Valence Force Fields as a Tool in Vibrational Spectroscopy and Molecular Mechanics

Force field calculations on conjugated molecules are discussed. The discussion is based on the experience of a series of overlay calculations, recently carried out, where the transferability of force constants was thoroughly studied. Successful applications as well as limitations of the constructed force field are described. The effects of nonbonded interactions are recognized as the most serious restriction of the transferability of valence force fields, and it is suggested that the molecular mechanics method, where the nonbonded interactions are taken explicitly into account, would be advantageous. The treatment of potential energy in the molecular mechanics method is briefly described and theconnections between valence force constants and potential energy parameters in this method are discussed

A study of galactic plane Planck galactic cold clumps observed by SCOPE and the JCMT plane survey

We have investigated the physical properties of Planck Galactic Cold Clumps (PGCCs) located in the Galactic Plane, using the JCMT Plane Survey (JPS) and the SCUBA-2 Continuum Observations of Pre-protostellar Evolution (SCOPE) survey. By utilising a suite of molecular-line surveys, velocities and distances were assigned to the compact sources within the PGCCs, placing them in a Galactic context. The properties of these compact sources show no large-scale variations with Galactic environment. Investigating the star-forming content of the sample, we find that the luminosity-to-mass ratio (L/M) is an order of magnitude lower than in other Galactic studies, indicating that these objects are hosting lower levels of star formation. Finally, by comparing ATLASGAL sources that are associated or are not associated with PGCCs, we find that those associated with PGCCs are typically colder, denser, and have a lower L/M ratio, hinting that PGCCs are a distinct population of Galactic Plane sources

Ensemble of transition state structures for the cis-trans isomerization of N-methylacetamide

The cis-trans isomerization of N-methylacetamide (NMA), a model peptidic fragment, is studied theoretically in vacuo and in explicit water solvent at 300 K using the metadynamics technique. The computed cis-trans free energy difference is very similar for NMA(g) and NMA(aq), in agreement with experimental measurements of population ratios and theoretical studies at 0 K. By exploiting the flexibility in the definition of a pair of recently introduced collective variables (Branduardi, D.; Gervasio, F. L.; Parrinello, M. J. Chem. Phys. 2007, 126, 054103), an ensemble of transition state structures is generated at finite temperature for both NMA(g) and NMA(aq), as verified by computing committor distribution functions. Ensemble members of NMA(g) are shown to have correlated values of the backbone dihedral angle and a second dihedral angle involving the amide hydrogen atom. The dynamical character of these structures is preserved in the presence of solvent, whose influence on the committor functions can be modeled using effective friction/noise terms