Intrachain Interactions Research Articles

The APS-bracket – A topological tool to classify lasso proteins, RNAs and other tadpole-like structures

The topology of biopolymers plays a crucial role in their function and properties. The standard knot-theory techniques allow one to distinguish the topology of linear polymers, however, they do not take into account the intrinsic and external interactions in the biopolymer chain, such as hydrogen or disulfide bonds. Here we introduce the APS-bracket – a topological tool developed to analyze the topology of biopolymers with intrachain interactions. We list the basic properties of the bracket and calculate its value for structures inspired by complex lasso proteins. We also introduce a set of basis structures and define the input of each separate basis structure. Finally, we discuss possible applications and generalizations of the bracket.

Coexisting spinons and magnons in the frustrated zigzag spin- 12 chain compound β−TeVO4

We investigate magnetic excitations in the frustrated zigzag spin-1/2 chain compound $\beta$-TeVO$_4$ by inelastic neutron scattering. In the magnetically ordered ground state, the excitation spectrum exhibits coexisting magnon dispersion, characteristic of long-range magnetic order, and a spinon-like continuum that prevails above 2 meV, indicating the dominance of intrachain interactions. Combining linear-spin-wave-theory and pre-calculated spinon-continuum results, we reproduce the experimental spectrum. Our analysis offers a minimal exchange-network model which determines dominant intrachain interactions, their anisotropies and weak interchain interactions. The obtained parameters explain the magnetic ordering vector and spin excitations in the magnetic ground state.

Structural‐Distortion‐Driven Magnetic Transformation from Ferro‐ to Ferrimagnetic Iron Chains in B6‐based Nb6FeIr6B8

AbstractWe report on a structural distortion of kinetically stable B6‐based ferromagnetic Nb6FeIr6B8 that induces an unprecedented transformation of a ferromagnetic Fe chain into two ferrimagnetic Fe chains through superstructure formation. Density functional theory calculations showed that the ferromagnetic Fe–Fe intrachain interactions found in the undistorted structure become ferrimagnetic in the distorted superstructure, mainly because the two independent iron atoms building each chain interact antiferromagnetically and carry different magnetic moments. High‐temperature SQUID magnetometry confirmed ferrimagnetic ordering at 525 K with a high and negative Weiss constant of −972 K indicating the presence of strong antiferromagnetic interactions, as predicted. This finding paves the way for the development of low‐dimensional magnetic intermetallic systems based on Heisenberg ferrimagnetic chains, which have previously been studied only in molecular‐based compounds.

Structural-Distortion-Driven Magnetic Transformation from Ferro- to Ferrimagnetic Iron Chains in B6 -based Nb6 FeIr6 B8.

We report on a structural distortion of kinetically stable B6 -based ferromagnetic Nb6 FeIr6 B8 that induces an unprecedented transformation of a ferromagnetic Fe chain into two ferrimagnetic Fe chains through superstructure formation. Density functional theory calculations showed that the ferromagnetic Fe-Fe intrachain interactions found in the undistorted structure become ferrimagnetic in the distorted superstructure, mainly because the two independent iron atoms building each chain interact antiferromagnetically and carry different magnetic moments. High-temperature SQUID magnetometry confirmed ferrimagnetic ordering at 525 K with a high and negative Weiss constant of -972 K indicating the presence of strong antiferromagnetic interactions, as predicted. This finding paves the way for the development of low-dimensional magnetic intermetallic systems based on Heisenberg ferrimagnetic chains, which have previously been studied only in molecular-based compounds.

Tuning the Gas Selectivity of Tröger's Base Polyimide Membranes by Using Carboxylic Acid and Tertiary Base Interactions.

Polyimide-based materials provide attractive chemistries for the development of gas-separation membranes. Modification of inter- and intra-chain interactions is a route to improve the separation performance. In this work, copolyimides with Tröger's base (TB) monomers are designed and synthesized. In particular, a series of copolyimides is synthesized with different contents of carboxylic acid groups (0-50 wt %) to alter the inter- and intra-chain interactions and enhance the basicity of the TB-polyimides. A detailed thermal and structural analysis is provided for the new copolyimides. Gas permeation data reveal a tunable trend in separation performance with increasing carboxylic acid group content. Importantly, this is one of the few examples of copolyimide membranes materials that show enhanced plasticization resistance to high-pressure gas feeds through physical cross-linking.

A comprehensive study of the magnetic properties of the pyroxenes series CaMgSi2O6–Co2Si2O6 as a function of Co content

We report a detailed study on the magnetic properties of the pyroxene series M2M1Si2O6, with M2 = Ca and M1 = Mg, where magnesium and then calcium are progressively substituted by cobalt. For cobalt site occupancy larger than 0.7 at the M1 site, a collinear antiferromagnetic phase is detected for T < TN1 = 12 K with a monodimensional character (i.e. M1 site intra-chain order parallel to c axis). Moreover the magnetization easy axis has been estimated to lie roughly along the [1 0 1] direction. Cobalt content ⩾0.5 at the M2 site (overall content 1.5) determines the formation of a new independent antiferromagnetic order with higher Néel temperature, involving only the M2 site intra-chain interactions. The incoming M2 site order is accompanied by a lowering of the space symmetry which yields to a weakly ferromagnetic resultant due to spin canted distribution of the magnetic moments either along the M1 or M2 chains. Furthermore, metamagnetic transitions are observed for both M1 and M2 site intra-chain orders at relatively low critical magnetic fields, around 2 T, suggesting that this series of pyroxenes can be used as a model system for investigating the fundamental aspects of magnetism in the matter.

A Bond-Fluctuation Model of Translational Dynamics of Chain-like Particles through Mucosal Scaffolds

Mucus scaffolds represent one of the most common barriers in targeted drug delivery and can remarkably reduce the outcome of pharmacological therapies. An efficient transport of drug particles through a mucus barrier is a precondition for an efficient drug delivery. Understanding the transport mechanism is particularly important for treatment of disorders such as cystic fibrosis. These are characterized by an onset of high-density mucus scaffolds imposing an increased steric filtering. In this study, we employed the bond-fluctuation model to analyze the effect of steric interactions on slowing the translational dynamics of compound chain-like particles traversing through scaffolds of different configurations (regular isotropic and anisotropic versus irregular random). The model, which accounts for both the geometry-imposed steric interaction as well as the intrachain steric interaction between the chain subunits, yields a transient subdiffusive motional pattern persists between the short-time and long-time Gaussian diffusion limits. The motion is analyzed in terms of a mean-squared displacement, diffusion coefficient, and radius of gyration. With higher levels of restriction or larger particles, the subdiffusive motional regime persists longer. The study also demonstrates that an important feature of the motion is also geometry-induced chain accommodation. The presented model is generic and could also be applied to studying the translational dynamics of other particles with more complex architecture such as dendrites or chain-decorated nanoparticles.

Conformational Changes and Dynamics during Adsorption of Macromolecules with Different Degree of Polymerization Studied by Monte Carlo Simulations

AbstractDynamics of multilayer adsorption of macromolecules with different degree of polymerization is studied by coarse‐grained Monte Carlo simulations, focusing on both the interface macromolecule‐surface and chain–chain interaction in and out of equilibrium conditions. The interfacial interaction between the solid flat surface and the macromolecules is modeled by means of a Lennard–Jones potential, and inter‐ and intrachain interactions are simulated using bond angle, bond length, and Lennard–Jones potentials. The results show that local and conformational motions near the glass transition temperature promote configurations with minimal energy, which induce better space efficiency and favor aligned conformations at the interface. In this context, it is also found that restriction of movement, together with the connectivity effect exerted by the partially adsorbed segments, leads to a range of chain lengths that maximizes the molecular groups adsorbed.

Relevance of Internal Friction and Structural Constraints for the Dynamics of Denatured Bovine Serum Albumin.

A general property of disordered proteins is their structural expansion that results in a high molecular flexibility. The structure and dynamics of bovine serum albumin (BSA) denatured by guanidinium hydrochloride (GndCl) were investigated using small-angle neutron scattering (SANS) and neutron spin-echo spectroscopy (NSE). SANS experiments demonstrated the relevance of intrachain interactions for structural expansion. Using NSE experiments, we observed a high internal flexibility of denatured BSA in addition to center-of-mass diffusion detected by dynamic light scattering. Internal motions measured by NSE were described using concepts based on polymer theory. The contribution of residue-solvent friction was accounted for using the Zimm model including internal friction (ZIF). Disulfide bonds forming loops of amino acids of the peptide backbone have a major impact on internal dynamics that can be interpreted with a reduced set of Zimm modes.

Synthesis, structure and magnetic behaviors of a new spin-1/2 chain compound Na4CuTeO6

A new tellurate compound Na4CuTeO6 was synthesized by a conventional high-temperature solid state reaction. The titled compound crystallizes in the monoclinic system of a space group C2/c and exhibits a unique spin-chain structure built by planar CuO4 squares and TeO6 octahedra along the [101] direction. Magnetic measurements confirm that Na4CuTeO6 possesses an antiferromagnetic ordering at TN = ∼2.5 K. The intrachain and interchain interactions are estimated by a spin-chain model, showing a less pronounced 1D character in the system.

Coupling Influences SMM Properties for Pure 4 f Systems.

Increasing both the energy barrier for magnetization reversal and the coercive field of the hysteresis loop are significant challenges in the field of single-molecule magnets (SMMs). Coordination geometries of lanthanide ions and magnetic interactions between lanthanide ions are both important for guiding the magnetic behavior of SMMs. We report a high energy barrier of 657 K (457 cm-1 ) in a diamagnetic-ion-diluted lanthanide chain compound with a constrained bisphenoid symmetry (D2d ); this energy barrier is substantially higher than the barrier of 567 K (394 cm-1 ) of the non-diluted chain compound with intrachain ferromagnetic interactions. Although intrachain magnetic interaction lowers the energy barrier for magnetization reversal, it can greatly enhance the coercive fields and zero-field remanence of the hysteresis loops, which is crucial for the rational design of high-performance SMMs. Factors related to the coordination sphere of the lanthanide center, which govern the high magnetic relaxation barriers through the second excited Kramer's doublets and the magnetic interactions that affect the hysteresis loops, were revealed through ab initio calculations.

Solvent effects on the dimensionality of oxamato-bridged manganese(II) compounds

Two new oxamate-containing manganese(II) complexes, [{Mn(H2edpba)(H2O)2}2]n (1) and [Mn(H2edpba)(dmso)2]∙dmso∙CH3COCH3∙H2O (2) (H4edpba = N,N′-ethylenediphenylenebis(oxamic acid) and dmso = dimethylsulfoxide), have been synthesized and the structures of 1 and 2 were characterized by single crystal X-ray diffraction. The structure of 1 consists of neutral honeycomb networks in which each manganese(II) is six-coordinate by one H2edpba2− ligand and two carboxylate–oxygens from two other H2edpba2− ligands building the equatorial plane. Each manganese is connected to its nearest neighbor through two carboxylate(monoprotonated oxamate) bridges in an anti-syn conformation. A dmso solution of single crystals of 1 was placed under acetone atmosphere affording 2, whereas putting 2 in equimolar water:ethanol mixture results in 1. The molecular structure of 2 is made up of mononuclear manganese(II) units which are interlinked by weak C–H⋯π and edge-to-face π-stacking interactions leading to supramolecular chains along the crystallographic b axis. Magnetic measurements reveal the occurrence of an antiferromagnetic coupling between two manganese(II) ions through anti-syn carboxylate bridges for 1 [J = −1.18 cm−1, the Hamiltonian being defined as H = −J S1.S2] and very weak intrachain ferromagnetic interactions in 2 [J = + 0.046 cm−1, H = −J ∑iSi.Si + 1].

Sizes of Macromolecules of Copolymers of N-Methyl-N-Vinylacetamide and N-Methyl-N-Vinylamine Hydrochloride with Low Charge Linear Density

Series of copolymers of N-methyl-N-vinylacetamide and N-methyl-N-vinylamine hydrochloride containing from 1.5 to 17% mol % of charged units were obtained by partial hydrolysis of poly(N-methyl-N-vinylacetamide). A complex of hydrodynamic investigations of their diluted solutions (viscous flow, velocity sedimentation, translational diffusion) was performed in 0.2 M NaCl in order to determine the molecular characteristics of copolymers. Viscosimetric investigations were performed in salt-free solution (ionic strength ~10–6 M) to study intrachain electrostatic interactions; the influence of charge linear density on the sizes of polyelectrolyte macromolecules was studied under these conditions. The examination of hydrodynamic volumes, equilibrium rigidity, and/or swelling coefficients of charged chains was performed.

Interpretation of the Vibrational Spectra of Glassy Polymers Using Coarse-Grained Simulations

The structure and vibrational density of states (VDOS) of polymer glasses are investigated using numerical simulations based on the classical Kremer-Grest bead-spring model. We focus on the roles of chain length and bending stiffness, the latter being set by imposing three-body angular potentials along chain backbones. Upon increasing the chain length and bending stiffness, structural reorganisation leads to volumetric expansion of the material and build-up of internal stresses. The VDOS has two dominant bands: a low frequency one corresponding to inter- and intra-chain non-bonding interactions and a high frequency one corresponding principally to vibrations of bonded beads that constitute skeletal chain backbones. Upon increasing the steepness of the angular potential, vibrational modes associated with chain bending gradually move from the low-frequency to the high-frequency band. This redistribution of modes is reflected in a reduction of the so-called Boson peak upon increasing chain stiffness. Remarkably, the finer structure and the peaks of the high-frequency band, and their variations with stiffness, can, for short chains, be explained using an analytical solution derived for a model triatomic molecule. For longer chains, the qualitative evolution of the VDOS with chain stiffness is similar, although the distinct peaks observed for short chains become increasingly smoothed-out. Our findings can be used to guide a systematic approach to interpretation of Brillouin and Raman scattering spectra of glassy polymers in future work, with applications in polymer processing diagnostics.

Magnetism in Heterobimetallic and Heterotrimetallic Chains Based on the Use of [WV(bipy)(CN)6]– as a Metalloligand

Two new heterobi‐ and trimetallic chains of formula ∞1[{MnII(pyim)2}{(µ‐NC)2WV(bipy)(CN)4}][WV(bipy)(CN)6] (1) and ∞1[{CuIIMnIIL}{(µ‐NC)3WV(bipy)(CN)3}][WV(bipy)(CN)6]·0.75H2O·2MeCN (2) were obtained by reacting the cyanido‐based AsPh4[W(bipy)(CN)6] heteroleptic complex with the pre‐formed [MnII(pyim)2]2+ (1) and [CuIIMnIIL]2+ (2) complexes [bipy = 2,2′‐bipyridine, pyim = 2‐(1H‐imidazol‐2‐yl)pyridine and H2L = macrocyclic Schiff‐base resulting from the stepwise condensation of 2,6‐diformyl‐p‐cresol with ethylenediamine and diethylenetriamine]. The structure of 1 consists of cationic cyanido‐bridged {MnIIWV} chains, assembled from [WV(bipy)(CN)6]– spacers, each one coordinating in a bis‐monodentate fashion, two [MnII(pyim)2]2+ nodes, and [WV(bipy)(CN)6]– counteranions. Compound 2 comprises a positively charged 1D coordination polymer, built from [WV(bipy)(CN)6]– cyanido metalloligands that act as tris‐monodentate spacers towards [CuIIMnIIL]2+ complexes, the entire assembly being neutralized by [WV(bipy)(CN)6]– anions. Each manganese(II) ion in 1 is six‐coordinate in a somewhat distorted octahedral surrounding. Five‐coordinate copper(II) and seven‐coordinate manganese(II) ions exhibiting distorted square pyramidal and monocapped trigonal prism environments respectively, occur in each {CuIIMnII} node of 2. The magnetic susceptibility of 1 and 2 investigated down to 1.9 K is characteristic of 1D ferrimagnetic behavior with minima in the χMT vs. T plots at 35 (1) and 20 K (2) (χM is the magnetic susceptibility per one MnII plus two WV ions). The magnetic data of 1 in the whole temperature range were analyzed through a model considering SMn = 5/2 as a classical spin and SW = 1/2 as a quantum spin, with two interaction parameters J1 = J(1 – α) and J2 = J(1 + α) {the spin Hamiltonian being defined as H = –JΣiSW,i[(1 + α)SMn,j + (1 – α)SMn,i+1] + Σi(gWSW,i + gMnSMn,i)βH}. The values of the intrachain antiferromagnetic interactions for 1 through this model were –3.0(1) (J1) and –32.0(1) cm–1 (J2). The complexity of the spin topology in 2, a branched chain with four different intrachain antiferromagnetic interactions (double phenoxido bridge between MnII and CuII, two single cyanido bridges between MnII and CuII, and one single cyanido bridge between CuII and WV) precluded any simulation of its magnetic data.

Relaxation of surface-tethered polymers under moderate confinement.

We study the relaxation of surface-tethered polymers in microchannels under moderate confinement (i.e. h ∼ Rg, where h is the channel height and Rg is the radius of gyration of the polymer) by experiments with fluorescence-marked DNA molecules and coupled lattice-Boltzmann/molecular dynamics simulations. The determined scaling exponent suggests that the relaxation is dominated by Zimm-dynamics with significant intra-chain hydrodynamic interactions. The relaxation of the DNA molecules is slower in shallower channels, indicating a pronounced effect of confinement on the longest relaxation time. An experimental correlation is obtained for the longest relaxation time as a function of the molecular contour length and the channel height. Good agreement between the experimental and the simulation results is found.

Exploring the interactions in binary mixtures of polyelectrolytes: Influence of mixture composition, concentration, and temperature on counterion condensation

The counterion condensation in the binary mixtures of like-charged polyelectrolytes with two different molecular weights, where both are negatively charged, has been studied by conductance measurement in aqueous medium. Sodium polystyrenesulfonate with two different chain lengths have been selected as model polyelectrolyte and the investigation has been carried out in the absence of any added salt. The specific conductance-polyelectrolyte concentration data were analyzed in the light of the scaling argument for the conformation of polyion chains in solutions to quantify the fractions of free counterions. Effects of polyelectrolyte concentration, molecular weights of the components of the mixture, and solution temperature on the condensation of counterions have been investigated to explore polyion–counterion interaction, and inter- and intra-chain interactions in these polyelectrolyte mixtures. This investigation revealed that the extent of counterion condensation is significantly influenced by the mixture composition, the polyelectrolyte concentration and the temperature. Evaluation of the polyion transference numbers provided important information as to the direction of the motion of the counterions under the action of the applied electric field.

Feasible D1–A–D2–A Random Copolymers for Simultaneous High‐Performance Fullerene and Nonfullerene Solar Cells

AbstractA series of PBDB‐TTn random donor copolymers is synthesized, consisting of an electron‐deficient benzo[1,2‐c:4,5‐c′]dithiophene‐4,8‐dione (BDD) unit and different ratios of two electron‐rich benzo[1,2‐b:4,5‐b′]dithiophene (BDT) and thieno[3,2‐b]thiophene (TT) units, with intention to modulate the intrachain and/or interchain interactions and ultimately bulk‐heterojunction morphology evolution. A comparative study using 4 × 2 polymer solar cell (PSC) performance maps and each of the [6,6]‐phenyl‐C71‐butyric acid methyl ester (PC71BM) and the fused‐aromatic‐ring‐based molecule (m‐ITIC) acceptors are carried out. Given the similarities in their absorption ranges and energy levels, the PBDB‐TTn copolymers clearly reveal a change in the absorption coefficients upon optimization of the BDT to TT ratio in the backbone. Among the given acceptor combination sets, superior performances are observed in the case of PBDB‐TT5 blended with PC71BM (8.34 ± 0.10%) or m‐ITIC (11.10 ± 0.08%), and the dominant factors causing power conversion efficiency differences in them are found to be distinctly different. For example, the performances of PC71BM‐based PSCs are governed by size and population of face‐on crystallites, while intermixed morphology without the formation of large phase‐separated aggregates is the key factor for achieving high‐performance m‐ITIC‐based PSCs. This study presents a new sketch of structure–morphology–performance relationships for fullerene‐ versus nonfullerene‐based PSCs.

Large exchange anisotropy in quasi-one-dimensional spin- 12 fluoride antiferromagnets with a d(z2)1 ground state

Hybrid density functional calculations are performed for a variety of systems containing d9 ions (Cu2+, Ag2+), and exhibiting quasi-one-dimensional magnetic properties. In particular we study fluorides containing these ions in a rarely encountered compressed octahedral coordination which forces the unpaired electron in the d(z2) orbital. We predict that such systems should exhibit magnetic anisotropies surpassing that of Sr2CuO3 - one of the best realizations of an one-dimensional system known to date. In particular we predict that the inter-chain coupling in the Ag2+ containing [AgF][BF4] should be nearly five orders of magnitude smaller than the intra-chain interaction. Our results indicate that quasi-one-dimensional spin-1/2 systems containing chains with spin sites in a d(z2)1 local ground state could constitute a versatile model for testing modern theories of quantum many-body physics in the solid state.

Spin-wave dynamics and exchange interactions in multiferroic NdFe3(BO3)4 explored by inelastic neutron scattering

Magnetic excitations and exchange interactions in multiferroic NdFe3(BO3)4 were studied by inelastic neutron scattering in the phase with commensurate antiferromagnetic structure. The observed spectra were analyzed in the frame of the linear spin-wave theory. It was shown that only the model, which includes the exchange interactions within eight coordination spheres, describes satisfactorily all observed dispersion curves. The calculation showed that the spin-wave dynamics is governed by the strongest antiferromagnetic intra-chain interaction and three almost the same inter-chain interactions. Other interactions, including ferromagnetic exchange, appeared to be insignificant. The overall energy balance of the antiferromagnetic inter-chain exchange interactions, which couple the moments from the adjacent ferromagnetic layers as well as within a layer, stabilizes ferromagnetic arrangement in the latter. It demonstrates that the pathway geometry plays a crucial role in forming of the magnetic structure.