Interchain Contacts Research Articles

HbQ-Iran [α75 (EF4) Asp→His]/−α3.7/β° IVSII.1 G→A in an Iranian Child: First Reported Case.

HbQ-Iran [α75 (EF4) Asp→His] is an α-chain variant first described in 1970, which substitution is not involved in the interchain contacts of hemoglobin. It has a slow-moving migration pattern on cellulose acetate at alkaline pH, that resembles the Hb S, but with normal solubility. The quantity of this variant in the heterozygous state has been reported to be 17–19%. Heterozygotes individuals with HbQ-Iran are hematologically asymptomatic and the combination with α+-thalassemia and β0- thalassemia has not been reported up to now.We here described the hematological characteristics of a 5 years old child referred to the clinic of Kermanshah University. Physical examination revealed no enlargement of the spleen, and the initial blood count indicated a mild microcytic anemia with low levels of Hb (10g/dL), a hematocrit of 30.5% and low MCV and MCH (59.3fL and 19.6pg) respectively. DNA analysis revealed the presence of HbQ-Iran, −α3.7 kb deletion of the alpha globin genes and also the presence of the mutation (IVSII.1.G→A) β0-thalassemia in the child. The study of the family revealed the presence of a minor β-thalassemia in the father and the HbQ-Iran in the mother. Both parents were heterozygous for the −α3.7 deletion (−α3.7/α α) in the α-globin genes. The coinheritance of HbQ-Iran with −α3.7 deletion and β-thalassemia resulted in an elevation of the levels of HbQ-Iran to 22.4%. However, the remainder hematological values of the young patient indicated a significant reduction in MCV (59.3 fL) and MCH (19.6 pg), an elevation of HbF (6.3%) and of HbA2 (3.7%) according to a picture of a minor β-thalassemia. This result demonstrated that HbQ-Iran is a benign structural variant, that in combination with β0-thalassemia and in the presence of a α+-thalassemia, produce a minor β-thalassemia picture with moderate anemia and elevation of HbF. The application of DNA technologies allowed the identification for the first time of the presence in one individual of three already known mutations, emphasizing the unique genetic heterogeneity of this population.

Challenges and opportunities in polymer theory

Challenges and opportunities in polymer theory

The effect of copolymer composition on the dynamics of random copolymers in a homopolymer matrix

The effect of copolymer composition on the dynamics of random copolymers in a homopolymer matrix is studied using computer simulations within the framework of the bond-fluctuation model on blends containing low concentrations (10%) of A-B copolymers, where A and B are two different types of monomers, dispersed in a homopolymer matrix of chains with only A-type monomers. Four copolymer compositions were studied, phi(A)=0.33, phi(A)=0.5, phi(A)=0.66, and phi(A)=0.82, while maintaining a statistically random sequence distribution. For this study, we have only included intermolecular interactions between A and B monomers. Our results indicate, in agreement with experimental data, that copolymer composition has an impact on system dynamics. Analysis of the structure reveals that copolymers with majority A content are expanded in the homopolymer matrix, have fewer interchain copolymer-copolymer contacts, and are well dispersed in the homopolymer matrix. On the other hand, copolymers with lower A content form a more compact structure, have more interchain contacts, and form aggregates that are short lived. This in turn leads to slower system dynamics. Both the radius of gyration (Rg) and copolymer end-to-end vectors (Re) increase with increasing A content until phi(A)=0.66 and then decrease. Copolymers with lower A content form more compact structures as the repulsive interactions between unlike species are minimized by the copolymers folding back on themselves and forming aggregates of copolymer chains. Thus, these results provide insight into the variation of copolymer dynamics with composition in the system by documenting the correlation between the thermodynamics of this mixture, the conformation of a copolymer chain in a homopolymer matrix, and the dynamics of both components in this blend.

3D supramolecular network constructed by intermolecular interactions in mixed ligand complex of zinc

New complex [Zn(quin-2-c) 2(Him) 2] (quin-2-c = quinoline-2-carboxylate ion, Him = imidazole) was synthesized by self assembly and its structure was determined by X-ray analysis. The compound crystallizes in P21/c space group. Four independent molecules of complex are present in the structure. Strong hydrogen bonds create three different 1D chains which are collected in two different layers. The alternately packed layers form the 3D supramolecular structure. The interchain and interlayer contacts are of the C–H⋯O, π⋯π and C–H⋯π type. The influence of strong hydrogen bond on the vibrational characteristics of the monodentately coordinated carboxylate group in zinc complexes with quin-2-c ion is discussed.

Controlling Optical Properties and Interchain Interactions in Semiconducting Polymers by Encapsulation in Periodic Nanoporous Silicas with Different Pore Sizes

The photophysics of MEH-PPV incorporated into the pores of periodic silica hosts has been investigated in an effort to understand the role played by interchain aggregation and chain morphology in polaron production. In this work, guest/host interactions were used to incorporate MEH-PPV into the straight, homogeneous pores of hexagonal surfactant- or polymer-templated mesoporous silicas of varying pore diameters. Polarized photoluminescence and photoluminescence excitation spectroscopy were then used to investigate the polymers' environment within the silica pores. Experiments exploiting luminescence peak shifts and depolarization indicate that depending on the pore size and preparation conditions, the alignment and packing of the polymer chains within the pores could be controlled. Samples could be produced with isolated chains, interacting straight chains, and coiled interacting chains. The sub-bandgap absorption by polarons was then measured with photoinduced absorption as a function of pore size. Small-diameter pores that allowed single polymer chains to reside within the pore showed little evidence of interchain contact and had a low polaron yield. Increasing the number of polymer chains within the pore increased the polaron yield. Finally, when the pores were large enough that the chains could coil, strong polaron absorption was observed, indicative of a further increase in polaron yield or an increase in polaron lifetime. The polaron absorption spectra also sharpen and red shift with increasing pore diameter, suggesting that excitons may migrate to lower energy polymer segments in samples where polymer chains are both coiled and interacting.

One‐dimensional Diamagnetic‐metal Nitronyl Nitroxide Radical Complexes with Dicyanoargentate(I) Bridges: M(NIT4Py)2[Ag(CN)2]2 (M= Zn, Cd)

AbstractTwo diamagnetic‐metal nitronyl nitroxide radical complexes with dicyanoargentate(I) bridges M(NIT4Py)2[Ag(CN)2]2 (M= Zn, Cd) were synthesized. X‐ray crystallography reveals that the two compounds are isomorphous, which crystallize in the triclinic ${\rm P}{\bar 3}$ space group. Their structures consist of infinite chains of M(NIT4Py)2 units linked by [Ag(CN)2]− μ2‐bridging ligands. The magnetic measurements showed that the χMT values are nearly constants at higher temperature for both complexes. The sharp decreasing of χMT values at lower temperature are related to intermolecular antiferromagnetic interactions, which result from the shortest interchain contacts of nitroxide groups in the crystals.

Influence of denatured and intermediate states of folding on protein aggregation

We simulate the aggregation thermodynamics and kinetics of proteins L and G, each of which self-assembles to the same alpha/beta [corrected] topology through distinct folding mechanisms. We find that the aggregation kinetics of both proteins at an experimentally relevant concentration exhibit both fast and slow aggregation pathways, although a greater proportion of protein G aggregation events are slow relative to those of found for protein L. These kinetic differences are correlated with the amount and distribution of intrachain contacts formed in the denatured state ensemble (DSE), or an intermediate state ensemble (ISE) if it exists, as well as the folding timescales of the two proteins. Protein G aggregates more slowly than protein L due to its rapidly formed folding intermediate, which exhibits native intrachain contacts spread across the protein, suggesting that certain early folding intermediates may be selected for by evolution due to their protective role against unwanted aggregation. Protein L shows only localized native structure in the DSE with timescales of folding that are commensurate with the aggregation timescale, leaving it vulnerable to domain swapping or nonnative interactions with other chains that increase the aggregation rate. Folding experiments that characterize the structural signatures of the DSE, ISE, or the transition state ensemble (TSE) under nonaggregating conditions should be able to predict regions where interchain contacts will be made in the aggregate, and to predict slower aggregation rates for proteins with contacts that are dispersed across the fold. Since proteins L and G can both form amyloid fibrils, this work also provides mechanistic and structural insight into the formation of prefibrillar species.

Spatial regimes in the dynamics of polyolefins: self-motion.

Molecular dynamics simulations are used to investigate the spatial dependence of dynamics in a series of polyolefins. The dynamic indicator used is the self-intermediate scattering function, which parallels the observable in an incoherent quasielastic neutron scattering experiment such as time of flight or backscattering. As with neutron time of flight experiments, two processes are evident. The fast process is a single exponential, and has relaxation times that scale as q(-2), where q is the momentum transfer. The slow process is the stretched exponential decay usually associated with the motion underlying the glass transition. The stretching exponent is a function of spatial scale, with the minimum values occurring near the spatial scale of interchain packing. Relaxation times for the slow process scale as q(-2/beta) for all materials investigated. The relative contribution of the two processes is a function of spatial scale, with the crossover from fast to slow dynamics at the location of closest possible interchain contacts, which is approximately three times the cage size. These observations apply equally well to the four materials considered. We consider the relative ordering of relaxation times of the series in light of their local chain architecture. This ordering varies depending on the observable calculated..

Molecular modelling of self-assembled alkynyl monolayer structures — Unnatural symmetry units, surface bonding, and topochemical polymerization1

Geometric modelling techniques are used to map the potential energies of packing for self-assembled alkyl- and phenyl-backboned monolayers across a range of intermolecular separations. Natural packing distances of 4.2–4.4 Å produce less stable, more isotropic monolayers because of repulsive interchain contacts. Optimizations at unnatural surface densities found thin films of lower energy and higher symmetry existed at increased chain–chain separations. Head-group bonding is therefore identified as a force for controlling monolayer order. Analysis of the natural monolayer structures on a silicon dioxide surface determined the favourable head-group structures, and allowed the topochemical polymerization of p-bis(butadiynyl)benzene monolayers to be rationalized.Key words: self-assembled monolayers, molecular modelling studies, repeating symmetry units, thin-film order, topochemical polymerization.

Ordering in Stretched Bernoullian Copolymers

AbstractA new approach is suggested to estimate the theoretical maximum capability to order for stretched Bernoullian copolymers AB, provided interchain AB contacts are unfavorable. A simple Monte Carlo procedure simulating the ordering of such copolymers via rotation of ring‐shaped chains reveals the capability to order even for quite long copolymer chains. The analytical probabilistic consideration is elaborated, which enables one to interpret the ordering via rotation in terms of a sliding of periodic Bernoullian chains. Using both the probabilistic analysis and Monte Carlo simulations it is shown that estimations of a capability to order given by the rotation procedure are also good for a sliding of true Bernoullian copolymers. Therefore, the simple Monte Carlo procedure seems suitable for estimating ordering in other classes of copolymers for which an analytical approach is more complicated. Such estimations might be useful for a consideration of various properties of irregular copolymers connected with their tendency to order.Ordering by rotation of rings. As an example, an ordering for M = 10 000 chains of length N = 20 and composition p = 0.50 (p is the mole fraction of A units) is shown. See text.imageOrdering by rotation of rings. As an example, an ordering for M = 10 000 chains of length N = 20 and composition p = 0.50 (p is the mole fraction of A units) is shown. See text.

Supramolecular structures of metronidazole and its copper(II), cobalt(II) and zinc(II) coordination compounds

In this work we present the synthesis and structural and spectroscopic characterization of CuII, CoII and ZnII coordination compounds with the antibiotic metronidazole (=emni). Coordination to metal ions is through its imidazolic nitrogen, while the hydroxyethyl and nitro groups act as supramolecular synthons. [Co(emni)2Br2], and [Zn(emni)2X2] (X−=Cl, Br) stabilize zig-zag chains, and a 2D supramolecular structure is formed by inter-chain contacts through inter-molecular hydrogen-bonding. Pleated sheet or layers are formed by [Co(emni)2Cl2] and [Cu(emni)2Cl(H2O)]2Cl2, respectively. The dinuclear CuII compound [Cu(emni)μ(O2CMe)2]2 gives a one-dimensional zig-zag arrangement. The contribution of metal ions in metronidazole coordination compounds is shown in the stabilization of the different aggregate structures.

Structural Properties of a Collagenous Heterotrimer that Mimics the Collagenase Cleavage Site of Collagen Type I

Collagens contain sequence- and conformation-dependent epitopes responsible for their digestion by collagenases at specific loci. A synthetic heterotrimer construct containing the collagenase cleavage site of collagen type I was found to mimic perfectly native collagen in terms of selectivity and mode of enzymatic degradation. The NMR conformational analysis of this molecule clearly revealed the presence of two structural domains, i.e. a triple helix spanning the Gly-Pro-Hyp repeats and a less ordered portion corresponding to the collagenase cleavage site where the three chains are aligned in extended conformation with loose interchain contacts. These structural properties allow for additional insights into the very particular mechanism of collagen digestion by collagenases.

Exploring protein aggregation and self-propagation using lattice models: phase diagram and kinetics.

Many seemingly unrelated neurodegenerative disorders, such as amyloid and prion diseases, are associated with propagating fibrils whose structures are dramatically different from the native states of the corresponding monomers. This observation, along with the experimental demonstration that any protein can aggregate to form either fibrils or amorphous structures (inclusion bodies) under appropriate external conditions, suggest that there must be general principles that govern aggregation mechanisms. To probe generic aspects of prion-like behavior we use the model of Harrison, Chan, Prusiner, and Cohen. In this model, aggregation of a structure, that is conformationally distinct from the native state of the monomer, occurs by three parallel routes. Kinetic partitioning, which leads to parallel assembly pathways, occurs early in the aggregation process. In all pathways transient unfolding precedes polymerization and self-propagation. Chain polymerization is consistent with templated assembly, with the dimer being the minimal nucleus. The kinetic effciency of R(n-1) + G --> R(n) (R is the aggregation prone state and G is either U, the unfolded state, or N, the native state of the monomer) is increased when polymerization occurs in the presence of a "seed" (a dimer). These results support the seeded nucleated-polymerization model of fibril formation in amyloid peptides. To probe generic aspects of aggregation in two-state proteins, we use lattice models with side chains. The phase diagram in the (T,C) plane (T is the temperature and C is the polypeptide concentration) reveals a bewildering array of "phases" or structures. Explicit computations for dimers show that there are at least six phases including ordered structures and amorphous aggregates. In the ordered region of the phase diagram there are three distinct structures. We find ordered dimers (OD) in which each monomer is in the folded state and the interaction between the monomers occurs via a well-defined interface. In the domain-swapped structures a certain fraction of intrachain contacts are replaced by interchain contacts. In the parallel dimers the interface is stabilized by favorable intermolecular hydrophobic interactions. The kinetics of folding to OD shows that aggregation proceeds directly from U in a dynamically cooperative manner without populating partially structured intermediates. These results support the experimental observation that ordered aggregation in the two-state folders U1A and CI2 takes place from U. The contrasting aggregation processes in the two models suggest that there are several distinct mechanisms for polymerization that depend not only on the polypeptide sequence but also on external conditions (such as C, T, pH, and salt concentration).

Characterization of the Protrimer Intermediate in the Folding Pathway of the Interdigitated β-Helix Tailspike Protein

P22 tailspike is a homotrimeric, thermostable adhesin that recognizes the O-antigen lipopolysaccharide of Salmonella typhimurium. The 70 kDa subunits include long beta-helix domains. After residue 540, the polypeptide chains change their path and wrap around one another, with extensive interchain contacts. Formation of this interdigitated domain intimately couples the chain folding and assembly mechanisms. The earliest detectable trimeric intermediate in the tailspike folding and assembly pathway is the protrimer, suspected to be a precursor of the native trimer structure. We have directly analyzed the kinetics of in vitro protrimer formation and disappearance for wild type and mutant tailspike proteins. The results confirm that the protrimer intermediate is an on-pathway intermediate for tailspike folding. Protrimer was originally resolved during tailspike folding because its migration through nondenaturing polyacrylamide gels was significantly retarded with respect to the migration of the native tailspike trimer. By comparing protein mobility versus acrylamide concentration, we find that the retarded mobility of the protrimer is due exclusively to a larger overall size than the native trimer, rather than an altered net surface charge. Experiments with mutant tailspike proteins indicate that the conformation difference between protrimer and native tailspike trimer is localized toward the C-termini of the tailspike polypeptide chains. These results suggest that the transformation of the protrimer to the native tailspike trimer represents the C-terminal interdigitation of the three polypeptide chains. This late step may confer the detergent-resistance, protease-resistance, and thermostability of the native trimer.

Conjugated polymers as molecular materials: how chain conformation and film morphology influence energy transfer and interchain interactions.

The electronic structure of conjugated polymers is of current interest because of the wide range of potential applications for such materials in optoelectronic devices. It is increasingly clear that the electronic properties of conjugated polymers depend sensitively on the physical conformation of the polymer chains and the way the chains pack together in films. This article reviews the evidence that interchain electronic species do form in conjugated polymer films, and that their number and chemical nature depend on processing conditions; the chain conformation, degree of interchain contact, and rate of energy transfer can be controlled by factors such as choice of solvent, polymer concentration, thermal annealing, presence of electrically charged side groups, and encapsulation of the polymer chains in mesoporous silica. Taken together, the results reconcile many contradictions in the literature and provide a prescription for the optimization of conjugated polymer film morphology for device applications.

Metamagnetism in linear chain electron-transfer salts based on decamethylferrocenium and metal–bis(dichalcogenate) acceptors

The crystal structure of the electron-transfer (ET) salts [Fe(Cp*) 2][M(tds) 2], with M=Ni ( 1) and Pt ( 2), consists of an array of parallel alternating donors, [Fe(Cp*) 2] +, and acceptors, [M(tds) 2] −, ⋯DADADA⋯, stacks. For T>20 K, the magnetic susceptibility follows a Curie–Weiss behavior, with θ values of 8.9 and 9.3 K for 1 and 2, respectively. A metamagnetic behavior was observed in 2, with T N=3.3 K and H C =3.95 kG at 1.7 K, resulting from a high magnetic anisotropy. A systematic study of the intra and interchain magnetic interactions was performed on 1, 2 and other ET salts based on decamethylferrocenium and on metal–bis(dichalcogenate) acceptors, with a similar crystal structure. The observed magnetic behavior of these compounds is consistent with the presence of strong ferromagnetic intrachain DA interactions and weaker antiferromagnetic interchain interactions, predicted by the McConnell I model. A variety of interionic interchain contacts were found in these ET salts (AA, DD and DA) and these contacts were observed to give rise to antiferromagnetic interchain coupling. Although it was only observed in the case of 2 and [Fe(Cp*) 2][Ni(edt) 2], metamagnetism is expected to occur at lower temperatures in the other ET salts due to weaker intra and interchain coupling.

Continuum percolation in macromolecular fluids

A heuristic treatment of the connectedness Ornstein–Zernike equation is developed for macromolecular fluids within the framework of the polymer reference interaction site model (PRISM). Results are presented for the critical volume fraction at the percolation threshold and for the mean number of interchain contacts per molecule for athermal rodlike and Gaussian coil-like particles. The results for rodlike particles are in qualitative agreement with prior investigations based on fully numerical solutions of the PRISM equations, and with computer simulations of ellipsoids. The method proposed here leads to the physically reasonable result that the percolation threshold for direct connectivity on the length scale of the molecular dimensions is closely related to the semidilute crossover concentration as usually defined, and can be generalized directly to multicomponent systems.

Crystal Structure and Magnetic Behavior of the Decamethylferrocenium and Decamethylchromocenium Salts of Bis(ethylenedithiolato)nickel, [M(Cp*)2][Ni(edt)2] − Magnetic Anisotropy and Metamagnetic Behavior of [Fe(Cp*)2][Ni(edt)2

New electron-transfer salts, [M(Cp*)2][Ni(edt)2], with M = Fe and Cr, were prepared and shown to be isostructural by X-ray crystallographic studies. The molecular structure of [Ni(edt)2]− is reported here for the first time. The solid-state structure consists of an array of parallel alternating donors, [Fe(Cp*)2]•+, and acceptors, [Ni(edt)2]•−, ··DADADA·· stacks along [101]. At high temperatures (T > 50−100 K), the magnetic susceptibility obeys the Curie−Weiss expression, with the θ values of −5 and −6.7 K for the Ni and Cr compounds respectively, revealing dominant AFM interactions. At low temperatures metamagnetic behavior was observed in case of [Fe(Cp*)2][Ni(edt)2], with TN = 4.2 K and HC = 14 kG at 2 K, resulting from high magnetic anisotropy, due to the coexistence of strong FM DA intrachain interactions and strong AFM (DA and AA) interchain interactions. Single-crystal magnetization measurements with [Fe(Cp*)2][Ni(edt)2] showed that the transition from the AFM state to the FM high-field state was induced by the application of a magnetic field parallel to the stacking axis. In these compounds the AFM interchain (DA and AA) interactions play a dominant role, due to the large spin density on the periphery of the acceptor and the close AA and DA interchain contacts. Above 4.2 K the 57Fe Mössbauer spectra of [Fe(Cp*][Ni(edt)2] exhibit the classical low spin FeIII ferrocenium singlet. Below this temperature a poorly resolved hyperfine pattern is observed (estimated hyperfine field ca. 350 kG at 3.5 K). The analysis of the spectra obtained in applied fields of 20 kG and 50 kG is consistent with a strongly anisotropic g tensor. A pronounced temperature dependence of the spectra in a field of 50 kG suggests the presence of spin-lattice relaxation effects.

Controlling Interchain Interactions in Conjugated Polymers: The Effects of Chain Morphology on Exciton−Exciton Annihilation and Aggregation in MEH−PPV Films

The presence of interchain species in the photophysics of conjugated polymer films has been the subject of a great deal of controversy. In this paper, we present strong evidence that interchain species do form in conjugated polymer films, and that the degree of interchain interactions can be controlled by varying the solvent and polymer concentration of the solution from which the films are cast. Thus, much of the controversy in the literature can be resolved by noting that the polymer samples in different studies had different side groups or were prepared in different ways and thus have different degrees of interchain interaction. The photoluminescence (PL) of poly(2-methoxy-5-(2′-ethylhexyloxy)-1,4-phenylene vinylene), MEH-PPV, changes both its spectral shape and quantum yield when the films are prepared from different solutions or when the morphology is varied by annealing. Increasing the amount of interchain interactions enhances the red portion of the film’s PL, a result assigned to a combination of changes in the vibronic structure of the PL of the exciton and increased numbers of weakly emissive interchain species. Photoluminescence excitation spectroscopy shows that excitation to the red edge of the absorption band preferentially enhances the red emission, suggesting that the interchain species are aggregates with a distinct ground state absorption. Scanning force microscopy shows topographic features that correlate with the degree of interchain interactions, verifying that the morphology of conjugated polymer films changes with polymer concentration, choice of solvent, and spin-casting speed. Even at low excitation intensities, photooxidative damage occurs quickly in MEH-PPV films excited in air, and the rate at which damage occurs is sensitive to the packing of the polymer chains. For samples under vacuum at low excitation intensity, a long-lived emissive tail, in combination with excitedstate absorption dynamics that do not match those of the emissive species, provide direct evidence for the production of interchain aggregates. Annealing an MEH-PPV film produces a photophysical signature similar to photooxidation, implying that defects in conjugated polymer films are intrinsic and depend on the details of how the chains are packed. At higher excitation intensities, we find that exciton -exciton annihilation occurs, and that the probability for annihilation can vary by an order of magnitude depending on the degree of interchain contact in the film. Finally, we show that changing the film morphology has a direct effect on the performance of MEH-PPV-based light-emitting diodes. Higher degrees of interchain interaction enhance the mobility of carriers at the expense of lower quantum efficiencies for electroluminescence. Taken together, the results reconcile much of the contradictory literature and provide a prescription for the optimization of conjugated polymer films for particular device applications.

Long-lived interchain contacts in polymer melts

We will study time dependence of interchain contacts in entangled and unentangled polymer melts. We find that “clusters” of contacts in entangled melts persist in time up to at least 0.2 of the longest relaxation time. The clusters of contacts in un-entangled melts disappear and reappear on at least two orders of magnitude shorter time scale. We also examine time-dependent correlation functions that try to quantify the properties of contacts.