Study of the Thymine Molecule: Equilibrium Structure from Joint Analysis of Gas-Phase Electron Diffraction and Microwave Data and Assignment of Vibrational Spectra Using Results of Ab initio Calculations

Abstract

Thymine is one of the nucleobases which forms the nucleic acid (NA) base pair with adenine in DNA. The study of molecular structure and dynamics of nucleobases can help to understand and explain some processes in biological systems and therefore it is of interest. Because the scattered intensities on the C, N, and O atoms as well as some bond lengths in thymine are close to each other the structural problem cannot been solved by the gas phase electron diffraction (GED) method alone. Therefore the rotational constants from microvawe (MW) studies and differences in the groups of N-C, C=O, N-H, and C-H bond lengths from MP2 (full)/cc-pVQZ calculations were used as supplementary data. The analysis of GED data was based on the C(s) molecular symmetry according to results of the structure optimizations at the MP2 (full) level using 6-311G (d,p), cc-pVTZ, and cc-pVQZ basis sets confirmed by vibrational frequency calculations with 6-311G (d,p) and cc-pVTZ basis sets. Mean-square amplitudes as well as harmonic and anharmonic vibrational corrections to the internuclear distances (r(e)-r(a)) and to the rotational constants (B(e)(k)-B(0)(k), where k = A, B, C) were calculated from the quadratic (MP2 (full)/cc-pVTZ) and cubic (MP2 (full)/6-311G (d,p)) force constants (the latter were used only for anharmonic corrections). The harmonic force field was scaled using published IR and Raman spectra of the parent and N1,N3-dideuterated species, which were for the first time completely assigned in the present work. The main equilibrium structural parameters of the thymine molecule determined from GED data supplemented by MW rotational constants and results of MP2 calculations are the following (bond lengths in Angstroms and bond angles in degrees with 3sigma in parentheses): r(e) (C5=C6) = 1.344 (16), r(e) (C5-C9) = 1.487 (8), r(e) (N1-C6) = 1.372 (3), r(e) (N1-C2) = 1.377 (3), r(e) (C2-N3) = 1.378 (3), r(e) (N3-C4) = 1.395 (3), r(e) (C2=O7) = 1.210 (1), r(e) (C4=O8) = 1.215 (1), angle e (N1-C6=C5) = 123.1 (5), angle e (C2-N1-C6) = 123.7 (5), angle e (N1-C2-N3) = 112.8 (5), angle e (C2-N3-C4) = 128.0 (5), angle e (N3-C4-C5) = 114.8 (5), angle e (C6=C5-C9) = 124.4 (9). The experimental structural parameters are in good agreement with those from MP2 (full) calculations with use of cc-pVTZ and cc-pVQZ basis sets.

IR spectra of nitrobenzene and nitrobenzene-15N in the gas phase, ab initio analysis of vibrational spectra and reliable force fields of nitrobenzene and 1,3,5-trinitrobenzene. Investigation of equilibrium geometry and internal rotation in these simplest aromatic nitro compounds with one and three rotors by means of electron diffraction, spectroscopic, and quantum chemistry data

“…The relative weights of rotational constants have been taken according to the errors calculated by summing up the standard deviations of the experimental B 0 (k) constants and uncertainties in the \(B e (k) -B 0 (k) )[ LAM corrections which are estimated to be 5 % of their total values. This procedure was successfully used in our previous studies [80,81]. The relative weights of the GED and MW data have been chosen so that standard deviations for the B 0 (k) constants determined in the joint analysis would be close to the above-mentioned estimated errors [78,79].…”

A benchmark study of molecular structure by experimental and theoretical methods: Equilibrium structure of thymine from microwave rotational constants and coupled-cluster computations

“…d Ref. [2]. e Parameters with equal superscripts were refined in one group; differences between parameters in each group were assumed at the values from MP2(AE)/cc-pVQZ calculation.…”

“…1), i.e. C s total symmetry [2]. The molecular structure with C s symmetry was optimized by the coupled-cluster method with single and double excitation [12] and a perturbative treatment of connected triples [13], CCSD(T), using the correlation-consistent polarized weighted core-valence triple-zeta basis set, cc-pwCVTZ, [14] with all electrons being correlated, AE.…”

“…Being of great importance for biochemistry, this molecule has been studied in the gas phase by several structural and spectroscopic methods (see, for example, review [1]). Thus, the molecular structure of the canonical tautomer of thymine has been determined both by gas-phase electron diffraction (ED) (thermal-average, r a , and semi-experimental equilibrium, r se e (ED), structures [2]) and by microwave spectroscopy (MW) (substitution structure, r s [3] However, the comparison of published data (see Section 'Discussion and general conclusions') demonstrates very strong discrepancies. Thus, the r s values for the C5@C6 and N3AC4 bond lengths are larger than the r a ones by 0.02 and 0.03 Å, although vibrational effects should be smaller in the r s structure that in the r a one.…”

Use of imaging plates (IPs) in the gas-phase electron diffraction (GED) experiments on the EG-100 M apparatus. The tetrachloromethane molecule as a test object

“…The GED experiment was carried out at room temperature at the Moscow State University on the EG-100 M apparatus using the r 3 sector from brass produced in the workshop of the University of Ulm (see [7] for the first application). The IPs were exposed for ca.…”