Dipoles of the tryptophan indole side chains have a direct impact on ion conductance in the gramicidin channel. Here, fluorination of the indoles (both 5- and 6-fluoro) is used to manipulate both the orientations and the magnitudes of the dipoles. The orientations and positions with respect to the channel axis were determined using (2)H solid state NMR of uniformly aligned lipid bilayer preparations. By exchange of the remaining four protons in the indole ring for deuterium, comparison could be made to d(5)-indole spectra that have previously been recorded for each of the four indoles of gramicidin A. After making the assignments which were aided by the observation of (19)F-(2)H dipolar interactions, we found that fluorination caused only minor changes in side chain conformation. With the high-resolution structural characterization of the fluorinated indoles in position 11, 13, and 15, the electrostatic interactions with a cation at the channel and bilayer center can be predicted and the influence of the modified dipoles on ion conductance estimated. The importance of the long-range electrostatic interaction was recently documented with the observation of alpha-helical dipoles oriented toward the bilayer center on the ion conductance pathway for the Streptomyces K(+) channel. We present direct measurements of the orientation of gramicidin channel F-Trp positions for use in analysis of dipole effects on channel permeation.

We examine consequences of the non-Boltzmann nature of probability distributions for one-particle kinetic energy, momentum, and velocity for finite systems of classical hard spheres with constant total energy and nonidentical masses. By comparing two cases, reflecting walls (NVE or microcanonical ensemble) and periodic boundaries (NVEPG or molecular dynamics ensemble), we describe three consequences of the center-of-mass constraint in periodic boundary conditions: the equipartition theorem no longer holds for unequal masses, the ratio of the average relative velocity to the average velocity is increased by a factor of [N/(N-1)]1/2, and the ratio of average collision energy to average kinetic energy is increased by a factor of N/(N-1). Simulations in one, two, and three dimensions confirm the analytic results for arbitrary dimension.

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Experimental and theoretical calculations indicate that the dipole moment of the four Trp side chains in gramicidin A (gA) channels modify channel conductance through long-range electrostatic interactions. Electrostatic ion/side-chain interaction energies along the channel were computed with CHARMM using ab initio atom charges for native and 4-, 5-, or 6-fluorinated Trp side chains. The bulk water reaction to the polar side chains was included using the method of images as implemented by, and channel waters in idealized structures were included. Ion/Trp interaction energies were approximately -0.6 kcal/mol throughout the channel for all four of the native Trp pairs. Channel waters produced a modest reduction in the magnitude of interactions, essentially offsetting images representing the bulk water outside the channel. The effects of side-chain fluorination depended on ring position and, to a lesser extent, residue number. Compared with native Trp, 5-fluorination reduces the translocation barrier with minor effects on the exit barrier. In contrast, 6-fluorination primarily reduces exit barrier. 4-Fluorination produces a more complex double-well energy profile. Effects of measured side-chain movements resulting from fluorination or change in lipid bilayer were negligible whereas thermal side chain librations cause large effects, especially in the region of the ion-binding sites.

Peroxy radicals can complex with water vapor. These complexes affect tropospheric chemistry. In this study, β-HEP (hydroxyethyl peroxy radical) serves as a model system for investigating the effect of water vapor on the kinetics and product branching ratio of the self-reaction of peroxy radicals. The self-reaction rate coefficient was determined at 274-296 K with water vapor between 1.0 × 10 15 and 2.5 × 10 17 molecules cm −3 at 200 Torr total pressure by slow-flow laser flash photolysis coupled with UV time-resolved spectroscopy and long-path, wavelength modulated, diode-laser spectroscopy. The overall self-reaction rate constant expressed as the product of both a temperature-dependent and water vapor-dependent term is k o = 7.8 × 10 −14 exp((8.3 ± 2.5kJ /mol)/RT ) + {(13.2 ± 1.56) × 10 −44 × exp((79.3 ± 17.18kJ /mol)/RT ) × [H 2 O]}, suggesting formation of a β-HEP-H 2 O complex is responsible for the increase in the self-reaction rate coefficient with increasing water concentration. Complex formation is supported by computational results identifying three local energy minima for the β-HEP-H 2 O complex. As the troposphere continues to get warmer and wetter, more of the peroxy radicals present will be complexed with water. Investigating the effect of water vapor on kinetics of atmospherically relevant radicals and determining the effects of these altered kinetics on tropospheric ozone concentrations is thus important. C 2015

the intramolecular absorption bands of the water-methylbenzene complexes, but we cannot exclude important contributions from complexes trapped in different sites. The results of this paper support the conclusion of ref 2, that water bound to a benzene ring has an unusual freedom to move relative to the ring.

Classical mechanics of intramolecular vibrational energy flow in benzene. V. Effect of zeropoint energy motion J. Chem. Phys. 91, 7490 (1989); 10.1063/1.457273 Semiclassical quantization of the scattering from a classically chaotic repellor Erratum: Approximate constants of motion for classically chaotic vibrational dynamics: Vague tori, semiclassical quantization, and classical intramolecular energy flow [J.Coupled nonlinear Hamiltonian systems are known to exhibit regular (quasiperiodic) and chaotic classical motions. In this and the preceding paper by Jam~ and Reinhardt, we find substantial short time regularity even in the chaotic regions of phase space for what appears to be a large class of systems. This regularity is demonstrated by the behavior of approximate constants of motion calculated by Pade summation of the BirkhotT-Gustavson normal form expansion and is attributed to remnants of destroyed invariant tori in phase space. The remnant toruslike manifold structures are used to suggest justification for use of Einstein-Brillouin-Keller semiclassical quantization procedures for obtaining quantum energy levels even in the absence of complete tori and to form a theoretical basis for the calculation of rate constants for intramolecular mode-mode energy transfer. These results are illustrated in a thorough analysis of the Henon-Heiles oscillator problem. Possible generality of the analysis is shown by brief consideration of classical dynamics for the Barbanis Hamiltonian, Zeeman etTect in hydrogen, and recent results of Wolf and Hase for the H-C-C fragment.