Dynamic Nuclear Polarization in Suspensions Consisting of Xylene Isomers and Asphaltene Extracted from MC‐800 Liquid Asphalt

Overhauser effect type dynamic nuclear polarization experiments were performed to study suspensions of asphaltene in the xylene isomers (o‐, m‐, p‐) at a low magnetic field of 1.44 mT and three different temperatures (15, 25, and 35°C). The asphaltene was extracted from MC‐800 liquid asphalt. Intermolecular spin‐spin interactions occur between nuclear spins of hydrogen in the solvent medium and the free electron spins in the asphaltene micelles. The electron paramagnetic resonance spectrum of the asphaltene was obtained and the saturation experiments were applied to the samples prepared in vacuum. For all media, the dipole‐dipole interaction is predominant due to the negative signal enhancements. In all temperatures, the ultimate enhancement is the smallest for the p‐xylene solvent medium which has the lowest electrical dipole moment. The normalized low frequency relaxation components were calculated for 25°C, and the behavior of the nuclear‐electron coupling parameter according to this component is in agreement with the other works in the literature.     

Conformational structure of peptides containing dehydroalanine: Formation of β‐bend ribbon structure

α,β‐Unsaturated amino acids (dehydroamino acids) have been found in naturally occurring antibiotics of microbial origin and in some proteins. Due to the presence of the C_αC_β double bond, the dehydroamino acids influence the main‐chain and the side‐chain conformations. The lowest‐energy conformational state of the model tripeptides, Ac–X–ΔAla–NHMe, (X=Ala, Val, Leu, Abu, or Phe) corresponds to ϕ₁=−30°, ψ₁=120° and ϕ₂=ψ₂=30°. This structure is stabilized by the hydrogen bond between CO of the acetyl group and the NH of the amide group, resulting in the formation of a 10‐membered ring. In the model heptapeptide containing ΔAla at alternate position with Ala, Abu, and Leu, the lowest‐energy conformation corresponds to ϕ=−30° and ψ=120° for all the Ala, Abu, and Leu residues and ϕ=ψ=30° for all ΔAla residues. A graphical view of the molecule in this conformation reveals the formation of three hydrogen bonds involving the CO moiety of the ith residue and the NH moiety of the i+3th residue, resulting in a 10‐membered ring formation. In this structure, only alternate peptide bonds are involved in the intramolecular hydrogen‐bond formation unlike the helices and it has been named the β‐bend ribbon structure. The helical structures were predicted to be the most stable structures in the heptapeptide Ac–(Aib–ΔAla)₃–NHMe with ϕ=±30°, ψ=±60° for Aib residues and ϕ=ψ=±30° for ΔAla residues. The computational results reveal that the ΔAla residue does not induce an inverse γ‐turn in the preceding residue. It is the competitive interaction of small solvent molecules with the hydrogen‐bonding sites of the peptide which gives rise to the formation of an inverse γ‐turn (ϕ₁=−54°, ψ₁=82°; ϕ₂=44°, ψ₂=3°) in the preceding residue to ΔAla. The computational studies for the positional preference of ΔAla in the peptide containing one ΔAla and nine Ala residues reveals the formation of a 3₁₀ helical structure in all the cases with the terminal preferences for ΔAla, consistent with the position of ΔAla in the natural antibiotics. The extended structures is found to be the most stable for poly‐ΔAla. ©1999 John Wiley & Sons, Inc. Int J Quant Chem 72: 15–23, 1999     

Aggregation of amyloid Aβ(1–40) peptide in perdeuterated 2,2,2‐trifluoroethanol caused by ultrasound sonication

Ultrasound sonication of protein and peptide solutions is routinely used in biochemical, biophysical, pharmaceutical and medical sciences to facilitate and accelerate dissolution of macromolecules in both aqueous and organic solvents. However, the impact of ultrasound waves on folding/unfolding of treated proteins, in particular, on aggregation kinetics of amyloidogenic peptides and proteins is not understood. In this work, effects of ultrasound sonication on the misfolding and aggregation behavior of the Alzheimer's Aβ_(1–40)‐peptide is studied by pulsed‐field gradient (PFG) spin–echo diffusion NMR and UV circular dichroism (CD) spectroscopy. Upon simple dissolution of Aβ_(1–40) in perdeuterated trifluoroethanol, CF₃‐CD₂‐OD (TFE‐d₃), the peptide is present in the solution as a stable monomer adopting α‐helical secondary structural motifs. The self‐diffusion coefficient of Aβ_(1–40) monomers in TFE‐d₃ was measured as 1.35 × 10^?10 m² s^?1, reflecting its monomeric character. However, upon ultrasonic sonication for less than 5 min, considerable populations of Aβ molecules (ca 40%) form large aggregates as reflected in diffusion coefficients smaller than 4.0 × 10^?13 m² s^?1. Sonication for longer times (up to 40 min in total) effectively reduces the fraction of these aggregates in ¹H PFG NMR spectra to ca 25%. Additionally, absorption below 230 nm increased significantly upon sonication treatment, an observation, which also clearly confirms the ongoing aggregation process of Aβ_(1–40) in TFE‐d₃. Surprisingly, upon ultrasound sonication only small changes in the peptide secondary structure were detected by CD: the peptide molecules mainly adopt α‐helical motifs in both monomers and aggregates formed upon sonication. Copyright © 2010 John Wiley & Sons, Ltd.     

Conformational polymorphism of the PrP106-126 peptide in different environments: a molecular dynamics study

Extensive molecular dynamic simulations (approximately 240 ns) have been used to investigate the conformational behavior of PrP106-126 prion peptide in four different environments (water, dimethyl sulfoxide, hexane, and trifluoroethanol) and under both neutral and acidic conditions. The conformational polymorphism of PrP106-126 in solution observed in the simulations supports the role of this fragment in the structural transition of the native to the abnormal form of prion protein in response to changes in the local environmental conditions. The peptide in solution is primarily unstructured. The simulations show an increased presence of helical structure in an apolar solvent, in agreement with the results from circular dichroism spectroscopy. In water solution, beta-sheet elements were observed between residues 108-112 and either residues 115-121 or 121-126. An alpha-beta transition was observed under neutral conditions. In DMSO, the peptide adopted an extended conformation, in agreement with nuclear magnetic resonance experiments.     

Negative surface potential produced by self-assembled monolayers of helix peptides oriented vertically to a surface

Self-assembled monolayers (SAMs) of helix peptides oriented vertically to a gold surface were prepared and the surface potential measured using the Kelvin technique up to 140°C. Negative surface potentials of a few hundred millivolts were observed for the helix peptide SAMs, indicating the occurrence of the large dipole moment of the helices directing toward the surface. The longer the helix peptide, the larger was the negative surface potential obtained. The absolute value of the surface potential decreased with increase in temperature due to thermal perturbation in the helical structure. However, Fourier transform infrared reflection–absorption spectroscopy revealed that perturbation is not significant and the α-helical conformation is stable even at 140°C.     

Investigating the interactions of the first 17 amino acid residues of Huntingtin with lipid vesicles using mass spectrometry and molecular dynamics

The first 17 amino acid residues of Huntingtin protein (Nt17 of htt) are thought to play an important role in the protein's function; Nt17 is one of two membrane binding domains in htt. In this study the binding ability of Nt17 peptide with vesicles comprised of two subclasses of phospholipids is studied using electrospray ionization ‐ mass spectrometry (ESI‐MS) and molecular dynamics (MD) simulations. Overall, the peptide is shown to have a greater propensity to interact with vesicles of phosphatidylcholine (PC) rather than phosphatidylethanolamine (PE) lipids. Mass spectra show an increase in lipid‐bound peptide adducts where the ordering of the number of such specie is 1,2‐dioleoyl‐sn‐glycero‐3‐phosphocholine (DOPC) > 1‐palmitoyl‐2‐oleoyl‐glycero‐3‐phosphocholine (POPC) > 1‐palmitoyl‐2‐oleoyl‐sn‐glycero‐3 phosphoethanolamine (POPE). MD simulations suggest that the compactness of the bilayer plays a role in governing peptide interactions. The peptide shows greater disruption of the DOPC bilayer order at the surface and interacts with the hydrophobic tails of lipid molecules via hydrophobic residues. Conversely, the POPE vesicle remains ordered and lipids display transient interactions with the peptide through the formation of hydrogen bonds with hydrophilic residues. The POPC system displays intermediate behavior with regard to the degree of peptide‐membrane interaction. Finally, the simulations suggest a helix stabilizing effect resulting from the interactions between hydrophobic residues and the lipid tails of the DOPC bilayer.     

Ethylbenzene solubility,diffusivity, and permeability in poly(dimethylsiloxane)

The pure‐gas sorption, diffusion, and permeation properties of ethylbenzene in poly(dimethylsiloxane) (PDMS) are reported at 35, 45, and 55 °C and at pressures ranging from 0 to 4.4 cmHg. Additionally, mixed‐gas ethylbenzene/N₂ permeability properties at 35 °C, a total feed pressure of 10 atm, and a permeate pressure of 1 atm are reported. Ethylbenzene solubility increases with increasing penetrant relative pressure and can be described by the Flory–Rehner model with an interaction parameter of 0.24 ± 0.02. At a fixed relative pressure, ethylbenzene solubility decreases with increasing temperature, and the enthalpy of sorption is −41.4 ± 0.3 kJ/mol, which is independent of ethylbenzene concentration and essentially equal to the enthalpy of condensation of pure ethylbenzene. Ethylbenzene diffusion coefficients decrease with increasing concentration at 35 °C. The activation energy of ethylbenzene diffusion in PDMS at infinite dilution is 49 ± 6 kJ/mol. The ethylbenzene activation energies of permeation decrease from near 0 to −34 ± 7 kJ/mol as concentration increases, whereas the activation energy of permeation for pure N₂ is 8 ± 2 kJ/mol. At 35 °C, ethylbenzene and N₂ permeability coefficients determined from pure‐gas permeation experiments are similar to those obtained from mixed‐gas permeation experiments, and ethylbenzene/N₂ selectivity values as high as 800 were observed. © 2000 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 38: 1461–1473, 2000     

Preparation and functions of self‐assembled monolayers of helix peptides

Self‐assembled monolayers (SAMs) of helix peptides oriented vertically to a gold surface were prepared. Negative surface potentials of a few hundred millivolts were observed for the helix peptide SAMs when they were immobilized on gold through the N terminal of the peptides. However, positive surface potentials were generated in the helix peptide SAMs when the N terminal of the peptides was directed the opposite way. The large dipole moment of the helical peptide was thought to be the major factor for generation of the surface potential. The effect of the dipole moment on the electron transfer through the helix peptide SAMs was investigated. Photocurrent generation by photoexcitation of the N‐ethylcarbazolyl group of the peptide SAMs was accelerated by the dipole moment directed toward the gold substrate. Helical peptides were thus shown to be a suitable medium for electron transfer. © 2000 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 38: 4826–4831, 2000     

Evaluation of the dioxane effect on the dipole moment of malonic acid

The dipole moment of malonic acid has been calculated taking into account its high conformational flexibility. The use of the MNDO method yields, at 25 °C, a value of 2.07 D, which is approximately 0.5 D lower than the values observed in dilute solution in liquid dioxane. A greater difference is obtained at higher temperatures. This result, which can be interpreted in terms of solute-solvent interactions, confirms the tendency of dioxane to increase the dipole moment of compounds dissolved in it. In the present case, the change in the conformational equilibria of malonic acid seems to be the main cause of this difference, whereas the effect of hydrogen bonding between the solute and the solvent is found to be of minor importance.     

Rhodium‐Catalyzed Highly Diastereo‐ and Enantioselective Synthesis of a Configurationally Stable S‐Shaped Double Helicene‐Like Molecule

An S‐shaped double helicene‐like molecule (>99 % ee), possessing stable helical chirality, has been synthesized by the rhodium(I)/difluorphos complex‐catalyzed highly diastereo‐ and enantioselective intramolecular double [2+2+2] cycloaddition of a 2‐naphthol‐ and benzene‐linked hexayne. The collision between two terminal naphthalene rings destabilizes the helical chirality of the S‐shaped double helicene‐like molecule, but the introduction of two additional fused benzene rings significantly increases the configurational stability. Thus, no epimerization and racemization were observed even at 100 °C. The enantiopure S‐shaped double helicene‐like molecule forms a trimer through the multiple C?H???π and C?H???O interactions in the solid‐state. The trimers stack to form columnar packing structures, in which neighboring stacks have opposite dipole directions. The accumulation of helical structures in the same direction in the S‐shaped double helicene‐like molecule enhanced the chiroptical properties.     

End‐group functionalization and postpolymerization modification of helical poly(isocyanide)s

This contribution presents the synthesis of helical alkyne‐terminated polymers using a functionalized Nickel complex to initiate the polymerization of menthylphenyl isocyanides. The resulting polymers display low dispersities and controlled molecular weights. Copper‐catalyzed azide/alkyne cycloadditions (CuAAC) are performed to attach various azide‐containing compounds to the polymer termini. After azido‐phosphonate moiety attachment the polymer displays a signal at 25.4 ppm in the ³¹P NMR spectrum demonstrating successful end‐group functionalization. End‐group functionalization of a fluorescent dye allows to determine the functionalization yield as 89% (±8). Successful ligation of an azide‐functionalized peptide sequence (M_KLA = 1547 g/mol) increases the M_n from 5100 for the parent polymer to 6700 for the bioconjugate as visualized by GPC chromatography. Analysis by CD spectroscopy confirms that the helical conformation of the poly(isocyanide) block in the peptide–polymer conjugate is maintained after postpolymerization modification. These results demonstrate an easy, generalizable, and versatile strategy toward mono‐telechelic helical polymers. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2016 , 54, 2766–2773     

Another way to view the chain conformation broadening of the line-width distribution measured in dynamic light scattering

In dynamic laser light scattering (LLS), for a given polydisperse sample, a line-width distribution G(Γ) or the translational diffusion coefficient distribution G(D) can be obtained from the measured time correlation function. For rigid colloid particles, G(Γ) can be directly related to the hydrodynamic size distribution. However, for flexible polymer chains, G(Γ) depends not only on the chain length distribution, but also on the relaxation of the chain conformation; that is, even for a monodisperse polymer sample there still exists a chain conformation distribution. If the time scale of the chain conformation relaxation is comparable to that of the translational diffusion, such as in the case of a very long polymer chain, the conformation relaxation might lead to an additional broadening in G (Γ). This "conformation broadening" has been directly observed for the first time by comparing two G(Γ) s obtained from a poly(N-isopropyl-acrylamide) solution at～25℃ and～32℃ at which the solution is ther     

Effect of association of dicarboxylic acids activated by TsCl/DMF/pyridine upon the copolycondensation with bisphenols

When a mixture of terephthalic acid (TPA) and various dicarboxylic acids was activated by tosyl chloride (TsCl)/dimethyl‐ formamide (DMF)/pyridine (Py), the resulting mixture became dissolved in Py, although the activated TPA was insoluble even at 120 °C. The temperature at which the mixture became soluble was varied with their compositions and the structure of diacids. Mixing the separately activated TPA and isophthalic acid (IPA) also improved the solubility of the activated TPA to some extent. The interesting phenomena were attributed to associations of the activated diacids through the dipole–dipole interactions between the carbonyl groups. The structures of associates were estimated in terms of transition temperatures of the thermotropic IPA/TPA‐methylhydroquinone and IPA/TPA‐chlorohydroquinone copolymers. The transition temperatures were significantly affected by the temperature of polycondensation, the preparative procedures of a mixture of the activated diacids, and several additives. © 2000 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 39: 196–201, 2001     

Structures of Peptidic H‐wires at Mercury Surface: Molecular Dynamics Study

Biopolymer immobilization strategies, self‐assembly systems and adsorption phenomenon in general are crucial for the development of methods that work on the basis of the surface‐detection principle, including electrochemistry. A mechanistic view into the interaction of biopolymers with electrode surfaces is also important for studying fundamental and dynamic processes such as electron/proton transport. In this sense, the utilization of new approaches for investigating the interfacial behavior of immobilized biomolecular architectures is a permanent focus. Here we use a molecular dynamics (MD) approach to simulate the structural changes and metallic surface interactions of a model 21‐mer peptide of His (H) and Ala (A), A₃(HA₂)₆, a peptidic proton wire (H‐wire). This H‐wire was previously proposed for the electrochemical study of proton transfer at mercury electrodes (Langmuir, 2018, 34, 6997). The rigid solid mercury mono‐atomic layer (α‐mercury lattice model) was used systematically in all our simulations. The calculations were performed in a simulation box with 1, 16 and 32 H‐wire strands attached covalently to the mercury layer via the thiol group of a cysteinamide residue appended to the H‐wire C‐terminus. The internal alpha‐helical configuration of H‐wires was maintained by the presence of 2,2,2‐trifluoroethanol. It was shown that both the surface density of H‐wires and the protonation state of His residues play a decisive role in the structural stability and orientation of the peptide to the surface, whereas the applied voltage only has a mild effect on it, especially in case of 16 and 32 H‐wire strand configurations. The MD simulations presented here could be used for the further investigation of other peptides at metallic surfaces and for electrochemical analyses of structural changes of surface‐attached peptides that depend on their protonation states and other external factors.     

A dipole moment study of the conformational properties of diaryl diselenides and related compounds

The electric dipole moments of the diaryl diselenides (RC₆H₄)₂Se₂ (R  H, 4-F, 4-Br, 4-CH₃, 3-F) were measured in benzene solution at 25 and 45°C. The conformations of these compounds were deduced by matching experimental moments with values calculated for a variety of possible conformations. In the dissolved state the diselenides exist at 25°C in fixed “skew” conformations characterized by dihedral angles of 75–106° between the CSeSe planes, corresponding to the conformational energy minima. At 45°C oscillations about the SeSe bonds are excited in the diphenyl and bis(4-methylphenyl) diselenides, whereas the 4-bromophenyl derivative exhibits free rotation. The fluoro compounds have temperature-independent dipole moments, suggesting “rigid conformations” with dihedral angles of 106° (4-F) and 74.4° (3-F). An analysis of the dipole moments at 25 and 45°C obtained for the compounds (RC₆H₄)₂X₂ (R  H, 3-F, 4-F, 4-Br, 4-CH₃; X  S, Se, Te) showed that the conformational properties of these derivatives change on passing from X  S to X  Te. The observed variations are explicable in terms of a decreasing repulsion between the lone electron pairs of the chalcogen atoms on going from the disulfides to the ditellurides and a concomitant reduction of the energy barrier to rotations about the XX bonds.     

Engineering a β‐Helical d,l‐Peptide for Folding in Polar Media

β Helices—helices formed by alternating d,l ‐peptides and stabilized by β‐sheet hydrogen bonding—are found naturally in only a handful of highly hydrophobic peptides. This paper explores the scope of β‐helical structure by presenting the first design and biophysical characterization of a hydrophilic d,l ‐peptide, 1 , that forms a β helix in methanol. The design of 1 is based on the β‐hairpin/β helix—a new supersecondary that had been characterized previously only for hydrophobic peptides in nonpolar solvents. Incorporating polar residues in 1 provided solubility in methanol, in which the peptide adopts the expected β‐hairpin/β‐helical structure, as evidenced by CD, analytical ultracentrifugation (AUC), NMR spectroscopy, and NMR‐based structure calculations. Upon titration with water (at constant peptide concentration), the structure in methanol ( 1 m ) transitions cooperatively to an extended conformation ( 1 w ) resembling a cyclic β‐hairpin; observation of an isodichroic point in the solvent‐dependent CD spectra indicates that this transition is a two‐state process. In contrast, neither 1 m nor 1 w show cooperative thermal melting; instead, their structures appear intact at temperatures as high as 65 °C; this observation suggests that steric constraint is dominant in stabilizing these structures. Finally, the ¹H NMR CαH spectroscopic resonances of 1 m are downfield‐shifted with respect to random‐coil values, a hitherto unreported property for β helices that appears to be a general feature of these structures. These results show for the first time that an appropriately designed β‐helical peptide can fold stably in a polar solvent; furthermore, the structural and spectroscopic data reported should prove useful in the future design and characterization of water‐soluble β helices.     

Conformational Transformation Exhibited by the Peptide Extracted from Crystalline Region of Bombyx mori Silk Fibroin in Solid and Solution States

The conformational transformation of a 30-residue peptide H（Ala-Gly-Ser-Gly-AIa-Gly）5OH, i.e., （AGSGAG）5, extracted from highly crystalline region of Bombyx mori （B. mori） silk fibroin was described by using the high resolution solid state 13^C NMR, and CD spectroscopies. Based on the conformation-dependent 13^C NMR chemical shifts of the Ala, Gly and Ser residues and the line-shape analysis of the conformation sensitive Ala Cβ resonance, the peptide revealed a strong preference for silk Ⅱ structural form, i,e,, an antiparallel fl-sheet structure （φ= - 140±20°and ψ= 135±20°） in solid state. On the contrary, the CD spectra of this peptide in the two non-native hexafluorinated fibre spinning solvents, hexafluoroisopropanol （HFIP） and hexafluoroacetone （HFA）, exhibited the existence of an unusual tightly-folded conformation resembling 310-helix （φ=- 60±20° and ψ=-30±20°）, as judged from the R ratio of [θ]222/[θ]203 in HFIP solution, whereas a dynamically averaged unordered structure in HFA, Taken together, the information inclined to hypothesis that the primary structure of the highly crystalline regions of B. mori silk fibroin may be easily accessible to the large conformational changes, which in turn may be critical for facilitating the structural transformation from unprocessed silk fibroin （silk I form） to processed silk fiber （silk Ⅱform）.     

Interactions of trifluoroethanol with [val5]angiotensin II

Intermolecular 1H{19F} NOE experiments have been used to explore the interactions of trifluoroethanol (TFE) with the octapeptide hormone [val5]angiotensin II at temperatures from 5 to 25 degrees C. Circular dichroism spectra indicate that 40% trifluoroethanol has an influence on the conformations of the peptide, probably leading to beta-structures. Diffusion experiments show that the mean hydrodynamic radius of the peptide in 40% trifluoroethanol-water is about 8 A, consistent with significant folding of the peptide in this medium. Distance constraints derived from intramolecular NOESY data along with observed vicinal coupling constants (3JCalphaHNH) were used to develop conformations consistent with available data. Assuming that intermolecular 1H{19F} NOEs are the result of diffusive encounters of TFE and peptide molecules, it is shown that no single conformation is consistent with the experimental values of the sigmaHF cross-relaxation parameters. It is argued that the disagreements between observed and expected values of sigmaHF are the result of formation of long-lived (approximately 0.5 ns) fluoroalcohol-peptide complexes, a conclusion consonant with similar studies of other peptide-fluoroalcohol systems. Complex formation appears to be especially prevalent near the charged amino acid side chains of the hormone.     

Ferroelectrically Switching Helical Columnar Assembly Comprising Cisoid Conformers of a 1,2,3‐Triazole‐based Liquid Crystal

The 1,2,3‐triazole molecule, which is a product of click chemistry, possesses a high dipole moment and can be a useful polar motif for ferroelectric columnar liquid crystal (LC) materials—though it has not been used to date. Herein, we report the helical assembly and ferroelectric switching properties of a columnar liquid crystal comprising a naphthalene core and 1,2,3‐triazolyl linkages. The molecule assembles into a double‐stranded helical columnar LC structure (Col_hel). The X‐ray simulations of cisoid and transoid columnar models suggest that the helical assembly comprises cisoid conformers with a non‐zero dipole moment. The helical columns in the Col_hel phase are aligned homeotropically under an electric field. The ferroelectric switching of the axial polarization can be observed in the temperature range of 105–115 °C in the Col_hel phase, wherein the triazolyl hydrogen bonding along the column axis is weakened. The ferroelectric switching event is attributed to the rotation of the polar triazolyl units in response to the electric field.     

Temperature dependence of positron lifetimes in water and ethanol

Positron lifetime spectra have been measured in water and ethanol between ?10°C and +80°C. In addition to the discontinuity at the ice—liquid water point (0 ± 0.5°C) we find a cusp-like singularity at 4.0 ± 0.5°C in the long lifetime component. At higher temperatures the lifetime falls with increasing temperature in agreement with the results of previous work. In ethanol an intermediate lifetime (1.7 ns) appears with small intensity (≈6%) at all temperatures. Its presence is tentatively attributed to a relaxation of the molecular structure on the bubble surface with a characteristic time of ≈4 ns.