Effects of orientation at the phthalocyanine-CdSe interface on the electron transfer characteristics.

A phthalocyanine molecule adsorbed on the (101[combining macron]0) surface of wurtzite CdSe is theoretically modeled by the DFT method. We have found that a linker does not affect substantially the redox properties of phthalocyanine, while saturation of the macrocycle with peripheral substituent groups causes a downward shift in the energy position of its frontier orbitals that can hinder electron injection to the CdSe surface. Tilting of the phthalocyanine molecule relative to the surface also leads to the lowering of its molecular electronic levels relative to the bands of CdSe. At a tilting angle of 30°, the LUMO level of the dye appears to be lower than the conduction band minimum of cadmium selenide, which makes the electron transfer to its hybridized surface unfavorable. By contrast, the HOMO level of the phenylbutyric acid linker provides a suitable intermediate channel for the hole transfer from the valence band of CdSe to the phthalocyanine that points to the possible acceptor behavior of the phthalocyanine molecule in its hybrids with CdSe nanostructures.

Electronic structure of p-type perylene monoimide-based donor-acceptor dyes on the nickel oxide (100) surface: a DFT approach.

A p-type dye-sensitized solar cell, where the dye injects a hole into the semiconductor, could be combined with a typical Grätzel cell to create an efficient tandem device. However, the current p-type devices suffer from low efficiency. Here, geometries and electronic structures of four perylenemonoimide-based dyes () both as free and adsorbed on the NiO(100) semiconductor surface have been investigated to gain a better understanding of the p-type devices. In particular, the electronic transitions relevant to charge transfer between the dye and the surface have been identified. Excitations have been evaluated using the time-dependent DFT calculations, and the roles of frontier orbitals and band edges in transitions have been assessed. The adsorbed dyes can adopt either upright or slightly tilted geometries depending on the structure of the anchoring group and the binding mode of the dye. The adsorption slightly lowers the NiO band gap, from 4.06 eV to 3.90-3.96 eV, depending on the surface-adsorbate system and the band gaps of the dye molecules by 0.1-0.2 eV. Additionally, the adsorption mode of dye moves the LUMO+1 level down by 0.5 eV. The effective mass of charge carrier holes is significantly smaller at the NiO surface than in the bulk indicating the importance of surface conductivity. We also found that the potential drop, i.e. the driving force for charge transfer from NiO to the dye molecule, depends on the adsorption mode of .

Electronic structure calculations with GPAW: a real-space implementation of the projector augmented-wave method.

Electronic structure calculations have become an indispensable tool in many areas of materials science and quantum chemistry. Even though the Kohn-Sham formulation of the density-functional theory (DFT) simplifies the many-body problem significantly, one is still confronted with several numerical challenges. In this article we present the projector augmented-wave (PAW) method as implemented in the GPAW program package (https://wiki.fysik.dtu.dk/gpaw) using a uniform real-space grid representation of the electronic wavefunctions. Compared to more traditional plane wave or localized basis set approaches, real-space grids offer several advantages, most notably good computational scalability and systematic convergence properties. However, as a unique feature GPAW also facilitates a localized atomic-orbital basis set in addition to the grid. The efficient atomic basis set is complementary to the more accurate grid, and the possibility to seamlessly switch between the two representations provides great flexibility. While DFT allows one to study ground state properties, time-dependent density-functional theory (TDDFT) provides access to the excited states. We have implemented the two common formulations of TDDFT, namely the linear-response and the time propagation schemes. Electron transport calculations under finite-bias conditions can be performed with GPAW using non-equilibrium Green functions and the localized basis set. In addition to the basic features of the real-space PAW method, we also describe the implementation of selected exchange-correlation functionals, parallelization schemes, ΔSCF-method, x-ray absorption spectra, and maximally localized Wannier orbitals.

Anomalous bismuth-stabilized (2x1) reconstructions on GaAs(100) and InP(100) surfaces.

First-principles phase diagrams of bismuth-stabilized GaAs- and InP(100) surfaces demonstrate for the first time the presence of anomalous (2x1) reconstructions, which disobey the common electron counting principle. Combining these theoretical results with our scanning-tunneling-microscopy and photoemission measurements, we identify novel (2x1) surface structures, which are composed of symmetric Bi-Bi and asymmetric mixed Bi-As and Bi-P dimers, and find that they are stabilized by stress relief and pseudogap formation.

Nitrogen interstitial defects in GaAs.

We have studied nitrogen interstitial defects in GaAs with first-principles calculations. On the basis of calculated formation energies we have determined the most common nitrogen defects and the transition levels for various charge states. The lowest energy interstitial-type defects are found to be N-N and N-As split interstitials for most of the experimentally relevant conditions. We have also compared two different methods of obtaining the potential correction needed in an accurate calculation of the formation energies and transition levels.

Apolipoprotein B gene polymorphisms and serum lipids: meta-analysis of the role of genetic variation in responsiveness to diet.

BACKGROUND: The genetic variance determining plasma lipid and lipoprotein concentrations may modify individual responsiveness to alterations in dietary fat and cholesterol content. OBJECTIVE: The aim was to examine the role of apolipoprotein (apo) B DNA polymorphisms in responsiveness of plasma lipids and lipoproteins to diet. DESIGN: A controlled dietary intervention study was conducted in 44 healthy, middle-aged subjects with a 3-mo baseline, a 1-mo fat-controlled, a 1-mo high-fat, and a 1-mo habitual diet period. We also conducted a meta-analysis of all published dietary trials, including our own. RESULTS: In our own dietary study, the apo B XbaI restriction-site polymorphism affected the responsiveness to diet of the plasma LDL-cholesterol concentration (P < 0.05, repeated-measures analysis of variance). Especially during the high-fat diet, homozygous absence of the XbaI restriction site (X(-)/X(-)) was associated with a greater increase in LDL cholesterol (44 +/- 5%) than was X(+)/X(+) (27 +/- 7%) or X(+)/X(-) (40 +/- 5%). The high-fat diet also induced a larger increase in plasma LDL cholesterol in subjects with the R(-)/R(-) genotype (homozygous absence of the EcoRI restriction site) (59 +/- 10%) than in those with the R(+)/R(-) (39 +/- 6%) or R(+)/R(+) (36 +/- 4%) genotype. The M(+)/M(+) genotype (homozygous presence of the MspI restriction site) was also more responsive (41 +/- 3% increase in LDL cholesterol) than the M(+)/M(-) genotype (27 +/- 10% increase). The meta-analysis supported the finding of the significant role of the EcoRI and MspI polymorphisms, but not that of the XbaI polymorphism. CONCLUSIONS: The present study indicated that the apo B EcoRI and MspI polymorphisms are associated with responsiveness to diet.

Structure and dynamic properties of diunsaturated 1-palmitoyl-2-linoleoyl-sn-glycero-3-phosphatidylcholine lipid bilayer from molecular dynamics simulation.

Unsaturated fatty acid chains are known to be an essential structural part of biomembranes, but only monounsaturated chains have been included in the molecular dynamics (MD) simulations of membrane systems. Here we present a 1-ns MD simulation for a diunsaturated 1-palmitoyl-2-linoleoyl-sn-glycero-3-phosphatidylcholine (PLPC; 16:0/18:2[delta9,12]) bilayer. The structural behavior of the phosphatidylcholine headgroup, the glycerol backbone, and the hydrating water were assessed and found to be consistent with the existing information about similar systems from both experimental and computational studies. Further analysis was focused on the structure of the double bond region and the effects of the diunsaturation on the bilayer interior. The behavior of the diunsaturated sn-2 chains is affected by the tilted beginning of the chain and the four main conformations of the double bond region. The double bonds of the sn-2 chains also influenced the characteristics of the saturated chains in the sn-1 position. Furthermore, extreme conformations of the sn-2 chains existed that are likely to be related to the functional role of the double bonds. The results here point out the importance of polyunsaturation for the biological interpretations deduced from the membrane MD simulations.

Solution structure of nodularin. An inhibitor of serine/threonine-specific protein phosphatases.

The three-dimensional solution structure of nodularin was studied by NMR and molecular dynamics simulations. The conformation in water was determined from the distance and dihedral data by distance geometry and refined by iterative relaxation matrix analysis. The cyclic backbone adopts a well defined conformation but the remote parts of the side chains of arginine as well as the amino acid derivative Adda have a large spatial dispersion. For the unusual amino acids the partial charges were calculated and nodularin was subjected to molecular dynamic simulations in water. A good agreement was found between experimental and computational data with hydrogen bonds, solvent accessibility, molecular motion, and conformational exchange. The three-dimensional structure resembles very closely that of microcystin-LR in the chemically equivalent segment. Therefore, it is expected that the binding of both microcystins and nodularins to serine/threonine-specific protein phosphatases is similar on an atomic level.

Conformational analysis of a toxic peptide from Trimeresurus wagleri which blocks the nicotinic acetylcholine receptor.

The 22-residue toxic peptide (WTX1) from the venom of the Southeast Asian snake Trimeresurus wagleri has multiple sites of action, but its lethal effect has been attributed to blocking the postsynaptic acetylcholine receptor at the neuromuscular junction. The 3-dimensional structure of WTX1 was studied using 2-dimensional nuclear magnetic resonance spectroscopy, circular dichroism, and computer simulations. In aqueous solution, WTX1 was shown to have extended and flexible "tails" defined by a short, rigid disulfide-bonded loop. The flexible regions can undergo structural rearrangement when moved from an aqueous to a less polar environment and may contribute to its effectiveness at different receptor sites. By substituting Gly or Phe for His at position 10, significant effects on the disulfide bond formation and, thereby, the activity of the peptide were observed. These results suggest that even subtle differences in single residues can have profound effects on the dynamics of folding, disulfide bond formation, and activity of this toxic peptide.