Identification of vibrational modes in thymine bases by broadband far-infrared absorption spectroscopy

Abstract

Far-infrared and THz absorption spectra were obtained for thymine bases. Quantum chemical calculations were also conducted to simulate the far-infrared spectrum using density functional theory. Three models were used for the simulations. In one model, a thymine monomer was assumed. The second model assumed a thymine dimer, where two pyrimidine rings were aligned antiparallel. The last model assumed a thymine trimer, in which four hydrogen bonds were formed in three pyrimidine rings placed on the same plane. By comparing the measurements and simulations, almost all the absorption peaks appearing from 100 to 600 cm−1 could be assigned to torsional or skeletal vibrations of a pyrimidine ring. On the other hand, absorption peaks appearing in the THz range from 16.7 to 167 cm−1 were assigned to intermolecular vibrations.

Broadband FIR absorption spectra of low‐density polyethylene sheets containing six different antioxidants and estimation of their contents by chemometric analysis

“…However, this relatively new THz absorption spectroscopy has not yet been widely used compared to Fourier‐transform mid‐infrared absorption spectroscopy, although several challenging and advanced trials to use quantum chemical calculations for analysing THz absorption spectra have recently been conducted [24, 25]. As an instrumental analysis tool that typically uses frequencies from 3.0 to 18.0 THz (100–600 cm −1 ), intermediate between the THz and the MIR frequency ranges, Fourier‐transform far‐infrared (FT‐FIR) absorption spectroscopy can mainly provide useful information on skeletal vibrations [21, 23, 25, 26].…”

Quantum Chemical and Spectroscopic Study on Hydrogen Bonds in Hairpin DNA

“…Next, the THz absorption spectra of guanine and cytosine acquired experimentally and shown, respectively, in Figs. 10(b) and 11(b) are compared with that of thymine reported in our previous paper [16]. The wave numbers of main absorption peaks Notes: δ = in-plane bending, γ = out-of-plane bending, τ = torsional vibration, s = symmetric, as = asymmetric, ring py = pyrimidine ring.…”

“…Here, all the assignments listed in Table I were determined based on the strengths and wave numbers of corresponding vibrational modes and the modes are listed in order of intensity when more than one is assigned to one absorption peak. In addition, the mode at 575 cm −1 in D is caused by the torsional vibration at H 15 N 14 H 16 and by the out-of-plane bending vibration at N 9 H 10 . Likewise, the mode at 577 cm −1 in T is caused by the torsional vibration at H 15 N 14 H 16 and by the out-of-plane bending vibration at N 1 H 13 .…”

“…In addition, the mode at 575 cm −1 in D is caused by the torsional vibration at H 15 N 14 H 16 and by the out-of-plane bending vibration at N 9 H 10 . Likewise, the mode at 577 cm −1 in T is caused by the torsional vibration at H 15 N 14 H 16 and by the out-of-plane bending vibration at N 1 H 13 . As mentioned above, a real sample should contain guanine in a variety of forms [17].…”

“…As for DNA and its constituent bases, although many papers have reported their MIR spectra [11,12], only few papers have reported on their FIR or THz absorption spectra [13][14][15][16]. Among the four constituent bases, we have already measured the absorption spectra of thymine in a range from 16.7 to 600 cm −1 and have assigned almost all the absorption peaks observed in the spectra by quantum chemical calculations using the density functional theory [16]. With this background, we measured FT-FIR and THz absorption spectra of guanine and cytosine experimentally and simulated the spectra quantum chemically in the present research.…”