Unconstrained Homooligomeric gamma-Peptides Show High Propensity for C-14 Helix Formation

Monosubstituted gamma(4)-residues (gamma(4)Leu, gamma(4)Ile, and gamma(4)Val) form helices even in short homooligomeric sequences. C-14 helix formation is established by X-ray diffraction in homooligomeric (gamma)(n) tetra-, hexa- and decapeptide sequences demonstrating the high propensity of gamma residues, with proteinogenic side chains, to adopt locally folded conformations.

Total internal reflection Raman spectroscopy of poly(alpha-olefin) oils in a lubricated contact

The rheology of a poly(alpha-olefin) base oil (PAO) in a sliding point contact has been investigated by total internal reflection (TIR) Raman spectroscopy. TIR Raman has the sensitivity to analyse nanometer-thick lubricant films in a tribological contact. The Raman signal generated from the sliding contact was used to determine the lubricant film thickness. The experimentally obtained film thicknesses were compared with theoretical calculations and a transition from Newtonian to non-Newtonian behaviour was observed at high shear rates. The Raman spectra showed no significant changes in the conformation of the PAO chains under the applied conditions of pressure and shear, but the polarisation dependence of the spectra revealed a preferred orientation of the hydrocarbon side chains in the shear-thinned region. Monolayers formed by a boundary lubricant, arachidic acid, dissolved in the PAO could be detected on the surfaces in the elastohydrodynamic regime.

Selenium in Diketopyrrolopyrrole-based Polymers: Influence on Electronic Properties and Charge Carrier Mobilities

Diketopyrrolopyrrole (DPP)-based pi-conjugated copolymers with thiophene have exceptionally high electron mobilities. This paper investigates electronic properties and charge carrier mobilities of selenophene containing analogues. Two new copolymers, with alternating thiophene DPP (TDPP) and selenophene DPP (SeDPP) units, were synthesized. Two side-chains, hexyl (Hex) and triethylene glycol (TEG) were employed, yielding polymers designated as PTDPPSeDPP-Hex and PTDPPSeDPP-TEG. Selenophene systems have smaller band gaps, with concomitant enhancement of the stability of the reduced state. For both polymers, ambipolar mobilities were observed in organic field-effect transistors (OFET). Grazing incidence X-ray diffraction (GIXD) data indicates preferential edge-on orientation of PTDPPSeDPP-TEG, which leads to superior charge transport properties of the TEG substituted polymer, as compared to its Hex analogue. Time-dependent-density functional theory (TDDFT) calculations corroborate the decrease in the optical band gap with the inclusion of selenophene. Ambipolar charge transport is rationalized by exceptionally wide conduction bands. Delta SCF calculations confirm the larger electron affinity, and therefore the greater stability, of the reduced form of the selenophene-containing DPP polymer in presence of chloroform.

Synthesis of 5,6-dihydro-4H-1,3-thiazine containing peptide mimics from N-(3-hydroxypropyl)thioamides and epimerization studies

The first synthesis of 1,3-thiazine fused peptide mimics is described from N-(3-hydroxypropyl)thioamides under MsCl/NEt3 conditions. The method is amenable to oligopeptidomimics with polar and apolar side chains. Substantial epimerization occurs at chiral C(2) exo methines in non-Pro fused mimics even under neutral conditions. H-1 NMR and crystal structure analyses indicate that the Thi analogues primarily associate with each other through intermolecular hydrogen bonds, involving the nitrogen of 1,3-thiazine and the N-H of the fused residue, which may be the basis for enamination-racemization process in these peptide mimics. (C) 2014 Elsevier Ltd. All rights reserved.

Temperature-Induced Reversible First-Order Single Crystal to Single Crystal Phase Transition in Boc-gamma(4)(R)Val-Val-OH: Interplay of Enthalpy and Entropy

Crystals of Boc-gamma y(4)(R)Val-Val-OH undergo a reversible first-order single crystal to single crystal phase transition at T-c approximate to 205 K from the orthorhombic space group P22(1)2(1) (Z' = 1) to the monoclinic space group P2(1) (Z' = 2) with a hysteresis of similar to 2.1 K. The low-temperature monoclinic form is best described as a nonmerohedral twin with similar to 50% contributions from its two components. The thermal behavior of the dipeptide crystals was characterized by differential scanning calorimetry experiments. Visual changes in birefringence of the sample during heating and cooling cycles on a hot-stage microscope with polarized light supported the phase transition. Variable-temperature unit cell check measurements from 300 to 100 K showed discontinuity in the volume and cell parameters near the transition temperature, supporting the first-order behavior. A detailed comparison of the room-temperature orthorhombic form with the low-temperature (100 K) monoclinic form revealed that the strong hydrogen-bonding motif is retained in both crystal systems, whereas the non-covalent interactions involving side chains of the dipeptide differ significantly, leading to a small change in molecular conformation in the monoclinic form as well as a small reorientation of the molecules along the ac plane. A rigid-body thermal motion analysis (translation, libration, screw; correlation of translation and libration) was performed to study the crystal entropy. The reversible nature of the phase transition is probably the result of an interplay between enthalpy and entropy: the low-temperature monoclinic form is enthalpically favored, whereas the room-temperature orthorhombic form is entropically favored.

Strategy for Enhancing the Dielectric Constant of Organic Semiconductors Without Sacrificing Charge Carrier Mobility and Solubility

Current organic semiconductors for organic photovoltaics (OPV) have relative dielectric constants (relative permittivities, epsilon(r)) in the range of 2-4. As a consequence, Coulombically bound electron-hole pairs (excitons) are produced upon absorption of light, giving rise to limited power conversion efficiencies. We introduce a strategy to enhance epsilon(r) of well-known donors and acceptors without breaking conjugation, degrading charge carrier mobility or altering the transport gap. The ability of ethylene glycol (EG) repeating units to rapidly reorient their dipoles with the charge redistributions in the environment was proven via density functional theory (DFT) calculations. Fullerene derivatives functionalized with triethylene glycol side chains were studied for the enhancement of epsilon(r) together with poly(p-phenylene vinylene) and diketo-pyrrolopyrrole based polymers functionalized with similar side chains. The polymers showed a doubling of epsilon(r) with respect to their reference polymers in identical backbone. Fullerene derivatives presented enhancements up to 6 compared with phenyl-C-61-butyric acid methyl ester (PCBM) as the reference. Importantly, the applied modifications did not affect the mobility of electrons and holes and provided excellent solubility in common organic solvents.

Narrow band gap conjugated polymer for improving the photovoltaic performance of P3HT:PCBM ternary blend bulk heterojunction solar cells

A new D-A structured conjugated polymer (PBDO-T-TDP) based on electron-rich benzo 1,2-b:4,5-b'] difuran (BDO) containing conjugated alkylthiophene side chains with an electron-deficient diketopyrrolopyrrole (DPP) derivative is designed and synthesized. The polymer shows a narrow band gap with broad UV-Visible absorption spectra, which is in contrast to that of the P3HT:PCBM binary blend. Furthermore, its energy levels can meet the energetic requirement of the cascaded energy levels of P3HT and PCBM. Therefore, PBDO-T-TDP is used as a sensitizer in P3HT: PCBM based BHJ solar cells and its effect on their photovoltaic properties was investigated by blending them together at various weight ratios. It is observed that the resulting ternary blend system exhibited a significant improvement in the device performance (similar to 3.10%) as compared with their binary ones (similar to 2.15%). Such an enhancement in the ternary blend system is ascribed to their balanced hole and electron mobility along with uniform distribution of PBDO-T-TDP in the blend system, as revealed by organic field effect transistors and AFM studies.

Periodically Grafted Amphiphilic Copolymers: Effects of Steric Crowding and Reversal of Amphiphilicity

Two series of periodically clickable polyesters were prepared; one of them carries alkylene segments along its backbone, whereas the other carries poly(ethylene glycol) (PEG) segments. These polyesters were clicked with either MPEG-350 azide or docosyl (C22) azide to yield periodically grafted amphiphilic copolymers (PGACs) carrying either flexible hydrophilic or crystallizable hydrophobic backbone segments. The immiscibility between hydrocarbon and PEG segments causes both of these systems to fold in either a zigzag or hairpin-like conformation; the hairpin-like conformation appears to be preferred when flexible PEG segments are present in the backbone. The folded chains further reorganize in the solid state to develop a lamellar morphology that permits the collocation of the PEG and hydrocarbon (HC) segments within alternate domains; evidence for the self-segregation was gained from DSC, SAXS, and AFM studies. SAXS studies revealed the formation of an extended lamellar structure, whereas AFM images showed uniform layered morphology with layer heights that matched reasonably well with the interlamellar spacing obtained from the SAXS study. Labeling One representative PGAC, carrying crystallizable long alkylene segments in the backbone and pendant PEG-350 side chains, with a small mole fraction of pyrene fluorophore permitted the examination of the conformational transition that occurs upon going from a good to a poor solvent; this single-chain folded conformation, we postulate, is the intermediate that organizes into the lamellar morphology.

Dissecting Ubiquitin Folding Using the Self-Organized Polymer Model

Folding of Ubiquitin (Ub), a functionally important protein found in eukaryotic organisms, is investigated at low and neutral pH at different temperatures using simulations of the coarse-grained self-organized-polymer model with side chains (SOP-SC). The melting temperatures (T-m's), identified with the peaks in the heat capacity curves, decrease as pH decreases, in qualitative agreement with experiments. The calculated radius of gyration, showing dramatic variations with pH, is in excellent agreement with scattering experiments. At T-m Ub folds in a two-state manner at low and neutral pH. Clustering analysis of the conformations sampled in equilibrium folding trajectories at T-m with multiple transitions between the folded and unfolded states, shows a network of metastable states connecting the native and unfolded states. At low and neutral pH, Ub folds with high probability through a preferred set of conformations resulting in a pH-dependent dominant folding pathway. Folding kinetics reveal that Ub assembly at low pH occurs by multiple pathways involving a combination of nucleation-collapse and diffusion collision mechanism. The mechanism by which Ub folds is dictated by the stability of the key secondary structural elements responsible for establishing long-range contacts and collapse of Ub. Nucleation collapse mechanism holds if the stability of these elements are marginal, as would be the case at elevated temperatures. If the lifetimes associated with these structured microdomains are on the order of hundreds of microseconds, then Ub folding follows the diffusion collision mechanism with intermediates, many of which coincide with those found in equilibrium. Folding at neutral pH is a sequential process with a populated intermediate resembling that sampled at equilibrium. The transition state structures, obtained using a P-fold analysis, are homogeneous and globular with most of the secondary and tertiary structures being native-like. Many of our findings for both the thermodynamics and kinetics of folding are not only in agreement with experiments but also provide missing details not resolvable in standard experiments. The key prediction that folding mechanism varies dramatically with pH is amenable to experimental tests.

Ab Initio Molecular Dynamics Simulations of Amino Acids in Aqueous Solutions: Estimating pK(a) Values from Metadynamics Sampling

Changes in the protonation and deprotonation of amino acid residues in proteins play a key role in many biological processes and pathways. Here, we report calculations of the free-energy profile for the protonation deprotonation reaction of the 20 canonical alpha amino acids in aqueous solutions using ab initio Car-Parrinello molecular dynamics simulations coupled with metad-ynamics sampling. We show here that the calculated change in free energy of the dissociation reaction provides estimates of the multiple pK(a) values of the amino acids that are in good agreement with experiment. We use the bond-length-dependent number of the protons coordinated to the hydroxyl oxygen of the carboxylic and the amine groups as the collective variables to explore the free-energy profiles of the Bronsted acid-base chemistry of amino acids in aqueous solutions. We ensure that the amino acid undergoing dissociation is solvated by at least three hydrations shells with all water molecules included in the simulations. The method works equally well for amino acids with neutral, acidic and basic side chains and provides estimates of the multiple pK(a) values with a mean relative error, with respect to experimental results, of 0.2 pK(a) units.

Crystal structure of a tripeptide containing aminocyclododecane carboxylic acid: a supramolecular twisted parallel -sheet in crystals

The crystal structure of a tripeptide Boc-Leu-Val-Ac(12)c-OMe (1) is determined, which incorporates a bulky 1-aminocyclododecane-1-carboxylic acid (Ac(12)c) side chain. The peptide adopts a semi-extended backbone conformation for Leu and Val residues, while the backbone torsion angles of the C-,C--dialkylated residue Ac(12)c are in the helical region of the Ramachandran map. The molecular packing of 1 revealed a unique supramolecular twisted parallel -sheet coiling into a helical architecture in crystals, with the bulky hydrophobic Ac(12)c side chains projecting outward the helical column. This arrangement resembles the packing of peptide helices in crystal structures. Although short oligopeptides often assemble as parallel or anti-parallel -sheet in crystals, twisted or helical -sheet formation has been observed in a few examples of dipeptide crystal structures. Peptide 1 presents the first example of a tripeptide showing twisted -sheet assembly in crystals. Copyright (c) 2016 European Peptide Society and John Wiley & Sons, Ltd.

Crystal structure of a tripeptide containing aminocyclododecane carboxylic acid: a supramolecular twisted parallel -sheet in crystals

The crystal structure of a tripeptide Boc-Leu-Val-Ac(12)c-OMe (1) is determined, which incorporates a bulky 1-aminocyclododecane-1-carboxylic acid (Ac(12)c) side chain. The peptide adopts a semi-extended backbone conformation for Leu and Val residues, while the backbone torsion angles of the C-,C--dialkylated residue Ac(12)c are in the helical region of the Ramachandran map. The molecular packing of 1 revealed a unique supramolecular twisted parallel -sheet coiling into a helical architecture in crystals, with the bulky hydrophobic Ac(12)c side chains projecting outward the helical column. This arrangement resembles the packing of peptide helices in crystal structures. Although short oligopeptides often assemble as parallel or anti-parallel -sheet in crystals, twisted or helical -sheet formation has been observed in a few examples of dipeptide crystal structures. Peptide 1 presents the first example of a tripeptide showing twisted -sheet assembly in crystals. Copyright (c) 2016 European Peptide Society and John Wiley & Sons, Ltd.

Three-dimensional self-assembly of brush block copolymers to photonic crystals

The development of Ring Opening Metathesis Polymerization has allowed the world of block copolymers to expand into brush block copolymers. Brush block copolymers consist of a polymer backbone with polymeric side chains, forcing the backbone to hold a stretched conformation and giving it a worm-like shape. These brush block copolymers have a number of advantages over tradition block copolymers, including faster self-assembly behavior, larger domain sizes, and much less entanglement. This makes them an ideal candidate in the development of a bottom-up approach to forming photonic crystals. Photonic crystals are periodic nanostructures that transmit and reflect only certain wavelengths of light, forming a band gap. These are used in a number of coatings and other optical uses. One and two dimensional photonic crystals are commercially available, though are often expensive and difficult to manufacture. Previous work has focused on the creation of one dimensional photonic crystals from brush block copolymers. In this thesis, I will focus on the synthesis and characterization of asymmetric brush block copolymers for self-assembly into two and three dimensional photonic crystals. Three series of brush block copolymers were made and characterized by Gel Permeation Chromatography and Nuclear Magnetic Resonance spectroscopy. They were then made into films through compressive thermal annealing and characterized by UV-Vis Spectroscopy and Scanning Electron Microscopy. Evidence of non-lamellar structures were seen, indicating the first reported creation of two or three dimensional photonic crystals from brush block copolymers.

Chemical-scale studies of G protein-coupled receptors and ligand-gated ion channels

This dissertation describes studies of G protein-coupled receptors (GPCRs) and ligand-gated ion channels (LGICs) using unnatural amino acid mutagenesis to gain high precision insights into the function of these important membrane proteins.

Chapter 2 considers the functional role of highly conserved proline residues within the transmembrane helices of the D2 dopamine GPCR. Through mutagenesis employing unnatural α-hydroxy acids, proline analogs, and N-methyl amino acids, we find that lack of backbone hydrogen bond donor ability is important to proline function. At one proline site we additionally find that a substituent on the proline backbone N is important to receptor function.

In Chapter 3, side chain conformation is probed by mutagenesis of GPCRs and the muscle-type nAChR. Specific side chain rearrangements of highly conserved residues have been proposed to accompany activation of these receptors. These rearrangements were probed using conformationally-biased β-substituted analogs of Trp and Phe and unnatural stereoisomers of Thr and Ile. We also modeled the conformational bias of the unnatural Trp and Phe analogs employed.

Chapters 4 and 5 examine details of ligand binding to nAChRs. Chapter 4 describes a study investigating the importance of hydrogen bonds between ligands and the complementary face of muscle-type and α4β4 nAChRs. A hydrogen bond involving the agonist appears to be important for ligand binding in the muscle-type receptor but not the α4β4 receptor.

Chapter 5 describes a study characterizing the binding of varenicline, an actively prescribed smoking cessation therapeutic, to the α7 nAChR. Additionally, binding interactions to the complementary face of the α7 binding site were examined for a small panel of agonists. We identified side chains important for binding large agonists such as varenicline, but dispensable for binding the small agonist ACh.

Chapter 6 describes efforts to image nAChRs site-specifically modified with a fluorophore by unnatural amino acid mutagenesis. While progress was hampered by high levels of fluorescent background, improvements to sample preparation and alternative strategies for fluorophore incorporation are described.

Chapter 7 describes efforts toward a fluorescence assay for G protein association with a GPCR, with the ultimate goal of probing key protein-protein interactions along the G protein/receptor interface. A wide range of fluorescent protein fusions were generated, expressed in Xenopus oocytes, and evaluated for their ability to associate with each other.

Hierarchical orientation of crystallinity by block-copolymer patterning and alignment in an electric field

Electron and hole conducting 10-nm-wide polymer morphologies hold great promise for organic electro-optical devices such as solar cells and light emitting diodes. The self-assembly of block-copolymers (BCPs) is often viewed as an efficient way to generate such materials. Here, a functional block copolymer that contains perylene bismide (PBI) side chains which can crystallize via π-π stacking to form an electron conducting microphase is patterned harnessing hierarchical electrohydrodynamic lithography (HEHL). HEHL film destabilization creates a hierarchical structure with three distinct length scales: (1) micrometer-sized polymer pillars, containing (2) a 10-nm BCP microphase morphology that is aligned perpendicular to the substrate surface and (3) on a molecular length scale (0.35-3 nm) PBI π-π-stacks traverse the HEHL-generated plugs in a continuous fashion. The good control over BCP and PBI alignment inside the generated vertical microstructures gives rise to liquid-crystal-like optical dichroism of the HEHL patterned films, and improves the electron conductivity across the film by 3 orders of magnitude. © 2013 American Chemical Society.