The molecular structure, photochemistry, and device physics of conjugated polymers have been investigated by single-molecule spectroscopy (SMS), using the unique ability of this technique to unravel complex spectra and dynamics. Surprisingly efficient and directional electronic energy funneling was observed for conjugated polymer molecules due to highly ordered conformations. Furthermore, recent studies on the SMS of conjugated polymers embedded in electronic devices demonstrate that SMS is a powerful tool for studying the photophysics and charge-transfer processes of conjugated polymers, giving new insights into the complex interactions among excited and charged species that exist in a device environment.

Programmed -1 ribosomal frameshifting (-1 RF) is an essential regulating mechanism of translation used by SARS-CoV (severe acute respiratory syndrome coronavirus) to synthesize the key replicative proteins encoded by two overlapping open reading frames. The integrity of RNA pseudoknot stability and structure in the -1 RF site is important for efficient -1 RF. Thus, small molecules interacting with high affinity and selectivity with the RNA pseudoknot in the -1 RF site of SARS-CoV (SARS-pseudoknot) would disrupt -1 RF and be fatal to viral infectivity and production. To discover ligands for the SARS-pseudoknot by virtual screening, we constructed a 3D structural model of the SARS-pseudoknot and conducted a computational screening of the chemical database. After virtual screening of about 80,000 compounds against the SARS-pseudoknot structure, high-ranked compounds were selected and their activities were examined by in vitro and cell-based -1 RF assay. We successfully identified a novel ligand 43 that dramatically inhibits the -1 RF of SARS-CoV. This antiframeshift agent is an interesting lead for the design of novel antiviral agents against SARS-CoV.

By utilizing oligonucleotide-modified Au nanoparticles encoded with sequences that act as biobarcodes, one can screen for multiple target polyvalent proteins simultaneously in one solution. This novel concept was demonstrated with two types of detection formats, a homogeneous assay and one based on oligonucleotide microarrays. With such an approach, one can prepare an extraordinarily large number of barcodes from synthetically accessible oligonucleotides (e.g., a 12-mer sequence offers 4(12) possible barcodes).

The structural properties of DNA-linked gold nanoparticle materials were examined using synchrotron smallangle X-ray scattering. The materials are composed of 12 or 19 nm diameter gold particles modified with 3′ or 5′ alkylthiol-capped 12-base oligonucleotides and linked with complementary oligonucleotides. Structure factors were derived from scattering intensities, and nearest-neighbor distances were determined from the primary peak in the pair distance distribution functions. The separation between particles was found to increase linearly with DNA linker length for 24, 48, and 72 base pair linkers. For assemblies formed in 0.3 M NaCl, 10 mM phosphate buffer solution, the increment in the interparticle distance was found to be 2.5 Å per base pair. Particle separations in assemblies at lower electrolyte concentration were larger, indicating that dielectric screening modulates the interactions. The effect of DNA sequence was studied with poly-adenine or polythymine spacer sequences incorporated between the alkylthiol and recognition sequences. The assemblies with poly-adenine spacer sequences showed significantly shorter particle separations than the assemblies involving poly-thymine spacers, a consequence of their different affinities for the gold surface. While the scattering data do not display evidence of long-range order, pair distance distribution functions indicate the presence of short-range order.

Doped carbon-based systems have been extensively studied over the past decade as active electrocatalysts for both the two-electron (2e-) and four-electron (4e-) oxygen reduction reaction (ORR). However, the mechanisms for ORR are generally poorly understood. Here we report an extensive experimental and first-principles theoretical study of the ORR at nitrogen-doped reduced graphene oxides (NrGO). We synthesize three distinct NrGO catalysts and investigate their chemical and structural properties in detail via X-ray photoelectron spectroscopy, infrared and Raman spectroscopy, high-resolution transmission electron microscopy and thin-film electrical conductivity. ORR experiments include the pH dependences of 2e-versus 4e-ORR selectivity, ORR onset potentials, Tafel slopes and H/D kinetic isotope effects. These experiments show very different ORR behavior for the three catalysts, both in terms of selectivity and the underlying mechanism which proceeds either via coupled proton-electron transfers (CPETs) or non-CPETs. Reasonable structural models developed from DFT rationalize this behavior. The key determinant between CPET vs. non-CPET mechanisms is the electron density at the Fermi level under operating ORR conditions. Regardless of the reaction mechanism or electrolyte pH, however, we identify the ORR active sites as sp2 carbons that are located next to oxide regions. This assignment highlights the importance of oxygen functional groups, while details of (modest) N-doping may still affect the overall catalytic activity, and likely also the selectivity, by modifying the general chemical environment around the active site. File list (2) download file view on ChemRxiv NrGO_ACS_Catal_updated.pdf (3.76 MiB) download file view on ChemRxiv NrGO_SI_ACS_Catal_updated.pdf (6.66 MiB)