Large Number Of Bonds Research Articles

Energetics of graphene flakes

Based on the idea that the binding energy of a graphene flake is a sum of atomic energy contributions, which depend on the local atomic environment of each atom of the flake, we propose a model for graphene flake energetics, which can very accurately predict the cohesive energy of graphene flakes. In our study, we calculate the cohesive energy of hexagonal graphene flakes with up to ≈1000 atoms using the tight binding molecular dynamics method and we show that the calculated values fit extremely accurately to the expression derived from the proposed model. For a further validation, we show that the proposed expression can very accurately predict the calculated values of other graphene flakes with random shapes. Based on that model, we show that the graphene flake stability obeys the following rules: (1) Between isomers the most stable are those with the larger number of bonds (or equivalently, with the smaller number of edge atoms) and (2) between isomers with the same number of bonds (or with the same number of edge atoms), the most stable are those with the smaller number of zig-zag atoms.

Analytical Model for the Deformation of a Fluid–Fluid Interface Beneath an AFM Probe

We present an analytical solution for the shape of a fluid-fluid interface near a nanoscale solid sphere, which is a configuration motivated by common measurements with an atomic force microscope. The forces considered are surface tension, gravity, and the van der Waals attraction. The nonlinear governing equation has been solved previously using the method of matched asymptotic expansions, and this requires that the surface tension forces far exceed those of gravity, i.e., the Bond number is much less than one. We first present this method using a physically relevant scaling of the equations, then offer a new analytical solution valid for all Bond numbers. We show that one configuration with a large effective Bond number, and thus one requiring our new solution, is a nanothick liquid film spread over a solid substrate. The scaling implications of both analytical methods are considered, and both are compared with numerical solutions of the full equation.

Syntheses, crystal structures and photophysical properties of Ag(I) coordination complexes

Three Ag(I) coordination complexes, [Ag(pyzca)]n (1) (Hpyzca=pyrazine-2-carboxylic acid), Ag[(HNA)(NA)(H2O)4] (2) (HNA=nicotinic acid) and [Ag1Ag2-(2,3-pydc)]n (3) (H2pydc=pyridine-2, 3-dicarboxylic acid) have been synthesized by the hydrothermal method. Their structures are determined by single-crystal X–ray diffractometer. Complex 1 possesses the 3D infinite structure. Complex 2 is a mononuclear coordination complex and exhibits one 3D infinite network by a large number of hydrogen bonds. In complex 3, two crystallographic independent Ag(I) ions exist, i.e., Ag1 is three-coordinate and Ag2 is two-coordinate, forming the 2D layer structure. At room temperature in the solid state, the IR, FP and UV–Vis spectra of all complexes were measured and investigated in detail. The emission and absorption spectra of the three complexes and their corresponding ligands are compared and analyzed.

DNA Looping Induced by Tubular Confinement

DNA looping is essential for the function and maintenance of genetic information. At short lengths the cyclization rate is limited by the semiflexible properties of DNA, while at long distances it is limited by the rapidly declining probability of colocation of the anchoring sequences of the loop. We propose that a facilitated diffusion process increases the rate of cyclization for large loops. The maze-like nuclear environment then becomes a major impediment for the required colocation.We have investigated the kinetic evolution of DNA loops (48500 bp) induced by T4 ligase inside a nanofabricated channel system with a channel cross-section of 100x100 nm2, and a few micron channel length. We found that addition of the ligase profoundly alters the behavior of DNA. In particular, ligase acts to stabilize hairpin geometries in which the extended forward and backward arms of the hairpin scan past each other. From the linear density of DNA inside the channel, we deduce that the effective excluded volume vanishes upon addition of T4 ligase and ATP.We conclude that the two strands are effectively stapled together through a large number of weak bonds involving T4 ligase. The absence of a similarly strong transformation of DNA in free solution points towards the necessity of parallel pre-alignment through the nanotube. We point to the fact that the formation of hairpins and the 1-d scanning of strands past each other solves the kinetic problem of forming a loop in a maze-like environment.

Improvement of electrical properties of silicon oxide thin film with ultraviolet and organic gas assisted annealings

In order to form a silicon oxide thin film at a low temperature, we employed the reaction between spin-coated silicone oil and ozone gas at a low temperature of 250°C. In the formed silicon oxide films, a large number of SiOH bonds were observed. To reduce the amount of impurities such as SiOH bonds, the silicon oxide film underwent ultraviolet (UV) light treatment and alcohol-assisted annealing. The combination of dipping in ethanol and thermal annealing in methanol gas effectively reduced SiOH bonds. It was hypothesized that the SiOH bonds were displaced with SiOCH3 bonds due to the alcohol treatment. After UV treatment and alcohol annealing, the network SiOSi bonds increased, and the cage SiOSi bonds decreased. It was predicted that the cage SiOSi bonds were broken by UV light and the bonds recombined to form the network SiOSi bond. The dielectric property after UV treatment and alcohol annealing was improved owing to the decrease in the cage SiOSi and SiOH bonds.

In-site observation of the crystallization of nylon-6 mediated by the interfacial hydrogen bonds

Hydrogen bonds exist in many polymer systems and play a large role in the physical and chemical properties. In this study, nylon-6, which consists of repeated amide groups and contains large number of hydrogen bonds, is chosen as an example. Meanwhile, the oxidized unzipped MWCNTs (μCNTs) with oxygenated species such as carboxyl and hydroxyl groups are used as mediator to regulate the crystallization process of nylon-6 thin films. In-site experimental techniques, including Fourier transform infrared spectroscopy, X-ray diffraction spectroscopy, and polarized optical microscopy were utilized to get more direct insights on the crystallization mechanism of nylon-6 and μCNTs systems.

Microstructural Investigation of Interfacial Features in Al Wire Bonds

In the present study the microstructure of ultrasonically bonded Al wires on AlSiCu and AlSi metallization was investigated by means of scanning electron microscopy, electron back-scattered diffraction, and high-resolution transmission electron microscopy techniques. Detailed microstructural investigations were conducted on samples in the as-bonded condition, subsequent to power cycling tests, and after long-time thermal exposure to reveal the temperature-dependent evolution of the interfaces and the metallization layer. Typical interfacial features were found to be ultrafine and nanoscaled grains of Al and Al2O3, amorphous Al oxide particles, voids, and pores, with regions of high density of dislocations and dislocation loops within the larger grains of the wire and metallization. The observed interface features confirm the suggested mechanism of formation of bonding interface by emergence of submicron grains at the thin interfacial boundary between the metallic pair as a result of dynamic recrystallization and interdiffusion. While isothermal and/or thermomechanical cycling lead to strong grain growth in the metallization layer and the Al wire, the nanostructured interfacial regions mainly remain, indicating a high thermal stability and strength of the interface. Furthermore, evaluation of a large number of wire bonds prepared using standard bonding conditions showed the presence of a certain percentage of nonbonded areas and microstructural variations between the interconnects processed under nominally identical conditions. However, it was found that, if a sufficient effective bonding interface is provided, the long-time reliability of Al wire bonds is maintained due to the stability and strength of the nanostructured interface.

Single amino acid exchange in bacteriophage HK620 tailspike protein results in thousand-fold increase of its oligosaccharide affinity

Bacteriophage HK620 recognizes and cleaves the O-antigen polysaccharide of Escherichia coli serogroup O18A1 with its tailspike protein (TSP). HK620TSP binds hexasaccharide fragments with low affinity, but single amino acid exchanges generated a set of high-affinity mutants with submicromolar dissociation constants. Isothermal titration calorimetry showed that only small amounts of heat were released upon complex formation via a large number of direct and solvent-mediated hydrogen bonds between carbohydrate and protein. At room temperature, association was both enthalpy- and entropy-driven emphasizing major solvent rearrangements upon complex formation. Crystal structure analysis showed identical protein and sugar conformers in the TSP complexes regardless of their hexasaccharide affinity. Only in one case, a TSP mutant bound a different hexasaccharide conformer. The extended sugar binding site could be dissected in two regions: first, a hydrophobic pocket at the reducing end with minor affinity contributions. Access to this site could be blocked by a single aspartate to asparagine exchange without major loss in hexasaccharide affinity. Second, a region where the specific exchange of glutamate for glutamine created a site for an additional water molecule. Side-chain rearrangements upon sugar binding led to desolvation and additional hydrogen bonding which define this region of the binding site as the high-affinity scaffold.

Molecular dynamics simulations of peptide adsorption on self-assembled monolayers

All-atom molecular dynamics simulations are performed to investigate the neuromedin-B peptide adsorption on the self-assembled monolayers (SAMs) of SH(CH2)10N+(CH3)2CH2CH(OH)CH2SO3− (SBT), SH(CH2)10OH and SH(CH2)10CH3. The force–distance profiles show that the surface resistance to peptide adsorption is mainly generated by the water molecules tightly bound to surfaces via hydrogen bonds (hydration water molecules); but surfaces themselves may also set an energy barrier for the approaching peptide. For the SBT-SAM, the surface first exerts a relatively high repulsive force and then a rather week attractive force on the approaching peptide; meanwhile the hydration water molecules exert a strong repulsive force on the peptide. Therefore, SBT-SAM has an excellent performance on resisting protein adsorption. For the OH-SAM and CH3-SAM, surfaces show low or little energy barrier but strong affinity to the peptide; and the hydration water molecules apply merely a repulsive force within a much narrower range and with lower intensity compared with the case for the SBT-SAM. The analysis of structural and dynamical properties of the peptide, surface and water indicates that possible factors contributing to surface resistance include the hydrogen-bond formation capability of surfaces, mobility of water molecules near surfaces, surface packing density and chain flexibility of SAMs. There are a large number of hydrogen bonds formed between the hydration water molecules and the functional groups of the SBT-SAM, which greatly lowers the mobility of water molecules near the surface. This tightly-bound water layer effectively reduces the direct contact between the surface and the peptide. Furthermore, the SBT-SAM also has a high flexibility and a low surface packing density, which allows water molecules to penetrate into the surface to form tightly-bound networks and therefore reduces the affinity between the peptide and the surface. The results show that the protein-resistant properties of the SAMs are in the decreasing order of SBT-SAM>OH-SAM>CH3-SAM, which provide mechanistic explanation on SBT materials’ excellent anti-fouling performance.

Freely Available Conformer Generation Methods: How Good Are They?

Conformer generation has important implications in cheminformatics, particularly in computational drug discovery where the quality of conformer generation software may affect the outcome of a virtual screening exercise. We examine the performance of four freely available small molecule conformer generation tools (Balloon, Confab, Frog2, and RDKit) alongside a commercial tool (MOE). The aim of this study is 3-fold: (i) to identify which tools most accurately reproduce experimentally determined structures; (ii) to examine the diversity of the generated conformational set; and (iii) to benchmark the computational time expended. These aspects were tested using a set of 708 drug-like molecules assembled from the OMEGA validation set and the Astex Diverse Set. These molecules have varying physicochemical properties and at least one known X-ray crystal structure. We found that RDKit and Confab are statistically better than other methods at generating low rmsd conformers to the known structure. RDKit is particularly suited for less flexible molecules while Confab, with its systematic approach, is able to generate conformers which are geometrically closer to the experimentally determined structure for molecules with a large number of rotatable bonds (≥10). In our tests RDKit also resulted as the second fastest method after Frog2. In order to enhance the performance of RDKit, we developed a postprocessing algorithm to build a diverse and representative set of conformers which also contains a close conformer to the known structure. Our analysis indicates that, with postprocessing, RDKit is a valid free alternative to commercial, proprietary software.

A theoretical method to determine unstressed off-rate from multiple bond force spectroscopy

Using dynamic force spectroscopy to measure the kinetic off-rates of intermolecular bonds currently requires the isolation of single molecules. This requirement arises in part because no tractable analytic method for determining kinetic off-rates from the rupture of a large number of bonds under dynamic forces is currently available. We introduce a novel method for determining the unstressed off-rate from dynamic force spectroscopy experiments involving a large number of bonds. Using both the Bell and Dembo models we show that the unstressed off-rate calculated using the proposed method is in good agreement with the prescribed unstressed off-rate used in Monte-Carlo simulations of multiple bond dynamic force spectroscopy experiments given initial number of bonds (50–500) and loading rate 103–106pN/s.

Density Functional Theory Investigations on the Structure and Dissolution Mechanisms for Cellobiose and Xylan in an Ionic Liquid: Gas Phase and Cluster Calculations

Density functional theory (DFT) calculations have been carried out for cellobiose and xylan chosen as models for cellulose and hemicellulose, respectively, in gas phase, implicit and explicit solvent (water, methanol, and the ionic liquid, 1,3-dimethylimidazolium acetate) media using plane wave and atom centered basis set approaches in order to find out lowest energy conformers and configurations. Geometry, vibrational properties, and (1)H and (13)C NMR chemical shift values have been discussed under all three conditions. Calculations predict that inter- and intramolecular hydrogen bonding play an important role in the dissolution processes. In the gas phase and in implicit solvent, the anti-anti conformer of cellobiose and the anti-syn conformer of xylan are the most stable due to the formation of a large number of intramolecular hydrogen bonds. However, in the cluster calculations containing ion pairs of the ionic liquid (IL) surrounding the cellulosic units, the anti-syn conformer of cellobiose is more stable as intramolecular hydrogen bonds are substituted by intermolecular ones formed with the ions of the IL. The complexes of cellobiose (or of xylan) with the ions of the ionic liquid are stable with large negative binding energies ranging between -21 and -55 kcal mol(-1). The predicted (1)H NMR values of the lowest energy cellobiose conformers are in good agreement with the experimental value. Xylan binds stronger with the IL than cellobiose does by 20 kcal mol(-1). Furthermore, the two pentose rings in xylan are rotated by 60° to each other in contrast to their coplanarity in cellobiose, which can explain the higher solubility and the amorphous nature of hemicellulose in ionic liquids. The fewer number of hydroxyl groups in xylan (relative to cellobiose) does not affect the number of cations present in its first solvation shell while the number of anions is reduced.

The complex structures of isocitrate dehydrogenase from Clostridium thermocellum and Desulfotalea psychrophila suggest a new active site locking mechanism

Isocitrate dehydrogenase (IDH) catalyzes the oxidative NAD(P)+-dependent decarboxylation of isocitrate into α-ketoglutarate and CO2 and is present in organisms spanning the biological range of temperature. We have solved two crystal structures of the thermophilic Clostridium thermocellum IDH (CtIDH), a native open apo CtIDH to 2.35Å and a quaternary complex of CtIDH with NADP+, isocitrate and Mg2+ to 2.5Å. To compare to these a quaternary complex structure of the psychrophilic Desulfotalea psychrophila IDH (DpIDH) was also resolved to 1.93Å. CtIDH and DpIDH showed similar global thermal stabilities with melting temperatures of 67.9 and 66.9°C, respectively. CtIDH represents a typical thermophilic enzyme, with a large number of ionic interactions and hydrogen bonds per residue combined with stabilization of the N and C termini. CtIDH had a higher activity temperature optimum, and showed greater affinity for the substrates with an active site that was less thermolabile compared to DpIDH. The uncompensated negative surface charge and the enlarged methionine cluster in the hinge region both of which are important for cold activity in DpIDH, were absent in CtIDH. These structural comparisons revealed that prokaryotic IDHs in subfamily II have a unique locking mechanism involving Arg310, Asp251′ and Arg255 (CtIDH). These interactions lock the large domain to the small domain and direct NADP+ into the correct orientation, which together are important for NADP+ selectivity.

Unusual thermodynamic properties of a compact state of IgG3 Kuc and Sur pFh fragments (Hinge region)

The pFh fragments from the hinge region of human IgG3 Kuc and Sur are able to fold into a compact structure, thereby giving proteins with secondary (supersecondary) structure, mainly represented by the left-handed polyproline II helix. It has been shown that thermal denaturation of a compact pFh from the hinge region of IgG3 Kuc and Sur comprises two stages. At the first stage, the compact protein structure unfolds according to the all-or-none model with retention of the secondary structure. At the second stage, the left-handed polyproline II helix, composed of four separate cooperative blocks formed of strands with a high content of proline residues, melts itself. A polyproline conformation of the secondary structure and a large number of disulfide bonds between the chains determine a high specific enthalpy of denaturation and a high thermal stability, respectively.

Alternative packing modes leading to amyloid polymorphism in five fragments studied with molecular dynamics

Amyloid aggregates have been implicated in the pathogenesis of diseases such as type 2 diabetes, Alzheimer's, Parkinson's, and prion disease. Recently determined microcrystal structures of several short peptide segments derived from fibril-forming proteins revealed coexistence of alternative aggregation modes (amyloid polymorphism) formed by the same segment. This polymorphism may help in understanding the influence of the side chain packing on the amyloid stability. Here we use molecular dynamics (MD) simulation to analyze the stability of five pairs of polar and nonpolar polymorphic oligomers. MD simulation shows polymorphs with steric zipper interface containing large polar and/or aromatic side chains (GNNQQNY, and NNQNTF) are more stable than steric zipper interfaces made of small or hydrophobic residues (SSTNGVG, VQIVYK, and MVGGVV). Several geometric analyses revealed that larger sheet to sheet interface of the dry steric zipper through polar Q/N rich side chains holds the sheets together. Mutant simulations (Q/N→G) show substitutions with glycine disrupt the steric zipper, leading to unstable oligomers. Stability of Q/N rich oligomers was found to result from the large average number of hydrogen bonds. The molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) method reports the nonpolar component of free energy to be favorable, while electrostatic solvation is unfavorable for β-sheet association. Knowledge of structural properties of these fibrils might be useful for developing therapeutic agents against amyloidoses as well as for developing biomaterials. © 2011 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 98: 131-144, 2012.

Conformational changes to deamidated wheat gliadins and β-casein upon adsorption to oil–water emulsion interfaces

The conformation of deamidated gliadins and β-casein in solution and adsorbed at the interface of oil-in-water emulsions was studied using synchrotron radiation circular dichroism (SRCD) and front-face-fluorescence spectroscopy. Deamidation led to partial unfolding of gliadins in solution. The α-helix content of the protein decreased from 35% (in the native form) to 16.3% while the percentage of β-sheet and unordered structure increased upon deamidation. The secondary structure of deamidated gliadins was largely unchanged upon adsorption to both tricaprin/water and hexadecane/water interfaces. In contrast, β-casein adopted a more ordered structure upon adsorption to these two oil/water interfaces, the α-helix content increased from 5.5% (in solution) to 20% and 22.5% respectively after adsorption to tricaprin/water and hexadecane/water interfaces. Both deamidated gliadins and β-casein have distinctive N-terminal hydrophilic and C-terminal hydrophobic domains. Unlike β-casein which contains no cysteine residue, gliadins have a large number of intramolecular disulphide bonds located in the C-terminal hydrophobic domain which constrains the conformational freedom of this protein upon adsorption to oil/water interfaces. The hydrophobicity of the oil phase also has an impact on the conformation of each protein upon adsorption to the oil/water interfaces – systematic trends were observed between oil phase polarity from: i) tryptophan fluorescence emission maxima, and ii) the α-helix content in the adsorbed state. Our results demonstrate that conformational re-arrangement of proteins upon adsorption to emulsion interfaces is dependent not only on the hydrophobicity of the oil phase, but more importantly on the conformational flexibility of the protein.

Molecular dynamics study of the human insulin B peptide SHLVEALYLVCGERGG complexed with HLA-DQ8 reveals important hydrogen bond interactions

The basis of proper recognition of pathogens and tumours is provided by adaptive immunity. This immunological reaction of the recognition function of T-cell receptors on T lymphocytes detects antigenic peptides bound to major histocompatibility complex (MHC) molecules. Structural insight into this process has few grown considerably in the last years. In some of the cases, antigens are self-protein fragments causing autoimmunity diseases. Type 1 diabetes is such a disease connected with the human leukocyte antigen-DQ8 molecule, a class II MHC glycoprotein. Its crystal structure, complexed with LVEALYLVCGERGG peptide (insulin B peptide), has been solved, and important information about the significance of P1, P4 and P9 binding pockets has been discovered. The complex structure also revealed an unusual large number of intermolecular hydrogen bonds between insulin B peptide and MHC molecule. To further investigate the dynamics of peptide/MHC interactions, we perform molecular dynamic simulations in explicit water. Analysis of the results provided useful information of the binding of the peptide antigen to MHC molecule, which is supported by numerous hydrogen bonds besides the electrostatic (P1 and P9 pockets) or hydrophobic interactions (P4). Results also allowed some implications to be drawn for the role of residues located outside of the binding groove.

High-efficient renaturation of immobilized recombinant C-terminal fragment of human alpha-fetoprotein

C-terminal fragment of a human oncofetal alpha-fetoprotein (AFP) may be used in targeted cytostatics delivery to malignant cells of many tumors. AFP fragment (from 404 to 595 amino acids residues of a full-sized protein) was cloned and produced in Escherichia coli cells, BL21 strain (DE3) in the form of inclusion bodies. To obtain a functionally active protein, is it necessary to renature the protein. The renaturation procedure of the AFP third domain (rAFP3D) is considerably complicated by the fact that the protein is hydrophobic and contains a large number of S-S bonds. A renaturation technique of rAFP3D immobilized on silicic metal chelate resin has been developed. The yield of renatured C-terminal fragment was no less than 60% with purity on the order of 98%. The developed technique has been applied for the first time for hydrophobic protein with a large number of S-S bonds. The approach can be applied for efficient renaturation of other hydrophobic proteins with a large number of disulfide bonds for scientific and practical purposes.

A novel electrochemical sensor surface for the detection of hydrogen peroxide using cyclic bisureas/gold nanoparticle composite

A novel electrochemical sensor surface with enhanced sensitivity for the detection of hydrogen peroxide has been developed based on the layer-by-layer assembly of mercapto propionic acid (MPA), cystine-based polymethylene-bridged cyclic bisureas (CBU)/gold nanoparticle (AuNP) and horseradish peroxidase (HRP) on gold electrode. Possibility of a large number of hydrogen bonds, allowed by the chemical and sterical structure of the CBU ensures the proper immobilization of the enzyme in favorable orientation and retention of enzymatic activity. Efficient electron tunneling property of AuNP together with its electrocatalytic activity leads to higher sensitivity in the detection of H2O2. In cyclic voltammetry measurements a cathodic current due to direct electron transfer of HRP is observed which, indicates excellent electrocatalytic activity of the sensor surface. The biosensor surface modified with gold nanoparticle and CBU showed a lower detection limit of 50nM for hydrogen peroxide. Chronoamperometry is performed at −0.3V and Michaelis–Menten constant KMapp value is estimated to be 4.5μM. The newly developed sensor surface showed very high stability, reproducibility and high sensitivity.

Synthesis, characterization and infrared emissivity property of optically active polyurethane derived from tyrosine

Optically active polyurethanes (LPU and DPU) and racemic polyurethane (RPU) were synthesized by the self-polyaddition of the isocyanate-phenols which derived from the chiral and racemic tyrosine. All of the polymers were characterized by FT-IR, 1H NMR, GPC, UV–Vis spectroscopy, circular dichroism (CD) spectroscopy, TGA and X-ray diffraction (XRD), and the infrared emissivity values were investigated in addition. LPU and DPU were two enantimorphs, they possessed helical configurations and higher degree of hydrogen bondings compared to the RPU which presented random coiled molecular chain. The crystallinity and thermal decomposition temperature of LPU and DPU were higher than that of the RPU due to the more regular secondary structure which facilitate the formation of a large number of inter-chain hydrogen bonds. Consequently, the LPU and DPU exhibited lower infrared emissivity values (8–14 μm), which came down to 0.611 and 0.625.