Reduced basis set for the gold atom in cluster complexes

To extend the metal cluster size used in interfacing between bulk metals and molecules in ab initio studies of molecular electronics and chemisorption, a reduced size atomic orbital basis set for the gold atom has been generated. Based on the SKBJ relativistic effective core potential set, the three component 5d Gaussian orbital basis set is completely contracted. Comparisons between the full and reduced basis set in Au atom clusters and cluster complexes for geometry, bond distances, dipole moments, atomic charges, spin, bond dissociation energies, lowest energy harmonic frequencies, electron affinities, ionization energies, and density of states distributions show the contracted set to be a viable replacement for the full basis set. This result is obtained using both the B3LYP and BPW91 exchange-correlation potentials in density functional theory.     

Electron tunneling through sensitizer wires bound to proteins

We report a quantitative theoretical analysis of long-range electron transfer through sensitizer wires bound in the active-site channel of cytochrome P450cam. Each sensitizer wire consists of a substrate group with high binding affinity for the enzyme active site connected to a ruthenium-diimine through a bridging aliphatic or aromatic chain. Experiments have revealed a dramatic dependence of electron transfer rates on the chemical composition of both the bridging group and the substrate. Using combined molecular dynamics simulations and electronic coupling calculations, we show that electron tunneling through perfluorinated aromatic bridges is promoted by enhanced superexchange coupling through virtual reduced states. In contrast, electron flow through aliphatic bridges occurs by hole-mediated superexchange. We have found that a small number of wire conformations with strong donor–acceptor couplings can account for the observed electron tunneling rates for sensitizer wires terminated with either ethylbenzene or adamantane. In these instances, the rate is dependent not only on electronic coupling of the donor and acceptor but also on the nuclear motion of the sensitizer wire, necessitating the calculation of average rates over the course of a molecular dynamics simulation. These calculations along with related recent findings have made it possible to analyze the results of many other sensitizer-wire experiments that in turn point to new directions in our attempts to observe reactive intermediates in the catalytic cycles of P450 and other heme enzymes.     

Book Review

Journal of Nanoparticle Research -     

Preparation and hydrophobizing properties of carboxylic acid <Emphasis Type="Italic">N</Emphasis>-[3-(dimethylamino)propyl]amide hydrochlorides

Carboxylic acid N-[3-(dimethylamino)propyl]amides were prepared in 90–95% yield by the reaction of carboxylic acid esters with N,N-dimethyl-1,3-diaminopropane in the presence of zeolites as catalysts. Hydrochlorides of these amides show promise as cationic surfactants for hydrophobization of the bottomhole formation zone of oil fields.     

Tunneling currents that increase with molecular elongation

We present a model molecular system with an unintuitive transport-extension behavior in which the tunneling current increases with forced molecular elongation. The molecule consists of two complementary aromatic units (1,4-anthracenedione and 1,4-anthracenediol) hinged via two ether chains and attached to gold electrodes through thiol-terminated alkenes. The transport properties of the molecule as it is mechanically elongated in a single-molecule pulling setting are computationally investigated using a combination of equilibrium molecular dynamics simulations of the pulling with gDFTB computations of the transport properties in the Landauer limit. Contrary to the usual exponential decay of tunneling currents with increasing molecular length, the simulations indicate that upon elongation electronic transport along the molecule increases 10-fold. The structural origin of this inverted trend in the transport is elucidated via a local current analysis that reveals the dual role played by H-bonds in both stabilizing π-stacking for selected extensions and introducing additional electronic couplings between the complementary aromatic rings that also enhance tunneling currents across the molecule. The simulations illustrate an inverted electromechanical single-molecule switch that is based on a novel class of transport-extension behavior that can be achieved via mechanical manipulation and highlight the remarkable sensitivity of conductance measurements to the molecular conformation.     

Guidelines for choosing molecular "alligator clip" binding motifs in electron transport devices

We employ a one-electron, tight-binding model of an electrode-molecule-electrode junction to explore the fundamental relationship between adsorption geometry and electron transport, producing exact results (within this model). By varying the chemisorption location (e.g., atop a surface atom or in a hollow site between surface atoms) and the molecule-electrode coupling, we find that the largest currents are realized when the molecule (i) is highly coordinated by the surface and (ii) has favorable overlap with electrode states near the Fermi level. We also show the importance of electrode-induced molecular level shifting for certain adsorption geometries, which can cause molecular levels far from the Fermi level to conduct better than those near the Fermi level. Since all of these factors are greatly influenced by the chemical moiety used to link the molecule to an electrode, these results present a set of guidelines to help choose "alligator clips" for molecular electronic devices.     

Multiplexed inkjet functionalization of silicon photonic biosensors

The transformative potential of silicon photonics for chip-scale biosensing is limited primarily by the inability to selectively functionalize and exploit the extraordinary density of integrated optical devices on this platform. Silicon biosensors, such as the microring resonator, can be routinely fabricated to occupy a footprint of less than 50 × 50 μm; however, chemically addressing individual devices has proven to be a significant challenge due to their small size and alignment requirements. Herein, we describe a non-contact piezoelectric (inkjet) method for the rapid and efficient printing of bioactive proteins, glycoproteins and neoglycoconjugates onto a high-density silicon microring resonator biosensor array. This approach demonstrates the scalable fabrication of multiplexed silicon photonic biosensors for lab-on-a-chip applications, and is further applicable to the functionalization of any semiconductor-based biosensor chip.     

Surface chemical composition and fibrinogen adsorption-retention of fluoropolymer films deposited from an RF glow discharge

Fluoropolymer films have been deposited in the glow and afterglow regions of radio frequency glow discharges fed with C₂F₆−H₂ mixtures. Structure, growth rate, composition, and wettability of the films have been investigated by means of atomic force microscopy, electron spectroscopy for chemical analysis, secondary ion mass spectrometry, and water contact angle measurements.¹²⁵I labeled baboon fibrinogen in baboon plasma has been used to study the adsorption of the protein onto the films. Protein retention, i.e., the binding affinity of the adsorbed protein, has been examined by elution with a sodium dodecyl sulfate solution. Adsorption and retention of fibrinogen were correlated using multivariate statistical methods with the wettability, the degree of film fluorination, and the CF _x (1≤x≤3) group distribution of the coatings. This correlation identified the influence of each variable on the adsorption and retention of fibrinogen onto these substrates. These variables or surface properties can be easily balanced by properly tuning the experimental conditions of the glow discharge deposition process.     

Fourier analysis,correlation functions and nonadiabatic electron transfer: Wavepackets and exact representations

Summary We investigate the validity of several common approximations in the analysis of nonadiabatic intramolecular electron transfer rate constants. Utilizing the Fourier representation of the golden rule form, we study the evolution of the vibrational correlation function that represents the density-of-states-weighted Franck-Condon factor. In particular, we test the validity of the perturbation theoretic golden rule form and of the Gaussian wavepacket representation for the vibrational wavefunctions against numerically exact quantum mechanical propagations. Although specific cases are found in which both of these break down, for a wide range of conditions (including anharmonic behavior and frequency changes), both the Gaussian wavepacket representation and the golden rule are excellent approximations.