Effect of the side-chain-distribution density on the single-conjugated-polymer-chain conformation

The spatial arrangement of the side chains of conjugated polymer backbones has critical effects on the morphology and electronic and photophysical properties of the corresponding bulk films. The effect of the side-chain-distribution density on the conformation at the isolated single-polymer-chain level was investigated with regiorandom (rra-) poly(3-hexylthiophene) (P3HT) and poly(3-hexyl-2,5-thienylene vinylene) (P3HTV). Although pure P3HTV films are known to have low fluorescence quantum efficiencies, we observed a considerable increase in fluorescence intensity by dispersing P3HTV in poly(methyl methacrylate) (PMMA), which enabled a single-molecule spectroscopy investigation. With single-molecule fluorescence excitation polarization spectroscopy, we found that rra-P3HTV single molecules form highly ordered conformations. In contrast, rra-P3HT single molecules, display a wide variety of different conformations from isotropic to highly ordered, were observed. The experimental results are supported by extensive molecular dynamics simulations, which reveal that the reduced side-chain-distribution density, that is, the spaced-out side-chain substitution pattern, in rra-P3HTV favors more ordered conformations compared to rra-P3HT. Our results demonstrate that the distribution of side chains strongly affects the polymer-chain conformation, even at the single-molecule level, an aspect that has important implications when interpreting the macroscopic interchain packing structure exhibited by bulk polymer films.

A simple atomic-level hydrophobicity scale reveals protein interfacial structure

Many amino acid residue hydrophobicity scales have been created in an effort to better understand and rapidly characterize water-protein interactions based only on protein structure and sequence. There is surprisingly low consistency in the ranking of residue hydrophobicity between scales, and their ability to provide insightful characterization varies substantially across subject proteins. All current scales characterize hydrophobicity based on entire amino acid residue units. We introduce a simple binary but atomic-level hydrophobicity scale that allows for the classification of polar and non-polar moieties within single residues, including backbone atoms. This simple scale is first shown to capture the anticipated hydrophobic character for those whole residues that align in classification among most scales. Examination of a set of protein binding interfaces establishes good agreement between residue-based and atomic-level descriptions of hydrophobicity for five residues, while the remaining residues produce discrepancies. We then show that the atomistic scale properly classifies the hydrophobicity of functionally important regions where residue-based scales fail. To illustrate the utility of the new approach, we show that the atomic-level scale rationalizes the hydration of two hydrophobic pockets and the presence of a void in a third pocket within a single protein and that it appropriately classifies all of the functionally important hydrophilic sites within two otherwise hydrophobic pores. We suggest that an atomic level of detail is, in general, necessary for the reliable depiction of hydrophobicity for all protein surfaces. The present formulation can be implemented simply in a manner no more complex than current residue-based approaches.

Transformation of the electrical characteristics of graphene field-effect transistors with fluoropolymer

We report on the improvement of the electronic characteristics of monolayer graphene field-effect transistors (FETs) by an interacting capping layer of a suitable fluoropolymer. Capping of monolayer graphene FETs with CYTOP improved the on-off current ratio from 5 to 10 as well as increased the field-effect mobility by as much as a factor of 2 compared to plain graphene FETs. Favorable shifts in the Dirac voltage toward zero with shift magnitudes in excess of 60 V are observed. The residual carrier concentration is reduced to ~2.8 × 10(11) cm(-2). Removal of the fluoropolymer from graphene FETs results in a return to the initial electronic properties before depositing CYTOP. This suggests that weak, reversible electronic perturbation of graphene by the fluoropolymer favorably tune the electrical characteristics of graphene, and we hypothesize that the origin of this improvement is in the strongly polar nature of the C-F chemical bonds that self-organize upon heat treatment. We demonstrate a general method to favorably restore or transform the electrical characteristics of graphene FETs, which will open up new applications.

Hot charge-transfer excitons set the time limit for charge separation at donor/acceptor interfaces in organic photovoltaics

Photocurrent generation in organic photovoltaics (OPVs) relies on the dissociation of excitons into free electrons and holes at donor/acceptor heterointerfaces. The low dielectric constant of organic semiconductors leads to strong Coulomb interactions between electron-hole pairs that should in principle oppose the generation of free charges. The exact mechanism by which electrons and holes overcome this Coulomb trapping is still unsolved, but increasing evidence points to the critical role of hot charge-transfer (CT) excitons in assisting this process. Here we provide a real-time view of hot CT exciton formation and relaxation using femtosecond nonlinear optical spectroscopies and non-adiabatic mixed quantum mechanics/molecular mechanics simulations in the phthalocyanine-fullerene model OPV system. For initial excitation on phthalocyanine, hot CT excitons are formed in 10(-13) s, followed by relaxation to lower energies and shorter electron-hole distances on a 10(-12) s timescale. This hot CT exciton cooling process and collapse of charge separation sets the fundamental time limit for competitive charge separation channels that lead to efficient photocurrent generation.

Thermal stability of hydrophobic helical oligomers: a lattice simulation study in explicit water

We investigate the thermal stability of helical hydrophobic oligomers using a three-dimensional, water-explicit lattice model and the Wang-Landau Monte Carlo method. The degree of oligomer helicity is controlled by the parameter ε(mm) < 0, which mimics monomer-monomer hydrogen bond interactions leading to the formation of helical turns in atomistic proteins. We vary |ε(mm)| between 0 and 4.5 kcal/mol and therefore investigate systems ranging from flexible homopolymers (i.e., those with no secondary structure) to helical oligomers that are stable over a broad range of temperatures. We find that systems with |ε(mm)| ≤ 2.0 kcal/mol exhibit a broad thermal unfolding transition at high temperature, leading to an ensemble of random coils. In contrast, the structure of conformations involved in a second, low-temperature, transition is strongly dependent on |ε(mm)|. Weakly helical oligomers are observed when |ε(mm)| ≤ 1.0 kcal/mol and exhibit a low-temperature, cold-unfolding-like transition to an ensemble of strongly water-penetrated globular conformations. For higher |ε(mm)| (1.7 kcal/mol ≤ |ε(mm)| ≤ 2.0 kcal/mol), cold unfolding is suppressed, and the low-temperature conformational transition becomes a "crystallization", in which a "molten" helix is transformed into a defect-free helix. The molten helix preserves ≥50% of the helical contacts observed in the "crystal" at a lower temperature. When |ε(mm)| = 4.5 kcal/mol, we find that conformational transitions are largely suppressed within the range of temperatures investigated.

Role of hydrophobic hydration in protein stability: a 3D water-explicit protein model exhibiting cold and heat denaturation

We investigate the microscopic mechanism of cold and heat denaturation using a 3D lattice model of a hydrated protein in which water is represented explicitly. The water model, which incorporates directional bonding and tetrahedral geometry, captures many aspects of water thermodynamics and properly describes hydrophobic hydration around apolar solutes because the hydrogen bonding rules in the model were gleaned from off-lattice atomistic simulations of water around representative protein structures. By incorporating local chain stiffness in the protein model, a homopolymer can fold into a β-hairpin. It is shown that the homopolymer can be folded by either attractive interactions between the monomers or as a direct consequence of the entropic cost of forming interfacial hydrogen bonds in the solvent. However, cold denaturation is not observed if the collapse transition is induced by intramolecular attractions. We further find that it is the changes in hydrophobic hydration with decreasing temperature that drive cold unfolding and that the overall process is enthalpically driven, whereas heat denaturation is entropically driven.

Predicting cavity formation free energy: how far is the Gaussian approximation valid?

We examine the range of validity of the Gaussian model for various water-like liquids whose intermolecular potentials differ from SPC/E water, to provide insight into the temperature dependence of the hydrophobic effect for small hard sphere solutes. We find that low compressibility liquids that have more close-packed network structures show much larger deviations from Gaussian fluctuations for low or zero occupancies relative to more compressible fluids with more open networks. Water appears to be a unique molecular fluid in possessing equilibrium density fluctuations that are faithfully described by the Gaussian theory. We ascribe this success to the fact, shown here, that the orientational correlations near a small hard sphere solute involve remarkably little reorganization from the bulk, which is a consequence of water's low solvent reorganization enthalpy and entropy.

Paul F. Barbara (1953–2010)

A chemical physicist who developed methods to study elementary reactions also explored the dynamics of complex polymers and biomolecules.

Dependence of electrochemical and electrogenerated chemiluminescence properties on the structure of BODIPY dyes. Unusually large separation between sequential electron transfers

Electrochemistry and electrogenerated chemiluminescence (ECL) of selected substituted BODIPY (4,4-difluoro-4-bora-3a,4a-diaza-s-indacene) dyes have been studied. The location and nature of substituents on positions 1-8 are important in predicting the behavior, and especially the stability, of the radical ions formed on electron transfer. Dyes with unsubstituted positions 2, 6, and 8 show a kinetic contribution to both oxidation and reduction. Dyes with only unsubstituted positions 2 and 6 and a substituted 8 position show chemically reversible reduction but irreversible oxidation. Unsubstituted positions 2 and 6 tend to show dimer formation on oxidation. Completely substituted dyes show nernstian oxidation and reduction. Oxidation and reduction studies of simple BODIPY dyes show an unusually large separation between the first and second reduction peaks and also the first and second oxidation peaks, of about 1.1 V, which is very different from that observed for polycyclic hydrocarbons and other heteroaromatic compounds, where the spacing is usually about 0.5 V. Electronic structure calculations confirmed this behavior, and this effect is attributed to a greater electronic energy required to withdraw or add a second electron and a lower relative solvation energy for the dianion or dication compared with those of the polycyclic hydrocarbons. ECL was generated for all compounds either by annihilation or by using a co-reactant.

Molecular origins of fluorocarbon hydrophobicity

We have undertaken atomistic molecular simulations to systematically determine the structural contributions to the hydrophobicity of fluorinated solutes and surfaces compared to the corresponding hydrocarbon, yielding a unified explanation for these phenomena. We have transformed a short chain alkane, n-octane, to n-perfluorooctane in stages. The free-energy changes and the entropic components calculated for each transformation stage yield considerable insight into the relevant physics. To evaluate the effect of a surface, we have also conducted contact-angle simulations of water on self-assembled monolayers of hydrocarbon and fluorocarbon thiols. Our results, which are consistent with experimental observations, indicate that the hydrophobicity of the fluorocarbon, whether the interaction with water is as solute or as surface, is due to its "fatness." In solution, the extra work of cavity formation to accommodate a fluorocarbon, compared to a hydrocarbon, is not offset by enhanced energetic interactions with water. The enhanced hydrophobicity of fluorinated surfaces arises because fluorocarbons pack less densely on surfaces leading to poorer van der Waals interactions with water. We find that interaction of water with a hydrophobic solute/surface is primarily a function of van der Waals interactions and is substantially independent of electrostatic interactions. This independence is primarily due to the strong tendency of water at room temperature to maintain its hydrogen bonding network structure at an interface lacking hydrophilic sites.