Single-molecule measurement of the strength of a siloxane bond

Increasing the mechanical stability of artificial polymer materials is an important task in materials science, and for this a profound knowledge of the critical mechanoelastic properties of its constituents is vital. Here, we use AFM-based single-molecule force spectroscopy measurements to characterize the rupture of a single silicon-oxygen bond in the backbone of polydimethylsiloxane as well as the force-extension behavior of this polymer. PDMS is not only a polymer used in a large variety of products but also an important model system for highly flexible polymers. In our experiments, we probe the entire relevant force range from low forces dominated by entropy up to the rupture of the covalent Si-O bonds in the polymer backbone at high forces. The resulting rupture-force histograms are investigated with microscopic models of bond rupture under load and are compared to density functional theory calculations to characterize the free-energy landscape of the Si-O bond in the polymer backbone.     

Molecular and nanoscale factors governing pressure‐sensitive adhesion strength of viscoelastic polymers

Pressure‐sensitive adhesives (PSAs) are finding increasing applications in various areas of industry and medicine. PSAs are a special class of viscoelastic polymers that form strong adhesive joints with substrates of varying chemical nature under application of light external bonding pressures (1–10 Pa) over short periods of time (1–5 s). To be a PSA, a polymer should possess both high fluidity under applied bonding pressure, to form good adhesive contact, and high cohesive strength and elasticity, which are necessary for resistance to debonding stresses and for dissipation of mechanical energy at the stage of adhesive bond failure under detaching force. For rational design of novel PSAs, molecular insight into mechanisms of their adhesive behavior is necessary. As shown in this review, strength of PSA adhesive joints is controlled by a combination of diffusion, viscoelastic, and relaxation mechanisms. At the molecular level, strong adhesion is the result of a narrow balance between two generally conflicting properties: high cohesive strength and large free volume. These conflicting properties are difficult to combine in a single polymer material. Individually, high cohesive interaction energy and large free volume are necessary but insufficient prerequisites for PSA strength. Evident correlations are observed between the adhesive bond strengths of different PSAs, and their relaxation behaviors are described by longer relaxation times. Innovative PSAs with tailored properties can be produced by physical mixing of nonadhesive long‐ and short‐chain linear parent polymers, with groups at the two ends of the short chains complementary to the functional groups in the recurring units of the long chains. Although chemical composition and molecular structure of such innovative adhesives are unrelated to those of conventional PSAs, their mechanical properties and adhesive behaviors obey the same general laws, such as the Dahlquist's criterion of tack. © 2012 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys, 2012     

Calculation of the entropy and free energy from monte carlo simulations of a peptide stretched by an external force

Hypothetical scanning Monte Carlo (HSMC) is a method for calculating the absolute entropy, S, and free energy, F, from a trajectory generated by any simulation technique. HSMC was applied initially to fluids (argon and water) and later to peptides and self-avoiding walks on a lattice. In this paper we make a step further and apply it to a model of decaglycine (at T = 300 K) in vacuum with constant bond lengths where external stretching forces are exerted at the end points; the changes in S and F are calculated as the forces are increased. The molecule is placed initially in a helical structure, which is changed to an extended structure after a short simulation time due to the exerted forces. This study has relevance to problems in polymers (e.g., rubber elasticity) and to the analysis of experiments where individual molecules are stretched by atomic force microscopy (AFM), for example. The results for S and F are accurate and are significantly better than those obtained by the quasi-harmonic approximation and the local states method. However, the molecule is quite stiff due to the strong bond angle potentials and the extensions are small even for relatively large forces. Correspondingly, as the force is increased the decrease in the entropy is relatively small while the potential energy is enhanced significantly. Still, differences, TDeltaS, for different forces are obtained with very good accuracy of approximately 0.2 kcal/mol.     

Intramolecular Cross-Linking: Addressing Mechanochemistry with a Bioinspired Approach

Many of the attractive properties in polymers are a consequence of their high molecular weight and therefore, scission of chains due to mechanochemistry leads to deterioration in properties and performance. Intramolecular cross-links are systematically added to linear chains, slowing down mechanochemical degradation to the point where the chains become virtually invincible to shear in solution. Our approach mimics the immunoglobulin-like domains of Titin, whose structure directs mechanical force towards the scission of sacrificial intramolecular hydrogen bonds, absorbing mechanical energy while unfolding. The kinetics of the mechanochemical reactions supports this hypothesis, as the polymer properties are maintained while high rates of mechanochemistry are observed. Our results demonstrate that polymers with intramolecular cross-links can be used to make solutions which, even under severe shear, maintain key properties such as viscosity.     

电喷雾离子源中样品离子化能量转移理论的初探

电喷雾离子源（electrospray ionization,ESI）不仅可以用于小分子的检测,也能够用于蛋白质、多肽等大分子的研究。本文通过对离子化过程的系统分析,提出了基于能量最低原理的离子化过程能量转移理论。样品分子在由液相转移到气相形成离子化气体的过程中受到静电力、分子间的范德华力等多种力的作用。样品的离子化是多种力共同作用的结果,在不同的离子化阶段,不同形式的力的作用也不尽相同。电荷在样品表面蒸发和多电荷离子的形成之间存在竞争。对不同结构的分子,分子形态、构象改变导致的两相间转移Gibbs自由能变化不同,可能导致离子蒸发、大分子形成多电荷离子、产生链弹射等行为。离子化能量转移理论不仅能够对已有的3种理论加以简化统一,也可以说明溶剂、电解质离子等在离子化过程中的作用,为优化不同结构与形态样品的质谱检测、了解离子化的真实过程提供了一种可能的依据。     

The Effect of Pulling and Twisting Forces on Chameleon Sequence Peptides**

Chameleon sequences are amino acid sequences found in several distinct configurations in experiment. They challenge our understanding of the link between sequence and structure, and provide insight into structural competition in proteins. Here, we study the energy landscapes for three such sequences, and interrogate how pulling and twisting forces impact the available structural ensembles. Chameleon sequences do not necessarily exhibit multiple structural ensembles on a multifunnel energy landscape when we consider them in isolation. The application of even small forces leads to drastic changes in the energy landscapes. For pulling forces, we observe transitions from helical to extended structures in a very small span of forces. For twisting forces, the picture is much more complex, and highly dependent on the magnitude and handedness of the applied force as well as the reference angle for the twist. Depending on these parameters, more complex and more simplistic energy landscapes are observed alongside more and less diverse structural ensembles. The impact of even small forces is significant, confirming their likely role in folding events. In addition, small forces exerted by the remaining scaffold of a protein may be sufficient to lead to the adoption of a specific structural ensemble by a chameleon sequence.     

Effect of Hydrodynamic Forces on meso‐(4‐Sulfonatophenyl)‐Substituted Porphyrin J‐Aggregate Nanoparticles: Elasticity,Plasticity and Breaking

The J aggregates of 4‐sulfonatophenyl meso‐substituted porphyrins are non‐covalent polymers obtained by self‐assembly that form nanoparticles of different morphologies. In the case of high aspect‐ratio nanoparticles (bilayered ribbons and monolayered nanotubes), shear hydrodynamic forces may modify their shape and size, as observed by peak force microscopy, transmission electron microscopy of frozen solutions, small‐angle X‐ray scattering measurements in a disk‐plate rotational cell, and cone–plate rotational viscometry. These nanoparticles either show elastic or plastic behaviour: there is plasticity in the ribbons obtained upon nanotube collapse on solid/air interfaces and in viscous concentrated nanotube solutions, whereas elasticity occurs in the case of dilute nanotube solutions. Sonication and strong shear hydrodynamic forces lead to the breaking of the monolayered nanotubes into small particles, which then associate into large colloidal particles.     

Surface forces,supramolecular polymers,and inversion symmetry

The effects of supramolecular equilibrium polymers on surface forces are studied by both a phenomenological Landau type analysis and a molecular model based on a Bethe-Guggenheim approximation. We point out that surface forces brought about by equilibrium polymers may be completely different from what can be found with "ordinary" polymers. The new feature is the role of inversion (a)symmetry or "directionality" of the associating unit molecules ("monomers"). Symmetric B-B monomers (where B denotes a self-complementary binding group) give rise to nondirectional chains and lead to attractive forces between similar surfaces. Asymmetric A-D monomers (where A and D denote complementary acceptor and donor groups, respectively) produce directional chains and can cause strong repulsion. The range of the attractive force has a maximum at intermediate concentration, while the range of the repulsive force increases over the whole concentration range.     

Elastic behavior of short compact polymers

In this paper, we investigate the elastic behaviors of short compact polymers using the enumeration calculation method and the HP model on a two-dimensional square lattice. Both the mean-square end-to-end distance R(2) and the ratio of R(2)/S(2) increase with lambda. However, when the elongation ratio becomes larger, the curves of R(2)/S(2) become smooth and they are close to the limit of 10.50 for different compact polymers. We also investigate the changes of interior conformations in the process of tensile elongation through calculating the probabilities of three bond angles (i.e., 90 degrees, 180 degrees, and 270 degrees). The average energy and Helmholtz free energy per bond are both negative and increase with elongation ratio lambda. In the meantime, the elastic force per bond (f ) also increases with elongation ratio lambda, and the energy contribution to the elastic force (f(U)) increases first and then drops, and there exists the maximum of f(U) in the region of lambda=1.40-1.80 for different sequences. The entropy contribution to force (f(S)) is close to zero at a small elongation ratio lambda and then increases with lambda. Some comparisons with different sequences (including nonfolding and folding sequences) are also made.     

Atomistic evidence of how force dynamically regulates thiol/disulfide exchange

The intricate coupling of mechanical force and chemical reactivity has been increasingly revealed in recent years by force spectroscopy experiments on the thiol/disulfide exchange reaction. We here aimed at elucidating the underlying dynamic effects of force on the reaction center for the case of disulfide bond reduction by dithiothreitol at forces of 200-2000 pN, by combining transition path sampling and quantum/classical mechanical simulations. Reaction rates and their dependence on force as quantified by Δx(r), the distance between reactant and transition state, are in good agreement with experiments but indicate a shift of the transition state structure at high forces. Indeed, while an associate S(N)2 mechanism prevails, force causes a move of the transition state to a longer length of the cleaving bond and a shorter length of the forming disulfide bond. Our results highlight the distribution of force into various degrees of freedom, which implies that care must be taken when correlating Δx(r) with a single order parameter of the reaction.     

Anomalously increased lifetimes of biological complexes at zero force due to the protein-water interface

A number of biological bonds show dramatically increased lifetimes at zero-force conditions, compared to lifetimes when even a small tensile force is applied to the ligand. The discrepancy is so great that it cannot be explained by the traditional receptor-ligand binding models. This generic phenomenon is rationalized here by considering the interaction of water with the receptor-ligand complex. It is argued that the water-protein interaction creates an energy barrier that prevents the ligand unbinding in the absence of the force. The properties of the interaction are such that even application of a relatively low force results in a dramatic drop of the bond lifetime due to the alteration of the water-receptor and water-ligand interaction network. The phenomenon is described by the presence of a second shallow interaction energy minimum for the bound ligand followed by a wide receptor-ligand dissociation barrier. The general analysis is applied quantitatively to the actin-myosin system, which demonstrates the gigantic drop of the bond lifetime at small forces and catch behavior (an increase in the lifetime) at moderate forces. The base hypothesis proposed to explain the small-force abnormal drop in the bond lifetime suggests that the majority of biological bonds may exhibit this phenomenon irrespectively whether they behave as slip or catch-slip bonds.     

Temperature dependent nano indentation of thin polymer films with the scanning force microscope

The scanning force microscope (SFM) was used to investigate the temperature dependent micro mechanical properties of polymethylmethacrylate (PMMA) films with a thickness of 35 nm in the range of the radius of gyration. Force-distance curves were performed in the glass transition range to create permanent nanometric indentations with maximal forces up to 4 μN. Quantitative measurements of the indentation depth during and after application of the force, hysteresis energy and slope of the loading part are carried out as function of sample temperature and applied force. The glass transition of the polymer film can be clearly identified by the change of the mechanical properties of the polymer. Surprisingly, only a small change of elasticity at the glass transition is observed.     

Highly covalent ferric-thiolate bonds exhibit surprisingly low mechanical stability

Depending on their nature, different chemical bonds show vastly different stability with covalent bonds being the most stable ones that rupture at forces above nanonewton. Studies have revealed that ferric-thiolate bonds are highly covalent and are conceived to be of high mechanical stability. Here, we used single molecule force spectroscopy techniques to directly determine the mechanical strength of such highly covalent ferric-thiolate bonds in rubredoxin. We observed that the ferric-thiolate bond ruptures at surprisingly low forces of ～200 pN, significantly lower than that of typical covalent bonds, such as C-Si, S-S, and Au-thiolate bonds, which typically ruptures at >1.5 nN. And the mechanical strength of Fe-thiolate bonds is observed to correlate with the covalency of the bonds. Our results indicated that highly covalent Fe-thiolate bonds are mechanically labile and display features that clearly distinguish themselves from typical covalent bonds. Our study not only opens new avenues to investigating this important class of chemical bonds, but may also shed new lights on our understanding of the chemical nature of these metal thiolate bonds.     

Molecular dynamics simulations for pure epsilon-CL-20 and epsilon-CL-20-based PBXs

Molecular dynamics has been employed to simulate the well-known high energy density compound epsilon-CL-20 (hexanitrohexaazaisowurtzitane) crystal and 12 epsilon-CL-20-based PBXs (polymer bonded explosives) with four kinds of typical fluorine polymers, i.e., polyvinylidenedifluoride, polychlorotrifluoroethylene, fluorine rubber (F(2311)), and fluorine resin (F(2314)) individually. The elastic coefficients, isotropic mechanical properties (tensile moduli, bulk moduli, shear moduli, and poission's ratios), and bonding energy are first reported for epsilon-CL-20 crystal and epsilon-CL-20-based polymer bonded explosives (PBXs). The mechanical properties of epsilon-CL-20 can be effectively improved by blending with a small amount of fluorine polymers, and the whole effect of the adding fluorine polymers to improve mechanical properties of PBXs along the three crystalline surfaces of epsilon-CL-20 is found to be (100) approximately (001) > (010). The interaction between each of the crystalline surfaces and each of the fluorine polymers is different, and the ordering of binding energy for the three surfaces is (001) > (100) > (010); F(2314) always has the strongest binding ability with the three different surfaces. F(2314) can best improve the ductibility and tenacity of PBX when it is positioned on epsilon-CL-20 (001) crystal surface. The calculations on detonation performances for pure epsilon-CL-20 crystal and the four epsilon-CL-20-based PBXs show that adding a small amount of fluorine polymer into pure epsilon-CL-20 will lower detonation performance, but each detonation parameter of the obtained PBXs is still excellent.     

Elastic Behaviors of Adsorbed Protein-like Chains

Elastic behaviors of protein-like chains are investigated by Pruned-Enriched-Rosenbluth method and modified orientation-dependent monomer-monomer interactions model. The protein-like chain is pulled away from the attractive surface slowly with elastic force acting on it. Strong adsorption interaction and no adsorption interaction are both considered. We calculate the characteristic ratio and shape factor of protein-like chains in the process of elongation. The conformation change of the protein-like chain is well depicted. The shape of chain changes from “rod” to “sphere” at the beginning of elongation. Then, the shape changes from “sphere” to “rod”. In the end, the shape becomes a “sphere” as the chain leaves away from the surface. In the meantime, we discuss average Helmoholtz free energy per bond, average energy per bond, average adsorbed energy per bond, average α-helical energy per bond, average β-sheet energy per bond and average contact energy per bond.On the other hand, elastic force is also studied. It is found that elastic force has a long plateau during the tensile elongation when there exists adsorption interaction. This result is consistent with SMFS experiment of general polymers. Energy contribution to elastic force and contact energy contribution to elastic force are both discussed. These investigations can provide some insights into the elastic behaviors of adsorbed protein chains.     

Force–Spectrum Relations for Molecular Optical Force Probes

Force probes allow real‐time monitoring of forces acting in different regions of large molecules and are potentially suited for the investigation of structural changes occurring in macromolecules during, e. g., folding processes. 1 – 10 Such information is crucial for the understanding of mechanochemical reactivity. 2 , 3 , 6 , 7 To this end, small molecular force probes can be incorporated into large molecules. 2 , 3 , 11 – 13 Some of the available systems are based on mechanochromism, the change of the UV/Vis absorption spectrum of a molecule under mechanical stress. 1 , 14 Herein we propose the idea of using molecular force probes in which the point‐group symmetry is reduced as a result of mechanical deformation. This effect leads to significant and characteristic changes in the UV/Vis, IR, and Raman spectra of the deformed molecules, which were determined using computational methods. Beneficially, these changes are reversible and occur even if the applied forces are small.     

Topography of the free-energy landscape probed via mechanical unfolding of proteins

Single-molecule experiments in which proteins are unfolded by applying mechanical stretching forces generally force unfolding to proceed along a reaction coordinate that is different from that in chemical or thermal denaturation. Here we simulate the mechanical unfolding and refolding of a minimalist off-lattice model of the protein ubiquitin to explore in detail the slice of the multidimensional free-energy landscape that is accessible via mechanical pulling experiments. We find that while the free-energy profile along typical "chemical" reaction coordinates may exhibit two minima, corresponding to the native and denatured states, the free energy G(z) is typically a monotonic function of the mechanical coordinate z equal to the protein extension. Application of a stretching force along z tilts the free-energy landscape resulting in a bistable (or multistable) free energy G(z)-fz probed in mechanical unfolding experiments. We construct a two-dimensional free-energy surface as a function of both chemical and mechanical reaction coordinates and examine the coupling between the two. We further study the refolding trajectories after the protein has been prestretched by a large force, as well as the mechanical unfolding trajectories in the presence of a large stretching force. We demonstrate that the stretching forces required to destabilize the native state thermodynamically are larger than those expected on the basis of previous experimental estimates of G(z). This finding is consistent with the recent experimental studies, indicating that proteins may refold even in the presence of a substantial stretching force. Finally, we show that for certain temperatures the free energy of a polyprotein chain consisting of multiple domains is a linear function of the chain extension. We propose that the recently observed "slow phase" in the refolding of proteins under mechanical tension may be viewed as downhill diffusion in such a linear potential.     

Investigations of heterogeneous ultrathin blends using lateral force microscopy

In order to study the glass transition of thin film polymer blends, high spatial resolution and temperature sensitivity is needed. In this paper, we emphasize the importance of the calibration of scanning parameters such as load and speed when measuring the glass transition temperature of polymers using lateral force microscopy. Once calibrated, this method is ideal for investigations of heterogeneous samples such as blends and co‐polymers. We present an analysis technique for lateral force imaging using a fast and stable cooling/heating stage. This approach involves mapping the friction forces over a certain area and identifying regions of different frictional properties. The difference in the average friction force can then be plotted as a function of temperature. The friction force is expected to vary around the glass transition. Therefore, the glass transition temperature can be defined as the temperature at which the difference in the average friction force undergoes a slope change. We present investigations of blends using polystyrene mixed with poly(butylmethacrylate). The transition temperatures obtained are in good agreement with the bulk values of corresponding homopolymeric films.     

Derivation of class II force fields. I. Methodology and quantum force field for the alkyl functional group and alkane molecules

A new method for deriving force fields for molecular simulations has been developed. It is based on the derivation and parameterization of analytic representations of the ab initio potential energy surfaces. The general method is presented here and used to derive a quantum mechanical force field (QMFF) for alkanes. It is based on sampling the energy surfaces of 16 representative alkane species. For hydrocarbons, this force field contains 66 force constants and reference values. These were fit to 128,376 quantum mechanical energies and energy derivatives describing the energy surface. The detailed form of the analytic force field expression and the values of all resulting parameters are given. A series of computations is then performed to test the ability of this force field to reproduce the features of the ab initio energy surface in terms of energies as well as the first and second derivatives of the energies with respect to molecular deformations. The fit is shown to be good, with rms energy deviations of less than 7% for all molecules. Also, although only two atom types are employed, the force field accounts for the properties of both highly strained species, such as cyclopropane and methylcyclopropanes, as well as unstrained systems. The information contained in the quantum energy surface indicates that it is significantly anharmonic and that important intramolecular coupling interactions exist between internals. The representation of the nature of these interactions, not present in diagonal, quadratic force fields (Class I force fields), is shown to be important in accounting accurately for molecular energy surfaces. The Class II force field derived from the quantum energy surface is characterized by accounting for these important intramolecular forces. The importance of each 4.2 to 18.2%. This fourfold increase in the second derivative error dramatically demonstrates the importance of bond anharmonicity in the ab initio potential energy surface. The Class II force field derived from the quantum energy surface is characterized by accounting for these important intramolecular forces. The importance of each of the interaction terms of the potential energy function has also been assessed. Bond anharmonicity, angle anharmonicity, and bond/angle, bond/torsion, and angle/angle/ torsion cross-term interactions result in the most significant overall improvement in distorted structure energies and energy derivatives. The implications of each energy term for the development of advanced force fields is discussed. Finally, it is shown that the techniques introduced here for exploring the quantum energy surface can be used to determine the extent of transferability and range of validity of the force field. The latter is of crucial importance in meeting the objective of deriving a force field for use in molecular mechanics and dynamics calculations of a wide range of molecules often containing functional groups in novel environments. © 1994 by John Wiley & Sons, Inc.