Exploring the conformational dynamics of alanine dipeptide in solution subjected to an external electric field: A nonequilibrium molecular dynamics simulation

In this paper, we investigate the conformational dynamics of alanine dipeptide under an external electric field by nonequilibrium molecular dynamics simulation. We consider the case of a constant and of an oscillatory field. In this context we propose a procedure to implement the temperature control, which removes the irrelevant thermal effects of the field. For the constant field different time-scales are identified in the conformational, dipole moment, and orientational dynamics. Moreover, we prove that the solvent structure only marginally changes when the external field is switched on. In the case of oscillatory field, the conformational changes are shown to be as strong as in the previous case, and non-trivial nonequilibrium circular paths in the conformation space are revealed by calculating the integrated net probability fluxes.Comment: 23 pages, 12 figure

PROBING THE ELECTRONIC STRUCTURE OF PEPTIDE BONDS USING METHYL GROUPS: EXPERIMENTAL MEASURES OF RESONANCE WEIGHTS

Author Institution: Optical Technology Division, National Institute of Standards and Technology, Gaithersburg, MD 20899; Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260The observed $V_{3}$ torsional barriers reported for nine methyl groups attached alpha to peptide bond linkages in five gas phase biomimetics are interpreted at the HF/6{-}311++G(d,p) level of theory in terms of the natural bonding orbitals and the natural resonance structures of the peptide bond. This decomposition has revealed that delocalization of the nitrogen lone pair electrons into anti-bonding orbitals of the carbonyl group is principally responsible for the torsional barriers and lowest energy staggered or $\it{anti}$ conformations of the carbonyl methyl groups. In contrast, the minimum energy configuration and $V_{3}$ barriers of the amide methyl groups are dominated by Lewis-like steric interactions that lead to $\it{syn}$ preferences. The Lewis vs non-Lewis energies are sufficiently well balanced that low barriers ($<$0.5 kcal/mole) result in both methyl group classes. These results reveal that a linear correlation exists between the barriers to internal rotation of attached methyl groups and the relative importance of the two principal resonance structures that contribute to the peptide bond. Predictions at the MP2 levels of theory are consistent with these trends but opposite to the conformational preferences calculated using popular force field models. The impact of the torsional state dependence of the resonance weights on internal rotation models also will be discussed

HIGH RESOLUTION FLUORESCENCE EXCITATION SPECTRA OF THE 1- AND 2-AMINONAPHTHALENES.1AMINONAPHTHALENES.^{1}

$^{1}$ Work supported by NSF. $^{2}$ J. M. Hollas. S. N. Thakur. Mol. Phys. 27. 1001 (1974).Author Institution: Department of Chemistry, University of PittsburghContinuing our study of internal motions of isoelectronic species attached to the naphthalene chromophore, we report here the observation and analysis of the $S_{1}\leftarrow S_{0}$ fluorescence excitation spectra of the 1- and 2- aminonaphtalenes at a resolution of - 15 MHz in the UV. We have determined the rotational constants and inertial defects of both $S_{0}$ and $S_{1}$ and the orientations of the transition moments for several vibronic bands in the spectrum. We find the $0^{o}_{o}$ band of 1-aminonapthalene (IAN) to be primarily b-axis polarized, contrary to earlier observations of IAN and related $species.^{2}$ We also obtain information about the magnitudes of the barriers to inversion of the amino group in both states. These results will be summarized and discussed in the framework of molecular orbital theory. A brief overview of the software developed to record and analyze the high resolution spectra of large polyatomic molecules also will be given