Interplay of Experiment and Theory: Determination of an Accurate Equilibrium Structure of 1-Methyluracil by the Gas Electron Diffraction Method and Coupled-Cluster Computations

Abstract

As far as fundamental knowledge is concerned, the methyl derivatives of uracil can be considered as the simplest objects for studying the structural effects due to the substitution in the pyrimidyne nucleobases. From this point of view, 1-methyluracil is of special importance in biochemistry because uracil attaches ribose in ribonucleic acid (RNA) just precisely at the N1 atom. The semi-experimental equilibrium structure (r(e)(se)) of 1-methyluracil has been determined for the first time by the gas electron diffraction (GED) method taking into account rovibrational corrections to the thermal-average internuclear distances calculated with harmonic and anharmonic (cubic) MP2/cc-pVTZ force constants with consideration of the methyl torsion as a large-amplitude motion. For the first time, the structure of the molecule has been optimized by the very time-consuming coupled-cluster method with single and double excitations and perturbative treatment of connected triples using the correlation-consistent polarized weighted core-valence triple-ζ basis set with all electrons being correlated (CCSD(T)(all)/cc-pwCVTZ) and extrapolated to the complete basis set (CBS) with the help of the MP2 calculations. Small differences between similar bond lengths of equilibrium configurations were assumed in the GED analysis at the CCSD(T)(all)/CBS values. A remarkable agreement between the semi-experimental and computed equilibrium structures points out the high accuracy of both the GED determination and the coupled-cluster computations. The effect of methylation on the structure of uracil has been analyzed.

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

“…Besides the elongation of the adjacent bond lengths, the methylation of uracil causes the decrease of the adjacent bond angle in pyrimidine ring, namely C4AC5@C6: from 119.5 to 117.9°, with corresponding increase of the further angles in the ring. Similar changes of the parameters adjacent to the N1 atom have been observed for 1-methyluracil [21].…”

“…[20][21][22][23][24]). As it has been shown for uracil [20], the diffuse function effects are negligibly small at the MP2(AE)/cc-pwCVQZ level.…”

“…Therefore, the methyl internal rotation cannot significantly affect the accuracy of the SE structure determined in the present study. On the other side, methyluracils can be remarkably flexible molecules, for example, 1-methyluracil with a methyl group almost freely rotating around the NAC bond (m 39 (A 00 ) = 64 cm À1 , MP2/cc-pVTZ) [21]. Indeed, this molecule could not be described by a rigid model in the electron diffraction investigation [21].…”

Anharmonic Thermal Motion Modelling in the Experimental XRD Charge Density Determination of 1-Methyluracil at T = 23 K

“…The electron population coefficients obtained from the least-squares refinements of the four multipolar models were used to generate experimental EDDs. Bader’s QTAIM [ 7 ] was applied to partition these experimental EDDs into atomic basins (Ω), and hence obtain, by integration, atomic volumes and charges. The calculations were made with the PAMoC code [ 32 ].…”

“…Following their footsteps on the path they traced, we here present the experimental charge density analysis of 1-methyluracil (hereinafter 1-MUR), based on a very low-T dataset collected at Caltech in Marsh’s laboratory in 1989 by one of us (RD). Experimental as well as theoretical and computational work on 1-methyluracil and its derivatives have been published a number of times [ 2 , 3 , 4 , 5 , 6 , 7 ], yet the experimental estimates for some of the fundamental properties of the molecule in a condensed phase, such as integrated atomic volumes and charges, as well as atomic and molecular electrostatic quadrupole moments, are not available, to the best of our knowledge, in the literature.…”