Structures and Vibrational Frequencies of Pure Halocarbon Clusters, and Mixed Clusters with Water

Spectroscopy and computation can be used to determine the structures of molecules. Recent work has been directed at two families of molecules, the azines, and the amino acids and their pseudo clusters, the dipeptides. For the former, ab initio calculations on the excited electronic states and their force fields have been conducted at high theoretical levels to assist in analyses of the spectra. The substituted azines are widespread in nature and knowledge of their stabilities and photochemical properties are of interest. Three-dimensional models of protein structures depend largely on knowledge of accurate geometries of the component amino acids. A novel experimental approach has been successfully used to measure resolved infrared spectra of the zwitterions isolated in a matrix. Molecular orbital calculations to determine the vibrational spectra and that are appropriate to the amino acid in its solid solvent environment have allowed for confident analyses of the infrared spectra. This combined approach marks an important breakthrough in amino acid structure determination.

Principal Investigator

Gad Fischer
Chemistry, Faculty of Science
Australian National University

Project

u54, u01

Co-Investigators

Nick Cox
Chemistry, Faculty of Science
Australian National University

LeHoa Scruton
Ultraviolet Physics Unit, RSPhysSE
Australian National University

RFCD Codes

250104, 250699, 250105

Significant Achievements, Anticipated Outcomes and Future Work

The predictive reliability of calculations of the excitation energies, geometries and vibration frequencies for the lower singlet states of NCCCCN is tested by similar calculations on well-characterised states of HCCCCH, HCCCN, NCCN, HCCCCCCH, and HCCCCCN. Their performance encourages confidence in the predictions for the so far unanalysed first singlet transition of NCCCCN.

The infrared absorption spectra of the dipeptide zwitterions, L-valyl-L-alanine and L-alanyl-L-valine have been measured using a novel infrared sampling technique. The two dipeptides are isomers and similar spectra are expected, and were measured. With the better resolved spectra obtained with the dissolution, spray and deposition (DSD) technique, small but significant differences were identified, not evident in the normal KBr pellet spectra. Ab initio molecular orbital calculations of the Self Consistent Reaction Field type using the Onsager dipole-sphere model were undertaken for structure determinations and spectral predictions at Hartree-Fock and Density Functional Theory levels. A number of conformers was identified, the structure of the calculated most stable one of L-valyl-L-alanine was found to be in excellent agreement with the X-ray crystallographically determined bond length and angles. The spectral resolution obtained, together with theoretical predictions of the absorption spectra, and comparisons with the spectra of related dipeptides and amino acids have enabled vibrational assignment of bands and identification of molecular conformer.

 

Computational Techniques Used

All calculations were from the Gaussian and Molpro suites of programs. Ab initio molecular orbital calculations of the Self Consistent Reaction Field type using the Onsager dipole-sphere model were undertaken for structure determinations and spectral predictions at Hartree-Fock and Density Functional Theory levels.

 

Publications, Awards and External Funding

External Funding and Awards

None.

Publications

R. Jacob and G. Fischer, Infrared Spectra and Structures of the Valyl-Alanine and Alanyl-Valine Zwitterions Isolated in a KBr Matrix, Journal of Physical Chemistry A 107: 6136-6143 (2003).
G. Fischer, Zheng-Li Cai, J. R. Reimers, and Paul Wormell, Singlet and Triplet Valence Excited States of Pyrimidine, Journal of Physical Chemistry A 107: 3093-3106 (2003).
G. Fischer and I. G. Ross, Electronic Spectrum of Dicyanoacetylene. 1. Calculations of the Geometries and Vibrations of Ground and Excited States of Diacetylene, Cyanoacetylene, Cyanogen, Triacetylene, Cyanodiacetylene, and Dicyanoacetylene, Journal of Physical Chemistry A 107: 10631-10636 (2003).
G. Fischer, G.D. Johnson, D. A. Ramsay, and I. G. Ross, Electronic Spectrum of Dicyanoacetylene. 2. Interpretation of the 2800 Å Transition, Journal of Physical Chemistry A 107: 10637-10641 (2003).