Analysis of the intermolecular interaction between CH(3)OCH(3), CF(3)OCH(3), CF(3)OCF(3), and CH(4): high level ab initio calculations

Hydrogen Abstraction from Fluorinated Ethyl Methyl Ether Systems by OH Radicals

A systematic computational investigation of hydrogen abstraction by OH from the full series of fluorinated ethyl methyl ethers (EME) containing at least one H and one F, C2HnX5-nOCHmX3-m (n=0–5, m=0–3; and n=m=0 not allowed), including 147 reactants and 469 transition states, has been carried out, employing the MP2/6-31G(d) level of theory. Results for optimized geometries, including evidence of intramolecular hydrogen bonding in transition states, and barrier heights are presented. Trends pertaining to the number of fluorines substituted, key bond lengths, barrier heights, and key bond angles were found with good correlations and were investigated. An increase in the number of F increases the barrier height of the reaction. An increase in some parameters such as C–H length of TS, relative change in C–H from reactants to TS, ∠COC of reactants, ∠HOH in the TS, and relative change in ∠HOH between TS and free water bond angle also correlates with increased barrier height. An increase in other parameters like C–H length in the reactants and hydrogen bonding can decrease the barrier height.

Molecular dynamics studies of the Nafion®, Dow® and Aciplex® fuel-cell polymer membrane systems

The Nafion, Dow and Aciplex systems--where the prime differences lies in the side-chain length--have been studied by molecular dynamics (MD) simulation under standard pressure and temperature conditions for two different levels of hydration: 5 and 15 water molecules per (H)SO(3) end-group. Structural features such as water clustering, water-channel dimensions and topology, and the dynamics of the hydronium ions and water molecules have all been analysed in relation to the dynamical properties of the polymer backbone and side-chains. It is generally found that mobility is promoted by a high water content, with the side-chains participating actively in the H(3)O(+)/H(2)O transport mechanism. Nafion, whose side-chain length is intermediate of the three polymers studied, is found to have the most mobile polymer side-chains at the higher level of hydration, suggesting that there could be an optimal side-chain length in these systems. There are also some indications that the water-channel network connectivity is optimal for high water-content Nafion system, and that this could explain why Nafion appears to exhibit the most favourable overall hydronium/water mobility.

Comparison of the Intermolecular Energy Surfaces of Amino Acids: Orientation-Dependent Chiral Discrimination

In the present work, we compare the intermolecular energy surfaces of the alanine molecule in its neutral and zwitterionic state using ab initio theory (HF/6-311++G) as a function of mutual orientation. Starting from the optimized structures of the nonbonded homochiral (l-l) and heterochiral (d-l) pairs of molecules, the energy surfaces are studied with rigid geometry by varying the distance and orientation. The potential energy surfaces of the l-l and d-l pairs are found to be dissimilar and reflect the underlying chirality of the homochiral pair and racemic nature of the heterochiral pair. The intermolecular energy surface of the l-l pair is more favorable than the corresponding energy surface of the d-l pair. The study, for the first time, reveals clear homochiral preference without use of parameters, which was unobserved in previous detailed simulations but predicted by theory. The electrostatic interaction further augments the chiral discrimination. The basis set superposition error (BSSE) corrected results show enhanced discrimination. Use of higher-level Møller-Plesset perturbation theory (MP2) and further BSSE correction do not change the conclusions made at the Hartree-Fock (HF) level. The major conclusions based on HF and MP2 level calculations remain unaltered when the calculations of the potential energy surfaces for the neutral and zwitterionic pairs are repeated using the density functional theory (DFT) (B3LYP/6-311++G). The observed orientation dependence has significance in the biological chiral recognition as well as peptide synthesis at the peptidyl transferase center where the amino terminal and peptidyl terminal undergo mutual rotatory motion.

Molecular Dynamics Simulation of Swollen Membrane of Perfluorinated Ionomer

Molecular dynamics simulations of the swollen membrane of perfluorinated ionomer, which is composed of poly(tetrafluoroethylene) backbones and perfluosulfonic pendant side chains, have been undertaken to analyze the static and dynamic properties of the water and the side chain in the membrane. The calculations were carried out for four different water contents, 5, 10, 20 and 40 wt %, at 358.15 K and 0.1 MPa. The results are summarized as follows: (1) The sulfonic acid is the unique site to which water molecules can bind, and the other sites in the pendant side chain have no bound water even at high water concentration. (2) Sulfonic acids aggregate in the short range within 4.6-7.7 A despite the electrostatic repulsion between them. In such aggregates, a water molecule bridges two sulfonic acids. (3) Pendant side chains prefer to orient perpendicular to the hydrophilic/hydrophobic interface, and long-range correlation of side chain orientations is observed at 20 and 40 wt % water uptake membranes. (4) In a low water uptake membrane, the dynamics of water is substantially restricted due to strong attractive interactions with acidic sites. In contrast, at high water content, even the water locating near the sulfonic acid is relatively mobile. The short residence time of the bound water reveals that such water can frequently exchange position with relatively free water, which locates in the center of water cluster, in highly swollen membranes.

Analysis of the intermolecular interactions between CH3OCH3, CF3OCH3, CF3OCF3, and CH2F2, CHF3

The intermolecular interaction energy curves of CH(3)OCH(3)-CH(2)F(2), CF(3)OCH(3)-CH(2)F(2), CF(3)OCF(3)-CH(2)F(2), CH(3)OCH(3)-CHF(3), CF(3)OCH(3)-CHF(3), and CF(3)OCF(3)-CHF(3) complexes were calculated by the MP2 level ab initio molecular orbital method using the 6-311G** basis set augmented with diffuse polarization functions. We investigate the fluorine substitution effects of both methane and dimethyl ether on intermolecular interactions. In addition, orientation dependence of intermolecular interaction energies is also studied with utilizing eight types of orientations. Our analyses demonstrate that partial fluorinations of methane make electrostatic interaction dominant, and consequently enhance attractive interaction at several specific orientations. On the contrary, fluorine substitutions of dimethyl ether substantially decrease the electrostatic interaction between ether and CH(2)F(2) or CHF(3); thus, there is no such characteristic interaction between the C-H of fluorinated methane and ether oxygen of CF(3)OCF(3) as conventional hydrogen bonding, due to reduced polarity of fluorinated ether. The combination of different pairs of the electrostatic interaction is therefore responsible for the intermolecular interaction differences among the complexes investigated herein and also their orientations.