Light-scattering of polyamide hydrazide solutions and conformational characteristics of its molecules

Light-scattering measurements have been carried out for 18 samples of polyamide hydrazide (PAH) in dimethylsulphoxide (DMS) with an over 10-fold variation in molecular weights. It was shown that the excluded volume effect in DMS does not appreciably affect the size of PAH molecules. The length of the Kuhn segment (A ≈ 240 · 10^?8 cm) was estimated from the experimental determinations of molecular weights $\text{M}{}_{\mathrm{w}}$ and the radii of gyration 〈R²〉_z. Viscometric determination of the rigidity of PAH chains yields the value of A ≈ 200 · 10^?8 cm and the hydrodynamic diameter d ≈ 5 · 10^?8 cm. The whole collection of data shows that PAH is a typical rigid-chain polymer; the extended conformation is due to the backbone rigidity tather than to the excluded volume effects.     

Flow birefringence and conformational characteristics of polyamide hydrazide molecules in dimethylsulphoxide

Flow birefringence (FB) and intrinsic viscosity of 19 samples of aromatic polyamide hydrazide (PAH) in dimethylsulphoxide (DMS), previously characterized by their weight-average molecular weights by the light scattering method, have been investigated. The molecular-weight dependence of reduced birefringence according to theory [12] was used to determine the optical anisotropy of a monomer unit Δa = (200 ± 20) 10^?25cm³ and the length of the Kuhn segment $\text{A = (250 ± 30)}\text{A}\text{?}$ of PAH molecules. The second independent evaluation of rigidity of the PAH chain $\text{A = (240 ± 30)}\text{A}\text{?}$ was obtained according to the theory of rotational friction of rigid wormlike chains by using the coefficients of rotational diffusion of PAH molecules determined from the characteristic values of orientation angles of FB. The value of rigidity of the PAH chain obtained by this method is in good agreement with the data on molecular dimensions obtained by light scattering.     

Humidity sensors using in situ synthesized sodium polystyrenesulfonate/ZnO nanocomposites

Thin film humidity sensors have been prepared using in situ synthesized inorganic/organic nanocomposites of sodium polystyrenesulfonate (NaPSS) and ZnO. Its humidity sensing characteristics and the sensing mechanism have been investigated by measuring the complex impedance spectra of the sensor at different humidities. The logarithm of the impedance of sensor based on composite film changes linearly by four-orders of magnitude over almost whole humidity range (11-97% RH). Furthermore, the sensor exhibits a quick response (absorption: 2 s, desorption: 2 s) and small hysteresis (less than 2% RH). The composite film shows better sensing properties than NaPSS film, such as better linearity, quicker response. Explanation to the improvement is attempted by taking into account of the composition and structure of the nanocomposites.     

An ant algorithm for the conformational analysis of flexible molecules

Originally, the ant system was developed for optimization in discrete search spaces such as the traveling salesman problem. We detail our adaptation of the algorithm to optimization in the continuous search space of conformational analysis. The parameters of the algorithm were tuned using a simple test molecule, undecane, and a drug molecule, imatinib. The algorithm is further tested on four more drug or drug-like molecules, on vitamin A and on alanine tetrapeptide.     

Scanning probe microscopy of adsorption layers of sodium polystyrenesulfonate/dodecyltrimethylammonium bromide complexes

Scanning probe microscopy is used to study adsorption films of sodium polystyrenesulfonate/dodecyltrimethylammonium bromide complexes, which are transferred from aqueous solution surfaces to the mica surface by the Langmuir-Blodgett method. It is established that the results obtained at surfactant concentrations below critical micelle concentration agree with the conclusions on the structure of the films dased on the data of the dilatational surface rheology (Noskov, B.A., Loglio, G., Miller, R., J. Phys. Chem. B, 2004, vol. 108, p. 18615). At low concentrations of the low-molecular-mass surfactant, a thin adsorption film containing a large number of holes is formed on the surface of an aqueous solution. As the surfactant concentration is increased to reach the region of a dramatic reduction in the dynamic surface elasticity, the morphology of the film drastically changes; i.e., dense three-dimensional aggregates are formed on the solution surface.     

Quantum and experimental conformational analysis of model molecules related to collagenic structures

Sequential polytripeptides comprising the repeating sequences (Gly-Pro-X) and (Gly-X-Pro) have been synthesized, and conformational analysis has been carried out using both quantum and experimental methods (X = Pro, Ala, Val, Ile R and Ile S, Leu, Nle, Met and Phe).PCILO computations were performed using appropriate model molecules, with a view to discussing the proline puckering, the cis/trans isomerism of Pro residue and the accessibility to different conformons (δ, R_α, L_α, β sheets and β bends) for the X residues, with the pyrrolidine rings free to adopt the most favorable puckering.Experimental studies show that, whatever sequence is considered in the triplet, the only ordered structures found are the obvious δ collagenlike structure and the β bend.Theoretical studies led to the conclusion that when Pro is in the δ conformation, the β bend is very probably of type II.On this basis, the microheterogeneity in collagen structure and the involvement of β bends in the enzymatic proline hydroxylation are discussed.     

Applications of simulated annealing to the conformational analysis of flexible molecules

We describe in this article our solution to the global minimum problem which uses the simulated annealing algorithm of Kirkpatrick. This method is a Metropolis (e-ΔE/kT) Monte Carlo sampling of conformation space with simultaneous constraint of the search by lowering the temperature T so that the search converges on the global minimum. The Anneal-Conformer program has been extensively tested with peptides and organic molecules using either the Amber or MM2 force fields. A history file of the simulated annealing process allows reconstruction of the random walk in conformation space for subsequent examination. Thus plots of distance and dihedral angle changes during the search for the global minimum can be examined to deduce molecular shape and flexibility. A separate program Conf-Gen reads the history file and extracts all low energy conformations visited during the run.     

Dependence of viscosity of organic nonassociated liquids on structural and conformational characteristics of the molecules

Semiempirical equations are obtained for the dependence of the viscosity of organic nonassociated liquids on the structural and conformational characteristics of the molecules. The equations are used to compute the viscosities of organic compounds of different structural classes. It is shown that they can be used to take into account the effect of isomerization of the carbon skeleton of the molecule on the viscosity and also the temperature dependence of the viscosity.Translated from Teoreticheskaya i Éksperimental'naya Khimiya, Vol. 25, No. 5, pp. 563–567, September–October, 1989.     

The application of Artificial Intelligence to the conformational analysis of strained molecules

An algorithm for predicting the conformations of strained molecules using Artificial Intelligence techniques is described and illustrated with some typical examples.     

Flow birefringence and conformational characteristics of molecules of para-and meta-isomers of polyoxyphenyl-benzoxazoleterephthalamides

Flow birefringence (FB) has been used to study sulphuric solutions of two homologous series of polyoxyphenylbenzoxazoleterephthalamides (POPhBT) differing in the position (para- or meta-) of phenyl ring in the chain. In the framework of the FB method alone by using the theory of flow birefringence for kinetically rigid wormlike chains, it was possible to determine quantitatively the optical anisotropy of the monomer unit Δa = (330 ± 30) 10^?25 cm^?3 and the length of the Kuhn segment $\text{A = (330 ± 30)}\text{A}\text{?}$ and $\text{A = (115 ± 20)}\text{A}\text{?}$ for para- and meta-isomers, respectively. Analysis of possible mechanisms of flexibility in the chains of both polymers gives theoretical values of the rigidity parameter A in good agreement with experimental values of A. confirming the validity of the molecular models used.     

Hydrodynamic and conformational properties of dendron-modified polystyrene molecules

The molecular characteristics of polystyrene modified by the Frechet type dendrons of 1–4 generations were studied in tetrahydrofuran by viscometry, isothermal diffusion, electric birefringence, and dynamic and static light scattering. It was shown that dendronized polystyrene molecules whose polymerization degree changes from 1640 to 930 with an increase in the generation number of dendrons occur in the coillike conformation. The equilibrium rigidity of macromolecules tends to increase with increasing the generation number of dendrons. The Kuhn segment length grows from 3.9 nm for polystyrene molecules modified by dendrons of the first generation to 23.3 nm for polystyrene molecules carrying dendrons of the fourth generation.     

Application of vibronic spectroscopy to conformational analysis. Investigations of molecules of carbonyl compounds

Application of vibronic spectroscopy to the conformational analysis of molecules in the ground and excited electronic states is reviewed. The basic concepts of the method as well as its methodological and technical aspects are discussed. The abilities of vibronic spectroscopy are exemplified by the results obtained for molecules of carbonyl compounds.The review is based on a report at the Vibrational Spectroscopy Conference dedicated to the 80th birthday of B. I. Stepanov (Minsk, Belarus', October 3–5, 1993).Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 5, pp. 783–791, May, 1994.This work was performed with the partial financial support of the Russian.Universities State Program.     

Efficient algorithm for conformational search of macrocyclic molecules

A new algorithm, complementarity, is developed for conformational search of macrocyclic molecules. The algorithm scans a large number of candidate conformations and energy-minimizes only the promising ones. These candidates can be generated by two operators that construct new conformations from known minima. The candidates have similar bonded-interaction energy as the known minima and possibly lower nonbonded interaction energy. This algorithm is 9 to 11 times faster than the existing methods when tested on two large rings, cycloheptadecane and rifamycin SV. © 1997 by John Wiley & Sons, Inc.     

Laser probes of conformational isomerization in flexible molecules and complexes

Molecules with several flexible coordinates have potential energy surfaces with a large number of minima and many transition states separating them. A general experimental protocol is described that is capable of studying conformational isomerization in such circumstances, measuring the product quantum yields following conformation-specific infrared excitation, and measuring energy thresholds for isomerization of specific X --> Y reactant-product isomer pairs following excitation via stimulated emission pumping (SEP). These methods have been applied to a series of molecules of varying size and conformational complexity, including 3-indolepropionic acid (IPA), meta-ethynylstyrene, N-acetyltryptophan methyl amide (NATMA), N-acetyltryptophan amide (NATA), and melatonin. Studies of isomerization in solute-solvent complexes are also described, including a measurement of the barrier to isomerization in the IPA-H2O complex, and a unique isomerization reaction in which a single water molecule is shuttled between H-bonding sites on the trans-formanilide (TFA) molecule.     

Hydrodynamic and conformational properties of cellulose myristate molecules in solution

Cellulose myristate samples with a degree of substitution of 230–250 have been studied by the methods of molecular hydrodynamics (viscometry, analytical ultracentrifugation (flotation), and isothermal translational diffusion) in chloroform in the range M = (56–652) × 10³. The experimental evidence has been interpreted within the framework of the generalized wormlike Yamakawa-Fuji model with the following parameters: the persistence length a = 115 × 10^?8 cm, the chain diameter d = 45 × 10^?8 cm, and the molecular mass per unit chain length M _L = 270 × 10⁸ cm^?1. It has been inferred that the polymer dissolves in chloroform in the form of dimers.     

Quantum theory of atoms in molecules analysis on the conformational preferences of vinyl alcohol and related ethers

Vinyl alcohol, methyl vinyl ether, and tert-butyl vinyl ether were studied within the framework of the quantum theory of atoms in molecules at the B3LYP/6-311++G(2d,2p) level. Local and integrated properties of the charge density indicate that the anti conformational preference of the tert-butyl derivative is not due to a differing resonance contribution with regard to the less bulky vinyl ethers but to steric effects. There is a small delocalization of charge density, either total or pi, between oxygen and the terminal vinyl carbon, which does not support the resonance picture of vinyl compounds.