Spectra and Molecular Structures

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
Faculty of Science


u01, u54

Facilities Used



Rebecca Jacob
Faculty of Science

RFCD Codes

250104, 250105, 250699

Significant Achievements, Anticipated Outcomes and Future Work

The first singlet–singlet and singlet–triplet band systems of the absorption spectrum of pyridazine vapour have been analysed using ab initio and vibronic coupling calculations. The lowest singlet–triplet absorption involves a comparatively unperturbed triplet B1 state, and contrasts with the highly perturbed singlet–singlet spectrum. The major source of vibronic perturbation in the singlet–singlet absorption is attributed to coupling between near-resonant singlet A2 and B1 states, with the former being slightly lower in energy. Many features of this complex and unusual spectrum, and its associated single vibronic level fluorescence spectrum, can be explained using a simple vibronic model. This provides experimental support for recent relaxed CASPT2 and EOM-CCSD calculations, but contrasts with earlier assignments of the spectrum. Similar studies have been carried out for pyrimidine. However, for pyrimidine the singlet and triplet spectra are not marked by major perturbations, and as a consequence the spectral analyses are relatively unambiguous. With the completion of the investigations of the diazines the triazines will be revisited using the more powerful compoutational techniques that are now available. The mid-IR spectra of a number of amino acids and their N-D3 deuterated isotopomers, and dipeptides and their N-D deuterated isotopomers, as isolated zwitterions in a KBr solid solvent have been obtained by means of a newly developed infrared sampling technique, which involves the production of thin films. Ab initio calculations of the non-aqueous Self-Consistent Reaction Field type, using the Onsager dipole-sphere model have been carried out for the prediction of the vibrational spectra and molecular structures of the zwitterions isolated in KBr matrices. For all the amino acids and dipeptides studied more than one conformer was determined by computation. Nevertheless, good agreement was established between the simulated and calculated spectra. This combined theoretical and experimental approach has allowed accurate determination of the amino acid structures. The work is to be extended to the polypeptides with a view to practical applications, such as the photosynthetic reaction centre in Photosystem II and synthetic photosynthesis.


Computational Techniques Used

Two computational packages were used in the two projects. In the one "Gaussian" ab initio calculations were conducted at the HF, HF/SCRF, DFT, DFT/SCRF, MP2 and CIS theoretical levels using basis sets ranging from 6-31G* to 6-311++G**. In the other, "Molpro", complete active space calculations were carried out using Multi and RS2. The high level calculations require much memory, large scratch disk space, and can take much CPU time, requirements successfully met by the available computers, PC, VPP and SC.


Publications, Awards and External Funding

G. Fischer, X. Cao, Vibrational analysis and ring-puckering inversion barrier of perfluorocyclopentene. J. Phys. Chem. A 103 (1999) 3726-3731.

X. Cao, G. Fischer, New infrared spectra and the tautomeric studies of purine and L-alanine with an innovative sampling technique. Spectrochim. Acta. 55A (1999) 2329-2342.

D.A. Kirkwood, M. Tulej, M.V. Pachkov, M. Schnaiter, F. Guthe, M. Grutter, M. Wyss, J.P. Maier, G. Fischer, Electronic Spectra of the Carbon Chain Anions- C2nH- (n=5-12). J. Chem. Phys. 111 (1999) 9280-9286.

M. Tulej, F. Guthe, M. Schnaiter, M.V. Pachkov, D.A. Kirkwood, J.P. Maier, G. Fischer, Electronic Spectra of the Carbon Chain Anions C2n-1H- (n=5-8) in the Gas Phase. J. Phys. Chem. A 103 (1999) 9712-9716.

X. Cao, G. Fischer, Infrared Spectral, Structural, and Conformational Studies of Zwitterionic L-Tryptophan. J. Phys. Chem. A 103 (1999) 9995-10003.

X. Cao, G. Fischer, The infrared spectra and molecular structure of zwitterionic L-phenylalanine. J. Mol. Structure 519 (2000) 153-163.

X. Cao, G. Fischer, Infrared spectra of monomeric L-alanine and L-alanine-N-D3 zwitterions isolated in a KBr matrix. Chem. Phys. 255 (2000) 195-204.

G. Fischer, P. Wormell, Vibronic analyses of the lowest singlet-singlet and singlet-triplet band systems of pyridazine. Chem. Phys. 257 (2000) 1-20.

G. Fischer, R. Jacob and X. Cao, The infrared spectra and structures of the valyl-glycine zwitterion isolated in a KBr matrix. Chem. Phys. 263 (2001) 243-253.

X. Cao, G. Fischer, Reply to comment on new infrared spectra and the tautomeric studies of purine and L-alanine with an innovative sampling technique. Spectrochim. Acta A57 (2001) 2719-2720.

G. Fischer, T. Wydrzynski, Isotope effects in FTIR difference spectra of the photosynthetic oxygen-evolving catalytic site determined by ab initio calculations on model compounds. J. Phys. Chem. B In press.

X. Cao, G. Fischer, Conformational and infrared studies of L-methionine and its N-deuterated isotopomer as isolated zwitterions. J. Phys. Chem. A In press.