New determination of structure parameters in strong field tunneling ionization theory of molecules

In the strong field molecular tunneling ionization theory of Tong et al. [Phys. Rev. A 66, 033402 (2002)], the ionization rate depends on the asymptotic wavefunction of the molecular orbital from which the electron is removed. The orbital wavefunctions obtained from standard quantum chemistry packages in general are not good enough in the asymptotic region. Here we construct a one-electron model potential for several linear molecules using density functional theory (DFT). We show that the asymptotic wavefunction can be improved with an iteration method and after one iteration accurate asymptotic wavefunctions and structure parameters are determined. With the new parameters we examine the alignment-dependent tunneling ionization probabilities for several molecules and compare with other calculations and with recent measurements, including ionization from inner molecular orbitals

Spontaneous formation and stability of small GaP fullerenes

We report the spontaneous formation of a GaP fullerene cage in ab-initio Molecular Dynamics simulations starting from a bulk fragment. A systematic study of the geometric and electronic properties of neutral and ionized GaP clusters suggests the stability of hetero-fullerenes formed by a compound with zincblend bulk structure. We find that GaP fullerenes up to 28 atoms have high symmetry, closed electronic shells, large HOMO-LUMO energy gaps and do not dissociate when ionized. We compare our results for GaP with those obtained by other groups for the corresponding BN clusters.Comment: To appear on PRL, 4 pages, 1 figure, Late

Thermodynamic aspects of materials' hardness: prediction of novel superhard high-pressure phases

In the present work we have proposed the method that allows one to easily estimate hardness and bulk modulus of known or hypothetical solid phases from the data on Gibbs energy of atomization of the elements and corresponding covalent radii. It has been shown that hardness and bulk moduli of compounds strongly correlate with their thermodynamic and structural properties. The proposed method may be used for a large number of compounds with various types of chemical bonding and structures; moreover, the temperature dependence of hardness may be calculated, that has been performed for diamond and cubic boron nitride. The correctness of this approach has been shown for the recently synthesized superhard diamond-like BC5. It has been predicted that the hypothetical forms of B2O3, diamond-like boron, BCx and COx, which could be synthesized at high pressures and temperatures, should have extreme hardness

Electronic entropy, shell structure, and size-evolutionary patterns of metal clusters

We show that electronic-entropy effects in the size-evolutionary patterns of relatively small (as small as 20 atoms), simple-metal clusters become prominent already at moderate temperatures. Detailed agreement between our finite-temperature-shell-correction-method calculations and experimental results is obtained for certain temperatures. This agreement includes a size-dependent smearing out of fine-structure features, accompanied by a measurable reduction of the heights of the steps marking major-shell and subshell closings, thus allowing for a quantitative analysis of cluster temperatures.Comment: Latex/Revtex, 4 pages with 3 Postscript figure

Molecular basis for passive immunotherapy of Alzheimer's disease

Amyloid aggregates of the amyloid-{beta} (A{beta}) peptide are implicated in the pathology of Alzheimer's disease. Anti-A{beta} monoclonal antibodies (mAbs) have been shown to reduce amyloid plaques in vitro and in animal studies. Consequently, passive immunization is being considered for treating Alzheimer's, and anti-A{beta} mAbs are now in phase II trials. We report the isolation of two mAbs (PFA1 and PFA2) that recognize A{beta} monomers, protofibrils, and fibrils and the structures of their antigen binding fragments (Fabs) in complex with the A{beta}(1–8) peptide DAEFRHDS. The immunodominant EFRHD sequence forms salt bridges, hydrogen bonds, and hydrophobic contacts, including interactions with a striking WWDDD motif of the antigen binding fragments. We also show that a similar sequence (AKFRHD) derived from the human protein GRIP1 is able to cross-react with both PFA1 and PFA2 and, when cocrystallized with PFA1, binds in an identical conformation to A{beta}(1–8). Because such cross-reactivity has implications for potential side effects of immunotherapy, our structures provide a template for designing derivative mAbs that target A{beta} with improved specificity and higher affinity

Structure of an archaeal PCNA1-PCNA2-FEN1 complex: elucidating PCNA subunit and client enzyme specificity.

The archaeal/eukaryotic proliferating cell nuclear antigen (PCNA) toroidal clamp interacts with a host of DNA modifying enzymes, providing a stable anchorage and enhancing their respective processivities. Given the broad range of enzymes with which PCNA has been shown to interact, relatively little is known about the mode of assembly of functionally meaningful combinations of enzymes on the PCNA clamp. We have determined the X-ray crystal structure of the Sulfolobus solfataricus PCNA1-PCNA2 heterodimer, bound to a single copy of the flap endonuclease FEN1 at 2.9 A resolution. We demonstrate the specificity of interaction of the PCNA subunits to form the PCNA1-PCNA2-PCNA3 heterotrimer, as well as providing a rationale for the specific interaction of the C-terminal PIP-box motif of FEN1 for the PCNA1 subunit. The structure explains the specificity of the individual archaeal PCNA subunits for selected repair enzyme 'clients', and provides insights into the co-ordinated assembly of sequential enzymatic steps in PCNA-scaffolded DNA repair cascades

Structure of a bacterial cell surface decaheme electron conduit

Some bacterial species are able to utilize extracellular mineral forms of iron and manganese as respiratory electron acceptors. In Shewanella oneidensis this involves decaheme cytochromes that are located on the bacterial cell surface at the termini of trans-outer-membrane electron transfer conduits. The cell surface cytochromes can potentially play multiple roles in mediating electron transfer directly to insoluble electron sinks, catalyzing electron exchange with flavin electron shuttles or participating in extracellular intercytochrome electron exchange along “nanowire” appendages. We present a 3.2-Å crystal structure of one of these decaheme cytochromes, MtrF, that allows the spatial organization of the 10 hemes to be visualized for the first time. The hemes are organized across four domains in a unique crossed conformation, in which a staggered 65-Å octaheme chain transects the length of the protein and is bisected by a planar 45-Å tetraheme chain that connects two extended Greek key split ß-barrel domains. The structure provides molecular insight into how reduction of insoluble substrate (e.g., minerals), soluble substrates (e.g., flavins), and cytochrome redox partners might be possible in tandem at different termini of a trifurcated electron transport chain on the cell surface

Benzene at 1GHz. Magnetic field-induced fine structure

The deuterium NMR spectrum of benzene-d6 in a high field spectrometer (1 GHz protons) exhibits a magnetic field-induced deuterium quadrupolar splitting ??. The magnitude of ?? observed for the central resonance is smaller than that observed for the 13C satellite doublets ???. This difference, ?(??) = ??? ? ??, is due to unresolved fine structure contributions to the respective resonances. We determine the origins of and simulate this difference, and report pulse sequences that exploit the connectivity of the peaks in the 13C and 2H spectra to determine the relative signs of the indirect coupling, JCD, and ??. The positive sign found for ?? is consonant with the magnetic field biasing of an isolated benzene molecule—the magnetic energy of the aromatic ring is lowest for configurations where the C6 axis is normal to the field. In the neat liquid the magnitude of ?? is decreased by the pair correlations in this prototypical molecular liquid

UV-induced ligand exchange in MHC class I protein crystals

High-throughput structure determination of protein−ligand complexes is central in drug development and structural proteomics. To facilitate such high-throughput structure determination we designed an induced replacement strategy. Crystals of a protein complex bound to a photosensitive ligand are exposed to UV light, inducing the departure of the bound ligand, allowing a new ligand to soak in. We exemplify the approach for a class of protein complexes that is especially recalcitrant to high-throughput strategies: the MHC class I proteins. We developed a UV-sensitive, “conditional”, peptide ligand whose UV-induced cleavage in the crystals leads to the exchange of the low-affinity lytic fragments for full-length peptides introduced in the crystallant solution. This “in crystallo” exchange is monitored by the loss of seleno-methionine anomalous diffraction signal of the conditional peptide compared to the signal of labeled MHC β2m subunit. This method has the potential to facilitate high-throughput crystallography in various protein families

An extracellular steric seeding mechanism for Eph-ephrin signaling platform assembly

Erythropoetin-producing hepatoma (Eph) receptors are cell-surface protein tyrosine kinases mediating cell-cell communication. Upon activation, they form signaling clusters. We report crystal structures of the full ectodomain of human EphA2 (eEphA2) both alone and in complex with the receptor-binding domain of the ligand ephrinA5 (ephrinA5 RBD). Unliganded eEphA2 forms linear arrays of staggered parallel receptors involving two patches of residues conserved across A-class Ephs. eEphA2-ephrinA5 RBD forms a more elaborate assembly, whose interfaces include the same conserved regions on eEphA2, but rearranged to accommodate ephrinA5 RBD. Cell-surface expression of mutant EphA2s showed that these interfaces are critical for localization at cell-cell contacts and activation-dependent degradation. Our results suggest a 'nucleation' mechanism whereby a limited number of ligand-receptor interactions 'seed' an arrangement of receptors which can propagate into extended signaling arrays