Influence of N−H···O and C−H···O Hydrogen Bonds on the ¹⁷O NMR Tensors in Crystalline Uracil:  Computational Study

Abstract

We report a computational study for the 17O NMR tensors (electric field gradient and chemical shielding tensors) in crystalline uracil. We found that N-H...O and C-H...O hydrogen bonds around the uracil molecule in the crystal lattice have quite different influences on the 17O NMR tensors for the two C=O groups. The computed 17O NMR tensors on O4, which is involved in two strong N-H...O hydrogen bonds, show remarkable sensitivity toward the choice of cluster model, whereas the 17O NMR tensors on O2, which is involved in two weak C-H...O hydrogen bonds, show much smaller improvement when the cluster model includes the C-H...O hydrogen bonds. Our results demonstrate that it is important to have accurate hydrogen atom positions in the molecular models used for 17O NMR tensor calculations. In the absence of low-temperature neutron diffraction data, an effective way to generate reliable hydrogen atom positions in the molecular cluster model is to employ partial geometry optimization for hydrogen atom positions using a cluster model that includes all neighboring hydrogen-bonded molecules. Using an optimized seven-molecule model (a total of 84 atoms), we were able to reproduce the experimental 17O NMR tensors to a reasonably good degree of accuracy. However, we also found that the accuracy for the calculated 17O NMR tensors at O2 is not as good as that found for the corresponding tensors at O4. In particular, at the B3LYP/6-311++G(d,p) level of theory, the individual 17O chemical shielding tensor components differ by less than 10 and 30 ppm from the experimental values for O4 and O2, respectively. For the 17O quadrupole coupling constant, the calculated values differ by 0.30 and 0.87 MHz from the experimental values for O4 and O2, respectively.

Study of hydrogen bonds in crystalline 5-nitrouracil. Density functional theory calculations of the O-17, N-14, and H-2 nuclear quadrupole resonance parameters

“…In uracil, O1 contributes to N-H … O type of HB interactions with two neighbor molecules and O2 contributes to C-H … O type of HB interactions with two neighbor molecules. Wu et al [20,21] have recently reported the 17 O NQR parameters of uracil either experimentally or computationally. Because of different HB interaction properties between uracil and 5NU, the calculated NQR parameters of uracil at the same level of calculations are observed in lower fields in comparison with those of 5NU.…”

“…H1 is chemically bonded to N1 and [19,20] for oxygen and from Ref. [21] for nitrogen nuclei. The values in parentheses are calculated at the same level of theory of this study.…”

Hydrogen Bonds of Peptide Group in Four Acetamide Derivatives: DFT Study of Oxygen and Nitrogen NQR and NMR Parameters

“…However, the positions of hydrogen atoms due to low electron density are not accurately located by x-ray diffraction. Therefore, following the earlier work of Ida et al [26], only the hydrogen positions of peptide group in the single and cluster structures are separately optimized at the level of B3LYP method and 6-311++G** standard basis set while the other atoms positions are kept frozen during the process.…”

Study of hydrogen bonds in N-methylacetamide by DFT calculations of oxygen, nitrogen, and hydrogen solid-state NMR parameters

“…As mentioned above, since NMR tensors are very sensitive to the electrostatic environment of nuclei, such environment must be included in the calculations to have reliable results. A way for this purpose is including the charge points in the calculations; however, two recent studies [18,19] showed that if the target molecule is surrounded by those possible interacting neighbor molecules, the calculated NMR tensors are also reliable. Therefore, trimer forms of NMA were created using coordinates transforming to surround the target molecule by the interacting neighbor ones (see Scheme 1 and Table 1 for details).…”