The Functional Form of Angular Forces around Transition Metal Ions in Biomolecules

A method for generating angular forces around $\sigma$-bonded transition metal ions is generalized to treat $\pi$-bonded configurations. The theoretical approach is based on an analysis of a ligand-field Hamiltonian based on the moments of the electron state distribution. The functional forms that are obtained involve a modification of the usual expression of the binding energy as a sum of ligand-ligand interactions, which however requires very little increased in CPU time. The angular interactions have simple forms involving sin and cos functions, whose relative weights depend on whether the ligands are $\sigma$- or $\pi$-bonded. They describe the ligand-field stabilization energy to an accuracy of about 10%. The resulting force field is used to model the structure of small clusters, including fragments of the copper blue protein structure. Large deviations from the typical square copper coordination are found when $\pi$-bonded ligands are present.Comment: Latex source, 9 postscript figure

Adsorption of Ethylene on Neutral, Anionic and Cationic Gold Clusters

The adsorption of ethylene molecule on neutral, anionic and cationic gold clusters consisting of up to 10 atoms has been investigated using density-functional theory. It is demonstrated that C2H4 can be adsorbed on small gold clusters in two different configurations, corresponding to the pi- and di-sigma-bonded species. Adsorption in the pi-bonded mode dominates over the di-sigma mode over all considered cluster sizes n, with the exception of the neutral C2H4-Au5 system. A striking difference is found in the size-dependence of the adsorption energy of C2H4 bonded to the neutral gold clusters in the pi and di-sigma configurations. The important role of the electronic shell effects in the di-sigma mode of ethylene adsorption on neutral gold clusters is demonstrated. It is shown that the interaction of C2H4 with small gold clusters strongly depends on their charge. The typical shift in the vibrational frequencies of C2H4 adsorbed in the pi- and the di-sigma configurations gives a guidance to experimentally distinguish between the two modes of adsorption.Comment: 30 pages, 10 figure

Redetermination of para-aminopyridine (fampridine, EL-970) at 150 K

The structure of fampridine (EL-970) or 4-aminopyridine, C₅H₆N₂, has been redetermined at 150 K. The room-temperature structure has been reported previously [Chao & Schempp (1977). Acta Cryst. B33, 1557-1564]. Pyramidalization at the amine N atom occurs in fampridine, with the N atom 0.133 (11) Å from the plane of the three C/H/H atoms to which it is bonded; the interplanar angle between the pyridyl ring and NH2 group is 21 (2)°. Aggregation in the solid state occurs by N-H...N and N-H...[pi](pyridine) interactions with N...N and N...[pi](centroid) distances of 2.9829 (18) and 3.3954 (15) Å, respectively; a C-H...[pi](pyridine) contact completes the intermolecular interactions [C...[pi](centroid) = 3.6360 (16) Å]

Quantum size effect in Pb(100) films: the role of symmetry and implication for film growth

We show from density-functional calculations that Pb(100) thin films exhibit quantum size effect with a bilayer periodicity in film energies, film relaxations, and work functions, which originate from different symmetry of the stacking geometry of odd and even layer films. The bilayer periodicity of the film energy is argued to survive on a semiconductor substrate, which should allow the growth of ``magically'' thick even-layer Pb(100) films. Furthermore, it is found that the quantum well states in a simple metal film can be classified into $\sigma$-bonded and $\pi$-bonded states, which quantize independently

Ab Initio Molecular Dynamics Study of Aqueous Solvation of Ethanol and Ethylene

The structure and dynamics of aqueous solvation of ethanol and ethylene are studied by DFT-based Car-Parrinello molecular dynamics. We did not find an enhancement of the structure of the hydrogen bonded network of hydrating water molecules. Both ethanol and ethylene can easily be accommodated in the hydrogen-bonded network of water molecules without altering its structure. This is supports the conclusion from recent neutron diffraction experiments that there is no hydrophobic hydration around small hydrophobic groups. Analysis of the electronic charge distribution using Wannier functions shows that the dipole moment of ethanol increases from 1.8 D to 3.1 D upon solvation, while the apolar ethylene molecule attains an average dipole moment of 0.5 D. For ethylene, we identified configurations with $\pi$-H bonded water molecules, that have rare four-fold hydrogen-bonded water coordination, yielding instantaneous dipole moments of ethylene of up to 1 D. The results provide valuable information for the improvement of empirical force fields, and point out that for an accurate description of the aqueous solvation of ethanol, and even of the apolar ethylene, polarizable force fields are required.Comment: 15 pages, 10 figures, 4 tables, revtex4, submitted to J. Chem. Phy

Atomic-scale characterization of nitrogen-doped graphite: Effects of dopant nitrogen on the local electronic structure of the surrounding carbon atoms

We report the local atomic and electronic structure of a nitrogen-doped graphite surface by scanning tunnelling microscopy, scanning tunnelling spectroscopy, X-ray photoelectron spectroscopy, and first-principles calculations. The nitrogen-doped graphite was prepared by nitrogen ion bombardment followed by thermal annealing. Two types of nitrogen species were identified at the atomic level: pyridinic-N (N bonded to two C nearest neighbours) and graphitic-N (N bonded to three C nearest neighbours). Distinct electronic states of localized {\pi} states were found to appear in the occupied and unoccupied regions near the Fermi level at the carbon atoms around pyridinic-N and graphitic-N species, respectively. The origin of these states is discussed based on the experimental results and theoretical simulations.Comment: 6 Pages, with larger figure

Noninvasive Embedding of Single Co Atoms in Ge(111)2x1 Surfaces

We report on a combined scanning tunneling microscopy (STM) and density functional theory (DFT) based investigation of Co atoms on Ge(111)2x1 surfaces. When deposited on cold surfaces, individual Co atoms have a limited diffusivity on the atomically flat areas and apparently reside on top of the upper pi-bonded chain rows exclusively. Voltage-dependent STM imaging reveals a highly anisotropic electronic perturbation of the Ge surface surrounding these Co atoms and pronounced one-dimensional confinement along the pi-bonded chains. DFT calculations reveal that the individual Co atoms are in fact embedded in the Ge surface, where they occupy a quasi-stationary position within the big 7-member Ge ring in between the 3rd and 4th atomic Ge layer. The energy needed for the Co atoms to overcome the potential barrier for penetration in the Ge surface is provided by the kinetic energy resulting from the deposition process. DFT calculations further demonstrate that the embedded Co atoms form four covalent Co-Ge bonds, resulting in a Co4+ valence state and a 3d5 electronic configuration. Calculated STM images are in perfect agreement with the experimental atomic resolution STM images for the broad range of applied tunneling voltages.Comment: 19 pages, 15 figures, 3 table

Highly Conducting pi-Conjugated Molecular Junctions Covalently Bonded to Gold Electrodes

We measure electronic conductance through single conjugated molecules bonded to Au metal electrodes with direct Au-C covalent bonds using the scanning tunneling microscope based break-junction technique. We start with molecules terminated with trimethyltin end groups that cleave off in situ resulting in formation of a direct covalent sigma bond between the carbon backbone and the gold metal electrodes. The molecular carbon backbone used in this study consist of a conjugated pi-system that has one terminal methylene group on each end, which bonds to the electrodes, achieving large electronic coupling of the electrodes to the pi-system. The junctions formed with the prototypical example of 1,4-dimethylenebenzene show a conductance approaching one conductance quantum (G0 = 2e2/h). Junctions formed with methylene terminated oligophenyls with two to four phenyl units show a hundred-fold increase in conductance compared with junctions formed with amine-linked oligophenyls. The conduction mechanism for these longer oligophenyls is tunneling as they exhibit an exponential dependence of conductance with oligomer length. In addition, density functional theory based calculations for the Au-xylylene-Au junction show near-resonant transmission with a cross-over to tunneling for the longer oligomers.Comment: Accepted to the Journal of the American Chemical Society as a Communication

Ab-initio study of model guanine assemblies: The role of pi-pi coupling and band transport

Several assemblies of guanine molecules are investigated by means of first-principle calculations. Such structures include stacked and hydrogen-bonded dimers, as well as vertical columns and planar ribbons, respectively, obtained by periodically replicating the dimers. Our results are in good agreement with experimental data for isolated molecules, isolated dimers, and periodic ribbons. For stacked dimers and columns, the stability is affected by the relative charge distribution of the pi orbitals in adjacent guanine molecules. pi-pi coupling in some stacked columns induces dispersive energy bands, while no dispersion is identified in the planar ribbons along the connections of hydrogen bonds. The implications for different materials comprised of guanine aggregates are discussed. The bandstructure of dispersive configurations may justify a contribution of band transport (Bloch type) in the conduction mechanism of deoxyguanosine fibres, while in DNA-like configurations band transport should be negligible.Comment: 21 pages, 6 figures, 3 tables, to be published in Phys. Rev.