Changes In Chain Conformation Research Articles

Molecular Origin of the Odd-Even Effect of Macroscopic Properties of n-Alkanethiolate Self-Assembled Monolayers: Bulk or Interface?

Elucidating the influence of the monolayer interface versus bulk on the macroscopic properties (e.g., surface hydrophobicity, charge transport, and electron transfer) of organic self-assembled monolayers (SAMs) chemically anchored to metal surfaces is a challenge. This article reports the characterization of prototypical SAMs of n-alkanethiolates on gold (CH3(CH2)nSAu, n = 6-19) at the macroscopic scale by electrochemical impedance spectroscopy and contact angle goniometry, and at the molecular level, by infrared reflection absorption spectroscopy. The SAM capacitance, dielectric constant, and surface hydrophobicity exhibit dependencies on both the length (n) and parity (nodd or neven) of the polymethylene chain. The peak positions of the CH2 stretching modes indicate a progressive increase in the chain conformational order with increasing n between n = 6 and 16. SAMs of nodd have a greater degree of structural gauche defects than SAMs of neven. The peak intensities and positions of the CH3 stretching modes are chain length independent but show an odd-even alternation of the spatial orientation of the terminal CH3. The correlations between the different data trends establish that the chain length dependencies of the dielectric constant and surface hydrophobicity originate from changes in the polymethylene chain conformation (bulk), while the odd-even variation arises primarily from a difference in the chemical composition of the interface related to the terminal group orientation. These findings provide new physical insights into the structure-property relation of SAMs for the design of ultrathin film dielectrics as well as the understanding of stereostructural effects on the electrical characteristics of tunnel junctions.

Stereospecific synthesis of methyl 2-amino-2,4-dideoxy-6S-deuterio-α-D-xylo-hexopyranoside and methyl 2-amino-2,4-dideoxy-6S-deuterio-4-propyl-α-d-glucopyranoside: Side chain conformation of the novel aminoglycoside antibiotic propylamycin

The stereospecific syntheses of methyl 2-amino-2,4-dideoxy-4-C-propyl-α-d-glucopyranoside and of methyl 2-amino-2,4-dideoxy-α-D-xylo-hexopyranoside and of their 6S-deuterioisotopomers are described as models for ring I of the aminoglycoside antibiotics propylamycin and 4′-deoxyparomomycin, respectively. Analysis of the 1H NMR spectra of these compounds and of methyl 2-amino-2-deoxy-α-d-glucopyranoside, a model for paromomycin itself, reveals that neither deoxygenation at the 4-position, nor substitution of the C–O bond at the 4-postion by a C–C bond significantly changes the distribution of the side chain population between the three possible staggered conformations. From this it is concluded that the beneficial effect on antiribosomal and antibacterial activity of the propyl group in propylamycin does not derive from a change in side chain conformation. Rather, enhanced basicity of the ring oxygen and increased hydrophobicity and/or solvation effects are implicated.

Electrical monitoring of photoisomerization of block copolymers intercalated into graphene sheets

Insulating polymers have received little attention in electronic applications. Here, we synthesize a photoresponsive, amphiphilic block copolymer (PEO-b-PVBO) and further control the chain growth of the block segment (PVBO) to obtain different degrees of polymerization (DPs). The benzylidene oxazolone moiety in PEO-b-PVBO facilitated chain-conformational changes due to photoisomerization under visible/ultraviolet (UV) light illumination. Intercalation of the photoresponsive but electrically insulating PEO-b-PVBO into graphene sheets enabled electrical monitoring of the conformational change of the block copolymer at the molecular level. The current change at the microampere level was proportional to the DP of PVBO, demonstrating that the PEO-b-PVBO-intercalated graphene nanohybrid (PGNH) can be used in UV sensors. Additionally, discrete signals at the nanoampere level were separated from the first derivative of the time-dependent current using the fast Fourier transform (FFT). Analysis of the harmonic frequencies using the FFT revealed that the PGNH afforded sawtooth-type current flow mediated by Coulomb blockade oscillation.

Impact of water on the hydrogen bonding between halide‐based ion‐pairs investigated by Raman scattering and density functional theory calculations

AbstractWe present a study of the impact of water on the size‐ and electronegativity‐dependent hydrogen bonds between cation and anion of imidazolium‐based ionic liquids (ILs) with halide anions. We have combined Raman spectroscopy with density functional theory (DFT) computations to characterize the intermolecular associations of cation–anion–water moieties. The Raman band at ~1,422 cm−1, which is assigned to the ν(N─CH2─CH3) vibration of the ethyl chain in the neat ion pairs (pure ion pairs), is blue shifted by +7, +4, and +3 cm−1 for 1‐ethyl‐3‐methylimidazolim (C2mim) cation‐based C2mim X ion pairs with X = Cl, Br, and I, respectively, in a water‐rich environment. Simultaneously, upon dilution, a new peak at ~1,438 cm−1 starts to appear at the high‐wavenumber side with continuously increasing intensity. These significant perturbations of the ν(N─CH2─CH3) vibrational mode in water environment are a clear indication of the change in the alkyl chain conformation. Further, the relative intensities of the Raman bands at ~2,946 and ~2,950 cm−1 corresponding to νs (CH2) and νas (CH3) of the ethyl chain, respectively, were significantly changed upon dilution, which also confirms the conformational change of the alkyl chain. The Raman band belonging to the C4/5─H stretch mode was significantly blue shifted by +33, +41, and +42 cm−1 going from the studied neat ion pairs having Cl, Br, and I anions to the corresponding water mixtures, respectively. Significant changes were also observed for the ν(C2─H) vibrational mode of the ion pairs in water environment; here, we observed blue shifts of +60, +51, and +50 cm−1 for ion pairs having Cl, Br, and I anions, respectively. These results confirm the weakening of the ion‐pair interaction due to the interaction with water molecules. In contrast to the ILs with halide anions, C2mim BF4 does not show any variation in the Raman peak positions upon dilution. Experimental results are nicely supported by the results of DFT calculations, and a sensible connection was established.

Chain conformation: A key parameter driving clustering or dispersion in polyelectrolyte – Colloid systems

The work presents the characterization of Pluronic F127 micellar solutions in presence of hyaluronic acid in semi-dilute regime. The effects of the nature and salt concentration are investigated by differential scanning calorimetry and small angle neutron scattering. Hyaluronic acid reduces the critical micellar temperature to the same extend as an increase of the ionic strength. Within the investigated HA concentration range, the size and shape of the micelles are not modified by the addition of HA but their dispersion state depends on the salt concentration. By increasing the ionic strength we observe the formation of small micellar clusters which organize into a face-centered cubic liquid crystalline phase at high salt concentration. This behavior is reinforced by increasing the HA concentration or molecular weight. The nature of the salt plays also a role and divalent cations such as Ca2+ promote the clustering of micelles and their crystallization. The origin of the aggregative behavior is the change of the HA chain conformation –from stretched to coil- by addition of salt which in turn induces an excluded volume around the micelles and exerts a depletion interaction.

Identification of a pH sensor in Influenza hemagglutinin using X-ray crystallography

Hemagglutnin (HA) mediates entry of influenza virus through a series of conformational changes triggered by the low pH of the endosome. The residue or combination of residues acting as pH sensors has not yet been fully elucidated. In this work, we assay pH effects on the structure of H5 HA by soaking HA crystallized at pH 6.5 in a series of buffers with lower pH, mimicking the conditions of the endosome. We find that HA1-H38, which is conserved in Group 1 HA, undergoes a striking change in side chain conformation, which we attribute to its protonation and cation-cation repulsion with conserved HA1-H18. This work suggests that x-ray crystallography can be applied for studying small-scale pH-induced conformational changes providing valuable information on the location of pH sensors in HA. Importantly, the observed change in HA1-H38 conformation is further evidence that the pH-induced conformational changes of HA are the result of a series of protonation events to conserved and non-conserved pH sensors.

Electromechanical Decoupling by Porous Aerogel Conducting Polymer

In the field of biointerface electronics, electromechanical decoupling—electrical performance independent of mechanical deformation—can ensure reliability of measured signals, which is critical in stable electrode. Herein, Chen et al. report such a decoupled and stretchable conductive polymer foam.

Crystal structure of a ligand-free stable TSH receptor leucine-rich repeat domain.

The crystal structures of the thyroid-stimulating hormone receptor (TSHR) leucine-rich repeat domain (amino acids 22-260; TSHR260) in complex with a stimulating human monoclonal autoantibody (M22TM) and in complex with a blocking human autoantibody (K1-70™) have been solved. However, attempts to purify and crystallise free TSHR260, that is not bound to an autoantibody, have been unsuccessful due to the poor stability of free TSHR260. We now describe a TSHR260 mutant that has been stabilised by the introduction of six mutations (H63C, R112P, D143P, D151E, V169R and I253R) to form TSHR260-JMG55TM, which is approximately 900 times more thermostable than wild-type TSHR260. These six mutations did not affect the binding of human TSHR monoclonal autoantibodies or patient serum TSHR autoantibodies to the TSHR260. Furthermore, the response of full-length TSHR to stimulation by TSH or human TSHR monoclonal autoantibodies was not affected by the six mutations. Thermostable TSHR260-JMG55TM has been purified and crystallised without ligand and the structure solved at 2.83 Å resolution. This is the first reported structure of a glycoprotein hormone receptor crystallised without ligand. The unbound TSHR260-JMG55TM structure and the M22 and K1-70 bound TSHR260 structures are remarkably similar except for small changes in side chain conformations. This suggests that neither the mutations nor the binding of M22TM or K1-70TM change the rigid leucine-rich repeat domain structure of TSHR260. The solved TSHR260-JMG55TM structure provides a rationale as to why the six mutations have a thermostabilising effect and provides helpful guidelines for thermostabilisation strategies of other soluble protein domains.

FRET-Based Semiconducting Polymer Dots for pH Sensing.

Förster resonance energy transfer (FRET)-based polymer dots (Pdots), fabricated by semiconducting polymers and exhibiting excellent properties, have attracted much interest in the last decade, however, full polymer-dot-based pH sensors are seldom systematically exploited by researchers. In this work, we constructed a kind of blend polymer dot, utilizing poly[(9,9-dihexyl-9H-fluorene-2,7-vinylene)-co-(1-methoxy-4-(2-ethylhexyloxy)-2,5-phenylenevinylene)] (PFV) as the donor, poly[2,5-bis(3′,7′-dimethyloctyloxy)-1,4-phenylenevinylene] (BDMO-PPV) as the acceptor, and polysytrene graft EO functionalized with carboxy (PS-PEG-COOH) to generate surface carboxyl groups. This type of Pdot, based on the FRET process, was quite sensitive to pH value changes, especially low pH environments. When the pH value decreases down to 2 or 1, the fluorescence spectrum of Pdots-20% exhibit spectral and intensity changes at the same time, and fluorescence lifetime changes as well, which enables pH sensing applications. The sharpening of the emission peak at ~524 nm, along with the weakening and blue shifts of the emission band at ~573 nm, imply that the efficiency of the energy transfer between PFV and BDMO-PPV inside the Pdots-20% decreased due to polymer chain conformational changes. The time-resolved fluorescence measurements supported this suggestion. Pdots constructed by this strategy have great potential in many applications, such as industrial wastewater detection, in vitro and intracellular pH measurement, and DNA amplification and detection.

Investigation of Extracellular Gate Movement in a Glutamate Homologue

Glutamate transporters harness the ionic gradients across cell membranes to carry out the concentrative uptake of glutamate. The sodium coupled Asp symporter, GltPh is an archaeal homologue of glutamate transporters which has been extensively used to understand the transport mechanism. A critical aspect of the transport mechanism is the coupled binding of sodium and aspartate. The crystal structures of GltPh shows that the Na+ ions do not form direct interactions with the substrate, suggesting that the binding of Na+ and substrate is coupled through an allosteric mechanism. Previous studies have suggested a critical role for hairpin-2 (HP2), the extracellular gate for the substrate binding site, in coupling the binding of sodium and asparate to GltPh. We have developed a fluorescence assay for monitoring HP2 movement by incorporating tryptophan and the unnatural amino acid, p-cyanophenylalanine into GltPh. We use the HP2 fluorescence assay in concert with traditional Na+ and Asp binding assays to investigate how key residues in the substrate binding sites modulate HP2 movement. Our studies reveal the intricate choreography of side chain conformational changes linked to HP2 opening and closing that is the basis for the coupled binding of Na+ and Asp to GltPh.

Untying of Complex Knots on Stretched Polymers in Elongational Fields

Knotting is a prevalent phenomenon which occurs in long polymer chains. We perform Brownian dynamics simulations and single-molecule DNA experiments to investigate knot untying in elongational fields that is induced by the knot being convected off the chain. The change in knot size as the knot moves off the chain and unties causes a change in the effective Weissenberg number, which in turn leads to a change in chain extension. Large-scale chain conformational changes are observed in both simulations and experiments for complex knots at low Weissenberg numbers (Wi). We investigate the knot untying time and untying-induced change in extension for a range of knot types and field strengths. Simulations predict a quadratic relationship between the change in extension due to knot untying and initial knot size for Wi ≥ 1.5. Due to the changes in chain extension as a knot unties, the untying process can be diffusion- or convection-driven.

Prediction of properties of silica nanoparticle/hydroxyapatite fiber reinforced Bis-GMA/TEGDMA composites using molecular dynamics

In this study, molecular dynamics simulations have been used to investigate the effects of organic/inorganic components on the properties of silica nanoparticle/hydroxyapatite fiber reinforced Bis-GMA/TEGDMA dental composite materials. Characterization at the atomic scale is highly important for an advancement of the understanding of properties of resin based materials. Various combinations of Bis-GMA/TEGDMA (20–80% by weight) were modelled using molecular dynamics. The silica nanoparticle weight percentage was varied from 0 to 11% and the hydroxyapatite fiber weight percentage was varied from 0 to 12%. It was observed that the radius of gyration, in various blends of resin, lie in the range of 16–17 Å and thus was approximately independent of Bis-GMA/TEGDMA weight percentage. It was found that a small percentage of silica nanoparticle improved the mechanical properties significantly because of an increase in the volumetric hydrogen bonds and polymer chain contraction. As the weight percentage of TEGDMA in dental resin blends was increased from 20 to 80%, the hydrogen bonds per unit volume were found to decrease from 1.3 × 10−3 to 0.3 × 10−3 Å−3. The elastic and shear moduli of dental composites containing varying percentage of hydroxyapatite fibers (0–12%) increased by 8.13 and 10% respectively. In comparison to the hydroxyapatite fibers, the silica nanoparticles provided significant mechanical reinforcement effect. The diffusion coefficient falls approximately by 46%, from 1.15 × 10−11 to 0.62 × 10−11 m2/s with an increase in the silica nanoparticle weight percentage from 0 to 11 %. This indicated a strong dependency on change in chain conformation as well as hydrogen bonds. These findings will be of great importance in improving the understanding of the mechanical and dynamic properties of dental materials at the atomic/nanoscale.

Large unsaturated room temperature negative magnetoresistance in graphene foam composite for wearable and flexible magnetoelectronics

Room temperature positive magnetoresistance (PMR) in graphene is a conventional phenomenon but we observed large negative magnetoresistance (NMR) in GF/polydimethylsiloxane (GF/PDMS) at room temperature for the first time. The largest NMR ~ 35% was detected at 250 K, while PMR is observed below 200 K. Furthermore, PMR at all temperatures is observed in regular GF specimens, hence, NMR is the result of the infiltration with the electrically insulating polymer. Forward interference and wavefunction shrinkage model has been employed to understand the transport mechanism in GF/PDMS. A critical temperature ~ 224 K for switching between NMR and PMR is observed at the crystallization temperature of PDMS, suggesting a change in polymer chain conformation may be a major reason leading to NMR in GF/PDMS specimens thus role of mechanical properties of PDMS in NMR cannot be ignored and observed locally via specially resolved atomic force microscopy. In addition, storage modulus and heat flow study shows similar transition temperature (~ 200 K) of NMR to PMR and provide an evidence of mechanical stable specimens. As is known, large, tunable, and unsaturated NMR at room temperature is very useful for future facile practical shapeable magnetoelectronic devices.

Conformational Transitions of Polymer Chains in Solutions Characterized by Fluorescence Resonance Energy Transfer.

The critical overlap concentration C* is an important concept in polymer solutions and is defined as the boundary between dilute and semidilute regimes. In this study, the chain conformational changes of polystyrene (PS) with both high (Mn = 200,000 Da) and low (Mn = 13,000 Da) molecular weights in cis-decalin were compared by intrachain fluorescence resonance energy transfer (FRET). The random labeling of donor and acceptor chromophores strategy was employed for long PS chains, whereas chain-end labeling was used for short PS chains. By monitoring the spectroscopic intensity ratio between acceptor and donor, the concentration dependence on chain conformation from dilute to semidilute solutions was determined. Both long and short chains exhibit a conformational transition concentration, above which the polymer chains begin to collapse with concentration significantly. Interestingly, for randomly labeled polymer long chains, such concentration is consistent with C* determined from the viscosity result, below which only slight conformational change of polymer chain takes place. However, for the chain-end labeled short chain, the conformational transition concentration takes place earlier than C*, below which no significant polymer conformation change is observed.

Effect of polysaccharide chain conformation on ultrasonic degradation of curdlan in alkaline solution

This study was to investigate the effects of polysaccharide chain conformation on ultrasonic degradation of curdlan, a high MW β-glucan with wide applications. The ultrasonic degradation was performed in alkaline solution at 0.1 M and 0.3 M NaOH, in which the curdlan chain was mainly in triple helical conformation and random coil form, respectively. The degradation rate was represented by the kinetic model, 1/Mt − 1/Mo = kt, with the rate constant k increasing with the ultrasonic power. The degradation rate was much higher in 0.3 M NaOH than in 0.1 M NaOH, suggesting that curdlan in random coil conformation was more liable to degradation than in helical conformation. Curdlan in 0.1 M NaOH was changed from triple helices to single helices and eventually to random coils with a higher solubility. In summary, ultrasonic degradation of curdlan in alkaline solution had a close and complex relationship to the chain conformation changes.

Insights into the helix-sense inversion of poly(β-phenethyl-L-aspartate) by two-dimensional Raman correlation spectroscopy.

In this study, the transition process of the helix-sense inversion of poly(β-phenethyl-L-aspartate) was investigated by Raman scattering and 2-dimensional correlation spectroscopy. Temperature-dependent Raman spectra were obtained during the helix-sense inversion. The results of 2-dimensional correlation analysis in the spectral regions of 1600-1800 and 3200-3400cm-1 showed that the intensity changes of the side-chain ester C═O stretching bands occurred prior to those of amide A and amide I bands in the unwinding process of αR-helix on heating. The sequential order of the intensity changes for amide A, amide I, and the side-chain ester C═O stretching bands during the inversion process was determined. It was found that the conformation change of the side chain occurred prior to that of the main chain for the αR-helix on heating. Thus, we concluded that the transformation of the backbone chain from right-handed to left-handed is triggered by the conformational change of the side chains.

Mechanical and dynamic properties of resin blend and composite systems: A molecular dynamics study

Molecular characterization of polymer resin systems is significantly important in prediction and advancing understanding of properties and phenomena of resin-based composites. In this work, molecular dynamics simulations of a resin composite model, i.e., silica nanoparticle reinforced Bis-GMA/TEGDMA resin composite, were performed to investigate the effects of organic and inorganic components on the structure and properties of the resulting composites. It was revealed that even a small amount of silica nanoparticles (up to 10 wt%) could improve the mechanical properties considerably due to increased intermolecular hydrogen bonds and polymer chain contraction. The reinforcement effect induced by silica nanoparticles is much more intensive than that caused by the stiff resin monomer of Bis-GMA. The composite modulus, increasing with the silica nanoparticle content, was further compared with micromechanics methods and exhibited good agreement with the Counto model, indicating strong matrix-particle interactions. Moreover, it was found that the diffusion dynamics of the resin matrix is significantly suppressed at higher contents of Bis-GMA or silica nanoparticles, which signifies a strong dependence on the hydrogen bonds and chain conformational changes. The findings in this work are believed to provide the atomic/molecular scale understanding of the structures and performances of Bis-GMA/TEGDMA resin blend and composite systems.

Collapse Transition of Cyclic Homopolymers and Block Copolymers

AbstractIn order to determine the structure of cyclic homopolymer and multiblock copolymer polymers (rings) at various solvent qualities (temperatures), an idealized model of macromolecules is developed and studied. All atomic details are suppressed and chains are represented as a sequence of identical beads embedded in a square lattice. A simple square‐well potential is used for polymer–polymer interactions in order to mimic the influence of nonselective solvent. An efficient Monte Carlo sampling algorithm using local and nonlocal changes of chain conformation as well as the Replica Exchange technique is used to sample the conformational space. Simulation results concerning the structure of globules formed at low temperature are discussed and compared with theoretical predictions. The influence of the arrangements of blocks in the chain on its structure in different temperatures is shown.

Studying compaction-decompaction of DNA molecules induced by surfactants

The mechanism and detailed processes of DNA compaction and decompaction are essential for the life activities, as well as for the researches in the molecular biology, genetics and biomedicine. The compaction of two kinds of DNA molecules caused by Cetyltrimethyl Ammonium Bromide (CTAB) and their decompaction induced with sodium dodecyl sulfate (SDS) or excessive amount of CTAB have been investigated with multiple perspectives such as the UV-VIS spectrophotometry, dynamic light scattering, and zeta potential. The compaction phenomenon of DNA can easily be observed when the CTAB combines with the DNA, not just when the molar ratio QCTAB/QDNA is approximately equal to 1 as the conventional recognition, but also when QCTAB/QDNA <1,DNA can be compacted; Molecular state of DNA is only changed in the conformational structure, but not in the chemical structure. Finally, a model is suggested to help catch on the biophysical mechanism of DNA chain conformational change.

Influence of molecular distortion on the exciton quenching for quaterthiophene-terminated self-assembled monolayers on Au(111)

We have studied the dynamics of photoexcited electronic states for structure-specific alkanethiolate-based self-assembled monolayers (SAMs) on Au(111). At the even numbers of methylene units (n) in the alkylene chain, a molecular distortion due to strong interference between the end substituents is expected. Focused on this geometrical perturbation, here, we examine the influence of the molecular distortion on the quenching process of photoexcited quaterthiophene (4T)-terminated alkanethiolate SAMs (4TCnS-SAMs) for even n (= 6 and 8). The occupied and unoccupied electronic levels of 4TCnS-SAMs are specified by ultraviolet photoelectron spectroscopy (UPS) and two-photon photoemission (2PPE) spectroscopy, respectively. The quenching rate, i.e., lifetime (τn), of the photoexcited state for 4TCnS-SAMs is evaluated by the time-resolved 2PPE measurements. In comparison to the previously reported results for odd n [J. Phys. Chem. C 119 (2015) 7400–7407], we find that τn for even n is not in the middle of those for n ± 1 but close to that for n − 1, i.e., τ6 ≈ τ5 and τ8 ≈ τ7, in contrast to the negligible difference in the electronic levels for all n. By the examination of molecular configurations using scanning tunneling microscopy (STM) and infrared reflection absorption spectroscopy (IRAS), we elucidate the weak n dependence of the 4T group orientation and the n-parity-dependent conformation change of alkylene chain. We conclude that the n parity dependence of τn results from a structural distortion of the aliphatic alkylene chain, in which a skewed alkylene chain appears for even n, rather than the electronic modification of the aromatic 4T groups.