DNA-based optomechanical molecular motor

An azobenzene-capped DNA hairpin coupled to an AFM is presented as an optically triggered single-molecule motor. The photoinduced trans to cis isomerization of azobenzene affects both the overall length of the molecule and the ability of the DNA bases to hybridize. Using a combination of molecular dynamics simulations and free energy calculations the unfolding of both isomers along the O5'-O3' extension coordinate is monitored. The potentials of mean force (PMFs) along this coordinate indicate that there are two major differences induced by photoisomerization. The first is that the interbase hydrogen bond and stacking interactions are stable for a greater range of extensions in the trans system than in the cis system. The second difference is due to a decreased chain length of the cis isomer with respect to the trans isomer. These differences are exploited to extract work in optomechanical cycles. The disruption of the hairpin structure gives a maximum of 3.4 kcal mol(-1) of extractable work per cycle with an estimated maximum efficiency of 2.4%. Structure-function insights into the operation of this motor are provided, and the effect of the cantilever stiffness on the extractable work is characterized.     

Nanoscale clustering of carbohydrate thiols in mixed self-assembled monolayers on gold

Self-assembled monolayers (SAMs) bearing pendant carbohydrate functionality are frequently employed to tailor glycan-specific bioactivity onto gold substrates. The resulting glycoSAMs are valuable for interrogating glycan-mediated biological interactions via surface analytical techniques, microarrays, and label-free biosensors. GlycoSAM composition can be readily modified during assembly by using mixed solutions containing thiolated species, including carbohydrates, oligo(ethylene glycol) (OEG), and other inert moieties. This intrinsic tunability of the self-assembled system is frequently used to optimize bioavailability and antibiofouling properties of the resulting SAM. However, until now, our nanoscale understanding of the behavior of these mixed glycoSAMs has lacked detail. In this study, we examined the time-dependent clustering of mixed sugar + OEG glycoSAMs on ultraflat gold substrates. Composition and surface morphologic changes in the monolayers were analyzed by X-ray photoelectron spectroscopy (XPS) and atomic force microscopy (AFM), respectively. We provide evidence that the observed clustering is consistent with a phase separation process in which surface-bound glycans self-associate to form dense glycoclusters within the monolayer. These observations have significant implications for the construction of mixed glycoSAMs for use in biosensing and glycomics applications.     

Interlaboratory comparison of test results of an ordinal or nominal binary property: analysis of variation

Applications of a new statistical method Ordinal Analysis of Variance (ORDANOVA) for interlaboratory comparisons of measurement or test results of semi-quantitative (ordinal) and qualitative (binary) properties are discussed. ORDANOVA can be helpful for validation of measurement or test methods, proficiency testing of laboratories, development of reference materials with certified semi-quantitative and qualitative properties, that is, probably in every field where ANOVA is applied for quantitative properties. A statistics and criteria are proposed for performance assessment of laboratories active in semi-quantitative and qualitative testing and for other purposes of statistical analysis of such test results.     

Calculation of transition dipole moment in fluorescent proteins--towards efficient energy transfer

F?rster Resonance Energy Transfer (FRET) between fluorescent proteins (FPs) is widely used to construct fluorescent sensor proteins, to study intracellular protein-protein interactions and to monitor conformational changes in multidomain proteins. Although FRET depends strongly on the orientation of the transition dipole moments (TDMs) of the donor and acceptor fluorophores, this orientation dependence is currently not taken into account in FRET sensor design. Similarly, studies that use FRET to derive structural constrains typically assume a κ(2) of 2/3 or use the TDM of green fluorescent protein, as this is the only FP for which the TDM has been determined experimentally. Here we used time-dependent density functional theory (TD-DFT) methods to calculate the TDM for a comprehensive list of commonly used fluorescent proteins. The method was validated against higher levels of calculation. Validation with model compounds and the experimentally determined TDM of GFP shows that the TDM is mostly determined by the structure of the π-conjugated fluorophore and is insensitive to non-conjugated side chains or the protein surrounding. Our calculations not only provide TDM for most of the currently used FPs, but also suggest an empirical rule that can be used to obtain the TDMs for newly developed fluorescent proteins in the future.     

Controlling the rate of electron transfer between a quantum dot and a tri-ruthenium molecular cluster by tuning the chemistry of the interface

Ultrafast transient absorption measurements reveal that the rate of photoinduced electron transfer (PET) from colloidal CdSe quantum dots (QDs) to oxo-centered triruthenium clusters (Ru(3)O) depends on the structure of the chemical headgroup by which the Ru(3)O clusters adsorb to the QDs. Complexes comprising QDs and Ru(3)O clusters adsorbed through a pyridine-4-carboxylic acid ligand (nic-Ru(3)O) have an intrinsic PET rate constant of (4.9 ± 0.9) × 10(9) s(-1) whereas complexes comprising QDs and Ru(3)O clusters adsorbed through a 4-mercaptopyridine ligand (thiol-Ru(3)O) have an intrinsic PET rate constant of (36 ± 7) × 10(9) s(-1). Cyclic voltammetry measurements of nic-Ru(3)O and thiol-Ru(3)O yield reduction potentials vs. Ag/AgCl of -0.93 V for both clusters, and density functional theory calculations of the nic-Ru(3)O and thiol-Ru(3)O clusters yield internal reorganization energies for the cluster radical anion of -0.17 eV and -0.19 eV, respectively. The small differences in driving force and reorganization energy between the two complexes rule out these parameters as possible explanations for the factor-of-seven difference in the rate constants for PET. The difference in the observed rates of PET for the two complexes is therefore attributable to a difference in donor-acceptor electronic coupling, which, according to electronic structure calculations, is modulated by the torsional angle between the Ru(3)O core of the cluster and the functionalized pyridine ligand that bridges the cluster to the QD surface.     

Phenacyl–Thiophene and Quinone Semiconductors Designed for Solution Processability and Air‐Stability in High Mobility n‐Channel Field‐Effect Transistors

Electron‐transporting organic semiconductors (n‐channel) for field‐effect transistors (FETs) that are processable in common organic solvents or exhibit air‐stable operation are rare. This investigation addresses both these challenges through rational molecular design and computational predictions of n‐channel FET air‐stability. A series of seven phenacyl–thiophene‐based materials are reported incorporating systematic variations in molecular structure and reduction potential. These compounds are as follows: 5,5′′′‐bis(perfluorophenylcarbonyl)‐2,2′:5′,‐ 2′′:5′′,2′′′‐quaterthiophene ( 1 ), 5,5′′′‐bis(phenacyl)‐2,2′:5′,2′′: 5′′,2′′′‐quaterthiophene ( 2 ), poly[5,5′′′‐(perfluorophenac‐2‐yl)‐4′,4′′‐dioctyl‐2,2′:5′,2′′:5′′,2′′′‐quaterthiophene) ( 3 ), 5,5′′′‐bis(perfluorophenacyl)‐4,4′′′‐dioctyl‐2,2′:5′,2′′:5′′,2′′′‐quaterthiophene ( 4 ), 2,7‐bis((5‐perfluorophenacyl)thiophen‐2‐yl)‐9,10‐phenanthrenequinone ( 5 ), 2,7‐bis[(5‐phenacyl)thiophen‐2‐yl]‐9,10‐phenanthrenequinone ( 6 ), and 2,7‐bis(thiophen‐2‐yl)‐9,10‐phenanthrenequinone, ( 7 ). Optical and electrochemical data reveal that phenacyl functionalization significantly depresses the LUMO energies, and introduction of the quinone fragment results in even greater LUMO stabilization. FET measurements reveal that the films of materials 1 , 3 , 5 , and 6 exhibit n‐channel activity. Notably, oligomer 1 exhibits one of the highest μ_e (up to ≈0.3 cm² V^?1 s^?1) values reported to date for a solution‐cast organic semiconductor; one of the first n‐channel polymers, 3 , exhibits μ_e≈10^?6 cm² V^?1 s^?1 in spin‐cast films (μ_e=0.02 cm² V^?1 s^?1 for drop‐cast 1 : 3 blend films); and rare air‐stable n‐channel material 5 exhibits n‐channel FET operation with μ_e=0.015 cm² V^?1 s^?1, while maintaining a large I_on:off=10⁶ for a period greater than one year in air. The crystal structures of 1 and 2 reveal close herringbone interplanar π‐stacking distances (3.50 and 3.43 Å, respectively), whereas the structure of the model quinone compound, 7 , exhibits 3.48 Å cofacial π‐stacking in a slipped, donor‐acceptor motif.     

Erratum to “The primes contain arbitrarily long polynomial progressions”

In our previous paper “The primes contain arbitrarily long polynomial progressions” [Acta Math., 201 (2008), 213–305] there were some minor errors in our definition of the polynomial forms and polynomial correlation conditions, which is unreasonably strong as written due to the overly loose bound on the degree of the polynomials involved. In this erratum we repair this issue by capping the degree of the polynomials more strongly, and adjusting some other relevant components of the argument accordingly.     

Triplet topology of self-assembled zinc porphyrin-pyridylfullerene complex

This work extends a recent EPR study on light-driven electron and energy transfer in a self-assembled zinc porphyrin-pyridylfullerene (ZnP-PyrF) complex. We report on a triplet line shape analysis of the photoexcited PyrF monomer and the ZnP-PyrF complex dissolved in isotropic and anisotropic matrixes of different polarity, namely, toluene, tetrahydrofuran (THF), and the nematic liquid crystals (LCs), E-7 and ZLI-4389. The line shape of the unbound *(3)PyrF obtained in both isotropic matrixes exhibits triplet parameters similar to those obtained for other monoadducts of C(60) under similar experimental conditions. On the other hand, 8(3)PyrF oriented in the LCs shows a complicated line shape, which is attributed to two conformers: (a) an axial dominant (85%) configuration characterized by triplet parameters, similar to those obtained in the isotropic matrixes and (b) a bent configuration associated with spin density localized about the poles accompanied by sign reversal of the ZFS parameter D of the *(3)C(60) moiety. Further, since in both LCs the ZnP-PyrF complex mainly exhibits a conformation with axial symmetry, the differences between the electron and the energy transfer routes in each LC are attributed to their different polarity. This study reflects the strength of LC matrixes to serve as a topological tool, enabling us to determine the conformers' distribution and to differentiate between electron and energy transfer routes.     

Protic ionic liquids: solvents with tunable phase behavior and physicochemical properties

The phase behavior, including glass, devitrification, solid crystal melting, and liquid boiling transitions, and physicochemical properties, including density, refractive index, viscosity, conductivity, and air-liquid surface tension, of a series of 25 protic ionic liquids and protic fused salts are presented along with structure-property comparisons. The protic fused salts were mostly liquid at room temperature, and many exhibited a glass transition occurring at low temperatures between -114 and -44 degrees C, and high fragility, with many having low viscosities, down to as low as 17 mPa.s at 25 degrees C, and ionic conductivities up to 43.8 S/cm at 25 degrees C. These protic solvents are easily prepared through the stoichiometric combination of a primary amine and Br?nsted acid. They have poor ionic behavior when compared to the far more studied aprotic ionic liquids. However, some of the other physicochemical properties possessed by these solvents are highly promising and it is anticipated that these, or analogous protic solvents, will find applications beyond those already identified for aprotic ionic liquids. This series of protic fused salts was employed to determine the effect of structural changes on the physicochemical properties, including the effect of hydroxyl groups, increasing alkyl chain lengths, branching, and the differences between inorganic and organic anions. It was found that simple structural modifications provide a mechanism to manipulate, over a wide range, the temperature at which phase transitions occur and to specifically tailor physicochemical properties for potential end-use applications.     

Geometry dependent features of optically induced forces between silver nanoparticles

A recently devised, discrete-dipole approximation (DDA) based method for computing optical forces is used to explore geometry dependent aspects of the light induced interactions between pairs of silver nanoparticles, including the influence of particle shape, relative positioning of the particles, and incident field orientation. The interactions are observed to have a large degree of generic character, independent of the details of the particle shape. The size of the optical forces is also compared to estimates for the van der Waals forces, and the results are used to assess the potential importance of radiation forces on recent experiments demonstrating photoinduced self-assembly of triangular silver nanoprisms.