Predicting the NMR spectra of nucleotides by DFT calculations: cyclic uridine monophosphate

Bagno, Alessandro; Rastrelli, Federico; Saielli, Giacomo

doi:10.1002/mrc.2204

Cited by 47 publications

(76 citation statements)

References 40 publications

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“…The contributions from these factors have been discussed in many works devoted to QM chemical shift prediction. [20,23,50,51] Figs 9 and 10 show plots of the HOSE-and QM-calculated 13 C chemical shifts versus experimental shifts for all atoms included in the structures presented in Table 2S, 274 shifts in total.…”

Section: Statistical Comparison Of Methodsmentioning

confidence: 99%

“…Stereoisomer 5 was ranked as the most likely isomer with MAE(HOSE) = 2.93 ppm and MAE(NN) = 3.89 ppm while the MAE(QM) value found for structure 5 using the GIAO approach was 5.3 ppm. [30] In a separate study, [51] Bagno et al carried out QM 13 C chemical shift calculations for structure 6. The MAE(QM) value = 6.83 ppm and the authors concluded that the QM approach allows 13 C NMR prediction for a polar, flexible molecule in aqueous solution with a high level of accuracy, comparable to that obtained for less complex systems.…”

Section: Statistical Comparison Of Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Empirical and DFT GIAO quantum‐mechanical methods of ¹³C chemical shifts prediction: competitors or collaborators?

Elyashberg¹,

Blinov²,

Smurnyy³

et al. 2010

Magnetic Reson in Chemistry

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The accuracy of (13)C chemical shift prediction by both DFT GIAO quantum-mechanical (QM) and empirical methods was compared using 205 structures for which experimental and QM-calculated chemical shifts were published in the literature. For these structures, (13)C chemical shifts were calculated using HOSE code and neural network (NN) algorithms developed within our laboratory. In total, 2531 chemical shifts were analyzed and statistically processed. It has been shown that, in general, QM methods are capable of providing similar but inferior accuracy to the empirical approaches, but quite frequently they give larger mean average error values. For the structural set examined in this work, the following mean absolute errors (MAEs) were found: MAE(HOSE) = 1.58 ppm, MAE(NN) = 1.91 ppm and MAE(QM) = 3.29 ppm. A strategy of combined application of both the empirical and DFT GIAO approaches is suggested. The strategy could provide a synergistic effect if the advantages intrinsic to each method are exploited.

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Section: Statistical Comparison Of Methodsmentioning

confidence: 99%

Section: Statistical Comparison Of Methodsmentioning

confidence: 99%

Empirical and DFT GIAO quantum‐mechanical methods of ¹³C chemical shifts prediction: competitors or collaborators?

Elyashberg¹,

Blinov²,

Smurnyy³

et al. 2010

Magnetic Reson in Chemistry

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show abstract

“…First, we consider the 11 The relationship between the theoretical and experimental chemical shifts can be seen easily from the linear fitting of the theoretical dataset to the experimental one. [19,29,33,35] The linear regression equations for the four sets of calculated chemical shifts can be expressed as…”

Section: Chemical Shieldings/shifts Of Species Other Than (Cf 3 ) 3 Bcomentioning

confidence: 99%

Theoretical investigation on multinuclear NMR chemical shifts of some tris(trifluoromethyl)boron complexes

Zhang

Cai

Zhong

2009

Magnetic Reson in Chemistry

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Tris(trifluoromethyl)boron complexes have unusual properties and may find applications in many fields of chemistry, biology, and physics. To gain insight into their NMR properties, the isotropic 11B, 13C, and 19F NMR chemical shifts of a series of tris(trifluoromethyl)boron complexes were systematically studied using the gauge-included atomic orbitals (GIAO) method at the levels of B3LYP/6-31 + G(d,p)//B3LYP/6-31G* and B3LYP/6-311 + G(d,p)//B3LYP/6-311 + G(d,p). Solvent effects were taken into account by polarizable continuum models (PCM). The calculated results were compared with the experimental values. The reason that the structurally inequivalent fluorine atoms in a specific species give a same chemical shift in experimental measurements is attributed to the fast rotation of CF3 group around the B-C(F3) bond because of the low energy barrier. The calculated 11B, 13C(F3), and 19F chemical shifts are in good agreement with the experimental measurements, while the deviations of calculated 13C(X, X = O, N) chemical shifts are slightly large. For the latter, the average absolute deviations of the results from B3LYP/6-311 + G(d,p)//B3LYP/6-311 + G(d,p) are smaller than those from B3LYP/6-31 + G(d,p)//B3LYP/6-31G*, and the inclusion of PCM reduces the deviation values. The calculated 19F and 11B chemical shieldings of (CF3)3BCO are greatly dependent on the optimized structures, while the influence of structural parameters on the calculated 13C chemical shieldings is minor.

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“…[2][3][4][5][6] Characterization of the structural arrangements of such polar organometallics in solution is now generally performed by using NMR spectroscopy, which affords convenient access to important physiA C H T U N G T R E N N U N G cochemical characteristics. [7][8][9] In particular, the 1 J Li,C coupling constant is a useful parameter which can be directly related to the degree of aggregation of the organolithium compound, independent of the nature of the organic chain. Indeed Bauer, Winchester, and Schleyer have proposed an empirical formula [BWS rule; Eq.…”

Section: Introductionmentioning

confidence: 99%

First‐Principles Molecular Dynamics Evaluation of Thermal Effects on the NMR ¹J_Li,C Spin–Spin Coupling

Lande¹,

Fressigné²,

Gérard³

et al. 2007

Chemistry A European J

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Car-Parrinello (CP) molecular dynamics were applied to sample conformations of various models of organolithium aggregates which are chosen to estimate (1)J(Li,C) NMR coupling constants. The results show that the deviations from the values computed using static (optimized) geometries are small provided no large-amplitude motions occur within the timescale of the simulations. In the case of the vinyllithium dimer, for which rotation of the vinyl chain is observed, this approach allows analysis of the various contributions to the experimentally measured constants. For the trisolvated methyllithium monomer, partial decoordination of solvating dimethyl ether is observed and results in a significant shift of (1)J(Li,C). All these results highlight that a varied physicochemical machinery is hidden behind general empirical formulas, such as the Bauer-Winchester-Schleyer rule used experimentally.

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Predicting the NMR spectra of nucleotides by DFT calculations: cyclic uridine monophosphate

Cited by 47 publications

References 40 publications

Empirical and DFT GIAO quantum‐mechanical methods of ¹³C chemical shifts prediction: competitors or collaborators?

Empirical and DFT GIAO quantum‐mechanical methods of ¹³C chemical shifts prediction: competitors or collaborators?

Theoretical investigation on multinuclear NMR chemical shifts of some tris(trifluoromethyl)boron complexes

First‐Principles Molecular Dynamics Evaluation of Thermal Effects on the NMR ¹J_Li,C Spin–Spin Coupling

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Predicting the NMR spectra of nucleotides by DFT calculations: cyclic uridine monophosphate

Cited by 47 publications

References 40 publications

Empirical and DFT GIAO quantum‐mechanical methods of 13C chemical shifts prediction: competitors or collaborators?

Empirical and DFT GIAO quantum‐mechanical methods of 13C chemical shifts prediction: competitors or collaborators?

Theoretical investigation on multinuclear NMR chemical shifts of some tris(trifluoromethyl)boron complexes

First‐Principles Molecular Dynamics Evaluation of Thermal Effects on the NMR 1JLi,C Spin–Spin Coupling

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Empirical and DFT GIAO quantum‐mechanical methods of ¹³C chemical shifts prediction: competitors or collaborators?

Empirical and DFT GIAO quantum‐mechanical methods of ¹³C chemical shifts prediction: competitors or collaborators?

First‐Principles Molecular Dynamics Evaluation of Thermal Effects on the NMR ¹J_Li,C Spin–Spin Coupling