On the aromaticity of uracil and its 5-halogeno derivatives as revealed by theoretically derived geometric and magnetic indexes

Rzepiela, Kacper; Buczek, Aneta; Kupka, Teobald; Broda, Małgorzata A.

doi:10.1007/s11224-020-01682-x

Cited by 5 publications

(3 citation statements)

References 52 publications

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“…Uracil is an important component related to information transfer and replication in living systems. Its 5-halogen modifications are used in anticancer and antifungal treatment [ 59 , 61 , 62 , 63 ]. Modifications of uracil, including replacing the oxygen atom with sulfur [ 64 ], also changes its biological activity.…”

Section: Resultsmentioning

confidence: 99%

Electron Correlation or Basis Set Quality: How to Obtain Converged and Accurate NMR Shieldings for the Third-Row Elements?

et al. 2022

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The quality of theoretical NMR shieldings calculated at the quantum-chemical level depends on various theoretical aspects, of which the basis set type and size are among the most important factors. Nevertheless, not much information is available on the basis set effect on theoretical shieldings of the NMR-active nuclei of the third row. Here, we report on the importance of proper basis set selection to obtain accurate and reliable NMR shielding parameters for nuclei from the third row of the periodic table. All calculations were performed on a set of eleven compounds containing the elements Na, Mg, Al, Si, P, S, or Cl. NMR shielding tensors were calculated using the SCF-HF, DFT-B3LYP, and CCSD(T) methods, combined with the Dunning valence aug-cc-pVXZ, core-valence aug-cc-pCVXZ, Jensen polarized-convergent aug-pcSseg-n and Karlsruhe x2c-Def2 basis set families. We also estimated the complete basis set limit (CBS) values of the NMR parameters. Widely scattered nuclear shieldings were observed for the Dunning polarized-valence basis set, which provides irregular convergence. We show that the use of Dunning core-valence or Jensen basis sets effectively reduces the scatter of theoretical NMR results and leads to their exponential-like convergence to CBS. We also assessed the effect of vibrational, temperature, and relativistic corrections on the predicted shieldings. For systems with single bonds, all corrections are relatively small, amounting to less than 4% of the CCSD(T)/CBS value. Vibrational and temperature corrections were less reliable for H3PO and HSiCH due to the high anharmonicity of the molecules. An abnormally high relativistic correction was observed for phosphorus in PN, reaching ~20% of the CCSD(T)/CBS value, while the correction was less than 7% for other tested molecules.

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Section: Resultsmentioning

confidence: 99%

Electron Correlation or Basis Set Quality: How to Obtain Converged and Accurate NMR Shieldings for the Third-Row Elements?

et al. 2022

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“…Aromaticity of uracil and its 5-chalogen derivatives were tested using GIAO NMR calculations of NICS magnetic indexes. 126 Kleinpeter and Koch employed NICS calculation for testing the nature of carbon-boron bond in boron trapped N-heterocyclic carbenes. 127 In addition, Kleinpeter et al 128 reported on a 29 Si and 13 C NMR conformational equilibrium study of 1-phenyl-1-tert-butylsilacyclohexane.…”

Section: Other Examples Of Nuclear Shielding Modelingmentioning

confidence: 99%

Nuclear Magnetic Resonance

米本理¹

2022

Nuclear Magnetic Resonance

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The selected research papers on theoretical aspects of nuclear magnetic shielding published from 1 January to 31 December 2021 are shortly reviewed in this chapter. Among the reported studies are mainly density functional theory (DFT) predictions of nuclear shielding for free molecules, as well as in solution, modeled by the polarizable continuum model (PCM). The calculations for solids are getting more common in the reviewed period of time. Due to their relatively high computational price, the number of ab initio and highlevel calculated nuclear shieldings is significantly lower. In several reports the theoretical results are additionally improved by inclusion of zero-point vibration and temperature correction (ZPVC and TC), As before, most calculations have been performed using the non-relativistic approach.

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“…1a, is most stable. [16][17][18][19] According to X-ray studies, uracil is found only in the diketo form in the solid phase, and in the same form, it exists in water. As shown in Fig.…”

Section: Introductionmentioning

confidence: 99%

Uracil–water interaction revisited – in search of single H-bonded secondary minima

Buczek,

Rzepiela,

Kupka

et al. 2024

Phys. Chem. Chem. Phys.

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On the aromaticity of uracil and its 5-halogeno derivatives as revealed by theoretically derived geometric and magnetic indexes

Cited by 5 publications

References 52 publications

Electron Correlation or Basis Set Quality: How to Obtain Converged and Accurate NMR Shieldings for the Third-Row Elements?

Electron Correlation or Basis Set Quality: How to Obtain Converged and Accurate NMR Shieldings for the Third-Row Elements?

Nuclear Magnetic Resonance

Uracil–water interaction revisited – in search of single H-bonded secondary minima

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