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To develop a viable detection system for 2,4-dinitrotoluene (DNT), its unimolecular decomposition mechanisms were studied by using the density functional theory. Three decomposition mechanisms were investigated: (1) homolytic cleavage; (2) migration of one of the O atoms in the NO2 groups to its neighboring C atoms; (3) migration of one of the H atoms in the methyl group to a neighboring O atom in the NO2 group. Only homolytic cleavage of the CN bond yields NO2 radicals with a total energy of 61 kcal/mol or more. Initial migration of the O atom to its second-nearest-neighbor C atom requires about 56 kcal/mol, but subsequent homolysis produces NO fragments with less energy ∼15 kcal/mol. NO formation from both NO2 groups in 2,4-DNT is possible with a total energy of ∼63 kcal/mol. The H-migration has the lowest energy barrier of 39 kcal/mol among the three initial decomposition mechanisms. Removing O directly from 2,4-DNT requires ∼90 kcal/mol, while NO2 radical decomposes to NO and O with ∼73 kcal/mol. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008

Grafting various groups onto cellulose is found to substantially increase acid hydrolysis of the β-(1,4)-glycosidic linkages. Molecular modeling is used to explain how various substituents such as esters and ethers cause this phenomenon. A substituent helps stabilize hydrolyzed cellulose by serving as an anchor to the end of the cleaved cellulose to which it is bonded, making it less mobile, and allowing it to have stronger interactions than those in pure hydrolyzed cellulose. Hydrolysis increases with increasing size of the substituent. Molecules sorbed but not grafted to cellulose do not increase hydrolysis. Hydrolysis mainly occurs at glucoses bonded to the substituent, and supporting experiments show that hydrolysis approaches equilibrium when no substituent remains on the cellulose fiber.

In recent years, molecular modeling has been used to predict structure and chemical behavior of molecules in order to design drugs and enhance the performance of pharmaceuticals. The size and complexity of molecules studied computationally has grown as the computational power available has increased, along with the creation and formulation of new theories and methods. We will apply these methods to a unique set of steroid-nucleoside conjugates in order to interpret their differences in activity. In the set of four studied in this work (three acids bonded to AZT through an ester bond and an additional isomer of the second in the series), only the cholenic acid-conjugated species (Conjugate 1) has exhibited antitumor behavior, while the other two, P-16-acid and P-21-oic acid (prednisolone with an ester linkage to zidovudine, AZT), do not. In this study, we use molecular mechanics and semiempirical techniques to compare structures and to examine rotational barriers and solvation effects on many of the low-lying conformations of these four conjugates, as well as to use electrostatic potential isosurfaces in order to gain insight into the contributions to the activity or inactivity of these potential antitumor drugs.

Molecular modeling techniques were applied to predicting binding energies for nanocomposites comprising exfoliated clay layers treated with ammonium salts (usually quaternary) and dispersed in nylon 6,6 resin. For each of 12 selected ammonium ions (quats), a molecular dynamics simulation was performed at 600 K for 100–300 ps with a time step of 0.001 ps on a computer model built from 20 repeating units of nylon 6,6 polymer, six quat molecules and a montmorillonite platelet. Several conformations were selected from the equilibrated time region, energy minimization carried out and binding energies calculated between nylon 6,6 and the clay platelet, between nylon 6,6 and the quat, and between the quat and the platelet. It was found that the binding energy between nylon 6,6 and the clay platelet decreases almost linearly with the volume of adsorbed quat. Consequently, pristine clay yields the highest binding strength to the nylon. Clays partially substituted by long quats were found to be equivalent to those fully substituted with short quats.

In the interests of carrying out computer simulations efficiently for systems of rodlike molecules, the model proposed by Berne and coworkers, in which each rod is represented by an anisotropic Lennard-Jones potential, was extensively compared with a site-site model. Using this potential, Monte Carlo simulations were carried out for rodlike molecules with aspect ratio (R a ) ranging from 3 to 50. Short rods such as R a 20) show an isotropic phase at only very low Φ < 0.07. The attractive part of the potential makes rodlike molecules associate as well as align even at low Φ. At high Φ around or above the transition, the repulsive potential dominates and the attractive potential becomes secondary. Based on simulation results, some implications for designing molecular composites are offered.

Monte Carlo simulations have been performed on a self-avoiding simple cubic lattice chain with the nearest-neighbor interactions for a range of chain lengths N from 40 to 1000 segments to investigate equilibrium properties of polymer chains from an athermal to a collapsed state. Both the fraction of segments in the clusters and the number of contacts exhibit the three stage process for the chain collapse, consistent with our previous molecular dynamics simulations of a fully atomistic chain. In the collapse region corresponding to the nearest-neighbor interaction parameter larger than 0.5 for a segment-solvent pair, polymer chains are quite spherical and both ends lie nearly randomized within the sphere. The peak height of the specific heat is proportional to N(lnN) 3/11 ', as predicted by the renormalization group theory.

In order to study the collapse of polymer chains, atomistic simulations of atactic poly(vinyl chloride) (PVC) were performed. An isolated PVC chain with a degree of polymerization (DP) larger than 40 quickly folds from an all-trans zigzag form into a nearly spherical compact state, whose density is close to the bulk one. PVC chains with DP < 30 remain unperturbed. The radius of gyration (S) and the monomer clustering exhibit two-stage and three-stage processes for the chain collapse, respectively. In the first stage, nearest monomers stick together and both the end-to-end distance and S sharply decrease. The shape of the chain changes from a thin wire to a sausage. The second stage corresponds to the transition from a sharp to gradual decrease in S. During this stage, distant monomers along the contour start coming within an interaction radius of each other. The third stage is characterized by an appearance of self-entanglements. In the collapsed chain, no new torsion states develop but the distribution becomes richer in gauche ± states than in the unperturbed chain.

The introduction of conformational constraints into a flexible peptide hormone can be exploited to develop models for the conformation required for receptor binding and activity. In this review, we illustrate this approach to analog design using our work on antagonists of gonadotropin-releasing hormone (GnRH). Design of a conformationally constrained, competitive antagonist of GnRH, cyclo[delta 3,4 Pro-D4ClPhe-DTrp-Ser-Tyr-DTrp-NMeLeu-Arg-Pro-bet a Ala] led to the prediction of its bioactive conformation. Template forcing experiments show that this conformation is accessible to other active GnRH analogs. Two-dimensional NMR studies verified the predicted conformation in solution. The predicted binding conformation has recently been used to design two new analogs incorporating side chain-side chain linkages suggested by the conformational model: Ac-delta 3,4Pro-D4FPhe-DTrp-Dap-Tyr-DTrp-Leu-Arg-Asp-Gly- NH2 and Ac-delta 3,4Pro-D4FPhe-DTrp-Dap-Tyr-D2Nal-Leu-Arg-Pro-Asp -NH2. These analogs were synthesized and the one predicted to be most similar to the parent conformation had equivalent potency while the second, designed to refine the conformational hypothesis, was found to exhibit enhanced potency, thus confirming the original binding conformation hypothesis. These compounds and their derivatives now provide a new class of GnRH antagonists possessing both high biological potency and limited conformational flexibility, thus making them ideal for both biophysical and structure-activity studies.

A correlation function formalism for the intrinsic viscosity of polymers is studied. For this purpose, a Fokker‐Planck equation and the momentum flux equation in the full phase space of the polymer are derived by an application of the projection operator method to the whole system consisting of the polymer and solvent molecules. These relations are further reduced to Kirkwood's Fokker‐Planck equation and the corresponding flux in the polymer coordinate space. These steps give a molecular‐theoretical basis to the Kirkwood equation, and the reduced flux obtained is essentially equivalent to that suggested previously by Stockmayer and co‐workers. Some comments are made on related studies, particularly that of Doi and Okano, which is considered to be erroneous.

Influence sur le coefficient de diffusion moyen translationnel et sur la viscosite intrinseque d'apres un modele de tige en arc

In order to test the two‐parameter theory of dilute polymer solutions, light‐scattering and intrinsic‐viscosity measurements were carried out on fractions of poly‐p‐methylstyrene in toluene, dichloroethane, cyclohexane, and methyl ethyl ketone at 30°C, and in diethyl succinate at temperatures ranging from 16 to 60°C. The theta temperature for this polymer in diethyl succinate was found to be 16.4°C. With the data for the statistical‐radius expansion factor αS and the interpenetration function Ψ appearing in the second virial coefficient, validity of a theory of these quantities was examined using the two criteria introduced previously: (1) consistency in the values of the excluded‐volume parameter z determined from αS and Ψ, and (2) linearity between z and the square root of the molecular weight. It was found that the Yamakawa–Tanaka theory of αS and the Kurata–Yamakawa theory of Ψ were a self‐consistent pair of intramolecular and intermolecular theories of interaction which satisfied both of the two crit...

Further Test of the Two-Parameter Theory of Dilute Polymer Solutions: Poly( p -bromostyrene)

The intrinsic viscosity of polymer chains with small excluded volume is calculated on the basis of the Fixman—Pyun theory for unperturbed chains. The eigenfunctions of the unperturbed free‐draining time evolution operator are chosen as the basis set, and the formulation is made so as to take into account the coupling of the normal coordinates for excluded‐volume interactions but not for hydrodynamic interactions. An additional approximation introduced is the preaveraging of the Oseen hydrodynamic interaction tensor. Therefore, the present theory gives the same result as the Zimm theory in Hearst's version for vanishing excluded volume. Evaluation is carried out only in the nondraining limit, and the cubed viscosity—expansion factor is obtained as αη3= 1+1.06z –···, where z is the well‐known excluded‐volume parameter. This is consistent with the recent experimental results. Furthermore, it is emphasized that the present value for the coefficient of z is smaller than the corresponding value of 1.80 predicte...

Light‐scattering and intrinsic‐viscosity measurements were carried out on fractions of poly‐p‐chlorostyrene and poly‐p‐bromostyrene in toluene at 30°C. Unperturbed dimensions were estimated from the Berry plots of second virial coefficients and also from the Stockmayer–Fixman plots of intrinsic viscosities. Values of the binary‐cluster integral β per monomeric unit were determined by the two methods proposed in the previous paper; one is based on the use of the Yamakawa–Tanaka equation for the statistical‐radius expansion factor, and the other the modified Stockmayer–Fixman plot. The results by the two methods were in excellent agreement with each other. The differences in β between poly‐p‐chlorostyrene and poly‐p‐methylstyrene, and between poly‐p‐bromostyrene and poly‐p‐methylstyrene in toluene, were analyzed using the theory of dilute solutions of polar polymers developed by Yamakawa and Rice on the basis of the cavity field and reaction field arguments. The agreement between theory and experiment was found to be satisfactory. The difference in β between polystyrene and poly‐p‐methylstyrene in toluene is also discussed. It is suggested that a complete theoretical calculation of the whole β should be based on the theory of simple liquids.

Further comments on the analysis of dilute solution data are provided. Light-scattering and intrinsic-viscosity data used for this purpose are those obtained for monodisperse polystyrenes, prepared anionically in tetrahydrofuran, in benzene, toluene, and dichloroethane at 30°C and in cyclohexane at temperatures ranging from 32.2 to 60.1°C. The value of [η]θ/M1/2 is somewhat greater than the corresponding value for Berry’s polystyrenes prepared anionically in benzene, where [η]θ is the intrinsic viscosity at the theta temperature and M is the polymer molecular weight. This suggests that the two types of samples differ in microstructure, though the precise difference is unknown. However, it is shown that the two-parameter relationships established experimentally in the previous papers are well reproduced in the present data. The relationships are different from those determined by Kato, et al., for monodisperse poly(α-methylstyrene) prepared anionically. Since there is shown to be no essential difference between our and their methods of determining mean-square radii, it seems unlikely that the difference is related to measurements and subsequent treatments. It is suggested rather that the problem is related to Kato’s samples.

A hierarchy of differential equations for the expansion factor of a linear polymer chain is derived in a purely formal way by successive differentiation of the general equation of Fixman with respect to the binary‐cluster integral for a pair of chain segments. The hierarchy is truncated by a physically reasonable assumption to obtain an approximate solution. The assumption introduced is discussed in detail. In order to obtain numerical results, it is necessary to develop at least the third‐order perturbation theory, and the third expansion coefficient is evaluated to be 6.459 for the mean‐square end‐to‐end distance. Assuming that the third coefficients are the same for the end‐to‐end distance and the radius of gyration, there is obtained the equation for the expansion factor αS for the latter, αS2=0.541+0.459(1+6.04z)0.46, where z is the well‐known excluded‐volume parameter. Although this equation has the asymptotic form αS4.35=constant z at large z, a definite conclusion concerning the value of the expon...

The translational diffusion coefficient of a rodlike polymer is investigated in the Kirkwood‐Riseman scheme with the use of the modified Oseen tensor derived previously by Yamakawa for the finite bead model. If it is assumed that the friction coefficient of the beads may be described by Stokes' law, this tensor can remove the Zwanzig singularities from the possible range of the strength of the hydrodynamic interaction. It is pointed out that the preaveraging of the Oseen tensor may remove the singularities apparently in some cases. The correct asymptotic solution is also obtained without transforming a set of simultaneous equations determining the frictional forces to an integral equation. The results show that the finite bead model of a rodlike polymer is intermediate between the ellipsoid and cylinder models in transport behavior.

A second‐order perturbation theory of the expansion factor αS for the radius of gyration of a linear polymer molecule is presented. The result is αS2=1+1.276z−2.082z2+···, where z is the well‐known excluded‐volume parameter. A Ptitsyn‐type closed expression for αS is also presented. Upon combining this and the corresponding expression for the expansion factor αR for the end‐to‐end distance, there is obtained the relation αR2/αS2=1.06 at large z. This is in excellent agreement with the Monte Carlo result obtained by Wall and Erpenbeck.

The intrinsic viscosity of flexible ring polymers with small excluded volume is calculated on the basis of the theory presented previously by Yamakawa and Tanaka for linear chains. The cubed viscosity-radius expansion factor is obtained as αη,r3=1+1.21z+···, so that αη,r3/αη,13=1+0.15z+···, where the subscripts r and 1 refer to ring and linear forms, respectively, and z is the well-known excluded-volume parameter. This result supports the prediction derived by Fukatsu and Kurata by an approximate perturbation method. Some comments on the Bloomfield–Zimm theory and the Yu–Fujita theory are also given.

First-order perturbation expressions are developed for the first cumulant (initial time derivative) of the dynamic structure factor observable by photon-correlation measurements of the light scattered by flexible chain molecules in solution. A dimensionless coefficient C , which measures the initial departure of the first cumulant from proportionality to the square of the scattering vector, is found to be only slightly altered by excluded-volume effects.

The Fixman-Kovac formulation of chain dynamics with constraints is used to calculate the first cumulant Q(q) of the dynamic scattering function. This general formalism is applied to the case of freely jointed chains. It is shown that the large q limit (q being the scattering wavenumber) of Q(q) for a chain of N bonds in the absence of hydrodynamic interaction is proportional to the ratio (2N+3)/3(N+l) representing the fraction of unconstrained degrees of freedom of the chain. The inclusion of hydrodynamic interaction seems to enhance the apparent segmental diffusion. The use of constrained chain dynamics has no appreciable effects, however, on the behavior of Q(q) in the small and intermediate q regions for long enough chains. This formalism can be used to interpret neutron (spin echo) scattering experiments from semiflexible polymers in solution.