Kiril Tsemekhman

Cooperative hydrogen bonding in amyloid formation.

Amyloid diseases, including Alzheimers 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. Monomers of amyloid‐forming proteins can remain in dissolved form for long periods, before rapidly assembly into fibrils. The lag before growth has been attributed to slow kinetics of formation of a nucleus, on which other molecules can deposit to form the fibril. We have explored the energetics of fibril formation, based on the known molecular structure of a fibril‐forming peptide from the yeast prion, Sup35, using both classical and quantum (density functional theory) methods. We find that the energetics of fibril formation for the first three layers are cooperative using both methods. This cooperativity is consistent with the observation that formation of amyloid fibrils involves slow nucleation and faster growth.

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. The electronic structure of the porphyrin-gold wire is studied here by density functional theory, and the conductivity of the system is determined as a function of the photoexcitation energy. Photoexcitations of the dye are found to enhance the wire conductivity by orders of magnitude.

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.g., B3LYP and PBE0) have shown to promise in rectifying this type of failure, as well as producing more accurate band gaps and reaction barriers. The evaluation of exact exchange is challenging for large, solid state systems with periodic boundary conditions, especially when plane‐wave basis sets are used. We have developed parallel algorithms for implementing exact exchange into pseudopotential plane‐wave DFT program and we have implemented them in the NWChem program package. The technique developed can readily be employed in Γ‐point plane‐wave DFT programs. Furthermore, atomic forces and stresses are straightforward to implement, making it applicable to both confined and extended systems, as well as to Car‐Parrinello ab initio molecular dynamic simulations. This method has been applied to several systems for which conventional DFT methods do not work well, including calculations for band gaps in oxides and the electronic structure of a charge trapped state in the Fe(II) containing mica, annite.

New Development of Self-Interaction Corrected DFT for Extended Systems Applied to the Calculation of Native Defects in 3C-SiC

We recently developed a framework for implementing a scaled self-interaction corrected density functional theory (DFT-SIC) into pseudo-potential plane-wave DFT. The technique implements the original method of Perdew and Zunger by direct minimization of the DFT-SIC total energy functional. By using maximally localized Wannier functions, DFT-SIC calculation can be carried out efficiently even for extended systems. Using this new development, the formation energies of defects in 3C–SiC (silicon carbide) were calculated and compared to more standard DFT calculations. Differences of up to 1 eV were seen between DFT and DFT-SIC calculations of the formation energies. When compared to DFT, DFT-SIC produced less-stable vacancies and silicon interstitials, and more stable antisites and carbon interstitials. The most favourable interstitials were found to be C interstitials in a C+–C100 dumbbell configuration, with the formation energy of 5.91 eV with DFT and 5.65 eV with DFT-SIC. Si interstitials were not as stable as C interstitials. The most favourable Si interstitial was found to be Si tetrahedral surrounded by four C atoms, with a formation energy of 7.65 eV with DFT and 8.71 eV with DFT-SIC.

Optimization of functionals of orthonormal functions in the absence of unitary invariance

We discuss the optimization of a functional with respect to sets of orthonormal functions where unitary invariance does not apply. This problem arises, for example, when density functionals with explicit self-interaction correction are used for systems of electrons. There, unitary invariance cannot be used to reformulate the minimization of the energy with respect to each of the functions as an eigenvalue problem as can be done for the commonly used GGA-DFT and Hartree-Fock theory. By including optimization with respect to unitary transformations as an explicit step in the iterative minimization procedure, fast convergence can, nevertheless, be obtained. Furthermore, by working with two sets of orthonormal functions, the optimal functions and a set of eigenfunctions, the implementation of the extended functional form in existing software becomes easier. The additional computations arising from the lack of unitary invariance can largely be carried out in parallel.

Metal Oxides in the Environment

Oxides are ubiquitous in much of environmental chemistry. Silica and related glasses are potential vehicles by which radioactive elements may be sequestered and stored. The migration of toxic waste in ground water is largely influenced by interactions at the liquid-solid interface, with several metal oxides making up the bulk of soil. In addition, metal oxides with Bronsted acid or Lewis base functionality are potential replacements for many traditional liquid catalysis that are hazardous to work with and difficult to dispose. In this proposal, we targeted two such areas of oxide chemistry. The long-term behavior of silicate materials slated for use in the entombment of high-level waste (HLW), and the use of solid acid metal oxides as replacements for toxic sulfuric and hydrofluoric acid used in industry (referred to as Green Chemistry). Thus, this project encompassed technology that can be used to both remediate and prevent pollution. These oxide systems were studied using density functional theory (DFT). The comparatively large size and complexity of the systems that will bweree studied made use of high-accuracy electronic structure studies intractable on conventional computers. The 512 node parallel processor housed in the Molecular Science Computing Facility (MSCF) provided the required capability.