Biomedical subjects

Thomas Frauenheim

Publications and source records attributed to Thomas Frauenheim.

15 recordsLinked to original sources

PubMed2007

Silicon nanowire band gap modification.

Band gap modification for small-diameter (approximately 1 nm) silicon nanowires resulting from the use of different species for surface termination is investigated by density functional theory calculations. Because of quantum confinement, small-diameter wires exhibit a direct band gap that increases as the wire diameter narrows, irrespective of surface termination. This effect has been observed in previous experimental and theoretical studies for hydrogenated wires. For a fixed cross-section, the functional group used to saturate the silicon surface significantly modifies the band gap, resulting in relative energy shifts of up to an electronvolt. The band gap shifts are traced to details of the hybridization between the silicon valence band and the frontier orbitals of the terminating group, which is in competition with quantum confinement.

Molecular Structure↗

PubMed2006

"Proton holes" in long-range proton transfer reactions in solution and enzymes: A theoretical analysis.

Proton transfers are fundamental to chemical processes in solution and biological systems. Often, the well-known Grotthuss mechanism is assumed where a series of sequential "proton hops" initiates from the donor and combines to produce the net transfer of a positive charge over a long distance. Although direct experimental evidence for the sequential proton hopping has been obtained recently, alternative mechanisms may be possible in complex molecular systems. To understand these events, all accessible protonation states of the mediating groups should be considered. This is exemplified by transfers through water where the individual water molecules can exist in three protonation states (water, hydronium, and hydroxide); as a result, an alternative to the Grotthuss mechanism for a proton transfer through water is to generate a hydroxide by first protonating the acceptor and then transfer the hydroxide toward the donor through water. The latter mechanism can be most generally described as the transfer of a "proton hole" from the acceptor to the donor where the "hole" characterizes the deprotonated state of any mediating molecule. This pathway is distinct and is rarely considered in the discussion of proton-transfer processes. Using a calibrated quantum mechanical/molecular mechanical (QM/MM) model and an effective sampling technique, we study proton transfers in two solution systems and in Carbonic Anhydrase II. Although the relative weight of the "proton hole" and Grotthuss mechanisms in a specific system is difficult to determine precisely using any computational approach, the current study establishes an energetics motivated framework that hinges on the donor/acceptor pKa values and electrostatics due to the environment to argue that the "proton hole" transfer is likely as important as the classical Grotthuss mechanism for proton transport in many complex molecular systems.

Acetic Acid↗

PubMed2006

The symmetry of single-molecule conduction.

We introduce the conductance point group which defines the symmetry of single-molecule conduction within the nonequilibrium Green's function formalism. It is shown, either rigorously or to within a very good approximation, to correspond to a molecular-conductance point group defined purely in terms of the properties of the conducting molecule. This enables single-molecule conductivity to be described in terms of key qualitative chemical descriptors that are independent of the nature of the molecule-conductor interfaces. We apply this to demonstrate how symmetry controls the conduction through 1,4-benzenedithiol chemisorbed to gold electrodes as an example system, listing also the molecular-conductance point groups for a range of molecules commonly used in molecular electronics research.

Electric Conductivity↗

PubMed2006

Computational studies on polymer adhesion at the surface of gamma-Al2O3. I. The adsorption of adhesive component molecules from the gas phase.

We calculate the minimum energy paths and reaction energies of the adsorption of the epoxide adhesive components diglycidylesterbisphenol A (DGEBA), diethyltriamine (DETA), and the adhesion promoter 3-aminopropylmethoxysilane (AMEO) at two different sites on a model of the native Al2O3 surface, using the nudged elastic band algorithm in conjunction with self-consistent charge-density functional based tight binding. Our results show that the chosen combination of methods is well suited to obtain an overview of the reaction mechanisms and kinetics of the adsorption of organic molecules on inorganic surfaces. The obtained MEP-s show that there is preference for the adsorption of the adhesion promoter, AMEO, over the resin, DGEBA, while the adsorption of the curing agent, DETA, is unfavorable. Our approach also gives an insight into the ranges of the mechanical and electronic influences of the adsorption process on the interface, which neither full ab initio methods nor force field approaches can provide. These results will help to develop a quantum mechanics-molecular mechanics multiscale embedding scheme for more detailed studies of organic/inorganic hybrid interface reactions.

Journal Article↗

PubMed2006

Computational photochemistry of retinal proteins.

High spectral tunability and quantum yield are the striking features of rhodopsin photochemistry. They rely on a strong and complex interaction of their chromophore, the protonated Schiff base of retinal, with its protein environment. In this article, we review the progress in the computational modeling of these systems, focusing on the optical properties and the excited state dynamics. While the earlier success of atomistic theoretical models was based on the breakthrough in X-ray crystallography and combined quantum mechanical molecular mechanical (QM/MM) methodology, recent advances point out the importance of high-level QM methods and the incorporation of effects that are neglected in conventional QM/MM or ONIOM schemes, like polarization and charge transfer.

Computational Biology↗

PubMed2006

Color tuning in rhodopsins: the mechanism for the spectral shift between bacteriorhodopsin and sensory rhodopsin II.

The mechanism of color tuning in the rhodopsin family of proteins has been studied by comparing the optical properties of the light-driven proton pump bacteriorhodopsin (bR) and the light detector sensory rhodopsin II (sRII). Despite a high structural similarity, the maximal absorption is blue-shifted from 568 nm in bR to 497 nm in sRII. The molecular mechanism of this shift is still a matter of debate, and its clarification sheds light onto the general mechanisms of color tuning in retinal proteins. The calculations employ a combined quantum mechanical/molecular mechanical (QM/MM) technique, using a DFT-based method for ground state properties and the semiempirical OM2/MRCI method and ab initio SORCI method for excited state calculations. The high efficiency of the methodology has allowed us to study a wide variety of aspects including dynamical effects. The absorption shift as well as various mutation experiments and vibrational properties have been successfully reproduced. Our results indicate that several sources contribute to the spectral shift between bR and sRII. The main factors are the counterion region at the extracellular side of retinal and the amino acid composition of the binding pocket. Our analysis allows a distinction and identification of the different effects in detail and leads to a clear picture of the mechanism of color tuning, which is in good agreement with available experimental data.

Bacteriorhodopsins↗

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↗

PubMed2006

Molecular origins of conduction channels observed in shot-noise measurements.

Measurements of shot noise from single molecules have indicated the presence of various conduction channels. We present three descriptions of these channels in molecular terms showing that the number of conduction channels is limited by bottlenecks in the molecule and that the channels can be linked to transmission through different junction states. We introduce molecular-conductance orbitals, which allow the transmission to be separated into contributions from individual orbitals and contributions from interference between pairs of orbitals.

Electric Conductivity↗

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↗