Human Islet Amyloid Polypeptide N-Terminus Fragment Self-Assembly: Effect of Conserved Disulfide Bond on Aggregation Propensity

NASA Astrophysics Data System (ADS)

Ilitchev, Alexandre I.; Giammona, Maxwell J.; Do, Thanh D.; Wong, Amy G.; Buratto, Steven K.; Shea, Joan-Emma; Raleigh, Daniel P.; Bowers, Michael T.

2016-06-01

Amyloid formation by human islet amyloid polypeptide (hIAPP) has long been implicated in the pathogeny of type 2 diabetes mellitus (T2DM) and failure of islet transplants, but the mechanism of IAPP self-assembly is still unclear. Numerous fragments of hIAPP are capable of self-association into oligomeric aggregates, both amyloid and non-amyloid in structure. The N-terminal region of IAPP contains a conserved disulfide bond between cysteines at position 2 and 7, which is important to hIAPP's in vivo function and may play a role in in vitro aggregation. The importance of the disulfide bond in this region was probed using a combination of ion mobility-based mass spectrometry experiments, molecular dynamics simulations, and high-resolution atomic force microscopy imaging on the wildtype 1-8 hIAPP fragment, a reduced fragment with no disulfide bond, and a fragment with both cysteines at positions 2 and 7 mutated to serine. The results indicate the wildtype fragment aggregates by a different pathway than either comparison peptide and that the intact disulfide bond may be protective against aggregation due to a reduction of inter-peptide hydrogen bonding.

Elucidating How Wood Adhesives Bond to Wood Cell Walls using High-Resolution Solution-State NMR Spectroscopy

Treesearch

Daniel J. Yelle

2013-01-01

Some extensively used wood adhesives, such as pMDI (polymeric methylene diphenyl diisocyanate) and PF (phenol formaldehyde) have shown excellent adhesion properties with wood. However, distinguishing whether the strength is due to physical bonds (i.e., van der Waals, London, or hydrogen bond forces) or covalent bonds between the adherend and the adhesive is not fully...

Modeling single molecule junction mechanics as a probe of interface bonding

NASA Astrophysics Data System (ADS)

Hybertsen, Mark S.

2017-03-01

Using the atomic force microscope based break junction approach, applicable to metal point contacts and single molecule junctions, measurements can be repeated thousands of times resulting in rich data sets characterizing the properties of an ensemble of nanoscale junction structures. This paper focuses on the relationship between the measured force extension characteristics including bond rupture and the properties of the interface bonds in the junction. A set of exemplary model junction structures has been analyzed using density functional theory based calculations to simulate the adiabatic potential surface that governs the junction elongation. The junction structures include representative molecules that bond to the electrodes through amine, methylsulfide, and pyridine links. The force extension characteristics are shown to be most effectively analyzed in a scaled form with maximum sustainable force and the distance between the force zero and force maximum as scale factors. Widely used, two parameter models for chemical bond potential energy versus bond length are found to be nearly identical in scaled form. Furthermore, they fit well to the present calculations of N-Au and S-Au donor-acceptor bonds, provided no other degrees of freedom are allowed to relax. Examination of the reduced problem of a single interface, but including relaxation of atoms proximal to the interface bond, shows that a single-bond potential form renormalized by an effective harmonic potential in series fits well to the calculated results. This allows relatively accurate extraction of the interface bond energy. Analysis of full junction models shows cooperative effects that go beyond the mechanical series inclusion of the second bond in the junction, the spectator bond that does not rupture. Calculations for a series of diaminoalkanes as a function of molecule length indicate that the most important cooperative effect is due to the interactions between the dipoles induced by the donor-acceptor bond formation at the junction interfaces. The force extension characteristic of longer molecules such as diaminooctane, where the dipole interaction effects drop to a negligible level, accurately fit to the renormalized single-bond potential form. The results suggest that measured force extension characteristics for single molecule junctions could be analyzed with a modified potential form that accounts for the energy stored in deformable mechanical components in series.

Modeling single molecule junction mechanics as a probe of interface bonding

DOE PAGES

Hybertsen, Mark S.

2017-03-07

Using the atomic force microscope based break junction approach, applicable to metal point contacts and single molecule junctions, measurements can be repeated thousands of times resulting in rich data sets characterizing the properties of an ensemble of nanoscale junction structures. This paper focuses on the relationship between the measured force extension characteristics including bond rupture and the properties of the interface bonds in the junction. We analyzed a set of exemplary model junction structures using density functional theory based calculations to simulate the adiabatic potential surface that governs the junction elongation. The junction structures include representative molecules that bond tomore » the electrodes through amine, methylsulfide, and pyridine links. The force extension characteristics are shown to be most effectively analyzed in a scaled form with maximum sustainable force and the distance between the force zero and force maximum as scale factors. Widely used, two parameter models for chemical bond potential energy versus bond length are found to be nearly identical in scaled form. Furthermore, they fit well to the present calculations of N–Au and S–Au donor-acceptor bonds, provided no other degrees of freedom are allowed to relax. Examination of the reduced problem of a single interface, but including relaxation of atoms proximal to the interface bond, shows that a single-bond potential form renormalized by an effective harmonic potential in series fits well to the calculated results. This, then, allows relatively accurate extraction of the interface bond energy. Analysis of full junction models shows cooperative effects that go beyond the mechanical series inclusion of the second bond in the junction, the spectator bond that does not rupture. Calculations for a series of diaminoalkanes as a function of molecule length indicate that the most important cooperative effect is due to the interactions between the dipoles induced by the donor-acceptor bond formation at the junction interfaces. The force extension characteristic of longer molecules such as diaminooctane, where the dipole interaction effects drop to a negligible level, accurately fit to the renormalized single-bond potential form. Our results suggest that measured force extension characteristics for single molecule junctions could be analyzed with a modified potential form that accounts for the energy stored in deformable mechanical components in series.« less

Modeling single molecule junction mechanics as a probe of interface bonding

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hybertsen, Mark S.

Using the atomic force microscope based break junction approach, applicable to metal point contacts and single molecule junctions, measurements can be repeated thousands of times resulting in rich data sets characterizing the properties of an ensemble of nanoscale junction structures. This paper focuses on the relationship between the measured force extension characteristics including bond rupture and the properties of the interface bonds in the junction. We analyzed a set of exemplary model junction structures using density functional theory based calculations to simulate the adiabatic potential surface that governs the junction elongation. The junction structures include representative molecules that bond tomore » the electrodes through amine, methylsulfide, and pyridine links. The force extension characteristics are shown to be most effectively analyzed in a scaled form with maximum sustainable force and the distance between the force zero and force maximum as scale factors. Widely used, two parameter models for chemical bond potential energy versus bond length are found to be nearly identical in scaled form. Furthermore, they fit well to the present calculations of N–Au and S–Au donor-acceptor bonds, provided no other degrees of freedom are allowed to relax. Examination of the reduced problem of a single interface, but including relaxation of atoms proximal to the interface bond, shows that a single-bond potential form renormalized by an effective harmonic potential in series fits well to the calculated results. This, then, allows relatively accurate extraction of the interface bond energy. Analysis of full junction models shows cooperative effects that go beyond the mechanical series inclusion of the second bond in the junction, the spectator bond that does not rupture. Calculations for a series of diaminoalkanes as a function of molecule length indicate that the most important cooperative effect is due to the interactions between the dipoles induced by the donor-acceptor bond formation at the junction interfaces. The force extension characteristic of longer molecules such as diaminooctane, where the dipole interaction effects drop to a negligible level, accurately fit to the renormalized single-bond potential form. Our results suggest that measured force extension characteristics for single molecule junctions could be analyzed with a modified potential form that accounts for the energy stored in deformable mechanical components in series.« less

High-Resolution Crystal Structures of Protein Helices Reconciled with Three-Centered Hydrogen Bonds and Multipole Electrostatics

PubMed Central

Kuster, Daniel J.; Liu, Chengyu; Fang, Zheng; Ponder, Jay W.; Marshall, Garland R.

2015-01-01

Theoretical and experimental evidence for non-linear hydrogen bonds in protein helices is ubiquitous. In particular, amide three-centered hydrogen bonds are common features of helices in high-resolution crystal structures of proteins. These high-resolution structures (1.0 to 1.5 Å nominal crystallographic resolution) position backbone atoms without significant bias from modeling constraints and identify Φ = -62°, ψ = -43 as the consensus backbone torsional angles of protein helices. These torsional angles preserve the atomic positions of α-β carbons of the classic Pauling α-helix while allowing the amide carbonyls to form bifurcated hydrogen bonds as first suggested by Némethy et al. in 1967. Molecular dynamics simulations of a capped 12-residue oligoalanine in water with AMOEBA (Atomic Multipole Optimized Energetics for Biomolecular Applications), a second-generation force field that includes multipole electrostatics and polarizability, reproduces the experimentally observed high-resolution helical conformation and correctly reorients the amide-bond carbonyls into bifurcated hydrogen bonds. This simple modification of backbone torsional angles reconciles experimental and theoretical views to provide a unified view of amide three-centered hydrogen bonds as crucial components of protein helices. The reason why they have been overlooked by structural biologists depends on the small crankshaft-like changes in orientation of the amide bond that allows maintenance of the overall helical parameters (helix pitch (p) and residues per turn (n)). The Pauling 3.613 α-helix fits the high-resolution experimental data with the minor exception of the amide-carbonyl electron density, but the previously associated backbone torsional angles (Φ, Ψ) needed slight modification to be reconciled with three-atom centered H-bonds and multipole electrostatics. Thus, a new standard helix, the 3.613/10-, Némethy- or N-helix, is proposed. Due to the use of constraints from monopole force fields and assumed secondary structures used in low-resolution refinement of electron density of proteins, such structures in the PDB often show linear hydrogen bonding. PMID:25894612

High-resolution crystal structures of protein helices reconciled with three-centered hydrogen bonds and multipole electrostatics.

PubMed

Kuster, Daniel J; Liu, Chengyu; Fang, Zheng; Ponder, Jay W; Marshall, Garland R

2015-01-01

Theoretical and experimental evidence for non-linear hydrogen bonds in protein helices is ubiquitous. In particular, amide three-centered hydrogen bonds are common features of helices in high-resolution crystal structures of proteins. These high-resolution structures (1.0 to 1.5 Å nominal crystallographic resolution) position backbone atoms without significant bias from modeling constraints and identify Φ = -62°, ψ = -43 as the consensus backbone torsional angles of protein helices. These torsional angles preserve the atomic positions of α-β carbons of the classic Pauling α-helix while allowing the amide carbonyls to form bifurcated hydrogen bonds as first suggested by Némethy et al. in 1967. Molecular dynamics simulations of a capped 12-residue oligoalanine in water with AMOEBA (Atomic Multipole Optimized Energetics for Biomolecular Applications), a second-generation force field that includes multipole electrostatics and polarizability, reproduces the experimentally observed high-resolution helical conformation and correctly reorients the amide-bond carbonyls into bifurcated hydrogen bonds. This simple modification of backbone torsional angles reconciles experimental and theoretical views to provide a unified view of amide three-centered hydrogen bonds as crucial components of protein helices. The reason why they have been overlooked by structural biologists depends on the small crankshaft-like changes in orientation of the amide bond that allows maintenance of the overall helical parameters (helix pitch (p) and residues per turn (n)). The Pauling 3.6(13) α-helix fits the high-resolution experimental data with the minor exception of the amide-carbonyl electron density, but the previously associated backbone torsional angles (Φ, Ψ) needed slight modification to be reconciled with three-atom centered H-bonds and multipole electrostatics. Thus, a new standard helix, the 3.6(13/10)-, Némethy- or N-helix, is proposed. Due to the use of constraints from monopole force fields and assumed secondary structures used in low-resolution refinement of electron density of proteins, such structures in the PDB often show linear hydrogen bonding.

B-spline tight frame based force matching method

NASA Astrophysics Data System (ADS)

Yang, Jianbin; Zhu, Guanhua; Tong, Dudu; Lu, Lanyuan; Shen, Zuowei

2018-06-01

In molecular dynamics simulations, compared with popular all-atom force field approaches, coarse-grained (CG) methods are frequently used for the rapid investigations of long time- and length-scale processes in many important biological and soft matter studies. The typical task in coarse-graining is to derive interaction force functions between different CG site types in terms of their distance, bond angle or dihedral angle. In this paper, an ℓ1-regularized least squares model is applied to form the force functions, which makes additional use of the B-spline wavelet frame transform in order to preserve the important features of force functions. The B-spline tight frames system has a simple explicit expression which is useful for representing our force functions. Moreover, the redundancy of the system offers more resilience to the effects of noise and is useful in the case of lossy data. Numerical results for molecular systems involving pairwise non-bonded, three and four-body bonded interactions are obtained to demonstrate the effectiveness of our approach.

Reversing Conventional Reactivity of Mixed Oxo/Alkyl Rare-Earth Complexes: Non-Redox Oxygen Atom Transfer.

PubMed

Hong, Jianquan; Tian, Haiwen; Zhang, Lixin; Zhou, Xigeng; Del Rosal, Iker; Weng, Linhong; Maron, Laurent

2018-01-22

The preferential substitution of oxo ligands over alkyl ones of rare-earth complexes is commonly considered as "impossible" due to the high oxophilicity of metal centers. Now, it has been shown that simply assembling mixed methyl/oxo rare-earth complexes to a rigid trinuclear cluster framework cannot only enhance the activity of the Ln-oxo bond, but also protect the highly reactive Ln-alkyl bond, thus providing a previously unrecognized opportunity to selectively manipulate the oxo ligand in the presence of numerous reactive functionalities. Such trimetallic cluster has proved to be a suitable platform for developing the unprecedented non-redox rare-earth-mediated oxygen atom transfer from ketones to CS 2 and PhNCS. Controlled experiments and computational studies shed light on the driving force for these reactions, emphasizing the importance of the sterical accessibility and multimetallic effect of the cluster framework in promoting reversal of reactivity of rare-earth oxo complexes. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

A single molecule assay to probe monovalent and multivalent bonds between hyaluronan and its key leukocyte receptor CD44 under force

NASA Astrophysics Data System (ADS)

Bano, Fouzia; Banerji, Suneale; Howarth, Mark; Jackson, David G.; Richter, Ralf P.

2016-09-01

Glycosaminoglycans (GAGs), a category of linear, anionic polysaccharides, are ubiquitous in the extracellular space, and important extrinsic regulators of cell function. Despite the recognized significance of mechanical stimuli in cellular communication, however, only few single molecule methods are currently available to study how monovalent and multivalent GAG·protein bonds respond to directed mechanical forces. Here, we have devised such a method, by combining purpose-designed surfaces that afford immobilization of GAGs and receptors at controlled nanoscale organizations with single molecule force spectroscopy (SMFS). We apply the method to study the interaction of the GAG polymer hyaluronan (HA) with CD44, its receptor in vascular endothelium. Individual bonds between HA and CD44 are remarkably resistant to rupture under force in comparison to their low binding affinity. Multiple bonds along a single HA chain rupture sequentially and independently under load. We also demonstrate how strong non-covalent bonds, which are versatile for controlled protein and GAG immobilization, can be effectively used as molecular anchors in SMFS. We thus establish a versatile method for analyzing the nanomechanics of GAG·protein interactions at the level of single GAG chains, which provides new molecular-level insight into the role of mechanical forces in the assembly and function of GAG-rich extracellular matrices.

Anti-Arrhenius cleavage of covalent bonds in bottlebrush macromolecules on substrate.

PubMed

Lebedeva, Natalia V; Nese, Alper; Sun, Frank C; Matyjaszewski, Krzysztof; Sheiko, Sergei S

2012-06-12

Spontaneous degradation of bottlebrush macromolecules on aqueous substrates was monitored by atomic force microscopy. Scission of C ─ C covalent bonds in the brush backbone occurred due to steric repulsion between the adsorbed side chains, which generated bond tension on the order of several nano-Newtons. Unlike conventional chemical reactions, the rate of bond scission was shown to decrease with temperature. This apparent anti-Arrhenius behavior was caused by a decrease in the surface energy of the underlying substrate upon heating, which results in a corresponding decrease of bond tension in the adsorbed macromolecules. Even though the tension dropped minimally from 2.16 to 1.89 nN, this was sufficient to overpower the increase in the thermal energy (k(B)T) in the Arrhenius equation. The rate constant of the bond-scission reaction was measured as a function of temperature and surface energy. Fitting the experimental data by a perturbed Morse potential V = V(0)(1 - e(-βx))(2) - fx, we determined the depth and width of the potential to be V(0) = 141 ± 19 kJ/mol and β(-1) = 0.18 ± 0.03 Å, respectively. Whereas the V(0) value is in reasonable agreement with the activation energy E(a) = 80-220 kJ/mol of mechanical and thermal degradation of organic polymers, it is significantly lower than the dissociation energy of a C ─ C bond D(e) = 350 kJ/mol. Moreover, the force constant K(x) = 2β(2)V(0) = 1.45 ± 0.36 kN/m of a strained bottlebrush along its backbone is markedly larger than the force constant of a C ─ C bond K(l) = 0.44 kN/m, which is attributed to additional stiffness due to deformation of the side chains.

Integrating a high-force optical trap with gold nanoposts and a robust gold-DNA bond.

PubMed

Paik, D Hern; Seol, Yeonee; Halsey, Wayne A; Perkins, Thomas T

2009-08-01

Gold-thiol chemistry is widely used in nanotechnology but has not been exploited in optical-trapping experiments due to laser-induced ablation of gold. We circumvented this problem by using an array of gold nanoposts (r = 50-250 nm, h approximately 20 nm) that allowed for quantitative optical-trapping assays without direct irradiation of the gold. DNA was covalently attached to the gold via dithiol phosphoramidite (DTPA). By using three DTPAs, the gold-DNA bond was not cleaved in the presence of excess thiolated compounds. This chemical robustness allowed us to reduce nonspecific sticking by passivating the unreacted gold with methoxy-(polyethylene glycol)-thiol. We routinely achieved single beads anchored to the nanoposts by single DNA molecules. We measured DNA's elasticity and its overstretching transition, demonstrating moderate- and high-force optical-trapping assays using gold-thiol chemistry. Force spectroscopy measurements were consistent with the rupture of the strepavidin-biotin bond between the bead and the DNA. This implied that the DNA remained anchored to the surface due to the strong gold-thiol bond. Consistent with this conclusion, we repeatedly reattached the trapped bead to the same individual DNA molecule. Thus, surface conjugation of biomolecules onto an array of gold nanostructures by chemically and mechanically robust bonds provides a unique way to carry out spatially controlled, repeatable measurements of single molecules.

Local vibrational modes of the water dimer - Comparison of theory and experiment

NASA Astrophysics Data System (ADS)

Kalescky, R.; Zou, W.; Kraka, E.; Cremer, D.

2012-12-01

Local and normal vibrational modes of the water dimer are calculated at the CCSD(T)/CBS level of theory. The local H-bond stretching frequency is 528 cm-1 compared to a normal mode stretching frequency of just 143 cm-1. The adiabatic connection scheme between local and normal vibrational modes reveals that the lowering is due to mass coupling, a change in the anharmonicity, and coupling with the local HOH bending modes. The local mode stretching force constant is related to the strength of the H-bond whereas the normal mode stretching force constant and frequency lead to an erroneous underestimation of the H-bond strength.

Why do receptor–ligand bonds in cell adhesion cluster into discrete focal-adhesion sites?

DOE PAGES

Gao, Zhiwen; Gao, Yanfei

2016-05-14

We report that cell adhesion often exhibits the clustering of the receptor–ligand bonds into discrete focal-adhesion sites near the contact edge, thus resembling a rosette shape or a contracting membrane anchored by a small number of peripheral forces. The ligands on the extracellular matrix are immobile, and the receptors in the cell plasma membrane consist of two types: high-affinity integrins (that bond to the substrate ligands and are immobile) and low-affinity integrins (that are mobile and not bonded to the ligands). Thus the adhesion energy density is proportional to the high-affinity integrin density. This paper provides a mechanistic explanation formore » the clustering/assembling of the receptor–ligand bonds from two main points: (1) the cellular contractile force leads to the density evolution of these two types of integrins, and results into a large high-affinity integrin density near the contact edge and (2) the front of a propagating crack into a decreasing toughness field will be unstable and wavy. From this fracture mechanics perspective, the chemomechanical equilibrium is reached when a small number of patches with large receptor–ligand bond density are anticipated to form at the cell periphery, as opposed to a uniform distribution of bonds on the entire interface. Finally, cohesive fracture simulations show that the de-adhesion force can be significantly enhanced by this nonuniform bond density field, but the de-adhesion force anisotropy due to the substrate elastic anisotropy is significantly reduced.« less

Why do receptor–ligand bonds in cell adhesion cluster into discrete focal-adhesion sites?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gao, Zhiwen; Gao, Yanfei

We report that cell adhesion often exhibits the clustering of the receptor–ligand bonds into discrete focal-adhesion sites near the contact edge, thus resembling a rosette shape or a contracting membrane anchored by a small number of peripheral forces. The ligands on the extracellular matrix are immobile, and the receptors in the cell plasma membrane consist of two types: high-affinity integrins (that bond to the substrate ligands and are immobile) and low-affinity integrins (that are mobile and not bonded to the ligands). Thus the adhesion energy density is proportional to the high-affinity integrin density. This paper provides a mechanistic explanation formore » the clustering/assembling of the receptor–ligand bonds from two main points: (1) the cellular contractile force leads to the density evolution of these two types of integrins, and results into a large high-affinity integrin density near the contact edge and (2) the front of a propagating crack into a decreasing toughness field will be unstable and wavy. From this fracture mechanics perspective, the chemomechanical equilibrium is reached when a small number of patches with large receptor–ligand bond density are anticipated to form at the cell periphery, as opposed to a uniform distribution of bonds on the entire interface. Finally, cohesive fracture simulations show that the de-adhesion force can be significantly enhanced by this nonuniform bond density field, but the de-adhesion force anisotropy due to the substrate elastic anisotropy is significantly reduced.« less

The Effect of Two Soft Drinks on Bracket Bond Strength and on Intact and Sealed Enamel: An In Vitro Study.

PubMed

Pasha, Azam; Sindhu, D; Nayak, Rabindra S; Mamatha, J; Chaitra, K R; Vishwakarma, Swati

2015-01-01

This study was conducted to evaluate the effect of two soft drinks, Coca-Cola and Mirinda orange on bracket bond strength, on adhesive remnant on teeth after debonding the bracket, and to observe by means of scanning electron microscope (SEM) the effect of these drinks on intact and sealed enamel. 120 non-carious maxillary premolar teeth already extracted for Orthodontic purposes were taken and divided into three groups, i.e., Coca-Cola drink, Mirinda orange, and control (artificial saliva) group. Brackets were bonded using conventional methods. Teeth were kept in soft drinks for 15 days, for 15 min, 3 times a day, separated by intervals of 2 h. At other times, they were kept in artificial saliva. The samples, thus obtained were evaluated for shear bond strength using the universal testing machine and subsequently subjected for adhesive remnant index (ARI) scores. SEM study on all the three groups was done for evaluating enamel surface of the intact and sealed enamel. The lowest mean resistance to shearing forces was shown by Mirinda orange group (5.30 ± 2.74 Mpa) followed by Coca-Cola group (6.24 ± 1.59 Mpa) and highest resistance to shearing forces by control group (7.33 ± 1.72 Mpa). The ARI scores revealed a cohesive failure in control samples and an adhesive failure in Mirinda and cola samples. SEM results showed areas of defect due to erosion caused by acidic soft drinks on intact and sealed enamel surface. Mirinda group showed the lowest resistance to shearing forces, followed by Coca-Cola group and with the highest resistance to shearing forces by the control group. There were significant differences between the control group and the study groups. Areas of defects, which were caused by erosion related to acidic soft drinks on the enamel surface around the adhesive, were seen. Areas of defects caused by Coca-Cola were more extensive when compared to Mirinda orange drink.

The influence of disulfide bonds on the mechanical stability of proteins is context dependent.

PubMed

Manteca, Aitor; Alonso-Caballero, Álvaro; Fertin, Marie; Poly, Simon; De Sancho, David; Perez-Jimenez, Raul

2017-08-11

Disulfide bonds play a crucial role in proteins, modulating their stability and constraining their conformational dynamics. A particularly important case is that of proteins that need to withstand forces arising from their normal biological function and that are often disulfide bonded. However, the influence of disulfides on the overall mechanical stability of proteins is poorly understood. Here, we used single-molecule force spectroscopy (smFS) to study the role of disulfide bonds in different mechanical proteins in terms of their unfolding forces. For this purpose, we chose the pilus protein FimG from Gram-negative bacteria and a disulfide-bonded variant of the I91 human cardiac titin polyprotein. Our results show that disulfide bonds can alter the mechanical stability of proteins in different ways depending on the properties of the system. Specifically, disulfide-bonded FimG undergoes a 30% increase in its mechanical stability compared with its reduced counterpart, whereas the unfolding force of I91 domains experiences a decrease of 15% relative to the WT form. Using a coarse-grained simulation model, we rationalized that the increase in mechanical stability of FimG is due to a shift in the mechanical unfolding pathway. The simple topology-based explanation suggests a neutral effect in the case of titin. In summary, our results indicate that disulfide bonds in proteins act in a context-dependent manner rather than simply as mechanical lockers, underscoring the importance of considering disulfide bonds both computationally and experimentally when studying the mechanical properties of proteins. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

The Impact of Thermocycling Process on the Dislodgement Force of Different Endodontic Cements

PubMed Central

Saghiri, Mohammad Ali; Asatourian, Armen; Garcia-Godoy, Franklin; Gutmann, James L.; Sheibani, Nader

2013-01-01

To evaluate the effects of thermocycling (500 cycles, 5°C/55°C) on the push-out bond strength of calcium silicate based cements including WMTA, Nano-WMTA, and Bioaggregate to root dentin. Forty-eight dentin slices were prepared and divided into 3 groups (n = 16) and filled with Angelus WMTA, Nano-WMTA, or Bioaggregate. After incubation, half of the samples were thermocycled while the other half remained untreated. Push-out bond strength was calculated, and the modes of the bond failures were determined by SEM. The highest bond strength was seen in nonthermocycled Nano-WMTA samples and the lowest in thermocycled Bioaggregate samples. The significant differences between nonthermocycled and thermocycled samples were only noticed in WMTA and Nano-WMTA groups (P < 0.001). The mode of failure for thermocycled samples of all three cements was mostly cohesive. Thermocycling process can drastically affect the push-out bond strength of calcium silicate based cements. The intrastructural damages occurred due to the thermal stresses, causing cohesive failures in set materials. Sealing property of endodontic cements which have experienced the thermal stresses can be jeopardized due to occlusal forces happening in furcation cites. PMID:24063004

Anisotropic mechanoresponse of energetic crystallites: a quantum molecular dynamics study of nano-collision

NASA Astrophysics Data System (ADS)

Li, Ying; Kalia, Rajiv K.; Misawa, Masaaki; Nakano, Aiichiro; Nomura, Ken-Ichi; Shimamura, Kohei; Shimojo, Fuyuki; Vashishta, Priya

2016-05-01

At the nanoscale, chemistry can happen quite differently due to mechanical forces selectively breaking the chemical bonds of materials. The interaction between chemistry and mechanical forces can be classified as mechanochemistry. An example of archetypal mechanochemistry occurs at the nanoscale in anisotropic detonating of a broad class of layered energetic molecular crystals bonded by inter-layer van der Waals (vdW) interactions. Here, we introduce an ab initio study of the collision, in which quantum molecular dynamic simulations of binary collisions between energetic vdW crystallites, TATB molecules, reveal atomistic mechanisms of anisotropic shock sensitivity. The highly sensitive lateral collision was found to originate from the twisting and bending to breaking of nitro-groups mediated by strong intra-layer hydrogen bonds. This causes the closing of the electronic energy gap due to an inverse Jahn-Teller effect. On the other hand, the insensitive collisions normal to multilayers are accomplished by more delocalized molecular deformations mediated by inter-layer interactions. Our nano-collision studies provide a much needed atomistic understanding for the rational design of insensitive energetic nanomaterials and the detonation synthesis of novel nanomaterials.At the nanoscale, chemistry can happen quite differently due to mechanical forces selectively breaking the chemical bonds of materials. The interaction between chemistry and mechanical forces can be classified as mechanochemistry. An example of archetypal mechanochemistry occurs at the nanoscale in anisotropic detonating of a broad class of layered energetic molecular crystals bonded by inter-layer van der Waals (vdW) interactions. Here, we introduce an ab initio study of the collision, in which quantum molecular dynamic simulations of binary collisions between energetic vdW crystallites, TATB molecules, reveal atomistic mechanisms of anisotropic shock sensitivity. The highly sensitive lateral collision was found to originate from the twisting and bending to breaking of nitro-groups mediated by strong intra-layer hydrogen bonds. This causes the closing of the electronic energy gap due to an inverse Jahn-Teller effect. On the other hand, the insensitive collisions normal to multilayers are accomplished by more delocalized molecular deformations mediated by inter-layer interactions. Our nano-collision studies provide a much needed atomistic understanding for the rational design of insensitive energetic nanomaterials and the detonation synthesis of novel nanomaterials. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr08769d

A short review on thermosonic flip chip bonding

NASA Astrophysics Data System (ADS)

Suppiah, Sarveshvaran; Ong, Nestor Rubio; Sauli, Zaliman; Sarukunaselan, Karunavani; Alcain, Jesselyn Barro; Shahimin, Mukhzeer Mohamad; Retnasamy, Vithyacharan

2017-09-01

This review is to study the evolution and key findings, critical technical challenges, solutions and bonding equipment of thermosonic flip chip bonding. Based on the review done, it was found that ultrasonic power, bonding time and force are the three main critical parameters need to be optimized in order to achieve sound and reliable bonding between the die and substrate. A close monitoring of the ultrasonic power helped to prevent over bonding phenomena on flexible substrate. Gold stud bumping is commonly used in thermosonic bonding compared to solder due to its better reliability obtained in the LED and optoelectronic packages. The review comprised short details on the available thermosonic bonding equipment in the semiconductor industry as well.

A classical mechanics model for the interpretation of piezoelectric property data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bell, Andrew J., E-mail: a.j.bell@leeds.ac.uk

2015-12-14

In order to provide a means of understanding, the relationship between the primary electromechanical coefficients and simple crystal chemistry parameters for piezoelectric materials, a static analysis of a 3 atom, dipolar molecule has been undertaken to derive relationships for elastic compliance s{sup E}, dielectric permittivity ε{sup X}, and piezoelectric charge coefficient d in terms of an effective ionic charge and two inter-atomic force constants. The relationships demonstrate the mutual interdependence of the three coefficients, in keeping with experimental evidence from a large dataset of commercial piezoelectric materials. It is shown that the electromechanical coupling coefficient k is purely an expressionmore » of the asymmetry in the two force constants or bond compliances. The treatment is extended to show that the quadratic electrostriction relation between strain and polarization, in both centrosymmetric and non-centrosymmetric systems, is due to the presence of a non-zero 2nd order term in the bond compliance. Comparison with experimental data explains the counter-intuitive, positive correlation of k with s{sup E} and ε{sup X} and supports the proposition that high piezoelectric activity in single crystals is dominated by large compliance coupled with asymmetry in the sub-cell force constants. However, the analysis also shows that in polycrystalline materials, the dielectric anisotropy of the constituent crystals can be more important for attaining large charge coefficients. The model provides a completely new methodology for the interpretation of piezoelectric and electrostrictive property data and suggests methods for rapid screening for high activity in candidate piezoelectric materials, both experimentally and by novel interrogation of ab initio calculations.« less

Protein S-sulfenylation is a fleeting molecular switch that regulates non-enzymatic oxidative folding

NASA Astrophysics Data System (ADS)

Beedle, Amy E. M.; Lynham, Steven; Garcia-Manyes, Sergi

2016-08-01

The post-translational modification S-sulfenylation functions as a key sensor of oxidative stress. Yet the dynamics of sulfenic acid in proteins remains largely elusive due to its fleeting nature. Here we use single-molecule force-clamp spectroscopy and mass spectrometry to directly capture the reactivity of an individual sulfenic acid embedded within the core of a single Ig domain of the titin protein. Our results demonstrate that sulfenic acid is a crucial short-lived intermediate that dictates the protein's fate in a conformation-dependent manner. When exposed to the solution, sulfenic acid rapidly undergoes further chemical modification, leading to irreversible protein misfolding; when cryptic in the protein's microenvironment, it readily condenses with a neighbouring thiol to create a protective disulfide bond, which assists the functional folding of the protein. This mechanism for non-enzymatic oxidative folding provides a plausible explanation for redox-modulated stiffness of proteins that are physiologically exposed to mechanical forces, such as cardiac titin.

Numerical simulation of linear fiction welding (LFW) processes

NASA Astrophysics Data System (ADS)

Fratini, L.; La Spisa, D.

2011-05-01

Solid state welding processes are becoming increasingly important due to a large number of advantages related to joining "unweldable" materials and in particular light weight alloys. Linear friction welding (LFW) has been used successfully to bond non-axisymmetric components of a range of materials including titanium alloys, steels, aluminum alloys, nickel, copper, and also dissimilar material combinations. The technique is useful in the research of quality of the joints and in reducing costs of components and parts of the aeronautic and automotive industries. LFW involves parts to be welded through the relative reciprocating motion of two components under an axial force. In such process the heat source is given by the frictional forces work decaying into heat determining a local softening of the material and proper bonding conditions due to both the temperature increase and the local pressure of the two edges to be welded. This paper is a comparative test between the numerical model in two dimensions, i.e. in plane strain conditions, and in three dimensions of a LFW process of AISI1045 steel specimens. It must be observed that the 3D model assures a faithful simulation of the actual threedimensional material flow, even if the two-dimensional simulation computational times are very short, a few hours instead of several ones as the 3D model. The obtained results were compared with experimental values found out in the scientific literature.

Quantitative Percussion Diagnostics For Evaluating Bond Integrity Between Composite Laminates

NASA Astrophysics Data System (ADS)

Poveromo, Scott Leonard

Conventional nondestructive testing (NDT) techniques used to detect defects in composites are not able to determine intact bond integrity within a composite structure and are costly to use on large and complex shaped surfaces. To overcome current NDT limitations, a new technology was utilized based on quantitative percussion diagnostics (QPD) to better quantify bond quality in fiber reinforced composite materials. Experimental results indicate that this technology is capable of detecting 'kiss' bonds (very low adhesive shear strength), caused by the application of release agents on the bonding surfaces, between flat composite laminates bonded together with epoxy adhesive. Specifically, the local value of the loss coefficient determined from quantitative percussion testing was found to be significantly greater for a release coated panel compared to that for a well bonded sample. Also, the local value of the probe force or force returned to the probe after impact was observed to be lower for the release coated panels. The increase in loss coefficient and decrease in probe force are thought to be due to greater internal friction during the percussion event for poorly bonded specimens. NDT standards were also fabricated by varying the cure parameters of an epoxy film adhesive. Results from QPD for the variable cure NDT standards and lap shear strength measurements taken of mechanical test specimens were compared and analyzed. Finally, experimental results have been compared to a finite element analysis to understand the visco-elastic behavior of the laminates during percussion testing. This comparison shows how a lower quality bond leads to a reduction in the percussion force by biasing strain in the percussion tested side of the panel.

Spontaneous adsorption on a hydrophobic surface governed by hydrogen bonding.

PubMed

Dang, Fuquan; Hasegawa, Takeshi; Biju, Vasudevanpillai; Ishikawa, Mitsuru; Kaji, Noritada; Yasui, Takao; Baba, Yoshinobu

2009-08-18

Spontaneous adsorption from solution onto solid surface is a common phenomenon in nature, but the force that governs adsorption is still a matter of considerable debate. (1, 2) We found that surfactants and cellulose adsorb from solution onto a poly(methyl methacrylate) (PMMA) surface in an ordered and cooperative way governed by hydrogen bonding. The glucose rings of n-dodecyl-beta-D-maltoside (DDM) and hydroxyethylcellulose (HEC) stand perpendicular to the surface, H-bond to the surface COOMe groups with their C=O and Me-O bonds parallel to the surface, and form a tight monolayer. The non-H-bonded COOMe groups orient their C=O bonds perpendicular to the surface. In contrast, the glucose rings of hydrophobically modified hydroxyethylcellulose (HMHEC) lie flat with the side chains perpendicular to the surface and H-bond to the perpendicular-oriented C=O groups. The non-H-bonded COOMe groups orient their C=O bonds parallel but Me-O bonds near-perpendicular to the surface for stabilizing HMHEC. The current work provides a detailed picture of how surface-active molecules interact with a solid surface and self-assemble into greatly different architectures.

Design of fluidic self-assembly bonds for precise component positioning

NASA Astrophysics Data System (ADS)

Ramadoss, Vivek; Crane, Nathan B.

2008-02-01

Self Assembly is a promising alternative to conventional pick and place robotic assembly of micro components. Its benefits include parallel integration of parts with low equipment costs. Various approaches to self assembly have been demonstrated, yet demanding applications like assembly of micro-optical devices require increased positioning accuracy. This paper proposes a new method for design of self assembly bonds that addresses this need. Current methods have zero force at the desired assembly position and low stiffness. This allows small disturbance forces to create significant positioning errors. The proposed method uses a substrate assembly feature to provide a high accuracy alignment guide to the part. The capillary bond region of the part and substrate are then modified to create a non-zero positioning force to maintain the part in the desired assembly position. Capillary force models show that this force aligns the part to the substrate assembly feature and reduces sensitivity of part position to process variation. Thus, the new configuration can substantially improve positioning accuracy of capillary self-assembly. This will result in a dramatic decrease in positioning errors in the micro parts. Various binding site designs are analyzed and guidelines are proposed for the design of an effective assembly bond using this new approach.

[Cleavage time for a hydrogen bond under a load].

PubMed

Bespalov, S V; Tolpygo, K B

1993-01-01

Statistics of the hydrogen bond formation and break in a bundle of actin and myosin filaments realizing the attractive force in the sarcomere of a muscle is studied. Purely mechanical problem of the attractive-force formation and motion of myosin heads and action globules under their action is supplemented by accounting for the irreversible processes: 1. Thermal de-excitation of the latter in the chain of hydrogen bond during the elementary act of the ATP energy use resulting in fixing the extended actin filament. 2. Break of the hydrogen bonds, realizing this fixing, due to thermal fluctuations for the time tau. The average life-time turns out to be the order of time necessary for the movement of z-membrane sarcomere for the value of action filament extension delta 1, which is necessary for the process of muscle contraction to be continued.

Computational investigation of non-covalent interactions in 1-butyl 3-methylimidazolium/bis(trifluoromethylsulfonyl)imide [bmim][Tf2N] in EMD and NEMD

NASA Astrophysics Data System (ADS)

Blanco-Díaz, Edgar G.; Vázquez-Montelongo, Erik A.; Cisneros, G. Andrés; Castrejón-González, Edgar Omar

2018-02-01

Non-covalent interactions (NCIs) play a crucial role in the behavior and properties of ionic liquids (ILs). These interactions are particularly important for non-equilibrium properties such as the change in viscosity due to shearing forces (shear viscosity). Therefore, a detailed understanding of these interactions can improve our understanding of these important classes of liquids. Here, we have employed quantum mechanical energy decomposition analysis (EDA) and NCI analysis to investigate a series of representative 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ([bmim][Tf2N]) ion pairs extracted from classical equilibrium and non-equilibrium molecular dynamics simulations. EDA based on symmetry-adapted perturbation theory (SAPT) for the complete monomers, as well as fragment SAPT (FSAPT), for the functional fragments has been carried out. In general, the electrostatic component comprises ≈80% of the intermolecular interaction, and significant contributions from other components (induction and dispersion) are also observed, especially for interactions involving bifurcated hydrogen bonds. The FSAPT analysis suggests that caution is warranted when employing simplified assumptions for non-bonded interactions, e.g., focusing only on hydrogen bonds between functional fragments, since this view may not provide a complete picture of the complicated interactions between the ions. In non-equilibrium molecular dynamics, the total interaction energies of some fragments have a significant qualitative change as the shear rate increases. Our results indicate that the inter-fragment interactions play a fundamental role in the viscous behavior of ILs, suggesting that the exclusive use of geometric criteria to analyze inter-molecular interactions in these systems is not sufficient to investigate shear-thinning effects.

The role of peel stresses in cyclic debonding

NASA Technical Reports Server (NTRS)

Everett, R. A., Jr.

1982-01-01

When an adhesively bonded joint is undergoing cyclic loading, one of the possible damage modes that occurs is called cyclic debonding - progressive separation of the adherends by failure of the adhesive bond under cyclic loading. In most practical structures, both peel and shear stresses exist in the adhesive bonding during cyclic loading. The results of an experimental and analytical study to determine the role of peel stresses on cyclic debonding in a mixed mode specimen are presented. Experimentally, this was done by controlling the forces that create the peel stresses by applying a clamping force to oppose the peel stresses. Cracked lap shear joints were chosen for this study. A finite element analysis was developed to assess the effect of the clamping force on the strain energy release rates due to shear and peel stresses. The results imply that the peel stress is the principal stress causing cyclic debonding.

Anti-Arrhenius cleavage of covalent bonds in bottlebrush macromolecules on substrate

PubMed Central

Lebedeva, Natalia V.; Nese, Alper; Sun, Frank C.; Matyjaszewski, Krzysztof; Sheiko, Sergei S.

2012-01-01

Spontaneous degradation of bottlebrush macromolecules on aqueous substrates was monitored by atomic force microscopy. Scission of C─C covalent bonds in the brush backbone occurred due to steric repulsion between the adsorbed side chains, which generated bond tension on the order of several nano-Newtons. Unlike conventional chemical reactions, the rate of bond scission was shown to decrease with temperature. This apparent anti-Arrhenius behavior was caused by a decrease in the surface energy of the underlying substrate upon heating, which results in a corresponding decrease of bond tension in the adsorbed macromolecules. Even though the tension dropped minimally from 2.16 to 1.89 nN, this was sufficient to overpower the increase in the thermal energy (kBT) in the Arrhenius equation. The rate constant of the bond-scission reaction was measured as a function of temperature and surface energy. Fitting the experimental data by a perturbed Morse potential V = V0(1 - e-βx)2 - fx, we determined the depth and width of the potential to be V0 = 141 ± 19 kJ/mol and β-1 = 0.18 ± 0.03 Å, respectively. Whereas the V0 value is in reasonable agreement with the activation energy Ea = 80–220 kJ/mol of mechanical and thermal degradation of organic polymers, it is significantly lower than the dissociation energy of a C─C bond De = 350 kJ/mol. Moreover, the force constant Kx = 2β2V0 = 1.45 ± 0.36 kN/m of a strained bottlebrush along its backbone is markedly larger than the force constant of a C─C bond Kl = 0.44 kN/m, which is attributed to additional stiffness due to deformation of the side chains. PMID:22645366

Assessing the attractive/repulsive force balance in axial cyclohexane C-Hax ···Yax contacts: A combined computational analysis in monosubstituted cyclohexanes.

PubMed

Silva Lopez, Carlos; Nieto Faza, Olalla; De Proft, Frank; Kolocouris, Antonios

2016-11-15

The interactions of axial substituents in monosubstituted cyclohexane rings are studied in this work using an array of different computational techniques. Additionally, the anomalous axial preference for some bulky substituents is related to stabilizing dispersion interactions. We find that the C-H ax ···Y ax contacts for various substituents with distances ranging from 2 to ∼5 Å may include attractive dispersion forces that can affect the conformational equilibrium; these forces co-exist with Pauli repulsive forces effected by Y ax group due to van der Waals sphere penetration. At distances between 2 and 3 Å stabilizing electron transfer interactions were calculated and the combination of natural bond orbital and QTAIM analysis showed that, in certain cases, Y ax  =  t Bu, C ax -O or C ax  = O or S ax  = O or C ax  = S this interaction can be characterized as an improper H-bond. DFT-D3 and non-covalent interactions calculations (NCIs) in cyclohexane derivatives with Y ax  = SiOR 3 including H Yax ···H cy surfaces at distances ranging between 4 and 6 Å suggest that dispersion has a clear effect on the experimentally observed stabilization of the axial conformer. NCIs computed from the reduced density gradient help to visually identify and analyze these interactions. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Very empirical treatment of solvation and entropy: a force field derived from Log Po/w

NASA Astrophysics Data System (ADS)

Kellogg, Glen Eugene; Burnett, James C.; Abraham, Donald J.

2001-04-01

A non-covalent interaction force field model derived from the partition coefficient of 1-octanol/water solubility is described. This model, HINT for Hydropathic INTeractions, is shown to include, in very empirical and approximate terms, all components of biomolecular associations, including hydrogen bonding, Coulombic interactions, hydrophobic interactions, entropy and solvation/desolvation. Particular emphasis is placed on: (1) demonstrating the relationship between the total empirical HINT score and free energy of association, ΔG interaction; (2) showing that the HINT hydrophobic-polar interaction sub-score represents the energy cost of desolvation upon binding for interacting biomolecules; and (3) a new methodology for treating constrained water molecules as discrete independent small ligands. An example calculation is reported for dihydrofolate reductase (DHFR) bound with methotrexate (MTX). In that case the observed very tight binding, ΔG interaction≤-13.6 kcal mol-1, is largely due to ten hydrogen bonds between the ligand and enzyme with estimated strength ranging between -0.4 and -2.3 kcal mol-1. Four water molecules bridging between DHFR and MTX contribute an additional -1.7 kcal mol-1 stability to the complex. The HINT estimate of the cost of desolvation is +13.9 kcal mol-1.

Increasing FSW join strength by optimizing feed rate, rotating speed and pin angle

NASA Astrophysics Data System (ADS)

Darmadi, Djarot B.; Purnowidodo, Anindito; Siswanto, Eko

2017-10-01

Principally the join in Friction Stir Welding (FSW) is formed due to mechanical bonding. At least there are two factors determines the quality of this join, first is the temperature in the area around the interface and secondly the intense of mixing forces in nugget zone to create the mechanical bonding. The adequate temperature creates good flowability of the nugget zone and an intensive mixing force produces homogeneous strong bonding. Based on those two factors in this research the effects of feed rate, rotating speed and pin angle of the FSW process to the tensile strength of resulted join are studied. The true experimental method was used. Feed rate was varied at 24, 42, 55 and 74 mm/minutes and from the experimental results, it can be concluded that the higher feed rate decreases the tensile strength of weld join and it is believed due to the lower heat embedded in the material. Inversely, the higher rotating speed increases the join’s tensile strength as a result of higher heat embedded in base metal and higher mixing force in the nugget zone. The rotating speed were 1842, 2257 and 2904 RPMs. The pin angle determines the direction of mixing force. With variation of pin angle: 0°, 4°, 8° and 12° the higher pin angle generally increases the tensile strength because of more intensive mixing force. For 12° pin angle the lower tensile strength is found since the force tends to push out the nugget area from the joint gap.

Influence of van der Waals forces on increasing the strength and toughness in dynamic fracture of nanofibre networks: a peridynamic approach

NASA Astrophysics Data System (ADS)

Bobaru, F.

2007-07-01

The peridynamic method is used here to analyse the effect of van der Waals forces on the mechanical behaviour and strength and toughness properties of three-dimensional nanofibre networks under imposed stretch deformation. The peridynamic formulation allows for a natural inclusion of long-range forces (such as van der Waals forces) by considering all interactions as 'long-range'. We use van der Waals interactions only between different fibres and do not need to model individual atoms. Fracture is introduced at the microstructural (peridynamic bond) level for the microelastic type bonds, while van der Waals bonds can reform at any time. We conduct statistical studies to determine a certain volume element for which the network of randomly oriented fibres becomes quasi-isotropic and insensitive to statistical variations. This qualitative study shows that the presence of van der Waals interactions and of heterogeneities (sacrificial bonds) in the strength of the bonds at the crosslinks between fibres can help in increasing the strength and toughness of the nanofibre network. Two main mechanisms appear to control the deformation of nanofibre networks: fibre reorientation (caused by deformation and breakage) and fibre accretion (due to van der Waals interaction). Similarities to the observed toughness of polymer adhesive in the abalone shell composition are explained. The author would like to dedicate this work to the 60th anniversary of Professor Subrata Mukherjee.

Deep eutectic solvent formation: a structural view using molecular dynamics simulations with classical force fields

NASA Astrophysics Data System (ADS)

Mainberger, Sebastian; Kindlein, Moritz; Bezold, Franziska; Elts, Ekaterina; Minceva, Mirjana; Briesen, Heiko

2017-06-01

Deep eutectic solvents (DES) have gained a reputation as inexpensive and easy to handle ionic liquid analogues. This work employs molecular dynamics (MD) to simulate a variety of DES. The hydrogen bond acceptor (HBA) choline chloride was paired with the hydrogen bond donors (HBD) glycerol, 1,4-butanediol, and levulinic acid. Levulinic acid was also paired with the zwitterionic HBA betaine. In order to evaluate the reliability of data MD simulations can provide for DES, two force fields were compared: the Merck Molecular Force Field and the General Amber Force Field with two different sets of partial charges for the latter. The force fields were evaluated by comparing available experimental thermodynamic and transport properties against simulated values. Structural analysis was performed on the eutectic systems and compared to non-eutectic compositions. All force fields could be validated against certain experimental properties, but performance varied depending on the system and property in question. While extensive hydrogen bonding was found for all systems, details about the contribution of individual groups strongly varied among force fields. Interaction potentials revealed that HBA-HBA interactions weaken linearly with increasing HBD ratio, while HBD-HBD interactions grew disproportionally in magnitude, which might hint at the eutectic composition of a system.

Superstrong encapsulated monolayer graphene by the modified anodic bonding

NASA Astrophysics Data System (ADS)

Jung, Wonsuk; Yoon, Taeshik; Choi, Jongho; Kim, Soohyun; Kim, Yong Hyup; Kim, Taek-Soo; Han, Chang-Soo

2013-12-01

We report a superstrong adhesive of monolayer graphene by modified anodic bonding. In this bonding, graphene plays the role of a superstrong and ultra-thin adhesive between SiO2 and glass substrates. As a result, monolayer graphene presented a strong adhesion energy of 1.4 J m-2 about 310% that of van der Waals bonding (0.45 J m-2) to SiO2 and glass substrates. This flexible solid state graphene adhesive can tremendously decrease the adhesive thickness from about several tens of μm to 0.34 nm for epoxy or glue at the desired bonding area. As plausible causes of this superstrong adhesion, we suggest conformal contact with the rough surface of substrates and generation of C-O chemical bonding between graphene and the substrate due to the bonding process, and characterized these properties using optical microscopy, atomic force microscopy, Raman spectroscopy, and X-ray photoelectron spectroscopy.We report a superstrong adhesive of monolayer graphene by modified anodic bonding. In this bonding, graphene plays the role of a superstrong and ultra-thin adhesive between SiO2 and glass substrates. As a result, monolayer graphene presented a strong adhesion energy of 1.4 J m-2 about 310% that of van der Waals bonding (0.45 J m-2) to SiO2 and glass substrates. This flexible solid state graphene adhesive can tremendously decrease the adhesive thickness from about several tens of μm to 0.34 nm for epoxy or glue at the desired bonding area. As plausible causes of this superstrong adhesion, we suggest conformal contact with the rough surface of substrates and generation of C-O chemical bonding between graphene and the substrate due to the bonding process, and characterized these properties using optical microscopy, atomic force microscopy, Raman spectroscopy, and X-ray photoelectron spectroscopy. Electronic supplementary information (ESI) available. See DOI: 10.1039/c3nr03822j

Atomic Forces for Geometry-Dependent Point Multipole and Gaussian Multipole Models

PubMed Central

Elking, Dennis M.; Perera, Lalith; Duke, Robert; Darden, Thomas; Pedersen, Lee G.

2010-01-01

In standard treatments of atomic multipole models, interaction energies, total molecular forces, and total molecular torques are given for multipolar interactions between rigid molecules. However, if the molecules are assumed to be flexible, two additional multipolar atomic forces arise due to 1) the transfer of torque between neighboring atoms, and 2) the dependence of multipole moment on internal geometry (bond lengths, bond angles, etc.) for geometry-dependent multipole models. In the current study, atomic force expressions for geometry-dependent multipoles are presented for use in simulations of flexible molecules. The atomic forces are derived by first proposing a new general expression for Wigner function derivatives ∂Dlm′m/∂Ω. The force equations can be applied to electrostatic models based on atomic point multipoles or Gaussian multipole charge density. Hydrogen bonded dimers are used to test the inter-molecular electrostatic energies and atomic forces calculated by geometry-dependent multipoles fit to the ab initio electrostatic potential (ESP). The electrostatic energies and forces are compared to their reference ab initio values. It is shown that both static and geometry-dependent multipole models are able to reproduce total molecular forces and torques with respect to ab initio, while geometry-dependent multipoles are needed to reproduce ab initio atomic forces. The expressions for atomic force can be used in simulations of flexible molecules with atomic multipoles. In addition, the results presented in this work should lead to further development of next generation force fields composed of geometry-dependent multipole models. PMID:20839297

Effects of rheology and viscosity of biobased adhesives on bonding performance

USDA-ARS?s Scientific Manuscript database

Rheology is the science of deformation and flow of the matter due to the application of a force. Most rheological tests involve applying a force to a material and measuring its flow or change in shape. Rheological characterization is useful to study the flowability and viscoelastic properties of adh...

The Effect of Two Soft Drinks on Bracket Bond Strength and on Intact and Sealed Enamel: An In Vitro Study

PubMed Central

Pasha, Azam; Sindhu, D; Nayak, Rabindra S; Mamatha, J; Chaitra, K R; Vishwakarma, Swati

2015-01-01

Background and Objectives: This study was conducted to evaluate the effect of two soft drinks, Coca-Cola and Mirinda orange on bracket bond strength, on adhesive remnant on teeth after debonding the bracket, and to observe by means of scanning electron microscope (SEM) the effect of these drinks on intact and sealed enamel. Methods: 120 non-carious maxillary premolar teeth already extracted for Orthodontic purposes were taken and divided into three groups, i.e., Coca-Cola drink, Mirinda orange, and control (artificial saliva) group. Brackets were bonded using conventional methods. Teeth were kept in soft drinks for 15 days, for 15 min, 3 times a day, separated by intervals of 2 h. At other times, they were kept in artificial saliva. The samples, thus obtained were evaluated for shear bond strength using the universal testing machine and subsequently subjected for adhesive remnant index (ARI) scores. SEM study on all the three groups was done for evaluating enamel surface of the intact and sealed enamel. Results: The lowest mean resistance to shearing forces was shown by Mirinda orange group (5.30 ± 2.74 Mpa) followed by Coca-Cola group (6.24 ± 1.59 Mpa) and highest resistance to shearing forces by control group (7.33 ± 1.72 Mpa). The ARI scores revealed a cohesive failure in control samples and an adhesive failure in Mirinda and cola samples. SEM results showed areas of defect due to erosion caused by acidic soft drinks on intact and sealed enamel surface. Conclusion: Mirinda group showed the lowest resistance to shearing forces, followed by Coca-Cola group and with the highest resistance to shearing forces by the control group. There were significant differences between the control group and the study groups. Areas of defects, which were caused by erosion related to acidic soft drinks on the enamel surface around the adhesive, were seen. Areas of defects caused by Coca-Cola were more extensive when compared to Mirinda orange drink. PMID:26668477

Water's role in the force-induced unfolding of ubiquitin.

PubMed

Li, Jingyuan; Fernandez, Julio M; Berne, B J

2010-11-09

In atomic force spectroscopic studies of the elastomeric protein ubiquitin, the β-strands 1-5 serve as the force clamp. Simulations show how the rupture force in the force-induced unfolding depends on the kinetics of water molecule insertion into positions where they can eventually form hydrogen bonding bridges with the backbone hydrogen bonds in the force-clamp region. The intrusion of water into this region is slowed down by the hydrophobic shielding effect of carbonaceous groups on the surface residues of β-strands 1-5, which thereby regulates water insertion prior to hydrogen bond breakage. The experiments show that the unfolding of the mechanically stressed protein is nonexponential due to static disorder. Our simulations show that different numbers and/or locations of bridging water molecules give rise to a long-lived distribution of transition states and static disorder. We find that slowing down the translational (not rotational) motions of the water molecules by increasing the mass of their oxygen atoms, which leaves the force field and thereby the equilibrium structure of the solvent unchanged, increases the average rupture force; however, the early stages of the force versus time behavior are very similar for our "normal" and fictitious "heavy" water models. Finally, we construct six mutant systems to regulate the hydrophobic shielding effect of the surface residues in the force-clamp region. The mutations in the two termini of β-sheets 1-5 are found to determine a preference for different unfolding pathways and change mutant's average rupture force.

Ab initio folding of mixed-fold FSD-EY protein using formula-based polarizable hydrogen bond (PHB) charge model

NASA Astrophysics Data System (ADS)

Zhang, Dawei; Lazim, Raudah; Mun Yip, Yew

2017-09-01

We conducted an all-atom ab initio folding of FSD-EY, a protein with a ββα configuration using non-polarizable (AMBER) and polarizable force fields (PHB designed by Gao et al.) in implicit solvent. The effect of reducing the polarization effect integrated into the force field by the PHB model, termed the PHB0.7 was also examined in the folding of FSD-EY. This model incorporates into the force field 70% of the original polarization effect to minimize the likelihood of over-stabilizing the backbone hydrogen bonds. Precise folding of the β-sheet of FSD-EY was further achieved by relaxing the REMD structure obtained in explicit water.

Electronegativity determination of individual surface atoms by atomic force microscopy.

PubMed

Onoda, Jo; Ondráček, Martin; Jelínek, Pavel; Sugimoto, Yoshiaki

2017-04-26

Electronegativity is a fundamental concept in chemistry. Despite its importance, the experimental determination has been limited only to ensemble-averaged techniques. Here, we report a methodology to evaluate the electronegativity of individual surface atoms by atomic force microscopy. By measuring bond energies on the surface atoms using different tips, we find characteristic linear relations between the bond energies of different chemical species. We show that the linear relation can be rationalized by Pauling's equation for polar covalent bonds. This opens the possibility to characterize the electronegativity of individual surface atoms. Moreover, we demonstrate that the method is sensitive to variation of the electronegativity of given atomic species on a surface due to different chemical environments. Our findings open up ways of analysing surface chemical reactivity at the atomic scale.

Electronegativity determination of individual surface atoms by atomic force microscopy

PubMed Central

Onoda, Jo; Ondráček, Martin; Jelínek, Pavel; Sugimoto, Yoshiaki

2017-01-01

Electronegativity is a fundamental concept in chemistry. Despite its importance, the experimental determination has been limited only to ensemble-averaged techniques. Here, we report a methodology to evaluate the electronegativity of individual surface atoms by atomic force microscopy. By measuring bond energies on the surface atoms using different tips, we find characteristic linear relations between the bond energies of different chemical species. We show that the linear relation can be rationalized by Pauling's equation for polar covalent bonds. This opens the possibility to characterize the electronegativity of individual surface atoms. Moreover, we demonstrate that the method is sensitive to variation of the electronegativity of given atomic species on a surface due to different chemical environments. Our findings open up ways of analysing surface chemical reactivity at the atomic scale. PMID:28443645

Fastening hardware to honeycomb panels

NASA Technical Reports Server (NTRS)

Kenger, A.

1979-01-01

Adhesive bonding reduces likelihood of skin failure due to excessive forces or torques by utilizing an adhesive to honeycomb skin. Concept is useful in other applications of composites such as aircraft, automobiles, and home appliances.

Importance of anisotropy in detachment rates for force production and cargo transport by a team of motor proteins.

PubMed

Takshak, Anjneya; Kunwar, Ambarish

2016-05-01

Many cellular processes are driven by collective forces generated by a team consisting of multiple molecular motor proteins. One aspect that has received less attention is the detachment rate of molecular motors under mechanical force/load. While detachment rate of kinesin motors measured under backward force increases rapidly for forces beyond stall-force; this scenario is just reversed for non-yeast dynein motors where detachment rate from microtubule decreases, exhibiting a catch-bond type behavior. It has been shown recently that yeast dynein responds anisotropically to applied load, i.e. detachment rates are different under forward and backward pulling. Here, we use computational modeling to show that these anisotropic detachment rates might help yeast dynein motors to improve their collective force generation in the absence of catch-bond behavior. We further show that the travel distance of cargos would be longer if detachment rates are anisotropic. Our results suggest that anisotropic detachment rates could be an alternative strategy for motors to improve the transport properties and force production by the team. © 2016 The Protein Society.

Dynamic stability of stacked disk type flywheels

NASA Astrophysics Data System (ADS)

Younger, F. C.

1981-04-01

A flywheel assembly formed from adhesively bonded stacked fiber composite disks was analyzed. The stiffness and rigidity of the assembly required to prevent uncontrolled growth in the deformations due to centrifugal force was determined. It is shown that stacked disk type flywheels become unstable when the speed exceeds a critical value. This critical value of speed depends upon the stiffness of the bonded attachments between the disks. It is found that elastomeric bonds do not provide adequate stiffness to insure dynamic stability for high speed stacked disk type flywheels.

Microwave Spectrum of the Isopropanol-Water Dimer

NASA Astrophysics Data System (ADS)

Mead, Griffin; Finneran, Ian A.; Carroll, Brandon; Blake, Geoffrey

2016-06-01

Microwave spectroscopy provides a unique opportunity to study model non-covalent interactions. Of particular interest is the hydrogen bonding of water, whose various molecular properties are influenced by both strong and weak intermolecular forces. More specifically, measuring the hydrogen bonded structures of water-alcohol dimers investigates both strong (OH ··· OH) and weak (CH ··· OH) hydrogen bond interactions. Recently, we have measured the pure rotational spectrum of the isopropanol-water dimer using chirped-pulse Fourier transform microwave spectroscopy (CP-FTMW) between 8-18 GHz. Here, we present the spectrum of this dimer and elaborate on the structure's strong and weak hydrogen bonding.

Parametrization of a force field for metals complexed to biomacromolecules: applications to Fe(II), Cu(II) and Pb(II)

NASA Astrophysics Data System (ADS)

David, Laurent; Amara, Patricia; Field, Martin J.; Major, François

2002-08-01

Although techniques for the simulation of biomolecules, such as proteins and RNAs, have greatly advanced in the last decade, modeling complexes of biomolecules with metal ions remains problematic. Precise calculations can be done with quantum mechanical methods but these are prohibitive for systems the size of macromolecules. More qualitative modeling can be done with molecular mechanical potentials but the parametrization of force fields for metals is often difficult, particularly if the bonding between the metal and the groups in its coordination shell has significant covalent character. In this paper we present a method for deriving bond and bond-angle parameters for metal complexes from experimental bond and bond-angle distributions obtained from the Cambridge Structural Database. In conjunction with this method, we also introduce a non-standard energy term of gaussian form that allows us to obtain a stable description of the coordination about a metal center during a simulation. The method was evaluated on Fe(II)-porphyrin complexes, on simple Cu(II) ion complexes and a number of complexes of the Pb(II) ion.

Investigating the settling dynamics of cohesive silt particles with particle-resolving simulations

NASA Astrophysics Data System (ADS)

Sun, Rui; Xiao, Heng; Sun, Honglei

2018-01-01

The settling of cohesive sediment is ubiquitous in aquatic environments, and the study of the settling process is important for both engineering and environmental reasons. In the settling process, the silt particles show behaviors that are different from non-cohesive particles due to the influence of inter-particle cohesive force. For instance, the flocs formed in the settling process of cohesive silt can loosen the packing, and thus the structural densities of cohesive silt beds are much smaller than that of non-cohesive sand beds. While there is a consensus that cohesive behaviors depend on the characteristics of sediment particles (e.g., Bond number, particle size distribution), little is known about the exact influence of these characteristics on the cohesive behaviors. In addition, since the cohesive behaviors of the silt are caused by the inter-particle cohesive forces, the motions of and the contacts among silt particles should be resolved to study these cohesive behaviors in the settling process. However, studies of the cohesive behaviors of silt particles in the settling process based on particle-resolving approach are still lacking. In the present work, three-dimensional settling process is investigated numerically by using CFD-DEM (Computational Fluid Dynamics-Discrete Element Method). The inter-particle collision force, the van der Waals force, and the fluid-particle interaction forces are considered. The numerical model is used to simulate the hindered settling process of silt based on the experimental setup in the literature. The results obtained in the simulations, including the structural densities of the beds, the characteristic lines, and the particle terminal velocity, are in good agreement with the experimental observations in the literature. To the authors' knowledge, this is the first time that the influences of non-dimensional Bond number and particle polydispersity on the structural densities of silt beds have been investigated separately. The results demonstrate that the cohesive behavior of silt in the settling process is attributed to both the cohesion among silt particles themselves and the particle polydispersity. To guide to the macro-scale modeling of cohesive silt sedimentation, the collision frequency functions obtained in the numerical simulations are also presented based on the micromechanics of particles. The results obtained by using CFD-DEM indicate that the binary collision theory over-estimated the particle collision frequency in the flocculation process at high solid volume fraction.

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