Competition between H-bonded and stacked dimers of pyrimidine: IR and theoretical ab-initio study

W. Mccarthy, J. Smets, L. Adamowicz, A. M. Plokhotnichenko, E. D. Radchenko, Ludwik Adamowicz, S. G. Stepanian

Research output: Contribution to journalArticle

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Abstract

A combined matrix isolation Fourier transform infrared experimental and ab-initio theoretical approach has been used to examine the vibrational spectra of pyrimidine dimers. It was found that the presence of pyrimidine dimers resulted in experimentally observed frequencies shifted relative to those of the pyrimidine monomer. Four stable pyrimidine dimer conformers were found via ab-initio calculations. Two of these conformers namely a stacked geometry and a H-bonded geometry in which pyrimidine monomer dipole moments orient antiparallel, had the lowest but very similar energies. Ab-initio harmonic frequencies of these two dimers and their shifts relative to the monomer's values were determined. The effect of Basis Set Superposition error on these calculated frequency shifts was also investigated. The comparison of the ab-initio predicted and experimentally observed frequency shifts and an accompanying potential energy distribution analysis suggest that the lowest-energy H-bonded configuration is responsible for the experimentally observed phenomena.

Original languageEnglish (US)
Pages (from-to)513-525
Number of pages13
JournalMolecular Physics
Volume91
Issue number3
StatePublished - Jun 20 1997

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Pyrimidine Dimers
pyrimidines
Monomers
dimers
monomers
Geometry
Dipole moment
frequency shift
Vibrational spectra
Fourier Analysis
Potential energy
Dimers
Fourier transforms
Infrared radiation
geometry
vibrational spectra
isolation
energy distribution
dipole moments
potential energy

ASJC Scopus subject areas

  • Atomic and Molecular Physics, and Optics

Cite this

Mccarthy, W., Smets, J., Adamowicz, L., Plokhotnichenko, A. M., Radchenko, E. D., Adamowicz, L., & Stepanian, S. G. (1997). Competition between H-bonded and stacked dimers of pyrimidine: IR and theoretical ab-initio study. Molecular Physics, 91(3), 513-525.

Competition between H-bonded and stacked dimers of pyrimidine : IR and theoretical ab-initio study. / Mccarthy, W.; Smets, J.; Adamowicz, L.; Plokhotnichenko, A. M.; Radchenko, E. D.; Adamowicz, Ludwik; Stepanian, S. G.

In: Molecular Physics, Vol. 91, No. 3, 20.06.1997, p. 513-525.

Research output: Contribution to journalArticle

Mccarthy, W, Smets, J, Adamowicz, L, Plokhotnichenko, AM, Radchenko, ED, Adamowicz, L & Stepanian, SG 1997, 'Competition between H-bonded and stacked dimers of pyrimidine: IR and theoretical ab-initio study', Molecular Physics, vol. 91, no. 3, pp. 513-525.
Mccarthy W, Smets J, Adamowicz L, Plokhotnichenko AM, Radchenko ED, Adamowicz L et al. Competition between H-bonded and stacked dimers of pyrimidine: IR and theoretical ab-initio study. Molecular Physics. 1997 Jun 20;91(3):513-525.
Mccarthy, W. ; Smets, J. ; Adamowicz, L. ; Plokhotnichenko, A. M. ; Radchenko, E. D. ; Adamowicz, Ludwik ; Stepanian, S. G. / Competition between H-bonded and stacked dimers of pyrimidine : IR and theoretical ab-initio study. In: Molecular Physics. 1997 ; Vol. 91, No. 3. pp. 513-525.
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