No abstract

We present density functional (DF) calculations, using a pseudopotential scheme and plane waves as basis functions, for isolated molecules of the amino acids glycine and alanine, for small oligopeptides composed of glycine and alanine, and for periodic (infinite) polyalanine helices. We calculate relative energies and geometries for the low-lying isomers of glycine and alanine and for a variety of oligopeptide geometries using various DF formulations for electron exchange and correlation (LDA, PBE, BLYP, BP). Comparison is made with other theories and experiment where possible. The free molecule equilibrium geometries agree well with the limited experimental data and with post-Hartree−Fock (post-HF) calculations. The inclusion of gradient-corrected (nonlocal) functionals is essential when hydrogen bonds play a role in determining relative energies. This is especially true for hydrogen bonds of the type N···H−O, which appear in two isomers of glycine and alanine. We obtain the most reliable results with BLYP, but the best compromise, with a considerably smaller cutoff energy, is PBE. For the polypeptides we find that the peptide bonds in the equilibrium geometries are planar to high accuracy, with dihedral angles deviating from planarity by up to 15°. The relative energies of the low-lying isomers of alanine dipeptide agree very well with post-HF calculations. The equilibrium structure of the polyalanine α helix is very well reproduced by our calculations.

We recorded photoelectron spectra of antimony Sb−N=2–9 and of bismuth clusters Bi−N=2–9 with a photon energy of 4.03 eV, as well as of Bi−N=2–21 with a photon energy of 5.0 eV. The experimentally determined photoelectron thresholds and peak positions of Sb−N=2–5 and Bi−N=2–5 are compared with the results of ab initio density-functional (LCAO) calculations. The agreement between the experimental thresholds and the calculated adiabatic electron affinities, as well as between the first maxima in the spectra and the calculated vertical detachment energies is fair to good for the antimony clusters and qualitative for the bismuth systems. For the calculation of the ionization (detachment) energies we determined for the neutral and anionic clusters the most stable structures by LCAO calculations. In particular, the tetramer cluster anions have a ‘‘roof’’ structure, while the negatively charged pentamers are planar rings [with similarities to the (C5H5)− anion]; positive and negative trimers are nonlinear. Furthermore, the ionization energies and affinities of larger antimony and bismuth clusters are discussed qualitatively and compared to jellium calculations of Seidl and Brack.

The asymptotic form of the image interaction is derived for a classical external point charge at a distance z1 outside a periodic metallic surface, generalizing to real metals the analytical result of Lang and Kohn (1973) for jellium. The centre of gravity zc of the induced charge coincides with the position of the image plane z0 in the limit of linear response. However, whereas zc is shown to depend through non-linear response on the magnitude of the external charge q, z0 is independent of q. We show that surface periodicity does not modulate z0, but adds to the image interaction a periodic component decaying exponentially with z. In addition, the long-ranged effect of non-linearity on the interaction energy is a term attractive to a positive external charge and proportional to q3/(z1-z0)4. We report first-principles pseudopotential calculations of the interaction energy with three aluminium surfaces: (111), (100) and (110). A supercell geometry is used. A discrete classical model without adjustable parameters reproduces the effect of the surface periodicity on the image interaction at each of the three surfaces.

Molecular dynamics (MD) simulations are presented for five different compositions of liquid NaSn alloys, covering the range from 20 to 80% sodium. We apply an ab initio (Car-Parrinello) method as well as an approximate LCAO-DFT scheme. The two methods yield similar results: the tin atoms form large dynamic networks. Only for the sodium-rich composition are isolated tin atoms and dimers observed.From the ab initio MD trajectories the structure factors, the total and partial densities of states, the charge distributions and, by means of the Kubo-Greenwood formula, the electrical conductivities are calculated. The structure factors and the conductivities are obtained as functions of the composition and show good agreement with experimental data.We give a detailed discussion of the concentration dependence of the structure factors, the total and partial densities of states, the charge distributions and the electrical conductivities. The behaviour and the origin of the prepeak is discussed. For the equimolar composition the dependence of the conductivity on temperature is obtained and is in qualitative accord with experimental data.