A benchmark study of molecular structure by experimental and theoretical methods: Equilibrium structure of uracil from gas-phase electron diffraction data and coupled-cluster calculations

Vogt, N.; Khaikin, L. S.; Grikina, O. E.; Rykov, Anatolii N.

doi:10.1016/j.molstruc.2013.07.014

Cited by 36 publications

(42 citation statements)

References 36 publications

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“…For example, the diffuse-function effects for uracil are less than 0.001 Å at this level. 4 Therefore, the best ab initio structure was calculated according to the expression: …”

Section: Results Of Theoretical Calculations and Discussionmentioning

confidence: 99%

From the Determination of the Accurate Equilibrium Structure of 1-Methylthymine by Gas Electron Diffraction and Coupled Cluster Computations to the Observation of Methylation and Flexibility Effects in Pyrimidine Nucleobases

2014

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1-Methylthymine is of particular interest because it can be considered as a simple model of thymidine, in which deoxyribose attaches to thymine precisely at the N1 atom. The structure of this molecule is still unknown and so far has been experimentally studied for the first time in this work. The semiexperimental equilibrium structural parameters (r(e)(se)/∠(e)(se)) of 1-methylthymine have been determined by the gas electron diffraction (GED) method, taking into account vibrational corrections calculated with the use of the anharmonic (cubic) MP2/cc-pVTZ force constants. The methyl torsion around the C–N bond has been treated as a large-amplitude motion. For the first time, the structure of this molecule has been optimized by the very time-consuming coupled-cluster method (CCSD(T)(ae)) with the triple-ζ (cc-pwCVTZ) basis set. The obtained results have been extrapolated to the quadruple-ζ basis set at the MP2 level. It has been revealed that the methylation of uracil, especially at the nitrogen atom, leads to an increase in the flexibility of the nucleobase as well as a noticeable deformation of the pyrimidine ring.

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“…For example, the diffuse-function effects for uracil are less than 0.001 Å at this level. 4 Therefore, the best ab initio structure was calculated according to the expression: …”

Section: Results Of Theoretical Calculations and Discussionmentioning

confidence: 99%

From the Determination of the Accurate Equilibrium Structure of 1-Methylthymine by Gas Electron Diffraction and Coupled Cluster Computations to the Observation of Methylation and Flexibility Effects in Pyrimidine Nucleobases

2014

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“…The geometry of thymine is quite close to that of uracil [24] (see also [20]). The effect of the substitution of a hydrogen atom by a methyl group is quite small in the pyrimidine ring, except for the bond lengths and angles adjacent to C5 atom.…”

Section: Discussion and General Conclusionmentioning

confidence: 66%

“…[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, they were ignored here.…”

Section: Computational Details and Results Of Calculationsmentioning

confidence: 99%

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

Vogt

Demaison

Ksenafontov

et al. 2014

Journal of Molecular Structure

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“…The anharmonic effects themselves are very important for the successful interpretation of the experimental data. 20,[35][36][37] The cubic force field is required for all the models (i.e. GED, VSp and RSp).…”

Section: Theoretical Models For Intramolecular Vibrationsmentioning

confidence: 99%

Application of classical simulations for the computation of vibrational properties of free molecules

Tikhonov

Sharapa

Schwabedissen

et al. 2016

Phys. Chem. Chem. Phys.

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In this study, we investigate the ability of classical molecular dynamics (MD) and Monte-Carlo (MC) simulations for modeling the intramolecular vibrational motion. These simulations were used to compute thermally-averaged geometrical structures and infrared vibrational intensities for a benchmark set previously studied by gas electron diffraction (GED): CS 2 , benzene, chloromethylthiocyanate, pyrazinamide and 9,12-I 2 -1,2-closo-C 2 B 10 H 10 . The MD sampling of NVT ensembles was performed using chains of Nose-Hoover thermostats (NH) as well as the generalized Langevin equation thermostat (GLE). The performance of the theoretical models based on the classical MD and MC simulations was compared with the experimental data and also with the alternative computational techniques: a conventional approach based on the Taylor expansion of potential energy surface, path-integral MD and MD with quantum-thermal bath (QTB) based on the generalized Langevin equation (GLE). A straightforward application of the classical simulations resulted, as expected, in poor accuracy of the calculated observables due to the complete neglect of quantum effects. However, the introduction of a posteriori quantum corrections significantly improved the situation. The application of these corrections for MD simulations of the systems with large-amplitude motions was demonstrated for chloromethylthiocyanate. The comparison of the theoretical vibrational spectra has revealed that the GLE thermostat used in this work is not applicable for this purpose. On the other hand, the NH chains yielded reasonably good results.

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A benchmark study of molecular structure by experimental and theoretical methods: Equilibrium structure of uracil from gas-phase electron diffraction data and coupled-cluster calculations

Cited by 36 publications

References 36 publications

From the Determination of the Accurate Equilibrium Structure of 1-Methylthymine by Gas Electron Diffraction and Coupled Cluster Computations to the Observation of Methylation and Flexibility Effects in Pyrimidine Nucleobases

From the Determination of the Accurate Equilibrium Structure of 1-Methylthymine by Gas Electron Diffraction and Coupled Cluster Computations to the Observation of Methylation and Flexibility Effects in Pyrimidine Nucleobases

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

Application of classical simulations for the computation of vibrational properties of free molecules

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