George McLendon

From Molecules to Materials: Current Trends and Future Directions

The development, characterization, and exploitation of novel materials based on the assembly of molecular components is an exceptionally active and rapidly expanding field. For this reason, the topic of molecule-based materials (MBMs) was chosen as the subject of a workshop sponsored by the Chemical Sciences Division of the United States Department of Energy. The purpose of the workshop was to review and discuss the diverse research trajectories in the field from a chemical perspective, and to focus on the critical elements that are likely to be essential for rapid progress. The MBMs discussed encompass a diverse set of compositions and structures, including clusters, supramolecular assemblies, and assemblies incorporating biomolecule-based components. A full range of potentially interesting materials properties, including electronic, magnetic, optical, structural, mechanical, and chemical characteristics were considered. Key themes of the workshop included synthesis of novel components, structural control, characterization of structure and properties, and the development of underlying principles and models. MBMs, defined as auseful substances prepared from molecules or molecular ions that maintain aspects of the parent molecular frameworko are of special significance because of the capacity for diversity in composition, structure, and properties, both chemical and physical. Key attributes are the ability in MBMs to access the additional dimension of multiple length scales and available structural complexity via organic chemistry synthetic methodologies and the innovative assembly of such diverse components. The interaction among the assembled components can thus lead to unique behavior. A consequence of the complexity is the need for a multiplicity of both existing and new tools for materials synthesis, assembly, characterization, and

Zinc-dependent protein folding.

Studies of classic zinc-finger peptides over the past 15 years have offered insights into the coupled processes of metal binding and protein folding. Within the past two years, this insight has been used to increase our understanding of the importance of first and second shell contributions (i.e. contributions from direct and indirect metal ligands) to metal binding and protein-folding stability, and led to advances in de novo protein design and protein redesign.

RNA architecture dictates the conformations of a bound peptide.

BACKGROUND The biological function of several viral and bacteriophage proteins, and their arginine-rich subdomains, involves RNA-mediated interactions. It has been shown recently that bound peptides adopt either beta-hairpin or alpha-helical conformations in viral and phage peptide-RNA complexes. We have compared the structures of the arginine-rich peptide domain of HIV-1 Rev bound to two RNA aptamers to determine whether RNA architecture can dictate the conformations of a bound peptide. RESULTS The core-binding segment of the HIV-1 Rev peptide class II RNA aptamer complex spans the two-base bulge and hairpin loop of the bound RNA and the carboxy-terminal segment of the bound peptide. The bound peptide is anchored in place by backbone and sidechain intermolecular hydrogen bonding and van der Waals stacking interactions. One of the bulge bases participates in U*(A*U) base triple formation, whereas the other is looped out and flaps over the bound peptide in the complex. The seven-residue hairpin loop is closed by a sheared G*A mismatch pair with several pyrimidines looped out of the hairpin fold. CONCLUSIONS Our structural studies establish that RNA architecture dictates whether the same HIV-1 Rev peptide folds into an extended or alpha-helical conformation on complex formation. Arginine-rich peptides can therefore adapt distinct secondary folds to complement the tertiary folds of their RNA targets. This contrasts with protein-RNA complexes in which elements of RNA secondary structure adapt to fit within the tertiary folds of their protein targets.

How methanol affects the surface of blue and red emitting porous silicon

The effects of liquid methanol on the photoluminescence intensity and FTIR spectra of red and blue emitting porous silicon were investigated. Hydrogen passivated red emitting samples exhibit quenching and recovery of photoluminescence intensity and broadening of the Si‐Hx stretch bands upon exposure to liquid methanol. Oxygen passivated red emitting samples exhibit no photoluminescence quenching. The sensitivity of the red emitting sample is due to the microstructure of porous silicon at the surface and the ability of methanol to penetrate the pores. The blue photoluminescence of thermally oxidized samples is quenched upon exposure to methanol. This is attributed to the solvent’s ability to change the surface passivation which modifies existing traps and introduces competitive recombination channels for electrons.

Effect of the Asn52----Ile mutation on the redox potential of yeast cytochrome c. Theory and experiment.

Theoretical methods for correlation of sequence changes and redox potential of electron transport proteins are examined using the Asn52----Ile mutation in cytochrome c as a test case. The first approach uses the protein dipoles Langevin dipoles (PDLD) method and the high resolution X-ray structures of the native and the mutant proteins. This approach is found to give reliable results where all the solvent molecules are represented by Langevin dipoles and also when some bound water molecules are represented explicitly. A free energy perturbation method is also found to give reasonable results but at the expense of much more computer time. Finally, an approach that generates mutant structures from the native structure by molecular dynamics simulation and then uses these configurations in PDLD calculations is found to give a reasonable estimate of the effect of the mutation on the corresponding redox potential. The encouraging results obtained here and in a preliminary test case of the Phe82----Ser mutation indicates that the present strategies can provide a useful tool for structure-redox and sequence-redox correlation in proteins.

Formation of electrostatically-stabilized complex at low ionic strength inhibits interprotein electron transfer between yeast cytochrome c and cytochrome c peroxidase.

Electron transfer from yeast ferrous cytochrome c to H2O2-oxidized yeast cytochrome c peroxidase has been studied using flash photoreduction methods. At low ionic strength (mu less than 10 mM), where a strong complex is formed between cytochrome c and peroxidase, electron transfer occurs rather slowly (k approximately 200s-1). However, at high ionic strength where the electrostatic complex is largely dissociated, the observed first-order rate constant for peroxidase reduction increases significantly reaching a concentration independent limit of k approximately 1500 s-1. Thus, at least in some cases, formation of an electrostatically-stabilized complex can actually impede electron transfer between proteins.

Picosecond measurements of exciton trapping in semiconductor clusters

Abstract The formation of deep traps in 30 A CdS semiconductor clusters has been time resolved using picosecond single-photon counting. The trapping rates, measured by the risetime of recombinate or emission, vary inversely with trap depth ranging from ≈ 30 ps above 500 nm to

Photo-active and electro-active protein films prepared by reconstitution with metalloporphyrins self-assembled on gold

Long-chain thiol derivatives of metalloporphyrins (M–protoporphyrinate IX di[12-sulfanyldodecyl] ester; M = Fe3+, Zn2+) were synthesized and self-assembled onto a gold substrate. X-Ray photoelectron spectroscopy (XPS), fluorescence spectroscopy and electrochemistry were employed to characterize the surface-immobilized species. XP spectra of the Fe–porphyrin showed the characteristic core level signals for C 1s, O 1s, S 2p, N 1s and, in particular, Fe 2p. The compound also displayed chemically reversible and stable electrochemical reactivity in an aqueous electrolyte, and its voltammetric response was manipulated by co-adsorbing with a diluent component, sulfanylpropionic acid. Fluorescence excitation and emission spectra of the Zn derivative adsorbed on Au closely resembled those of Zn–protoporphyrins in solution. After immersion in a dilute solution of apomyoglobin, significant changes in the voltammetric response of the adsorbed Fe–porphyrin and fluorescence excitation spectra of the Zn derivative were observed, and were attributed to the formation of the respective Fe– and Zn–myoglobin protein at the interface. A control experiment using native myoglobin instead of the apoprotein in the reaction ruled out the possibility of non-specific protein binding as the cause for the observed changes.

The effect of size restriction on silver bromide. A dramatic enhancement of free exciton luminescence

Abstract The effect of size restriction on the low temperature emission of silver bromide is examined. The critical size for the onset of detectable free exciton emission is determined. The effect of deliberately introduced iodide traps on free exciton luminescence was examined. Several reasons for the enhancement of the free exciton are discussed.

Kinetics of proton-coupled electron-transfer reactions to the manganese-oxo "cubane" complexes containing the Mn4O4(6+) and Mn4O4(7+) core types.

The kinetics of proton-coupled electron-transfer (pcet) reactions are reported for Mn4O4(O2PPh2)6, 1, and [Mn4O4(O2PPh2)6]+, 1+, with phenothiazine (pzH). Both pcet reactions form 1H, by H transfer to 1 and by hydride transfer to 1+. Surprisingly, the rate constants differ by only 25% despite large differences in the formal charges and driving force. The driving force is proportional to the difference in the bond-dissociation energies (BDE >94 kcal/mol for homolytic, 1H → H + 1, vs. ≈127 kcal/mol for heterolytic, 1H → H− + 1+, dissociation of the O—H bond in 1H). The enthalpy and entropy of activation for the homolytic reaction (ΔH‡ = −1.2 kcal/mol and ΔS‡ = −32 cal/mol⋅K; 25–6.7°C) reveal a low activation barrier and an appreciable entropic penalty in the transition state. The rate-limiting step exhibits no H/D kinetic isotope effect (kH/kD = 0.96) for the first H atom-transfer step and a small kinetic isotope effect (1.4) for the second step (1H + pzH → 1H2 + pz•). These lines of evidence indicate that formation of a reactive precursor complex before atom transfer is rate-limiting (conformational gating), and that little or no N—H bond cleavage occurs in the transition state. H-atom transfer from pzH to alkyl, alkoxyl, and peroxyl radicals reveals that BDEs are not a good predictor of the rates of this reaction. Hydride transfer to 1+ provides a concrete example of two-electron pcet that is hypothesized for the O—H bond cleavage step during catalysis of photosynthetic water oxidation.