Velocity Structure of the ISM as Seen by the Spectral Correlation Function

(Abridged) We use the statistical tool known as the ``Spectral Correlation Function" [SCF] to intercompare simulations and observations of the atomic interstellar medium. The simulations considered mimic three distinct sets of physical conditions. One of them (run "ISM") is intended to represent a mixture of cool and warm atomic gas, and includes self-gravity and magnetic fields. For each simulation, H I spectral-line maps are synthesized and intercompared, both with each other, and with observations, using the SCF. We find that, when thermal broadening is large in comparison with fine-scale turbulent velocity structure, it masks sub-thermal velocity sub-structure in the synthesized spectra. The H I observations we use here for comparison are of the North Celestial Pole (NCP) Loop. None of the simulations match the NCP Loop data very well. The most realistic sets of line profiles and SCF statistics comes from artifically rescaling the velocity axis of run ISM. Without rescaling, almost all velocity structure is smeared out by thermal broadening. However, if the velocity axis is expanded by a factor of 6, the SCF distributions of run ISM an the NCP Loop match up fairly well. This means that the ratio of thermal to turbulent pressure in run ISM is much too large as it stands, and that the simulation is deficient in turbulent energy. This is a consequence of run ISM not including the effects of supernovae. We conclude that the SCF is a useful tool for understanding and fine-tuning simulations of interstellar gas, and in particular that realistic simulations of the atomic ISM need to include the effects of energetic stellar winds (e.g. supernovae) in order for the ratio of thermal-to-turbulent pressure to give spectra representative of the observed interstellar medium in our Galaxy.Comment: 25 pages, 24 figures. ApJ Accepted (May 20). Also available at: ftp://www.astrosmo.unam.mx/pub/j.ballesteros/Papers

Role of hydration in determining the structure and vibrational spectra of L-alanine and N-acetyl L-alanine N'-methylamide in aqueous solution: a combined theoretical and experimental approach

In this work we have utilised recent density functional theory Born-oppenheimer molecular dynamics simulations to determine the first principles locations of the water molecules in the first solvation shell which are responsible for stabilizing the zwitterionic structure of L-alanine. Previous works have used chemical intuition or classical molecular dynamics simulations to position the water molecules. In addition, a complete shell of water molecules was not previously used, only the water molecules which were thought to be strongly interacting (H-bonded) with the zwitterionic species. In a previous work by Tajkhorshid et al. (J Phys Chem B 102:5899) the l-alanine zwitterion was stabilized by 4 water molecules, and a subsequent work by Frimand et al. (Chem Phys 255:165) the number was increased to 9 water molecules. Here we found that 20 water molecules are necessary to fully encapsulate the zwitterionic species when the molecule is embedded within a droplet of water, while 11watermolecules are necessary to encapsulate the polar region with themethyl group exposed to the surface, where it migrates during the MD simulation. Here we present our vibrational absorption, vibrational circular dichroism and Raman and Raman optical activity simulations, which we compare to the previous simulations and experimental results. In addition, we report new VA, VCD, Raman and ROA measurements for l-alanine in aqueous solution with the latest commercially available FTIR VA/VCD instrument (Biotools, Jupiter, FL, USA) and Raman/ROA instrument (Biotools). The signal to noise of the spectra of l-alanine measured with these new instruments is significantly better than the previously reported spectra. Finally we reinvestigate the causes for the stability of the Pp structure of the alanine dipeptide, also called N-acetyl-l-alanine N-methylamide, in aqueous solution. Previously we utilized the B3LYP/6-31G* + Onsager continuum level of theory to investigate the stability of the ALANMA4WC Han et al. (J Phys Chem B 102:2587) Here we use the B3PW91 and B3LYP hybrid exchange correlation functionals, the aug-cc-pVDZ basis set and the PCMand CPCM (COSMO) continuum solvent models, in addition to the Onsager and no continuum solvent model. Here by the comparison of the VA, VCD, Raman and ROA spectra we can confirm the stability of the NALANMA4WC due to the strong hydrogen bonding between the fourwatermolecules and the peptide polar groups. Hence we advocate the use of explicit water molecules and continuum solvent treatment for all future spectral simulations of amino acids, peptides and proteins in aqueous solution, as even the structure (conformer) present cannot always be found without this level of theory