Demonstration of an alternative mechanism for G-to-G cross-link formation

The cross-link dG-to-dG is an important product of DNA nitrosation. Its formation has commonly been attributed to nucleophilic substitution of N2 in a guaninediazonium ion by guanine, while recent studies suggest guanine addition to a cyanoamine derivative formed after dediazoniation, deprotonation, and pyrimidine ring-opening. The chemical viability of the latter mechanism is supported here by the experimental demonstration of rG-to-aG formation via rG addition to a synthetic cyanoamine derivative. Thus, all known products of nitrosative guanine deamination are consistent with the postulate of pyrimidine ring-opening. This postulated mechanism not only explains what is already known but also suggests that other products and other cross-links also might be formed in DNA deamination. The study suggests one possible new product: the structure isomer aG(N1)-to-rG(C2) of the classical G(N2)-to-G(C2) cross-link. While the formation of aG(N2)-to-rG(C2) has been established by chemical synthesis, the structure isomer aG(N1)-to-rG(C2) has been assigned tentatively based on its MS/MS spectrum and because this assignment is reasonable from a mechanistic perspective. Density functional calculations show preferences for the amide-iminol tautomer of the classical cross-link G(N2)-to-G(C2) and the amide-amide tautomer of G(N1)-to-G(C2). Moreover, the results suggest that both cross-links are of comparable thermodynamic stability, and that there are no a priori energetic or structural reasons that would prevent the formation of the structure isomer in the model reaction or in DNA.     

Embedded conformon model of chain folding

The real-space renormalization-group technique is used to study the low lying energy states of a random copolymer composed of hydrophobic (H) and polar (P) beads on a simple cubic lattice. Application of a variety of boundary conditions to parts of the larger chain (embedded conformons) while progressively increasing the length scale gives the lowest energy states in agreement with exact calculations for a 17 bead chain with a random H,P sequence. These results are significant for studying minimalist models of the folding of complex molecules because the computation time is several orders of magnitude less than for other approaches.     

Vibrational analysis of chain folding in polyethylene crystals

The vibration frequencies of a polyethylene crystal lattice have been computed for various structures in which a fully deuterated chain is mixed with a normal chain. Intermolecular potential functions previously developed by the authors were used in the calculation. It is shown that such structures make it possible to distinguish experimentally between chain folding in the (110) plane and folding parallel to the (100) plane. Calculations have also been done for a regular polymer of (CH₂CD₂). Such a structure would permit the determination of the parity of the number of methylene groups in the fold.     

Mixed crystal infrared study of chain folding in crystalline polyethylene

Infrared spectroscopic studies have been made of mixed crystals of linear polyethylene and perdeuteropolyethylene. On the basis of normal vibration analyses by Tasumi and Krimm it had been shown that the study of crystal splittings of internal chain modes in such mixed crystals could provide information on the geometry of chain folding. The present results, which include a study of n-paraffin (C₃₆) mixed crystals, confirm these predictions. They show that (110) folding predominates in dilute solution grown crystals, and that this is transformed to (200) folding in melt-crystallized polymer. Folding with adjacent re-entry is favored, a random re-entry model being clearly eliminated.     

Molecular Dynamics Studies of Collapse Stages in the chain folding process of Polyethylene

Althoughtheequilibriumpropertiesofthepolymerhavebeenextensivelystudied,kineticphenomenasuchasthecondensingprocessandcollapsetransitionstillhavemanyunclearaspects,andmucheffortwastakentomakeathoroughinvestigationandstudy.Moleculardynamic(MD)simulationsofthefoldingandcollapseprocessforapolyethylenechainwasrecentlycarriedoutbymanyauthors1'2'3.Itwasreportedthatatwo-stagecollapseprocesswasseenwithouttorsionpotential',andthreestageswerefoundbysimplificationofthecomputationalmodel5.ButthecollaPsesta…     

On the possibility of chain folding in solutions of normal paraffins and polyethylene

A simple statistical thermodynamic argument is presented in which the probability of intramolecular chain folding of normal paraffins and polyethylene in solution is examined. This possibility is based on the existence of low-energy intramolecular conformations which are stable enough to overcome the tendency of a chain molecule to assume a random arrangement in solution. Some rough estimates of the magnitudes of energetic interaction in straight-chain hydrocarbons are made to demonstrate the plausibility of this hypothesis. The experimental support for this model arises from NMR spectra of normal paraffins in aromatic hydrocarbon solvents.     

Novel one-dimensional lanthanide acrylic acid complexes: an alternative chain constructed by hydrogen bonding

Novel one-dimensional (1D) chains of three lanthanide complexes La(L¹)₃(CH₃OH)]·CH₃OH (L¹=(E)-3-(2-hydroxyl-phenyl)-acrylic acid) 1, La(L²)₃(H₂O)₂]·2.75H₂O (L²=(E)-3-(3-hydroxyl-phenyl)-acrylic acid) 2, and La(L³)₃(CH₃OH)₂(H₂O)]·CH₃OH (L³=(E)-3-(4-hydroxyl-phenyl)-acrylic acid) 3 are reported. The crystal structure data are as follows for 1: C₂₉H₂₉LaO₁₁, monoclinic, P2₁/n, a=15.4289(12) Å, b=7.9585(6) Å, c=23.041(2) Å, β=99.657(2)°, Z=4, R₁=0.0637, wR₂=0.0919; for 2: C₂₇H_30.50LaO_13.75, triclinic, P−1, a=8.4719(17) Å, b=13.719(3) Å, c=14.570(3) Å, α=62.19(3)°, β=99.657(2)°, γ=78.22(3)°, Z=2, R₁=0.0384, wR₂=0.0820; and for 3: C₃₀H₃₅LaO₁₃, monoclinic, P2(1)/c, a=9.5667(6) Å, b=24.3911(15) Å, c=14.0448(9) Å, β=109.245(2)°, Z=4, R₁=0.0374, wR₂=0.0630. All the three structure data were collected using graphite monochromated molybdenum Kα radiation and refined using full-matrix least-squares techniques on F². These structures show that four kinds of the carboxylato bridge modes are included in these chains to link the La(III) ions. It is the first time that it has been found that the intra-chain hydrogen bonding can construct an alternative chain even, when the coordination bridge mode is the same along the chain (complex 2). There are 2D and 3D hydrogen bonding in the crystal lattices of complexes 1-3.     

Coordinated pair chain folding model for solution-grown polyethylene single crystal

A new regular chain folding model, namely the “coordinated pair chain folding model” (CPCFM) is proposed to revive the consideration that a polymer chain should fold regularly rather than randomly in solution-grown polyethylene single crystals.     

Relations between thermomechanical properties and chain folding of polyethylene terephthalate fibers

Summary The molecular mechanism of the nonlinear relationship between the transition temperatures (T _g resp.Tinm) and the outer tensile stress is discussed.On the basis of thermomechanical curves (deformation-temperature) taken at different external tensile force on drawn annealed PET fibers and films it has been shown that the transition temperatures depend nonlinearly on the applied tension stress. The maxima observed for bothT _g andT _m confirm the theoretical results ofCiferri andSmith andFrenkel assuming a crystallization of oriented polymer with chains in folded or helical conformation.A reasonable explanation is proposed for the increase ofT _m followed by decrease and again increase with progressively rising of the applied tension stress using the model ofBonart-Hosemann for structure of semicrystalline polymers: at low tension values an orientation of macromolecules in noncrystalline zones takes place followed by defolding of chains from crystallites and finally (at highest tension values) an extreme stretching with additional orientation proceeds. This mechanism is supported by infra-red measurements.The thermomechanical data plotted as external tension divided by the corresp. melting temperature versus deformation confirm the theoretical curve derived byFlory. The experimental curves demonstrate that (1) the crystallization under strain with negative elongation as well as (2) the regeneration of the amorphous phase and its additional stretching are physically realisable situations when the crystallization is accompanied by chain folding or building of helices. It is shown that the thermomechanical method could be used as a simple tool for investigating the chain folding problem.The data reported are an additional proof of the existence of regular folded chains in the crystalline PET too.

---

Zusammenfassung Es wird der molekulare Mechanismus des nichtlinearen Zusammenhangs zwischen den Übergangstemperaturen (T_g bzw. T_m) und der äußeren Spannung diskutiert. Auf Grund der thermomechanischen Kurven (Deformation - Temperatur), aufgenommen bei verschiedenen äußeren Spannungen an verstreckten und getemperten PET Fasern, wird festgestellt, daß die Übergangstemperaturen (T_g und T_m) von der äußeren Spannung abhängig sind. Die beobachteten Maxima für die beiden Temperaturen T_g und T_m bestätigen die theoretischen Ergebnisse vonCiferri undSmith undFrenkel, die eine Kristallisation der orientierten Polymeren mit Kettenfaltung oder Spiral-Bildung annehmen. Von dem Bonart-Hosemann-Modell ausgehend wird eine Erklärung für die festgestellte Zunahme von T_m, nach welcher eine Abnahme und wieder neue Zunahme folgt, mit progressiv wachsender äußerer Spannung vorgeschlagen: bei niedrigen Spannungswerten findet eine Orientierung von Makromolekülen in nichtkristallinen Bereichen statt, nach welcher eine Entfaltung von Ketten in den Kristalliten eintritt und zuletzt (bei höchsten Spannungen) eine extreme Verstreckung mit zusätzlicher Orientierung stattfindet. Dieser Mechanismus wird von Infrarotmessungen gestützt. Die dargestellten thermomechanischen Daten in den Koordinaten äußere Spannung/Schmelztemperatur gegen Deformation bestätigen die vonFlory theoretisch berechnete Kurve. Die experimentellen Kurven demonstrieren, daß (1) die Kristallisation mit negativer Deformation sowie (2) die Regenerierung der amorphen Phase und ihre zusätzliche Verstreckung physikalisch realisierbare Situationen sind, wenn die Kristallisation mit Kettenfaltung oder Spiral-Bildung auftritt. Es ist damit gezeigt, daß thermomechanische Messungen ein erfolgreiches Mittel zur Untersuchung des Kettenfaltungsproblems darstellen. Die experimentellen Daten sind ein neuer Beweis für die Existenz von regulärer Kettenfaltung auch im kristallinen PET.

---

---

With 11 figures     

The protein folding problem: Searching conformations of compact chain molecule

A simple model of self-avoiding chains of specific-sequence copolymers of H (hydrophobic) and P (polar) monomers on lattices gives many of the properties of proteins, including their tertiary structural symmetries.     

Instationary polymerization technique – an alternative route for the direct determination of the rate constant of chain propagation

Instationary polymerization technique (IPT) is a combination of nonstationary polymerization conditions and the controlled deactivation of all active radicals present in the system by reaction with an inhibitor at a certain time span after initiation. The special features of the resulting molecular weight distribution can be used for the direct determination of k_p in analogy to the pulsed‐laser polymerization (PLP) method. Furthermore, a qualitative information about the prevailing termination mechanism – i.e. disproportionation or combination – is also feasible from the distribution at a first glance.     

Dominant folding pathways of a peptide chain from ab initio quantum-mechanical simulations

Using the dominant reaction pathways method, we perform an ab initio quantum-mechanical simulation of a conformational transition of a peptide chain. The method we propose makes it possible to investigate the out-of-equilibrium dynamics of these systems, without resorting to an empirical representation of the molecular force field. It also allows to study rare transitions involving rearrangements in the electronic structure. By comparing the results of the ab initio simulation with those obtained by employing a standard force field, we discuss its capability to describe the nonequilibrium dynamics of conformational transitions.     

Potentials of an alternative scheme for ab initio polymer band structure calculations. Illustration on the chain of hydrogen atoms

An alternative scheme for ab initio polymer band structure calculations based on a Filon-type quadrature is proposed. This scheme avoids the explicit calculation and the storage of the “troublesome” Fourier transforms of the LCAO density matrix elements and is a first step towards a better control of the convergence of the different lattice sums appearing in the configuration space LCAO-SCF-CO method. The potential of the proposed technique is illustrated by a minimal basis set calculations on an infinite chain of H atoms.     

Occurrence of chain folding in micelles : A C NMR relaxation and photophysical study

¹³CT₁ relaxation times for the different carbons of the sodium dodecyl sulphate chain in micellar systems have been measured, using Gd³⁺ as a paramagnetic relaxation reagent. The fluorescence decay of ω-(-naphthyl) dodecanoic acid, solubflized in the sodium dodecyl sulphate micelles was obtained in the presence of various amounts of counterion quencher Both series of experiments point to the occurrence of chain folding and to the fact that the terminal group can approach the Stern region of the micelle.     

Rheology of polyacrylate binders produced via catalytic chain transfer polymerization as an alternative to bitumen in road pavement materials

Catalytic chain transfer polymerization has been successfully used to produce a range of methyl acrylate (MA) and butyl acrylate (BA) synthetic polymers of specific, targeted molecular weights, with polydispersity index values in the range of 2–4.5. The rheological properties of a subgroup of these synthetic binders consisting of four MA homo-polymers and one MA–BA co-polymer were then determined by means of oscillatory testing using a dynamic shear rheometer (DSR). The rheological tests consisted of a combination of stress/strain amplitude and frequency sweeps using a standard 8 mm diameter parallel plate testing geometry. The rheological parameters of phase angle and complex, storage and loss moduli were then shifted to form master curves at a reference temperature of 25 °C and isochronal plots at 0.1, 1 and 10 Hz. The rheological properties of the synthetic polymers were also compared to those of standard road pavement bitumens. The results show that it is possible to produce a range of synthetic polyacrylates with different rheological responses by altering the reactant type, reactant concentration and polymerization conditions to match the rheological properties of road bitumens. All the polyacrylate binders showed a similar rheological profile with a unique viscoelastic response as represented by the phase angle master curves together with an upper limiting stiffness and intermediate temperature/frequency ‘plateau’ region as shown in the complex modulus master curves. The results of the rheological examination of the binders showed that the key material property that influenced the performance of the polyacrylates in these specific application tests was glass transition temperature rather than molecular weight. Over this range of investigated molecular weights, it is the ratio between the two polymers which determines the glass transition and as such determines the material properties. These findings suggest that such sustainably sourced polyacrylate binders may allow for a move from petrochemical feed stocks to be made and allow for targeted road pavement design based on local climates, offering improved mechanical robustness.