Chapter IV IR electroabsorption spectroscopic study of 4(3H)-pyrimidinone in
IV- 4 Summary and future perspective
In this thesis, the author has presented an IREA spectroscopic study of an important model compound of pyrimidine bases, 4(3H)-pyrimidinone in p-dioxane. To our knowledge, the IREA spectrum of 4(3H)-Pyr in room-temperature solution has been successfuly measured for the first time. The results have revealed that the angle between the transition moment of the monomer C=O stretch band and the permanent dipole moment is very close to 54.7°, at which the orientational polarization signal vanishes. We also found that a base pair-like hydrogen bonded structure is plausible for the dimer structure. Accurate knowledge on the direction vibrational transition moment directions in the molecule is important in spectral assignment [51, 52]. Especially in complex biological molecules, the problems associated with resolving vibrational bands arise, because the vibrational frequencies of various tautomers can be very similar [27].
For molecules possessing C2v or higher symmetry, determination of the angle α is often obvious from the nature of the vibration. In contrast, for molecules of low-symmetry, the direction of vibrational transition moment directions are nontrivial and depends on the complicated motions that constitute the normal mode. Miller et al. developed an experimental method for determining the vibrational transition moment angle (VTMAs) using orientational polarization [27]. They applied this method to various biologically relevant compounds [31-33]. The molecules of interest are isolated in liquid helium nanodroplets, in which the molecules are cooled down to 0.37 K. In contrast, our IREA spectroscopy can measure the angle α in room-temperature liquids, which are much closer to a real biological system.
The present study has demonstrated the potential of our method to study biology-related molecules in more biologically relevant environments. The VTMAs and the dipole moment of association structures of base-pair model compounds can be obtained from IREA spectra simultaneously.
Figure IV-1. (a) Concentration dependent FT-IR spectra of 4(3H)-Pyr in p-dioxane at 12 different concentrations in the 1740−1640 cm−1 region. (b) Concentration dependence of the absorbance ratio (defined as A1675 cm−1 / A1706 cm−1).
Figure IV-2. Area intensities of the monomer and dimer bands as a function of total concentration. The solid line is the fitting result based on the model functions (Eqs. IV-5 and IV-6).
10
8
6
4
2
0
A re a in te n si ty
60 50
40 30
20 10
0
Concentration/mM
Area intensity of the monomer band
Area intensity of the dimer band
Fit
Figure IV-3. (a) ∆A spectra of 4(3H)-Pyr in p-dioxane (60 mM) measured with an applied voltage of 45, 55, 65, and 75V. (b) Absorption spectrum of 4(3H)-Pyr measured with a 50 µm path-length cell consisting CaF2 windows.
-4x10-6
Figure IV-4. Band area of the ∆A signals for the 1722−1700 (blue circles), 1700−1682 (red squares), and 1682−1658 cm−1 (green triangles) region as a function of the square of external electric field. Solid lines are a fit to a linear function having a zero intercept.
-30x10
Figure IV-5. Three independent sets of the ∆A spectra of 4(3H)-Pyr in p-dioxane (60 mM)
Figure IV-6. (a) Averaged χ-dependent ∆A spectra. (b) Plot of singular values obtained from the SVD of the averaged χ-dependent ∆A spectra shown in panel a. The components associated with the three largest singular values are denoted 1, 2, and 3. (c) Spectral components corresponding to the largest three singular values.
6x10-6
Figure IV-7. (a) Model functions (solid line) and reconstructed χ dependences (open triangles and circles). (b) χ-dependent (blue) and χ-independent (red) spectral components.
-1.0x10-6
Figure IV-8. Observed (solid line) and reconstructed (dotted line) ∆A spectra of 4(3H)-Pyr in p-dioxane measured at χ = 55, 66, 76, 83, and 90°.
6x10-6
4
2
0
-2
∆A
1760 1740 1720 1700 1680 1660 1640
Wavenumber/cm-1
χ = 90°
χ = 83°
χ = 76°
χ = 66°
χ = 55°
Figure IV-9. (a) IR absorption spectrum, the same as in Fig. IV-2(b). Also shown is the best fit to a sum of two Gaussian functions representing the C=O stretch bands of the monomer and the dimer of 4(3H)-Pyr. (b) χ-dependent (triangles) and χ-independent (squares) spectral components, and the best fit (solid curve) to a superposition of the zeroth, first, and second
Figure IV-10. Decomposition of the fitted results in Fig. IV-8 into the zeroth, first, and second derivative components: (a) χ-independent and (b) χ-independent components. (c) Fitted result of the absorption spectrum.
(a) (b)
Figure IV-11. Predicted direction of the transition moment from the experimental results and the optimized structure of 4(3H)-Pyr calculated at the RB3LYP/6-31+G(d,p) level.
Transition moment Dipole moment (calculated)
Table I. Assignments, peak positions, and bandwidths of the two IR bands observed in the wavenumber region 1740−1640 cm−1.
Assignments Peak position (cm−1) Bandwidth (cm−1)
C=O stretch of the monomer of 4(3H)-Pyr 1706 11
C=O stretch of the dimer of 4(3H)-Pyr 1675 15
Table II. Coefficients aχ, bχ, and cχ, of the zeroth, first, and second derivative terms of the absorption bands of 4(3H)-Pyr and its dimer. Note that aχ = ∆A/A and the absorbance A was taken from the spectrum measured with the 50-µm sample cell.
χ-independent χ-dependent
Monomer Dimer Monomer Dimer
aχ (10−6) −2.74 0a 0.58 0a
bχ (10−5) 2.32 0a 1.10 0a
cχ (10−4) 0.97 3.4 0a 1.78
aIn the spirit of reducing the number of adjustable parameters, we set those coefficients zero.
Table III. Stark parameters Aχ, Bχ, and Cχ. Note that f is the local field correction factor.
χ-independent χ-dependent
Monomer Dimer Monomer Dimer
Aχ (10−20m2V−2f−2) −1.75 0a 0.37 0a
Bχ (10−43Jm2V−2f−2) 4.42 0a 2.10 0a
Cχ (10−66J2m2V−2f−2) 0.73 2.58 0a 1.35
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