Kink Defects Research Articles

FTIR spectroscopy revealed nonplanar conformers, chain order, and packaging density in diOctadecylamine- and octadecylamine-passivated gold nanoparticles

This work reveals that diOctadecylamine (diODA) outperforms its primary amine counterpart ODA in intra- and intermolecular order, forming passivation monolayers on 5 nm small gold nanoparticles. We support this conclusion by meticulously analyzing the differences in the Fourier Transform Infrared (FTIR) spectrum of diODA and ODA molecules in their pure- and coordinated-to-gold-nanoparticle phases. Detailed diODA spectral data are scarce in the literature and are absent for diODA-passivated nanoparticles, whose merits have gone unnoticed. The analysis compares the signatures of defects and all indicators for molecular packing in the ligand. The results align with the High-Resolution Transmission Electron Microscopy (HR-TEM) based analysis. We observe unexpectedly that pure diODA molecules are not prone to form trans-gauche (TG) [CH3-CH2-gauche] end-conformation. At the same time, an intensive absorption structure at the relevant TG position around 760 cm−1 indicates its presence in pure ODA. The spectrum of pure ODA indicates higher energy of the internal kink defects in the vicinity of 1306 cm−1 than pure diODA. In the coordinated phase, both molecules reduce their initial energy. However, the observed better-pronounced red shift of the structures reveals a crystal-like chain arrangement for diODA. Consequently, the HR-TEM images reveal a spontaneous formation of 2D arrangement only for diODA passivated nanoparticles having nearly twice as large gold core separation as the one provided by ODA molecules. The present analysis can be used as a preliminary test in demanding applications where tightly packed coatings of nanoparticles with impenetrable organic passivation are essential.

Molecular insights into reversible and irreversible kinks formed in nanocellulose

Kink defects in nanocellulose are common, yet questions remain open regarding the unclear microstructure-mechanical property relationship. Various kink patterns without molecular-scale resolution cause confusion about how nanocellulose forms different kinks and what the fundamental mechanisms of reversible and irreversible kinks are. In atomic force microscopy images, bent nanofibrils usually exhibit small curvatures, while kinked nanofibrils feature sharp bends, in which kinks are notable due to their distinct disordered configurations. To identify the incipient kink defects formed in nanocellulose, molecular dynamics simulations of cellulose nanocrystals (CNCs) under curvature-dependent bending were subsequently carried out. Five typical bending/kinking modes were found, depending on the anisotropic microstructure and size of CNCs. More importantly, two contrasting cases of kinks were demonstrated, providing evidence that kink defects in nanocellulose depend mainly on the microstructure at the molecular scale. Kinks in CNCs with the (100) and (11¯0) crystal plane are recoverable with a few residual defects. While kinks in CNCs with the (010) crystal plane are irreversible with permanent microstructural damage. Compressive stresses accumulated in the bottom chains of CNC contribute to the main mechanism for forming incipient kinks in nanocellulose. The results can fundamentally answer the confusion in recent experiments why bond breakage did not necessarily occur even at high kink angles. The insights present intrinsic deformation mechanisms for understanding the widespread but mysterious kinks arising in nanocellulose.

Structural Anisotropy Governs the Kink Formation in Cellulose Nanocrystals

Understanding the defect structure is fundamental to correlating the structure and properties of materials. However, little is known about the defects of soft matter at the nanoscale beyond their external morphology. We report here on the molecular-level structural details of kink defects of cellulose nanocrystals (CNCs) based on a combination of experimental and theoretical methods. Low-dose scanning nanobeam electron diffraction analysis allowed for correlation of the local crystallographic information and nanoscale morphology and revealed that the structural anisotropy governed the kink formation of CNCs. We identified two bending modes along different crystallographic directions with distinct disordered structures at kink points. The drying strongly affected the external morphology of the kinks, resulting in underestimating the kink population in the standard dry observation conditions. These detailed defect analyses improve our understanding of the structural heterogeneity of nanocelluloses and contribute to the future exploitation of soft matter defects.

Nanomechanics of Incipient Kink Defects Formed in Nanocellulose

Nanomechanics of Incipient Kink Defects Formed in Nanocellulose

Elasticity of Semiflexible ZigZag Nanosprings with a Point Magnetic Moment.

Kinks can appear along the contour of semiflexible polymers (biopolymers or synthetic ones), and they affect their elasticity and function. A regular sequence of alternating kink defects can form a semiflexible nanospring. In this article, we theoretically analyze the elastic behavior of such a nanospring with a point magnetic dipole attached to one end while the other end is assumed to be grafted to a rigid substrate. The rod-like segments of the nanospring are treated as weakly bending wormlike chains, and the propagator (Green's function) method is used in order to calculate the conformational and elastic properties of this system. We analytically calculate the distribution of orientational and positional fluctuations of the free end, the force-extension relation, as well as the compressional force that such a spring can exert on a planar wall. Our results show how the magnetic interaction affects the elasticity of the semiflexible nanospring. This sensitivity, which is based on the interplay of positional and orientational degrees of freedom, may prove useful in magnetometry or other applications.

Intrinsic kink deformation in nanocellulose

Sharp bends can be widely observed in isolated cellulose nanofibrils (CNFs) after mechanical treatment, referred to as kink dislocations that are previously found in wood cell walls under compression. The non-Gaussian distribution of kink angle implies some inherent deformation behaviors of cellulose nanocrystals (CNCs) hidden in the formation of kink dislocations in CNFs. We herein perform molecular dynamics simulations to investigate the kink deformation of nanocellulose. It is interesting to find an intrinsic deformation mode of Iβ CNCs under uniaxial compression, in which the metastable structure of kinked CNCs turns out to be the triclinic Iα phase with twin boundaries originated from interlayer dislocation-induced allomorphic transition. An intrinsic kink angle (~60°) is defined based on geometric traits of stable kinked CNCs. Moreover, the weakened intrachain hydrogen bonds in twin boundaries lead to exposed glycosidic bonds and damaged hydrogen-bonding networks, which would act as the origin of kink defects in nanocellulose.

Atomistic Study of Interactions between Intrinsic Kink Defects and Dislocations in Twin Boundaries of Nanotwinned Copper during Nanoindentation.

In order to study the effects of kink-like defects in twin boundaries on deformation mechanisms and interaction between dislocations and defects in twin boundaries under localized load, nanotwinned Cu with two defective twin (TDT) boundaries is compared with the nanotwinned Cu with two perfect twin (TPT) boundaries, and nanotwinned Cu with single defective twin (SDT) boundary and single perfect twin boundary by simulating spherical nanoindentations using molecular mechanics. The indenter force-depth and hardness-contact strain responses were analyzed. Results show that the existence of intrinsic defects in twin boundary could reduce the critical load and critical hardness of nanotwinned material. A quantitative parameter was first proposed to evaluate the degree of surface atom accumulation around the indenter during nanoindentation, and it can be inferred that the surface morphology in TDT changes more frequently than the surface morphologies in TPT and SDT. The atomistic configurations of incipient plastic structures of three different models were also analyzed. We found that the intrinsic defects in twin boundary will affect the incipient plastic structures. The formation of twinning partial slip on the defective twin boundary happens before the contact of the dislocation and twin boundary. The kink-like defects could introduce Frank partial dislocation to the twin boundary during interaction between dislocation and twin boundary, which was not detected on the perfect twin boundary. In addition, the area of twinning partial slips on the upper twin boundary in the incipient plastic structures in SDT and TDT are larger than the twinning partial slip area in TPT, which results in the reduction of the critical hardness in SDT and TDT. The kink-like defects could also block the expansion of twinning partial slip on the twin boundary. Furthermore, we investigated the dislocation transmission processes in three different models. It is found that the dislocation transmission event could be delayed in model containing single defective twin boundary, while the transmission process could be advanced in model containing two consecutive defective twin boundaries. The quantitative analysis of dislocation length was also implemented. Result shows that the main emitted dislocation during nanoindentation is Shockley partial, and the dislocation nucleation in SDT and TDT is earlier than the dislocation nucleation in TPT due to the existence of defects. It is inferred that the intrinsic defects on twin boundaries could enhance the interaction between dislocations and twin boundaries, and could strongly change the structure evolution and promote the dislocation nucleation and emission. These findings about kink-like defects in twin boundaries show that the inherent kink-like defects play a crucial role in the deformation mechanisms and it should be taken into consideration in future investigations. Single defective twin boundary structure is recommended to delay the transmission and block the expansion of twin boundary migration. Some of the results are in good agreement with experiments.

Structure and the role of filling rate on model dsDNA packed in a phage capsid.

The conformation of DNA inside bacteriophages is of paramount importance for understanding packaging and ejection mechanisms. Models describing the structure of the confined macromolecule have depicted highly ordered conformations, such as spooled or toroidal arrangements that focus on reproducing experimental results obtained by averaging over thousands of configurations. However, it has been seen that more disordered states, including DNA kinking and the presence of domains with different DNA orientation can also accurately reproduce many of the structural experiments. In this work we have compared the results obtained through different simulated filling rates. We find a rate dependence for the resulting constrained states showing different anisotropic configurations. We present a quantitative analysis of the density distribution and the DNA orientation across the capsid showing excellent agreement with structural experiments. Second, we have analyzed the correlations within the capsid, finding evidence of the presence of domains characterized by aligned segments of DNA characterized by the structure factor. Finally, we have measured the number and distribution of DNA defects such as the emergence of bubbles and kinks as function of the filling rate. We find the slower the rate the fewer kink defects that appear and they would be unlikely at experimental filling rates with our model parameters. DNA domains of various orientation get larger with slower rates.

Nanomechanics of cellulose deformation reveal molecular defects that facilitate natural deconstruction

Technologies surrounding utilization of cellulosic materials have been integral to human society for millennia. In many materials, controlled introduction of defects provides a means to tailor properties, introduce reactivity, and modulate functionality for various applications. The importance of defects in defining the behavior of cellulose is becoming increasingly recognized. However, fully exploiting defects in cellulose to benefit biobased materials and conversion applications will require an improved understanding of the mechanisms of defect induction and corresponding molecular-level consequences. We have identified a fundamental relationship between the macromolecular structure and mechanical behavior of cellulose nanofibrils whereby molecular defects may be induced when the fibrils are subjected to bending stress exceeding a certain threshold. By nanomanipulation, imaging, and molecular modeling, we demonstrate that cellulose nanofibrils tend to form kink defects in response to bending stress, and that these macromolecular features are often accompanied by breakages in the glucan chains. Direct observation of deformed cellulose fibrils following partial enzymatic digestion reveals that processive cellulases exploit these defects as initiation sites for hydrolysis. Collectively, our findings provide a refined understanding of the interplay between the structure, mechanics, and reactivity of cellulose assemblies.

Some characterizations of a new metal–organic framework (n-C14H29NH3)2CdCl4 and the role of hydrogen bonding

ABSTRACTA cadmium-based organic–inorganic hybrid (n-C14H29NH3)2CdCl4 is synthesized and characterized, thermally and dielectrically. The differential scanning calorimetery (DSC) and the differential thermal analysis (DTA) thermograms were performed in a suitable range of temperature. The general feature of each thermogram indicates that the hybrid undergoes two structural phase transitions at Tmajor ≈ 351.5 K and Tminor ≈ 344.66 K in addition to an intermediate temperature which is located at ≈346.8 K. For further confirmation of the observed phase transitions, the complex dielectric permittivity ε* (ω,T) = ε′(ω,T) – iε″(ω,T) and ac conductivity σac(ω,T) were accurately measured in the wide range of temperature 100 K<T<400 K at some suitable range of frequencies. The data evidenced the existence of such transitions. Comparison with other hybrids reveals the absence of the odd–even effect whereas the transition temperature increases with the increase of the chain length. The mechanism of proton transfer and kink defects was outlined.

Tensile elasticity of semiflexible polymers with hinge defects.

It has become clear in recent years that the simple uniform wormlike chain model needs to be modified in order to account for more complex behavior which has been observed experimentally in some important biopolymers. For example, the large flexibility of short ds-DNA has been attributed to kink or hinge defects. In this paper, we calculate analytically, within the weak bending approximation, the force-extension relation of a wormlike chain with a permanent hinge defect along its contour. The defect is characterized by its bending energy (which can be zero, in the completely flexible case) and its position along the polymer contour. Besides the bending rigidity of the chain, these are the only parameters which describe our model. We show that a hinge defect causes a significant increase in the differential tensile compliance of a prestressed chain. In the small force limit, a hinge defect significantly increases the entropic elasticity. Our results apply to any pair of semiflexible segments connected by a hinge. As such, they may also be relevant to cytoskeletal filaments (F-actin, microtubules), where one may treat the cross-link connecting two filaments as a hinge defect.

Real-Time Monitoring Distance Changes in Surfactant-Coated Au Nanoparticle Films upon Volatile Organic Compounds (VOCs)

We explore into the role of the organic ligands composition surrounding Au nanoparticles (NPs) toward internanoparticles distance changes and film structure during vapor sensing by the use of in situ grazing-incidence small-angle X-ray scattering (GISAXS) and other relevant techniques. We observed distinct changes in core-to-core distance and film structure upon measured concentrations of polar ethanol (EtOH) and nonpolar toluene (Tol) vapors. As-formed tetraoctylammonium bromide (TOABr)-coated Au NPs (SNPs) film exhibited ∼0.4 nm core-to-core increase in distance and improved SNPs correlation upon 80% Tol. In the presence of EtOH, SNPs distance seems not to change and correlation critically diminishes, leading to an amorphous film. As-formed films were exchanged with nonanedithiol (NDT) and exposed to 100% Tol vapor. Interestingly, the incorporation of NDT increased distance between NPs and rendered film flexibility. It is determine that just a small number of S, from NDT ligands, binds to Au NPs, and those exchanged alkanedithiol chains adopted a loop conformation around the Au NPs as evidenced by X-ray absorption near-edge structure (XANES) and kink defects by Fourier transformed infrared (FT-IR) experiments, respectively. These findings may solve some fundamental questions about internanoparticle distance-dependent phenomena such as electron transport in chemiresistors and coupling effects in localized surface plasmon resonance (LSPR) solid-state sensors.

Soliton defects in one-gap periodic system and exotic supersymmetry

By applying Darboux--Crum transformations to the quantum one-gap Lam\'e system, we introduce an arbitrary countable number of bound states into forbidden bands. The perturbed potentials are reflectionless and contain two types of soliton defects in the periodic background. The bound states with a finite number of nodes are supported in the lower forbidden band by the periodicity defects of the potential well type, while the pulse-type bound states in the gap have an infinite number of nodes and are trapped by defects of the compression modulations nature. We investigate the exotic nonlinear $\mathcal{N}=4$ supersymmetric structure in such paired Schr\"odinger systems, which extends an ordinary $\mathcal{N}=2$ supersymmetry and involves two bosonic generators composed from Lax--Novikov integrals of the subsystems. One of the bosonic integrals has a nature of a central charge and allows us to liaise the obtained systems with the stationary equations of the Korteweg--de Vries and modified Korteweg--de Vries hierarchies. This exotic supersymmetry opens the way for the construction of self-consistent condensates based on the Bogoliubov--de Gennes equations and associated with them new solutions to the Gross--Neveu model. They correspond to the kink or kink-antikink defects of the crystalline background in dependence on whether the exotic supersymmetry is unbroken or spontaneously broken.

Competition of the connectivity with the local and the global order in polymer melts and crystals

The competition between the connectivity and the local or global order in model fully flexible chain molecules is investigated by molecular-dynamics simulations. States with both missing (melts) and high (crystal) global order are considered. Local order is characterized within the first coordination shell (FCS) of a tagged monomer and found to be lower than in atomic systems in both melt and crystal. The role played by the bonds linking the tagged monomer to FCS monomers (radial bonds), and the bonds linking two FCS monomers (shell bonds) is investigated. The detailed analysis in terms of Steinhardt's orientation order parameters Ql (l = 2 - 10) reveals that increasing the number of shell bonds decreases the FCS order in both melt and crystal. Differently, the FCS arrangements organize the radial bonds. Even if the molecular chains are fully flexible, the distribution of the angle formed by adjacent radial bonds exhibits sharp contributions at the characteristic angles θ ≈ 70°, 122°, 180°. The fractions of adjacent radial bonds with θ ≈ 122°, 180° are enhanced by the global order of the crystal, whereas the fraction with 70° ~/< θ ~/< 110° is nearly unaffected by the crystallization. Kink defects, i.e., large lateral displacements of the chains, are evidenced in the crystalline state.

Spontaneous nucleation and dynamics of kink defects in zigzag arrays of trapped ions

The spontaneous nucleation and dynamics of topological kink defects have been studied in trapped arrays of 41--43 Yb ions. The number of kinks formed as a function of quench rate across the linear-zigzag transition is measured in the underdamped regime of the inhomogeneous Kibble-Zurek theory. The experimental results agree well with molecular dynamics simulations, which show how losses mask the intrinsic nucleation rate. Simulations indicate that doubling the ion number and optimization of laser cooling can help reduce the effect of losses. A range of kink dynamics is observed including configural change, motion and lifetime, and behavioral sensitivity to ion number.

Role of kinks in the dynamics of contact lines receding on superhydrophobic surfaces.

We have investigated the depinning of the contact line on superhydrophobic surfaces with anisotropic periodic textures. By direct observation of the contact line conformation, we show that the mobility is mediated by kink defects. Full 3D simulations of the shape of the liquid surface near the solid confirm that kinks account for the measured wetting properties. This behavior, which is similar to the Peierls-Nabarro mechanism for dislocations, may open perspectives for the optimization of wetting hysteresis by design.

Exact solution for a quantum compass ladder

We introduce a spin ladder with antiferromagnetic Ising ZZ interactions along the legs, and interactions on the rungs which interpolate between the Ising ladder and the quantum compass ladder. We show that the entire energy spectrum of the ladder may be determined exactly for finite number of spins 2N by mapping to the quantum Ising chain and using Jordan-Wigner transformation in invariant subspaces. We also demonstrate that subspaces with spin defects lead to excited states using finite size scaling, and the ground state corresponds to the quantum Ising model without defects. At the quantum phase transition to maximally frustrated interactions of the compass ladder, the ZZ spin correlation function on the rungs collapses to zero and the ground state degeneracy increases by 2. We formulate a systematic method to calculate the partition function for a mesoscopic system, and employ it to demonstrate that fragmentation of the compass ladder by kink defects increases with increasing temperature. The obtained heat capacity of a large compass ladder consisting of 2N=104 spins reveals two relevant energy scales and has a broad maximum due to dense energy spectrum. The present exact results elucidate the nature of the quantum phase transition from ordered to disordered ground state found in the compass model in two dimensions.

Effects of kink and flexible hinge defects on mechanical responses of short double-stranded DNA molecules

We predict various detectable mechanical responses to the presence of local DNA defects which are defined as short DNA segments exhibiting mechanical properties obviously different from the 50 nm persistence length based semiflexible polymer model. The defects discussed are kinks and flexible hinges either permanently fixed on DNA or thermally excited. Their effects on extension shift, the effective persistence length, the end-to-end distance distribution, and the cyclization probability are computed using a transfer-matrix method. Our predictions will be useful in future experimental designs to study DNA nicks or mismatch base pairs, mechanics of specific DNA sequences, and specific DNA-protein interaction using magnetic tweezer, fluorescence resonance energy transfer, plasmon resonance techniques, and the traditional biochemistry cyclization probability measurements.

Lattice vibrations of armchair carbon nanotubes: phonons, soliton deformations and lattice discreteness effects

Radial solitons are investigated in armchair carbon nanotubes using a generalized Lennard-Jones potential. The radial solitons are found in terms of moving kink defects whose velocity obeys a dispersion relation. Effects of lattice discreteness on the shape of kink defects are examined by estimating the Peierls stress. Results suggest that the typical size for an unpinned kink phase is of the order of a lattice spacing.

Modeling branched polyethylene: copolymers possessing precisely placed ethyl branches.

A structural investigation of precise ethylene/1-butene (EB) copolymers has been completed using step polymerization chemistry. The synthetic methodology needed to generate four model copolymers is described; their primary and higher level structure is characterized. The copolymers possess an ethyl branch on every 9th, 15th, and 21st carbon along the backbone of linear polyethylene. Melting points and heats of fusion decrease with increased branch frequency. Differential scanning calorimetry and infrared spectroscopy show highly disordered crystal structures favoring ethyl branch inclusion. On the other hand, the EB copolymers contain high concentrations of kink and gauche defects independent of branch frequency. These model copolymers are compared with random copolymers produced using traditional chain chemistry and previously synthesized ADMET EP copolymers.