads to the formation of a weak bond with essentially no charge transfer between the molecule and the sheet or tube, as one would expect for a physisorptive bond. This result is independent on the approximation used for the exchange-correlation functional. The binding strength, however, depends strongly on the functional, reflecting the inability of current approximation functionals to deal correctly with dispersion forces. Gradient-corrected functionals yield very weak binding at distances around 4 A, whereas local density functional results yield substantially stronger binding for both graphene and the nanotube at distances of less than 3 A. The picture of oxygen physisorption is not substantially altered by the presence of topological defects such as 5–7 Stone–Wales pairs.

First-principle molecular dynamics with ultrasoft pseudopotentials: parallel implementation and application to extended bio-inorganic system

Abstract: We present a plane-wave ultrasoft pseudopotential implementation of first-principle molecular dynamics, which is well suited to model large molecular systems containing transition metal centers. We describe an efficient strategy for parallelization that includes special features to deal with the augmented charge in the contest of Vanderbilt's ultrasoft pseudopotentials. We also discuss a simple approach to model molecular systems with a net charge and/or large dipole/quadrupole moments. We present test applications to manganese and iron porphyrins representative of a large class of biologically relevant metallorganic systems. Our results show that accurate Density-Functional Theory calculations on systems with several hundred atoms are feasible with access to moderate computational resources.

The low frequency vibrational modes of green fluorescent proteins

Abstract: We report the observation and analysis of the low frequency vibrational modes of green fluorescent proteins (GFPs). Our study exploits the surface enhanced Raman scattering technique, which allowed the analysis of the vibrational modes of the proteins down to 300 cm � 1 . Here we present results on two GFP mutants, namely S65T/F64L GFP (EGFP) and S65T/F64L/T203Y GFP (E 2 GFP). These particularly bright mutants display almost inverted population ratio of anionic (B) to neutral (A) forms of the chromophore. By comparing the vibrational spectrum of the proteins with that of a synthetic model chromophore in solution and with the aid of first principle calculations based on density functional theory, we identify the Raman active bands in this region of frequencies. A dominant collective mode at 720 cm � 1 is found and assigned to a collective planar deformation of the chromophore. Low frequency vibrational modes belonging specifically to A and/or Bstructural configurations are also identified. This work demonstrates the possibility of monitoring the structural sub-states of GFPs through vibrational spectroscopy in a range of frequencies where collective modes peculiar of the double ring structure of the chromophore lie. 2002 Elsevier Science B.V. All rights reserved.

Nitrogen passivation by atomic hydrogen in GaAs y N 1 − y and In x Ga 1 − x As y N 1 − y alloys

Abstract: Previous theoretical studies on N-H complexes in GaAsN have been extended here to new di-hydrogen complex configurations and to N-H complexes in the In 0 . 2 5 Ga 0 . 7 5 As 0 . 9 7 N 0 . 0 3 alloy. Moreover, a deeper analysis has been performed on the structure, formation energies, chemical bonding and electronic properties of old and new N-H complexes in the above alloys. On the ground of the achieved results, the existence of a novel di-hydrogen complex is predicted that is characterized by a C 2 v symmetry and peculiar vibrational properties. Complexes with this symmetry are not stable in N-free GaAs. Further, we propose a sound model for the N passivation founded on the characteristics of the electronic states and the local atomic relaxations induced by the N-H complexes. This model explains why the N passivation is not achieved in the case of monohydrogen complexes and realized through the formation of the N-H* 2 dihydrogen complexes. Finally, it is suggested that different N-H complexes (and different vibrational spectra) should be observed in hydrogenated p-type and n-type N-containing alloys.