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Infrared spectra of hydrogen bonded crystals: Uracil
INFRARED
SPECTRA
OF HYDROGEN
Andrzej WITKOWSKI Deparrmenr
1 June 1974
CHEMICAL PHYSICS LETI’ERS
Volume 26. number 3
of l7reorerical
Chemistry.
Jagellonh
BONDED
CRYSTALS:
URACIL
and Marek WdJCIK University.
Cracow.
Knrpnicza
41, Poland
Received 23 October 1973
A theory of the infrared spectra of hydrogen bonds in molecular crystals of C:h symmetry, containing. like uracil, four molecules and eight hydrogen bonds in the unit cell, is presented. The theoretical spectra are in good agreement in both the frequency and intensity distribution with experiment. The changes in the fine structure introduced by deuteration are quantitatively reproduced.
The infrared spectra of hydrogen bonds in the uracil crystal as well as the spectra of its deuterated a forms were obtained by Suzi and Ard [ 11. In the present note we use the spectrum of the uracil crystal obtained in the Institute of Molecular Biology of the JageIIonian University with the UR-IO spectrometer because of its better resolution and the spectrum of the N,N dideutero uracil obtained by Suzi and Ard. The crystal symmetry is [2] C&, and its unit cell contains four molecules joined by eight hydrogen bonds. This consists of two diiers which are bonded 3200 00 2600 in addition by hydrogen bonds which form an angle b of I18O with the hydrogen bonds of the dirners. Four hydrogen bonds in the dimers and four between the dimers belong to different groups, and in each group these are related by the symmetry operations of inversion; a screw axis and a slide plane. The crystal IR spectrum of uracil shows a characteristic fme structure which is considerably changed by deuteration (figs. la, b). The quantitative theoretical reconstitution of the IR spectra associated with hydrogen bonds in crystals have been obtained only for imidazole [3] and I-methylthymine [4] crystals up till now. The theomticai results were in agreement with experiment and the deuteration effect was correctly explained. ?he present note .is the continuation of this work [4] and is based on similar a%rmptions.. We assume that the high frequency stretching ._ Fig. l._.Coinpen of theoretical and expeiimenti spectra N-H vibrations form the potential energy for the .,’ fyr,the urac? crystal (a) and ,me F$N dideutero until low frequency hydrogen bond stretching .?bratio& .._ .-;.Iaystal@).. :.‘. 327 .,. . -_: . ..---. ;
4
x
1
Volume
CHEMICAL PHYSICS LE?TERS
26, number 3
1 June 1974
For the change in the potential energy between the ground and excited states of the high frequency vibrztion, only the term linear in the normal coordinate of
Our theory predicts that after deuteration the distortion parameter describing the difference in the potential energy for the low frequency vibration be-
the low frequency
tween the ground and excited states of the high fre-
hydrogen bond vibration
is re-
tained. The degeneracy in &he high frequency modes which results from different-possible localizations of the vibrational exciton in the unit cell is split by the resonance type (Davydov) interaction. We neglect the interactions between the translationally equiva-
lent hydrogen bonds as they do nor markedly influence the spectral structure [S, 61. Some simplifications are required to obtain the numerical results. First, we neglect the inter-dimer resonance interactions_ This is justified by the fact
quency vibration should be divided by the 21J2 factor [3]. The substantially different structure of the IR
absorption band of the deuterated uracil was obtained with this prediction_ An extended version of the theory of the IR absorption spectra of hydrogen bonded crystals will be published later.
that the distance between the hydrogen bonds of
The financial support of the PAN-3 research project of the Polish Academy of Sciences is acknowl-
different dimers is substantially larger than the distance between the hydrogen bonds in the same dimer.
edged_ The authors are grateful to Mr_W. Bielafiski for his help in the experimental measurements.
Second, we neglect the interactions between the bifurcated hydrogen bonds directed along the 118O angle. The spectrum therefore contains two components: the first is the spectrum of d&e dimer and the second is the spectrum of the two lateral hydrogen bonds. The theoretical spectra are compared with the experimental ones in fig. 1 a for uracil and in fig. 1b for the deuterated form. The frequency and the intensity distributions of the fine structure are in good agreement with the ex@mental spectra. The calculations were performed on the Odra-1204 computer_
The dimer spectrum is shifted to low frequencies compared with the monomer’s spectrum by 290 cm-’ since the bond length of the imine group N-H in the dimer is 0.04 a longer than in the monomer. After deuteration this shift is lowered by the 2”* factor.
328. . ..
..
_.
:
References [1] H. Suzi and J.S. Ard, Spectrochim. Acta 27A (1971) 1549. [2] R.E. Stewart and L.H. Jensen, Acta Cryst. 23 (1967) 1102. [3] Y.Marbchal and A. Witkowski, J. Chem. Phys. 48 (1968) 3697. [4] A. Witkowski and M. Wbjcik, Chem. Phys. Letters 20 (1973) 615. (51 S. Bhagavantam and T. Venkatarayudy, Theory of groups and its application to physical problems (Andhra University, W&air, 195 1). [6] A. Witkowski and M. Zgierski, Phys. Stat. Sol. 46b (1971) 429.
..
SPECTRA
OF HYDROGEN
Andrzej WITKOWSKI Deparrmenr
1 June 1974
CHEMICAL PHYSICS LETI’ERS
Volume 26. number 3
of l7reorerical
Chemistry.
Jagellonh
BONDED
CRYSTALS:
URACIL
and Marek WdJCIK University.
Cracow.
Knrpnicza
41, Poland
Received 23 October 1973
A theory of the infrared spectra of hydrogen bonds in molecular crystals of C:h symmetry, containing. like uracil, four molecules and eight hydrogen bonds in the unit cell, is presented. The theoretical spectra are in good agreement in both the frequency and intensity distribution with experiment. The changes in the fine structure introduced by deuteration are quantitatively reproduced.
The infrared spectra of hydrogen bonds in the uracil crystal as well as the spectra of its deuterated a forms were obtained by Suzi and Ard [ 11. In the present note we use the spectrum of the uracil crystal obtained in the Institute of Molecular Biology of the JageIIonian University with the UR-IO spectrometer because of its better resolution and the spectrum of the N,N dideutero uracil obtained by Suzi and Ard. The crystal symmetry is [2] C&, and its unit cell contains four molecules joined by eight hydrogen bonds. This consists of two diiers which are bonded 3200 00 2600 in addition by hydrogen bonds which form an angle b of I18O with the hydrogen bonds of the dirners. Four hydrogen bonds in the dimers and four between the dimers belong to different groups, and in each group these are related by the symmetry operations of inversion; a screw axis and a slide plane. The crystal IR spectrum of uracil shows a characteristic fme structure which is considerably changed by deuteration (figs. la, b). The quantitative theoretical reconstitution of the IR spectra associated with hydrogen bonds in crystals have been obtained only for imidazole [3] and I-methylthymine [4] crystals up till now. The theomticai results were in agreement with experiment and the deuteration effect was correctly explained. ?he present note .is the continuation of this work [4] and is based on similar a%rmptions.. We assume that the high frequency stretching ._ Fig. l._.Coinpen of theoretical and expeiimenti spectra N-H vibrations form the potential energy for the .,’ fyr,the urac? crystal (a) and ,me F$N dideutero until low frequency hydrogen bond stretching .?bratio& .._ .-;.Iaystal@).. :.‘. 327 .,. . -_: . ..---. ;
4
x
1
Volume
CHEMICAL PHYSICS LE?TERS
26, number 3
1 June 1974
For the change in the potential energy between the ground and excited states of the high frequency vibrztion, only the term linear in the normal coordinate of
Our theory predicts that after deuteration the distortion parameter describing the difference in the potential energy for the low frequency vibration be-
the low frequency
tween the ground and excited states of the high fre-
hydrogen bond vibration
is re-
tained. The degeneracy in &he high frequency modes which results from different-possible localizations of the vibrational exciton in the unit cell is split by the resonance type (Davydov) interaction. We neglect the interactions between the translationally equiva-
lent hydrogen bonds as they do nor markedly influence the spectral structure [S, 61. Some simplifications are required to obtain the numerical results. First, we neglect the inter-dimer resonance interactions_ This is justified by the fact
quency vibration should be divided by the 21J2 factor [3]. The substantially different structure of the IR
absorption band of the deuterated uracil was obtained with this prediction_ An extended version of the theory of the IR absorption spectra of hydrogen bonded crystals will be published later.
that the distance between the hydrogen bonds of
The financial support of the PAN-3 research project of the Polish Academy of Sciences is acknowl-
different dimers is substantially larger than the distance between the hydrogen bonds in the same dimer.
edged_ The authors are grateful to Mr_W. Bielafiski for his help in the experimental measurements.
Second, we neglect the interactions between the bifurcated hydrogen bonds directed along the 118O angle. The spectrum therefore contains two components: the first is the spectrum of d&e dimer and the second is the spectrum of the two lateral hydrogen bonds. The theoretical spectra are compared with the experimental ones in fig. 1 a for uracil and in fig. 1b for the deuterated form. The frequency and the intensity distributions of the fine structure are in good agreement with the ex@mental spectra. The calculations were performed on the Odra-1204 computer_
The dimer spectrum is shifted to low frequencies compared with the monomer’s spectrum by 290 cm-’ since the bond length of the imine group N-H in the dimer is 0.04 a longer than in the monomer. After deuteration this shift is lowered by the 2”* factor.
328. . ..
..
_.
:
References [1] H. Suzi and J.S. Ard, Spectrochim. Acta 27A (1971) 1549. [2] R.E. Stewart and L.H. Jensen, Acta Cryst. 23 (1967) 1102. [3] Y.Marbchal and A. Witkowski, J. Chem. Phys. 48 (1968) 3697. [4] A. Witkowski and M. Wbjcik, Chem. Phys. Letters 20 (1973) 615. (51 S. Bhagavantam and T. Venkatarayudy, Theory of groups and its application to physical problems (Andhra University, W&air, 195 1). [6] A. Witkowski and M. Zgierski, Phys. Stat. Sol. 46b (1971) 429.
..