Parallel implementation of Γ-point pseudopotential plane-wave DFT with exact exchange.

Semi-local functionals commonly used in density functional theory (DFT) studies of solids usually fail to reproduce localized states such as trapped holes, polarons, excitons, and solitons. This failure is ascribed to self-interaction which creates a Coulomb barrier to localization. Pragmatic approaches in which the exchange correlation functionals are augmented with small amount of exact exchange (hybrid-DFT, e.

Photoinduced conductivity of a porphyrin-gold composite nanowire.

Negatively charged phosphine groups on the backbone of DNA are known to attract gold nanoclusters from a colloid, assembling the clusters at fixed intervals. Bridging these intervals with porphyrin-dye linkers forms an infinite conducting chain, a quantum wire whose carrier mobility can be enhanced by photoexcitation. The resulting nanoassembly can be used as a gate: a wire with a controllable conductivity.

Cooperative hydrogen bonding in amyloid formation.

Amyloid diseases, including Alzheimer's and prion diseases, are each associated with unbranched protein fibrils. Each fibril is made of a particular protein, yet they share common properties. One such property is nucleation-dependent fibril growth.

Electron density redistribution accounts for half the cooperativity of alpha helix formation.

The energy of alpha helix formation is well known to be highly cooperative, but the origin and relative importance of the contributions to helical cooperativity have been unclear. Here we separate the energy of helix formation into short range and long range components by using two series of helical dimers of variable length. In one dimer series two monomeric helices interact by forming hydrogen bonds, while in the other they are coupled only through long range, primarily electrostatic interactions.

Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum mechanical calculations.

Hydrogen bonding is a key contributor to the exquisite specificity of the interactions within and between biological macromolecules, and hence accurate modeling of such interactions requires an accurate description of hydrogen bonding energetics. Here we investigate the orientation and distance dependence of hydrogen bonding energetics by combining two quite disparate but complementary approaches: quantum mechanical electronic structure calculations and protein structural analysis. We find a remarkable agreement between the energy landscapes obtained from the electronic structure calculations and the distributions of hydrogen bond geometries observed in protein structures.