Interaction of aromatic compounds with xenon: spectroscopic and computational characterization for the cases of p-cresol and toluene.

We have investigated noncovalent interactions of two aromatic compounds (toluene and p-cresol) with Xe atoms by using infrared spectroscopy in a Ne matrix and quantum chemical calculations. The present results show that the methyl group of these molecules is a sensitive probe of the interaction with Xe. We have used the molecules with the deuterated methyl group, possessing a relatively simple spectrum, which allows us to detect characteristic vibrational shifts in the complexes, in which a Xe atom interacts with the aromatic π electron system (π structure). For the p-cresol···Xe complex, we also observed evidence of the 1:1 H-bonded structure. The amount of the H-bonded structure of the cresol···Xe complex is relatively small, which agrees with the calculated interaction energies (stronger interaction for the π structure). The bands of the 1:1 complexes of p-cresol and toluene with Xe appear at low Xe concentration and their intensities relative to the monomer bands are nearly proportional to the Xe/Ne concentration ratio. For the p-cresol-Xe system, additional OH stretching bands appear at higher Xe concentrations, which are suitable for the complexes with several Xe atoms. The π structures studied in this work can probably be formed in the case of aromatic amino acids, for which these simple aromatic compounds are useful models.

Toward molecular mechanism of xenon anesthesia: a link to studies of xenon complexes with small aromatic molecules.

The present study illustrates the steps toward understanding molecular mechanism of xenon anesthesia by focusing on a link to the structures and spectra of intermolecular complexes of xenon with small aromatic molecules. A primary cause of xenon anesthesia is attributed to inhibition of N-methyl-D-aspartate (NMDA) receptors by an unknown mechanism. Following the results of quantum mechanics/molecular mechanics (QM/MM) and molecular dynamics (MD) calculations we report plausible xenon action sites in the ligand binding domain of the NMDA receptor, which are due to interaction of xenon atoms with aromatic amino-acid residues. We rely in these calculations on computational protocols adjusted in combined experimental and theoretical studies of intermolecular complexes of xenon with phenol. Successful reproduction of vibrational shifts in molecular species upon complexation with xenon measured in low-temperature matrices allowed us to select a proper functional form in density functional theory (DFT) approach for use in QM subsystems, as well as to calibrate force field parameters for MD simulations. The results of molecular modeling show that xenon atoms can compete with agonists for a place in the corresponding protein cavity, thus indicating their active role in anesthetic action.

Interaction of phenol with xenon and nitrogen: spectroscopic and computational characterization.

Intermolecular complexes of phenol with xenon and nitrogen are studied by infrared absorption spectroscopy in a neon matrix and by quantum chemistry calculations. The π complex is theoretically the most stable 1:1 phenol⋅⋅⋅Xe structure, but it has no characteristic shifts in the calculated vibrational spectrum, which complicates its experimental characterization. However, the formation of the π complex finds indirect but significant support from the experimental results. The calculated spectrum of the less stable H-bonded complex shows a number of characteristic absorptions, but they are not observed in the experiment, indicating the lack of its formation. For the phenol⋅⋅⋅Xe(n) (n = 2-4) complexes, the calculations predict substantial changes in the vibrational spectra, and the corresponding bands are observed in the matrices with large concentrations of xenon. Our experiments show the high efficiency of the formation of large xenon clusters in a neon matrix that can accommodate a major part of phenol molecules. In contrast to the case of xenon, the H-bonded 1:1 phenol⋅⋅⋅N(2) complex is found in a neon matrix, and the formation of large N(2) clusters embedding phenol molecules is relatively inefficient.

Conformation-dependent chemical reaction of formic acid with an oxygen atom.

Conformation dictates many physical and chemical properties of molecules. The importance of conformation in the selectivity and function of biologically active molecules is widely accepted. However, clear examples of conformation-dependent bimolecular chemical reactions are lacking. Here we consider a case of formic acid (HCOOH) that is a valuable model system containing the -COOH carboxyl functional group, similar to many biomolecules including the standard amino acids. We have found a strong case of conformation-dependent reaction between formic acid and atomic oxygen obtained in cryogenic matrices. The reaction surprisingly leads to peroxyformic acid only from the ground-state trans conformer of formic acid, and it results in the hydrogen-bonded complex for the higher-energy cis conformer.