Modeling single chain elasticity of single-stranded DNA: A comparison of three models

The dominant models of polymers, i.e., the freely jointed chain (FJC) model, the wormlike chain (WLC) model and the freely rotating chain (FRC) model are modified by integrating the inherent single-molecule elasticity obtained from quantum mechanics (QM) ab-initio calculations. The QM modified models have been utilized to generate fitting curves for single-stranded DNA obtained in organic solvent. The analyses on the deviation between the fitting curve and the experimental force curve demonstrate that the QM-FRC and QM-FJC model are suitable for ssDNA, but not the QM-WLC model. We also find that one repeating unit of ssDNA is corresponding to a Kuhn segment in QM-FJC model or two rotating units in QM-FRC. Having close correlation to the inherent elasticity and real molecular structure of the polymer, QM-FJC and QM-FRC are emerging as structure relevant models.     

Numerical simulations of the cathodic delamination of adhesive bonded rubber/steel joints

Cathodic delamination of mechanically loaded rubber/steel adhesive bonds occurs due to bondline degradation (weakening) followed by crack growth under mechanical (here, mostly cleavage) load. In this paper, a mechano-chemical failure criterion is proposed, which couples fracture mechanics principles with the weakening mode of debonding due to environmental effects. The latter is mainly described by electrolyte type, cathodic potential, and temperature and may be analytically described according to the recently introduced [1] analytical model based on liquid-solid reactions and is capable of simulating the weakening mode of bond degradation. This paper extends the model advanced in [1] to where we now account for externally applied mechanical loading (mostly peel mode). Such loads cause already weakened bonds to delaminate thus resulting in physical separation of the rubber from the steel substrate.For the rubber/metal, variable-G, strip blister specimen (SBS) used in this work, progressive delamination proceeds as the applied strain energy release rate, G, decreases from an initial maximum value, G_T0 (of about 2.24 kJ/m² for the most utilized specimen configuration). As the applied G decreases, delamination correspondingly proceeds at progressively slower rates. The fact that delamination rates decrease with increasing delaminated bond lengths has already been established experimentally and simulated using empirical [2] and semi-empirical models [3] but will be simulated numerically in this paper. The model is validated using such experimental data of bond delamination under a variety of cathodic conditions. The validated methodology provides numerical simulations of joint delamination of the SBS under the combined action of mechanical peel loads and cathodic environment.     

Mechanistic study on the cellulose dissolution in ionic liquids by density functional theory☆

Ionic liquids (ILs) have attracted many attentions in the dissolution of cellulose due to their unique physicochem-ical properties as green solvents. However, the mechanism of dissolution is stil under debate. In this work, com-putational investigation for the mechanisms of dissolution of cellulose in [Bmim]Cl, [Emim]Cl and [Emim]OAc ILs was performed, and it was focused on the process of breakage of cel ulose chain and ring opening using cel obiose as a model molecule. The detailed mechanism and reaction energy barriers were computed for various possible pathways by density functional theoretical method. The key finding was that ILs catalyze the dissolution process by synergistic effect of anion and cation, which led to the cleavage of cellulose chain and formation of derivatives of cel ulose. The investigation on ring opening process of cellobiose suggested that carbene formed in ILs played an important role in the side reaction of cellulose, and it facilitated the formation of a covalent bond between cel-lulose and imidazolium core. These computation results may provide new perspective to understand and apply ILs for pretreatment of cellulose.     

褐煤无黏结剂成型理论的粉体工程分析

在分析多种褐煤无黏结剂成型假说的基础上,提出了影响褐煤成型特性的其他内因。介绍了褐煤无黏结剂成型的粉体力学模型,同时对无桥、液桥、固桥3种黏结类型下的平均颗粒抗拉强度的计算公式进行了推导。探讨了在褐煤成型过程中,不同阶段相应的主要黏结力,并得出褐煤型煤最终产品的强度取决于颗粒间形成的固桥黏结力。研究表明:确定合理的外部条件,使颗粒间形成合适的固桥黏结力,即可满足褐煤运输和加工利用所需强度。     

A molecular thermodynamic model for binary lattice polymer solutions

A molecular thermodynamic model for binary lattice polymer solutions with concise and accurate expressions for the Helmholtz energy of mixing and other thermodynamic properties is established. Computer simulation results are combined with the statistical mechanics to obtain the expressions. Yan et al.'s model for Ising lattice and the sticky-point model of Cumming, Zhou and Stell are incorporated in the derivation. Besides the nearest neighbor cavity correlation function obtained from the Ising lattice, the long range correlations beyond the close contact pairs are represented by a parameter λ, the linear chain-length dependence of which is obtained by fitting the simulated critical parameters of two systems with chain lengths of 4 and 200. The predicted critical temperatures and critical compositions, spinodals and coexistence curves as well as internal energies of mixing for systems with various chain lengths are in satisfactory agreement in comparison with the computer simulation results and experimental data indicating the superiority of the model over other theories. The model can serve as a basis to develop more efficient models for practical applications.     

Elastic behavior of compact polymer chain transporting through an infinite adsorption channel

The elastic behavior of a single compact chain transporting through an infinite adsorption channel is investigated using the pruned-enriched-Rosenbluth method (PERM). In our model, single compact chain is fixed with one of its first monomer at a position in an infinite adsorption channel, is then pulled slowly along the direction of z-axis. We first calculate the chain size and shape of compact chains transporting through an infinite channel, such as mean-square end-to-end distance per bond 〈R²〉/N, mean-square radii of gyration per bond 〈S²〉/N, 〈S²〉_xy/N and 〈S²〉_z/N, and shape factor 〈δ〉 for the changes in the size and shape of compact chains during the translocation process. If there are strong adsorption interactions between the monomers and the channel, some special behaviors for the size and shape of compact chains are obtained during the process. On the other hand, some thermodynamics properties are also investigated, such as average energy bond, average Helmholtz free energy per bond, elastic force per bond f and energy contribution to elastic force per bond f_E. During the translocation process, elastic force f is less than zero, and has some plateaus in some special regions for strong adsorption interaction, which may explain how the adsorption interaction drives chains through narrow channels or pores in many biological systems because f<0 means that the translocation process need no external force on the chains. These investigations can provide some insights into the mechanics of proteins infiltrating through membrane. In the meantime, by recording and comparing these force-extension curves, we may also investigate the complex interactions between biopolymers (such as protein, RNA, and DNA) and the membranes, and determine indirectly the complicated structure of the channel.     

Vibrational Spectroscopies Applied to Chemisorption and Catalysis

Vibrational (infrared) spectroscopy is often referred to as molecular spectroscopy to emphasize that it is the source of much of the known molecular-structure data, e.g., molecular symmetry, bond lengths, and bond angles [1]. Coupled with statistical mechanics, vibrational spectroscopy can also allow the calculation of thermodynamic properties [2]. Of course, catalysis is by definition a kinetic phenomena, and therefore it is noteworthy that vibrational spectroscopy has also been used to follow the transient response of kinetically significant (as opposed to stable, unreactive) intermediates on heterogeneous catalysts [3-5].     

A kinetic model for thermal degradation in polymers with specific application to proteins

We present a novel method for calculating degradation kinetics in polymers. Our calculations directly use the dissociation energy of chemical bonds in a polymer chain to predict weight loss as a function of time and temperature in an Arrhenius-type activation function. The novelty lies in quantifying the thermal energy term for skeletal bonds in the chain backbone in the activation function that initiates the bond fission process and that also quantifies the pre-exponential rate term. Our method allows prediction of TGA experiments with any time-temperature profile directly from the polymer structure using tools such as quantum mechanics simulations for bond dissociation energy. The model is demonstrated by application to a number of synthetic polymers with different temperature ramp rates. Application of the model to protein polymers shows significant differences from synthetic example polymers, since the synthetics use a single average dissociation energy, whereas proteins seem to degrade sequentially with the individual skeletal bond energies.     

Anisotropic mechanical behavior of magnetically oriented iron particle reinforced foams

Reinforced foams were prepared by exposing a polyurethane matrix filled with iron particles to a magnetic field during the foaming process. The magnetic field induced an alignment of the iron particles along the field direction, giving rise to columnar structures similar to fibrils, as observed by SEM and microtomographic 3D reconstructions. The anisotropic reinforcement induced by the fibrils improved the mechanical performances, yielding a threefold increase of both elastic modulus and yield stress in the alignment direction, whereas minor effects were observed in the transversal direction. In this case, the mechanical properties were comparable with those of randomly filled foams or, in some cases, of unfilled foam. The reinforcing efficiency of fibrils was evaluated through a theoretical model, based on the combination of the mechanics of foams with two micromechanical models for aligned short fibers composites (Halpin‐Tsai and Cox‐Krenchel). The theoretical predictions based on the Halpin‐Tsai equations showed a good agreement with the experimental data, whereas the model derived from Cox‐Krenchel equations overestimated data. © 2010 Wiley Periodicals, Inc. J Appl Polym Sci, 2011     

Crystallization of networks under stress

A theory of crystallization under stress is developed about the premise that the direction a chain takes through a crystallite, relative to its end-to-end vector, is determined by the first few links of a chain that initially deposit onto the crystallite surface. Since these few links are quickly trapped by subsequently crystallizing chains, their orientational probability prior to deposition governs the chain direction through the crystallite, and the properties of the system depend upon a statistical distribution of all vector orientations. Such a model leads to a relationship between the melting temperature and the degree of network orientation, and relates the retractive force to temperature in the crystallization region. The theory appears to adequately describe some of the published data on rubber and polychloroprene networks.     

Vibrational Spectroscopies Applied to Chemisorption and Catalysis

Abstract

Vibrational (infrared) spectroscopy is often referred to as molecular spectroscopy to emphasize that it is the source of much of the known molecular-structure data, e.g., molecular symmetry, bond lengths, and bond angles [1]. Coupled with statistical mechanics, vibrational spectroscopy can also allow the calculation of thermodynamic properties [2]. Of course, catalysis is by definition a kinetic phenomena, and therefore it is noteworthy that vibrational spectroscopy has also been used to follow the transient response of kinetically significant (as opposed to stable, unreactive) intermediates on heterogeneous catalysts [3–5].     

A New Model Compound for Studying Alkaline Cellulose Chain Cleavage Reactions

A conformationally rigid cellulose model, the 4′,6′-O-benzylidene derivative of 1,5-anhydrocellobiitol, has been studied to learn more about the mechanisms of chain cleavage reactions under alkaline pulping conditions. Heating the model at 170°C in 2.5N NaOH gave 55% glycon-oxygen (G-O) bond cleavage, and ～45% oxygen-aglycon (O-A) bond cleavage. The amount of observed O-A bond cleavage is significantly higher than that for 1,5-anhydrocellobiitol. The benzylidene model also degraded about ～35% faster than 1,5-anhydrocellobiitol; much of this rate increase can be attributed to a faster rate of O-A bond cleavage for the benzylidene model. The greater amount of O-A bond cleavage in the benzylidene case may be attributable to a more highly substituted glycosyl ring (making the ring a better anion leaving group) and/or to a more conformationally inflexible glycosyl ring. The inflexibility restricts one of the standard G-O bond cleavage mechanisms, namely the S_NicB(2′) mechanism. The results point out the value of choosing appropriate cellulose models.     

Effect of bond thickness on creep lifetime of adhesive joints under mode I

An experimental investigation has been carried out on double cantilever beam specimens with different bond thicknesses to study the effect of bond thickness on lifetime of adhesive joints under mode I. This paper describes an approach to predict the rate of crack propagation. The approach is based on principles of linear elastic fracture mechanics and uses elevated temperature to accelerate the crack propagation under constant loads. The fracture energy of the joint is studied as a function of bond thickness. The results from short-term tests are analyzed and a simple model has been proposed to predict the variation of two kinetic parameters of the Paris law with bond thickness.     

Impact resistance of poly(vinyl alcohol) fiber reinforced high-performance organic aggregate cementitious material

Poly(vinyl butyral) (PVB) which has many special engineering aggregate properties such as super lightweight, physical toughness, adhesion to a variety of surfaces and energy-absorbing characteristics is utilized as the sole aggregate in this study to develop a novel cementitious composite reinforced with Poly(vinyl alcohol) (PVA) fiber. Impact energy absorption capacity is evaluated based on the Charpy impact test. The results show that PVB composite material has lower density but higher impact energy absorption capability compared with conventional lightweight concrete and regular concrete. The addition of PVA fiber improves the impact resistance with fiber volume fractions. The remarkable change in the interfacial bond strength contributed by the non-covalent bond such as hydrogen bond and ether interactions at the interfaces between fiber, aggregate and matrix contributes to the improvement of the impact resistant capacity. A model based on fiber bridging mechanics and the rule of mixtures is developed to characterize the impact energy. A good correlation was obtained for the materials tested when experimental results are compared to those predicted by the developed model.     

Conformational origin of the molecular weight dependence of the characteristic ratio of the dipole moment in poly(A-B)

By poly(A-B) we denote a chain with repeating sequence -A-B-, such as polyoxymethylene. Here A and B stand for a single atom, e.g., -O-, or a group of atoms, e.g., -CH₂-. All n bond vectors are of the same length, l, as are all bond dipole moment vectors, m. The manner in which the characteristic ratio of the dipole moment, D_n≡〈μ²〉₀/nm² approaches its asymptotic limit is related quantitatively to the behavior of subchains of various sizes in poly(A-B). Illustrative numerical calculations with rotational isomeric state (RIS) models for several polymers are consistent with the predictions. The approach of D_n to its asymptotic limit is sensitive to longer subchains than is the approach of the characteristic ratio of the end-to-end distance, C_n≡〈r²〉₀/nl², to its asymptotic limit, due to the differences in the connectivity of the bond vectors (head-to-tail) and the bond dipole moment vectors (head-to-head, tail-to-tail).     

Multi-scale modeling of polyimides

A coarse-grained model for a set of three polyimide isomers is developed. Each polyimide is comprised of 3,3′,4,4′-biphenyltetracarboxylic dianhydride (BPDA) and one of three APB isomers: 1,3-bis(4-aminophenoxy)benzene, 1,4-bis(4-aminophenoxy)benzene or 1,3-bis(3-aminophenoxy)benzene. The coarse-grained model is constructed as a series of linked vectors following the contour of the polymer backbone. Beads located at the midpoint of each vector define centers for long range interaction energies between monomer subunits. A bulk simulation of each coarse-grained polyimide model is performed with a dynamic Monte Carlo procedure. These coarse-grained models are then reverse-mapped to fully atomistic models. The coarse-grained models show the expected trends in decreasing chain dimensions with increasing meta linkage in the APB section of the repeat unit, although these differences were minor due to the relatively short chains simulated here. Considerable differences are seen among the dynamic Monte Carlo properties of the three polyimide isomers. Decreasing relaxation times are seen with increasing meta linkage in the APB section of the repeat unit. The packing behavior of the three isomers is compared with the atomistic and coarse-grained models.     

Metal complexes containing allenylidene and higher cumulenylidene ligands: a theoretical perspective

Transition metal complexes containing unsaturated carbenes have enjoyed a recent surge in research interest. In addition to showing potential as molecular wires and as components of opto-electronic materials, they provide multifaceted reactive sites for organic synthesis. In this Account, we describe results of recent theoretical studies that delineate the main features of electronic structure and bonding in allenylidenes and higher cumulenylidene complexes, [L(m)M]═C(═C)(n)═CR(1)R(2) (where L represents the ligand, M the metal, and n ≥ 1). Although free cumulenylidene ligands, :C(═C)(n)═CR(1)R(2), are extremely unstable and reactive species, they can be stabilized by coordination to a transition metal. The σ-donation of the electron lone pair on the terminal carbon atom to an empty metal d-orbital, together with the simultaneous π back-donation from filled metal d(π)-orbitals to empty cumulene π* system orbitals, leads to the formation of a strong M═C bond with multiple character. Density functional theory studies on the model systems [(CO)(5)Cr(═C)(n)CH(2)] and [trans-Cl(PH(3))(4)Ru(═C)(n)CH(2)](+) (where n = 1-9) have been useful in interpreting the structural and spectroscopic properties and the reactivity of this class of complexes. Geometry optimizations significantly contributed to the generalization of the sparse structural data available for allenylidene, butatrienylidene, and pentatetraenylidene complexes to higher cumulenylidene complexes (with up to eight carbon atoms in the chain), which show a clear structural trend. In particular, the geometries of all even-chain cumulenes are consistent with an almost purely cumulenic structure, whereas the geometries of odd-chain cumulenes present a significant polyyne-like carbon-carbon bond length alternation. The calculated bond dissociation energies (BDEs) of the cumulenylidene ligand remain almost constant on lengthening the cumulene chain. These BDEs indicate that there is no thermodynamic upper limit to the cumulene chain length and suggest that the synthetic difficulties in preparing higher cumulenylidenes are due to an increase in reactivity. The calculated charges on the carbon atoms show no significant polarization along the cumulene chain, indicating that charge distribution is not important in determining the regioselectivity of either electrophilic or nucleophilic attack, which is instead determined by frontier orbital factors. The breakdown of the contributions from the metal and the carbon atoms along the chain to the HOMO and LUMO shows that the HOMO has contributions mainly from the metal and the carbon atoms in even positions along the chain (C(2), C(4), C(6), and higher). In contrast, the LUMO has contributions mainly from the carbon atoms in odd positions along the chain (C(1), C(3), C(5), and higher), thus explaining the experimentally observed regioselectivity of electrophilic and nucleophilic attacks, which are directed, respectively, to even and odd positions of the cumulenylidene chain. The study of the electronic structure of cumulenylidenes has allowed us not only to give a consistent rationale for the main structural and spectroscopic properties and for the reactivity of this emerging class of compounds but also to predict the effect of ancillary ligands on the metal center or substituents on the carbon end. The result is a useful guide to new developments in the still-underexplored fields of this fascinating class of compounds.     

Conformational properties of poly(alkene sulphone)s in solution: 2. A rotational isomeric state study of the poly(cyclohexene sulphone) chain

The rotational isomeric states model, coupled with the Flory matrix method, was applied to the calculation of the unperturbed mean-square end-to-end distance in poly(cyclohexene sulphone) as a function of several parameters. The calculations were performed for atactic, isotactic and syndiotactic chains; the tacticity arises from the two possible ways, D and L, in which the rings can be attached to the main chain, assuming that the CC bonds are all in the t conformation, as indicated by dielectric measurements. One of the three conformations about each CS bond is strongly hindered and was given zero statistical weight whereas the other two were assigned weights determined by second-order effects, operating over three or more consecutive bonds, and dependent on the chirality of the rings and the coulombic interactions between adjacent dipoles.The calculations for the atactic model, in which a Monte Carlo procedure was used to generate the chain, were found to agree with experiment only if the parameter α was given a value of 5 or greater. This parameter is determined by the relative orientation of successive sulphone dipoles and was expected to have a value less than unity. It appears that specific solvation effects help to stabilize (t, g) and (g, t) CSC bond pairs relative to t, t. Other parameters are not so important.The calculations for the isotactic and syndiotactic models show interesting features, particularly for certain limiting conditions when cyclic or helical structures are generated. For these models there is a greater sensitivity to the various parameters than in the atactic case.     

Molecular design and density functional theory investigation of novel low‐band‐gap copolymers between quinoid acceptors and aromatic donors

The structures and electronic properties of furo[3,4‐b]pyridine‐based alternating donor and acceptor conjugated oligomers, in which furan and pyrrole are used as donors, and their periodic polymers were investigated using density functional theory at the B3LYP/6‐31G(d) level. The bond lengths, bond length alternation, bond critical point (BCP) properties, nucleus‐independent chemical shift (NICS) and Wiberg bond index (WBI) were analyzed and correlated with conduction properties. The changes of bond length, BCP properties, NICS and WBI all show that the degree of conjugation increases with main chain extension. The changes of NICS also show that the conjugation is stronger in the central section than in the outer section. Hydrogen bonding interactions and nitrogen atom substitution in the acceptors play very important roles in the geometries, electronic structures and energy gaps. The theoretical results suggest that pyrrole‐based polymers are good candidates for conducting materials, compared with furan‐based polymers. With an increase of nitrogen atom substitution in the acceptors in these polymers, the intermolecular charge transfers along the polymeric axes are enhanced, and the bond length alternations and HOMO–LUMO energy gap for these polymers are decreased. The results suggest that the six polymers studied all have lower energy gaps (in the range 0.81–1.26 eV), which indicate that these proposed polymers are good candidates for n‐doping conductive materials, especially poly(7‐(furan‐2‐yl)furo[3,4‐e][1,2,4]triazine) and poly(7‐(1H‐pyrrol‐2‐yl)furo[3,4‐e][1,2,4]triazine). Copyright © 2011 Society of Chemical Industry