R. Di Felice

GolP: An atomistic force-field to describe the interaction of proteins with Au(111) surfaces in water

A classical atomistic force field to describe the interaction of proteins with gold (111) surfaces in explicit water has been devised. The force field is specifically designed to be easily usable in most common bio‐oriented molecular dynamics codes, such as GROMACS and NAMD. Its parametrization is based on quantum mechanical (density functional theory [DFT] and second order Möller‐Plesset perturbation theory [MP2]) calculations and experimental data on the adsorption of small molecules on gold. In particular, a systematic DFT survey of the interaction between Au(111) and the natural amino acid side chains has been performed to single out chemisorption effects. Van der Waals parameters have been instead fitted to experimental desorption energy data of linear alkanes and were also studied via MP2 calculations. Finally, gold polarization (image charge effects) is taken into account by a recently proposed procedure (Iori, F.; Corni, S. J Comp Chem 2008, 29, 1656). Preliminary validation results of GolP on an independent test set of small molecules show the good performances of the force field.

G-quartet biomolecular nanowires

We present a first-principle investigation of quadruple helix nanowires, consisting of stacked planar hydrogen-bonded guanine tetramers. Our results show that long wires form and are stable in potassium-rich conditions. We present their electronic band structure and discuss the interpretation in terms of effective wide-band-gap semiconductors. The microscopic structural and electronic properties of the guanine quadruple helices make them suitable candidates for molecular nanoelectronics.

Electronic rectification in protein devices

We show that the electron-transfer protein azurin can be used to fabricate biomolecular rectifiers exploiting its native redox properties, chemisorption capability and electrostatic features. The devices consist of a protein layer interconnecting nanoscale electrodes fabricated by electron beam lithography. They exhibit a rectification ratio as large as 500 at 10 V, and operate at room temperature and in air.

Solid‐State Molecular Rectifier Based on Self‐Organized Metalloproteins

Recently, great attention has been paid to the possibility of implementing hybrid electronic devices exploiting the self-assembling properties of single molecules. Impressive progress has been done in this field by using organic molecules and macromolecules. However, the use of biomolecules is of great interest because of their larger size (few nanometers) and of their intrinsic functional properties. Here, we show that electron-transfer proteins, such as the blue copper protein azurin (Az), can be used to fabricate biomolecular electronic devices exploiting their intrinsic redox properties, self assembly capability and surface charge distribution. The device implementation follows a bottom-up approach in which the self assembled protein layer interconnects nanoscale electrodes fabricated by electron beam lithography, and leads to efficient rectifying behavior at room temperature.

Energetics of AlN thin films on the Al2O3(0001) surface

We present an ab initio study of the energetics and atomic structure of films consisting of approximately 1 bilayer of AlN on the c-plane sapphire surface. We show that these films are unstable with respect to three-dimensional islands, and we attribute this instability to both strain and chemical mismatch between the oxide and the nitride. The relative stability of the AlN films depends on the chemical potentials of Al and N. Films having (0001) polarity are expected to form under Al-rich conditions. Films with (0001) polarity appear to form only for undersaturation conditions of bulk AlN in the initial stages of growth.

First-principles density-functional theory calculations of electron-transfer rates in azurin dimers

We have conceived and implemented a new method to calculate transfer integrals between molecular sites, which exploits few quantities derived from density-functional theory electronic structure computations and does not require the knowledge of the exact transition state coordinate. The method uses a complete multielectron scheme, thus including electronic relaxation effects. Moreover, it makes no use of empirical parameters. The computed electronic couplings can then be combined with estimates of the reorganization energy to evaluate electron-transfer rates that are measured in kinetic experiments: the latter are the basis to interpret electron-transfer mechanisms. We have applied our approach to the study of the electron self-exchange reaction of azurin, an electron-transfer protein belonging to the family of cupredoxins. The transfer integral estimates provided by the proposed method have been compared with those resulting from other computational techniques, from empirical models, and with available experimental data.

Towards metalated DNA-based structures

We present an overview of ab initio plane-wave density functional theory calculations performed on DNA-based model complexes and realistic helices. After elucidating the predictions concerning the effects of hydrogen pairing and stacking interactions on the formation of dispersive energy bands and delocalized orbitals, we focus our attention on metal–nucleotide coupling and hybridization. The latter effects are currently explored as a factor that may enhance DNA conductivity.

Hydrogen-induced surface metallization of beta-SiC(100)-(3x2) revisited by density functional theory calculations.

Recent experiments on the silicon terminated (3 x 2)-SiC(100) surface indicated an unexpected metallic character upon hydrogen adsorption. This effect was attributed to the bonding of hydrogen to a row of Si atoms and to the stabilization of a neighboring dangling bond row. Here, on the basis of density-functional calculations, we show that multiple-layer adsorption of H at the reconstructed surface is compatible with a different geometry: in addition to saturating the topmost Si dangling bonds, H atoms are adsorbed at rather unusual sites, i.e., stable bridge positions above third-layer Si dimers. The results thus suggest an alternative interpretation for the electronic structure of the metallic surface.

Maximally localized Wannier functions constructed from projector-augmented waves or ultrasoft pseudopotentials

We report a theoretical scheme that enables the calculation of maximally localized Wannier functions within the formalism of projector-augmented waves (PAW), which also includes the ultrasoft pseudopotential (USPP) approach. We give a description of the basic underlying formalism and explicitly write out all the required matrix elements using the common ingredients of the PAW/USPP theory. We report an implementation of the method in a form suitable for accepting the input electronic structure from USPP plane-wave DFT simulations. We apply the method to the calculation of Wannier functions, dipole moments and spontaneous polarizations for a range of test cases. A comparison with norm-conserving pseudopotentials is reported as a benchmark.

Hydrogen covered Si(111) surfaces

Abstract The recently discovered method for the production of an ideally H-terminated, stable and easily transferable Si(111)1 × 1 surface renews the interest for this prototypical system. Through a density functional description of the electronic structure based on pseudopotential and LMTO methods, we discuss in detail spectroscopical information, bond geometry, stretching frequency and the energetics of this surface. Further attention is devoted to the chemisorption of atomic hydrogen on the Si(111)2 × 1 surface and to the removal of the reconstruction, which leads to a less perfect 1 × 1 surface.