Biomedical subjects

Thomas Frauenheim

Publications and source records attributed to Thomas Frauenheim.

8 recordsLinked to original sources

PubMed2006

Strain-free polarization superlattice in silicon carbide: a theoretical investigation.

A strain-free superlattice of inversion domains along the hexagonal axis of SiC is investigated by theoretical calculations. The induced polarization causes a zigzag shape in the band edges, leading to spatial separation of photoexcited carriers and to an effective band gap narrowing tunable over a wide range by the geometry and on a smaller scale by the intensity of the excitation. Calculations on the SiC surface indicate that preparation of such a superlattice might be possible in atomic layer epitaxy with properly chosen sources and temperatures.

Journal Article↗

PubMed2006

Understanding the inelastic electron-tunneling spectra of alkanedithiols on gold.

We present results for a simulated inelastic electron-tunneling spectra (IETS) from calculations using the "gDFTB" code. The geometric and electronic structure is obtained from calculations using a local-basis density-functional scheme, and a nonequilibrium Green's function formalism is employed to deal with the transport aspects of the problem. The calculated spectrum of octanedithiol on gold(111) shows good agreement with experimental results and suggests further details in the assignment of such spectra. We show that some low-energy peaks, unassigned in the experimental spectrum, occur in a region where a number of molecular modes are predicted to be active, suggesting that these modes are the cause of the peaks rather than a matrix signal, as previously postulated. The simulations also reveal the qualitative nature of the processes dominating IETS. It is highly sensitive only to the vibrational motions that occur in the regions of the molecule where there is electron density in the low-voltage conduction channel. This result is illustrated with an examination of the predicted variation of IETS with binding site and alkane chain length.

Journal Article↗

PubMed2006

Structural evolution of anionic silicon clusters SiN (20 <or= N <or= 45).

Results of a combined photoelectron spectroscopy and first-principles density-functional study of SiN- clusters in the size range 20 or= 20. For 28 <or= N <or= 45, almost all low-lying near-spherical clusters SiN- adopt "stuffed-cage"-like structures where the cages are homologous to carbon fullerenes in the sense that they are composed of only five- and six-membered rings. However the arrangement of the "stuffing" atoms is not yet diamondlike.

Journal Article↗

PubMed2006

Structure and shape variations in intermediate-size copper clusters.

Using extensive, unbiased searches based on density-functional theory, we explore the structural evolution of Cu(n) clusters over the size range n=8-20. For n=8-16, the optimal structures are plateletlike, consisting of two layers, with the atoms in each layer forming a trigonal bonding network similar to that found in smaller, planar clusters (n<or=6). For n=17 and beyond, there is a transition to compact structures containing an icosahedral 13-atom core. The calculated ground-state structures are significantly different from those predicted earlier in studies based on empirical and semiempirical potentials. The evolution of the structure and shape of the preferred configuration of Cu(n), n<or=20, is shown to be nearly identical to that found for Na clusters, indicating a shell-model-type behavior in this size range.

Journal Article↗

PubMed2005

Theoretical study of the interaction between selected adhesives and oxide surfaces.

We investigate the competition of the various organic components of two representative adhesive systems for reactive defect sites at model surfaces of both SiO2 and Al2O3. The reaction energies of resin monomers, curing agents, and in some cases also of additional adhesion promoters with the defects are calculated. We applied a density-functional based tight-binding method including a self-consistent correction of the Mulliken charges, which has already proven to be a useful tool for computational materials science, delivering reliable structural and energetic information.

Journal Article↗

PubMed2005

Validation of the density-functional based tight-binding approximation method for the calculation of reaction energies and other data.

We investigated the performance of the approximative density functional method DFTB versus BLYP and G2 with respect to zero-point corrected reaction energies, vibrational frequencies, and geometry parameters for a set of 28 reactions and 22 representative molecules containing C, H, N, and O (DFTB--density-functional based tight-binding approximation). The DFTB reaction energies show a mean absolute deviation versus the G2 reference of 4.3 kcalmol only. The corresponding value for the vibrational frequencies amounts to 75 cm(-1) versus BLYP/cc-pVTZ. With very few exceptions bond lengths and angles are in excellent agreement with the results of higher-level methods.

Journal Article↗

PubMed2003

Modeling zinc in biomolecules with the self consistent charge-density functional tight binding (SCC-DFTB) method: applications to structural and energetic analysis.

Parameters for the zinc ion have been developed in the self-consistent charge density functional tight-binding (SCC-DFTB) framework. The approach was tested against B3LYP calculations for a range of systems, including small molecules that contain the typical coordination environment of zinc in biological systems (cysteine, histidine, glutamic/aspartic acids, and water) and active site models for a number of enzymes such as alcohol dehydrogenase, carbonic anhydrase, and aminopeptidase. The SCC-DFTB approach reproduces structural and energetic properties rather reliably (e.g., total and relative ligand binding energies and deprotonation energies of ligands and barriers for zinc-assisted proton transfers), as compared with B3LYP/6-311+G** or MP2/6-311+G** calculations.

Alcohol Dehydrogenase↗

PubMed2002

11-cis-retinal protonated Schiff base: influence of the protein environment on the geometry of the rhodopsin chromophore.

Density functional theory (DFT) calculations based on the self-consistent-charge tight-binding approximation have been performed to study the influence of the protein pocket on the 3-dimensional structure of the 11-cis-retinal Schiff base (SB) chromophore. Starting with an effectively planar chromophore embedded in a protein pocket consisting of the 27 next-nearest amino acids, the relaxed chromophore geometry resulting from energy optimization and molecular dynamics (MD) simulations has yielded novel insights with respect to the following questions: (i) The conformation of the beta-ionone ring. The protein pocket tolerates both conformations, 6-s-cis and 6-s-trans, with a total energy difference of 0.7 kcal/mol in favor of the former. Of the two possible 6-s-cis conformations, the one with a negative twist angle (optimized value: -35 degrees ) is strongly favored, by 3.6 kcal/mol, relative to the one in which the dihedral is positive. (ii) Out-of-plane twist of the chromophore. The environment induces a nonplanar helical deformation of the chromophore, with the distortions concentrated in the central region of the chromophore, from C10 to C13. The dihedral angle between the planes formed by the bonds from C7 to C10 and from C13 to C15 is 42 degrees. (iii) The absolute configuration of the chromophore. The dihedral angle about the C12-C13 bond is +170 degrees from planar s-cis, which imparts a positive helicity on the chromophore, in agreement with earlier considerations based on theoretical and spectroscopic evidence.

Animals↗