Computational studies of 13C NMR chemical shifts of saccharides

The (13)C NMR chemical shifts for alpha-D-lyxofuranose, alpha-D-lyxopyranose (1)C(4), alpha-D-lyxopyranose (4)C(1), alpha-D-glucopyranose (4)C(1), and alpha-D-glucofuranose have been studied at ab initio and density-functional theory levels using TZVP quality basis set. The methods were tested by calculating the nuclear magnetic shieldings for tetramethylsilane (TMS) at different levels of theory using large basis sets. Test calculations on the monosaccharides showed B3LYP(TZVP) and BP86(TZVP) to be cost-efficient levels of theory for calculation of NMR chemical shifts of carbohydrates. The accuracy of the molecular structures and chemical shifts calculated at the B3LYP(TZVP) level is comparable to those obtained at the MP2(TZVP) level. Solvent effects were considered by surrounding the saccharides by water molecules and also by employing a continuum solvent model. None of the applied methods to consider solvent effects was successful. The B3LYP(TZVP) and MP2(TZVP)(13)C NMR chemical shift calculations yielded without solvent and rovibrational corrections an average deviation of 5.4 ppm and 5.0 ppm between calculated and measured shifts. A closer agreement between calculated and measured chemical shifts can be obtained by using a reference compound that is structurally reminiscent of saccharides such as neat methanol. An accurate shielding reference for carbohydrates can be constructed by adding an empirical constant shift to the calculated chemical shifts, deduced from comparisons of B3LYP(TZVP) or BP86(TZVP) and measured chemical shifts of monosaccharides. The systematic deviation of about 3 ppm for O(1)H chemical shifts can be designed to hydrogen bonding, whereas solvent effects on the (1)H NMR chemical shifts of C(1)H were found to be small. At the B3LYP(TZVP) level, the barrier for the torsional motion of the hydroxyl group at C(6) in alpha-D-glucofuranose was calculated to 7.5 kcal mol(-1). The torsional displacement was found to introduce large changes of up to 10 ppm to the (13)C NMR chemical shifts yielding uncertainties of about +/-2 ppm in the chemical shifts.     

Vibrational, NMR spectral studies of 2-furoic hydrazide by DFT and ab initio HF methods

The Fourier transform infrared spectra, 1H NMR and 13C NMR spectra of 2-furoic hydrazide have been recorded. Optimized geometry, frequency and intensity of the vibrational bands of 2-furoic hydrazide were obtained by the density functional theory (DFT) and ab initio levels of theory and also 1H NMR, 13C NMR chemical shifts were calculated using 6-31G+(d,p) basis sets. The theoretical values were compared with experimental values.     

Toward direct determination of conformations of protein building units from multidimensional NMR experiments. V. NMR chemical shielding analysis of N-formyl-serinamide,a model for polar side-chain containing peptides

Knowledge of chemical shift-structure relationships could greatly facilitate the NMR chemical shift assignment and structure refinement processes that occur during peptide/protein structure determination via NMR spectroscopy. To determine whether such correlations exist for polar side chain containing amino acid residues the serine dipeptide model, For-L-Ser-NH(2), was studied. Using the GIAO-RHF/6-31+G(d) and GIAO-RHF/TZ2P levels of theory the NMR chemical shifts of all hydrogen ((1)H(N), (1)H(alpha), (1)H(beta1), (1)H(beta2)), carbon ((13)C(alpha), (13)C(beta), (13)C') and nitrogen ((15)N) atoms have been computed for all 44 stable conformers of For-L-Ser-NH(2). An attempt was made to establish correlation between chemical shift of each nucleus and the major conformational variables (omega(0), phi, psi, omega(1), chi,(1) and chi(2)). At both levels of theory a linear correlation can be observed between (1)H(alpha)/phi, (13)C(alpha)/phi, and (13)C(alpha)/psi. These results indicate that the backbone and side-chain structures of For-L-Ser-NH(2) have a strong influence on its chemical shifts.     

Calculated and experimental 1H and 13C NMR assignments for cannabicitran

Cannabicitran is an important cannabinoid natural product produced by Cannabis sativa and is often found at surprisingly high levels (up to ~10%) in “purified” commercial cannabidiol (CBD) extract preparations. Despite the prevalence of this molecule in CBD oil and other cannabinoid-related products, and the rapidly expanding interest in cannabinoids for treatment of a wide range of physiological conditions, only unassigned ¹H NMR data and partial unambiguous ¹³C assignments have been published. Herein, we report the complete ¹H and ¹³C NMR assignments of cannabicitran and comparatively evaluate the performance of several density functional theory (DFT) methods with varying levels of theory for the calculation of NMR chemical shifts.     

Visualization and quantification of the anisotropic effect of C=C double bonds on 1H NMR spectra of highly congested hydrocarbons-indirect estimates of steric strain

The anisotropic effect of the olefinic C=C double bond has been calculated by employing the NICS ( nucleus independent chemical shift) concept and visualized as an anisotropic cone by a through space NMR shielding grid. Sign and size of this spatial effect on (1)H chemical shifts of protons in norbornene, exo- and endo-2-methylnorbornenes, and in three highly congested tetracyclic norbornene analogs have been compared with the experimental (1)H NMR spectra as far as published. (1)H NMR spectra have also been calculated at the HF/6-31G* level of theory to get a full, comparable set of proton chemical shifts. Differences between delta( (1)H)/ppm and the calculated anisotropic effect of the CC double bond are discussed in terms of the steric compression that occurs in the compounds studied.     

TMS的NMR量子化学计算

分别用HF/4-31G(Si=6-21G)、B3LYP/6-31G(D)、B3LYP/6-31G、HF/6-31G、MP2/6-31G(D)对TMS进行了结构优化,在此基础上,用Hartree-Fock、B3LYP理论水平下,分别用不同的基组6-31G、6-31++G(D,P)、6-311+G(2D,P)、6-311++G(D,P)进行NMR的计算;在MP2理论水平上,用STO-3G、3-21G、4-31G、6-31G、6-31G(D)、6-31++G(D,P)等基组进行NMR的计算.并用GAUSSION98程序所给出的四种计算NMR的方法:GIAO、IGAIM、CSGT、SINGLE GAUGE ORIGIN,分别在上述基础上进行了TMS的屏蔽值的计算.研究结果表明,就理论水平而言,DFT(B3LYP)比HF计算结果要好,而且基组越大,计算精度越高,但有一饱和基组存在.就计算方法而言,用GIAO有利于计算精度的提高.计算结果与实验值基本上吻合.     

Solid-state 25Mg NMR spectroscopic and computational studies of organic compounds. square-pyramidal magnesium(II) ions in aqua(magnesium) phthalocyanine and chlorophyll a

We report a solid-state (25)Mg NMR spectroscopic study of two magnesium-containing organic compounds: monopyridinated aqua(magnesium) phthalocyanine (MgPc.H(2)O.Py) and chlorophyll a (Chla). Each of these compounds contains a Mg(II) ion coordinating to four nitrogen atoms and a water molecule in a square-pyramidal geometry. Solid-state (25)Mg NMR spectra for MgPc.H(2)O.Py were obtained at 11.7 T (500 MHz for (1)H) for a (25)Mg-enriched sample (99.1% (25)Mg atom) using both Hahn-echo and quadrupole Carr-Purcell Meiboom-Gill (QCPMG) pulse sequences. Solid-state (25)Mg NMR spectra for Chla were recorded at (25)Mg natural abundance (10.1%) at 19.6 T (830 MHz for (1)H). The (25)Mg quadrupole parameters were determined from spectral analyses: MgPc.H(2)O.Py, C(Q) = 13.0 +/- 0.1 MHz and eta(Q) = 0.00 +/- 0.05; Chla, C(Q) = 12.9 +/- 0.1 MHz and eta(Q) = 1.00 +/- 0.05. This work represents the first time that Mg(II) ions in a square-pyramidal geometry have been characterized by solid-state (25)Mg NMR spectroscopy. Extensive quantum mechanical calculations for electric-field-gradient (EFG) and chemical shielding tensors were performed at restricted Hartee-Fock (RHF), density functional theory (DFT), and second-order M?ller-Plesset perturbation theory (MP2) levels for both compounds. Computed (25)Mg nuclear quadrupole coupling constants at the RHF and MP2 levels show a reasonable basis-set convergence at the cc-pV5Z basis set (within 7% of the experimental value); however, B3LYP results display a drastic divergence beyond the cc-pVTZ basis set. A new crystal structure for MgPc.H(2)O.Py is also reported.     

Intramolecular hydrogen-bonding interactions in 2-nitrosophenol and nitrosonaphthols: ab initio, density functional, and nuclear magnetic resonance theoretical study

Intramolecular hydrogen bonding (IHB) interactions and molecular structures of 2-nitrosophenol, nitrosonaphthols, and their quinone-monooxime tautomers were investigated at ab initio and density functional theory (DFT) levels. The geometry optimization of the structures studied was performed without any geometrical restrictions. Possible conformations with different types of the IHB of the tautomers were considered to understand the nature of the HB among these conformers. The effect of solvent on hydrogen bond energies, conformational equilibria, and tautomerism in aqueous solution were studied. Natural bond orbital analysis was performed to study the IHB in the gaseous phase and in aqueous medium. The NMR 1H, 13C, 15N, and 17O chemical shifts in the gaseous phase and in solution for the studied compounds were calculated using the gauge-including atomic orbitals approach implemented in the Gaussian 03 program package. The optimized geometrical parameters and 1H NMR chemical shifts are in good agreement with previous theoretical and experimental data.     

Tautomeric equilibria of [1]benzopyrano[3,4-d]imidazol-4(3H)-ones, a theoretical and NMR study

[reaction: see text] Benzopyranoimidazolones could virtually exist in four tautomeric forms, namely N3-H, N1-H, coumarin O-H, and C2-H. Experimental evidence reported thus far has been unable to lead to a unique statement about the preferred tautomeric forms in solution. In this work, tautomeric equilibria for a series of 2-substituted [1]benzopyrano[3,4-d]imidazol-4(3H)-ones were investigated by DFT calculations, in both gas phase and solution. The influence of the solvent was included in the calculations by the CPCM solvent model. 13C chemical shifts of all tautomers were computed at different levels of theory and then compared with experiments to assign the preferred tautomers. Theoretical findings were then compared to dynamic 1H NMR experiments results.     

Chemical shifts in nucleic acids studied by density functional theory calculations and comparison with experiment

NMR chemical shifts are highly sensitive probes of local molecular conformation and environment and form an important source of structural information. In this study, the relationship between the NMR chemical shifts of nucleic acids and the glycosidic torsion angle, χ, has been investigated for the two commonly occurring sugar conformations. We have calculated by means of DFT the chemical shifts of all atoms in the eight DNA and RNA mono-nucleosides as a function of these two variables. From the DFT calculations, structures and potential energy surfaces were determined by using constrained geometry optimizations at the BP86/TZ2P level of theory. The NMR parameters were subsequently calculated by single-point calculations at the SAOP/TZ2P level of theory. Comparison of the (1) H and (13) C?NMR shifts calculated for the mono-nucleosides with the shifts determined by NMR spectroscopy for nucleic acids demonstrates that the theoretical shifts are valuable for the characterization of nucleic acid conformation. For example, a clear distinction can be made between χ angles in the anti and syn domains. Furthermore, a quantitative determination of the χ angle in the syn domain is possible, in particular when (13) C and (1) H chemical shift data are combined. The approximate linear dependence of the C1' shift on the χ angle in the anti domain provides a good estimate of the angle in this region. It is also possible to derive the sugar conformation from the chemical shift information. The DFT calculations reported herein were performed on mono-nucleosides, but examples are also provided to estimate intramolecularly induced shifts as a result of hydrogen bonding, polarization effects, or ring-current effects.     

Characterization of a new hexasodium diphosphopentamolybdate hydrate, Na6[P2Mo5O23]x7H2O, by 23Na MQMAS NMR spectroscopy and X-ray powder diffraction

A novel hexasodium disphosphopentamolybdate hydrate, Na6[P2Mo5O23]x7H2O, has been identified using X-ray powder diffraction, 1H, 23Na, and 31P magic-angle spinning (MAS) NMR, and 23Na multiple-quantum (MQ) MAS NMR. Powder XRD reveals that the hydrate belongs to the triclinic spacegroup P1 with cell dimensions a = 10.090(3) A, b = 15.448(5) A, c = 8.460(4) A, alpha = 101.45(6) degrees, beta = 104.09(2) degrees, gamma = 90.71(5) degrees, and Z = 2. The number of water molecules of crystallization has been determined on the basis of a quantitative evaluation of the 1H MAS NMR spectrum, the crystallographic unit cell volume, and a hydrogen content analysis. The 23Na MQMAS NMR spectra of Na6[P2Mo5O23]x7H2O, obtained at three different magnetic fields, clearly resolve resonances from six different sodium sites and allow a determination of the second-order quadrupolar effect parameters and isotropic chemical shifts for the individual resonances. These data are used to determine the quadrupole coupling parameters (CQ and eta Q) from simulations of the complex line shapes of the central transitions, observed in 23Na MAS NMR spectra at the three magnetic fields. This analysis illustrates the advantages of combining MQMAS and MAS NMR at moderate and high magnetic fields for a precise determination of quadrupole coupling parameters and isotropic chemical shifts for multiple sodium sites in inorganic systems. 31P MAS NMR demonstrates the presence of two distinct P sites in the asymmetric unit of Na6[P2Mo5O23].7H2O while the 31P chemical shielding anisotropy parameters, determined for this hydrate and for Na6[P2Mo5O23]x13H2O, show that these two hydrates can easily be distinguished using 31P MAS NMR.     

Benchmarking of density functionals for a soft but accurate prediction and assignment of 1H and 13C NMR chemical shifts in organic and biological molecules

A number of programs and tools that simulate ¹H and ¹³C nuclear magnetic resonance (NMR) chemical shifts using empirical approaches are available. These tools are user‐friendly, but they provide a very rough (and sometimes misleading) estimation of the NMR properties, especially for complex systems. Rigorous and reliable ways to predict and interpret NMR properties of simple and complex systems are available in many popular computational program packages. Nevertheless, experimentalists keep relying on these “unreliable” tools in their daily work because, to have a sufficiently high accuracy, these rigorous quantum mechanical methods need high levels of theory. An alternative, efficient, semi‐empirical approach has been proposed by Bally, Rablen, Tantillo, and coworkers. This idea consists of creating linear calibrations models, on the basis of the application of different combinations of functionals and basis sets. Following this approach, the predictive capability of a wider range of popular functionals was systematically investigated and tested. The NMR chemical shifts were computed in solvated phase at density functional theory level, using 30 different functionals coupled with three different triple–ζ basis sets. © 2016 Wiley Periodicals, Inc.     

Combining multinuclear high-resolution solid-state MAS NMR and computational methods for resonance assignment of glutathione tripeptide

We present a complete set of experimental approaches for the NMR assignment of powdered tripeptide glutathione at natural isotopic abundance, based on J-coupling and dipolar NMR techniques combined with (1)H CRAMPS decoupling. To fully assign the spectra, two-dimensional (2D) high-resolution methods, such as (1)H-(13)C INEPT-HSQC/PRESTO heteronuclear correlations (HETCOR), (1)H-(1)H double-quantum (DQ), and (1)H-(14)N D-HMQC correlation experiments, have been used. To support the interpretation of the experimental data, periodic density functional theory calculations together with the GIPAW approach have been used to calculate the (1)H and (13)C chemical shifts. It is found that the shifts calculated with two popular plane wave codes (CASTEP and Quantum ESPRESSO) are in excellent agreement with the experimental results.     

Formation, isolation, spectroscopic properties, and calculated properties of some isomers of C(60)H(36)

Isomers of C(60)H(36) and He@C(60)H(36) have been synthesized by the Birch or dihydroanthracene reduction of C(60) and isolated by preparative high-pressure liquid chromatography. (3)He, (13)C, and (1)H NMR spectroscopic properties were then determined. A comparison of experimental chemical shifts against those computed using density functional theory (B3LYP) with polarized triple- and double-zeta basis sets for He and C,H, respectively, allowed provisional assignment of structure for several isomers to be made. Theoretical calculations have also been carried out to identify low-energy structures. The transfer hydrogenation method using dihydroanthracene gives a major C(60)H(36) isomer and a minor C(60)H(36) isomer with C(3) symmetry as determined by the (13)C NMR spectrum of C(60)H(36) and the (3)He NMR spectrum of the corresponding sample of (3)He@C(60)H(36). In view of the HPLC retention times and the (3)He chemical shifts observed for the Birch and dihydroanthracene reduction products, the two isomers generated by the latter procedure can be only minor isomers of the Birch reduction. A significant energy barrier apparently exists in the dihydroanthracene reduction of C(60) for the conversion of the C(3) and C(1) symmetry isomers of C(60)H(36) to the T symmetry isomer previously predicted by many calculations to be among the most stable C(60)H(36) isomers. Many of the (1)H NMR signals exhibited by C(60)H(36) (and C(60)H(18), previously reported) are unusually deshielded compared to "ordinary" organic compounds, presumably because the unusual structures of C(60)H(36) and C(60)H(18) result in chemical shift tensors with one or more unusual principal values. Calculations clearly show a relationship between exceptionally deshielded protons beta to a benzene ring in C(60)H(18) and C(60)H(36) and relatively long C-C bonds associated with these protons. The additional information obtained from 1D and 2D (1)H NMR spectra obtained at ultrahigh field strengths (up to 900 MHz) will serve as a critical test of chemical shifts to be obtained from future calculations on different C(60)H(36) isomers.     

Investigation of structure, vibrational and NMR spectra of oxycodone and naltrexone: a combined experimental and theoretical study

In this work, two important opioid antagonists, naltrexone and oxycodone, were prepared from thebaine and were characterized by IR, (1)H NMR and (13)C NMR spectroscopy. Moreover, computational NMR and IR parameters were obtained using density functional theory (DFT) at B3LYP/6-311++G** level of theory. Complete NMR and vibrational assignment were carried out using the observed and calculated spectra. The IR frequencies and NMR chemical shifts, determined experimentally, were compared with those obtained theoretically from DFT calculations, showed good agreements. The RMS errors observed between experimental and calculated data for the IR absorptions are 85 and 105 cm(-1), for the (1)H NMR peaks are 0.87 and 0.17 ppm and for those of (13)C NMR are 5.6 and 5.3 ppm, respectively for naltrexone and oxycodone.     

Theoretical prediction and assignment of vicinal 1H-1H coupling constants of diastereomeric 3-alkoxy-6,7-epoxy-2-oxabicyclo[3.3.0]octanes

Spin-spin coupling constants between nuclei in NMR spectroscopy reflect their spatial arrangement. A number of calculation methods, applying different levels of theory, have been developed to support the stereochemical assignment of novel compounds. Nevertheless, revisions of the assignment of structures in the literature are not rare. In the present work, the reliability of the calculation methods amenable for a theoretical prediction of spin-spin coupling constants of vicinal protons to support correct stereochemical assignment of substitution at five-membered rings of 3-alkoxy-6,7-epoxy-2-oxabicyclo[3.3.0]octanes was studied. Experimental (3)J(H,H) coupling constants were compared with the coupling constants calculated for all possible diastereomers. The fully quantum chemical approach provided theoretical (3)J(H,H) coupling constants with an absolute deviation of no more than 1.1 Hz for 91% of the experimentally studied coupled spins, whereas the methods without quantum chemical geometry optimization resulted in completely unreliable predictions. Consequently, for a reliable stereochemical assignment of small and medium size molecules, the protocol for calculating the coupling constants based on the results of the quantum chemical geometry optimization is recommended.     

Analysis of a cycloheptenone derivative: an experimental and theoretical approach

A detailed analysis with total assignment of (1)H and (13)C NMR spectral data for a cycloheptenone derivative, a key intermediate for the synthesis of perhydroazulene terpenoids, is related. These assignments are based on 1D (1)H and (13)C NMR and on 2D NMR techniques including gCOSY, gHSQC, gHMBC, J-resolved and NOEDIF experiments. The unequivocal assignments were supported by theoretical chemical shifts and scalar coupling constant calculations at GIAO B3LYP/cc-pVDZ level from optimized structures at the same level of theory.     

DFT and AIM study of the protonation of nitrous acid and the pKa of nitrous acidium ion

The gas phase and aqueous thermochemistry, NMR chemical shifts, and the topology of chemical bonding of nitrous acid (HONO) and nitrous acidium ion (H(2)ONO(+)) have been investigated by ab initio methods using density functional theory. By the same methods, the dissociation of H(2)ONO(+) to give the nitrosonium ion (NO(+)) and water has also been investigated. We have used Becke's hybrid functional (B3LYP), and geometry optimizations were performed with the 6-311++G(d,p) basis set. In addition, highly accurate ab initio composite methods (G3 and CBS-Q) were used. Solvation energies were calculated using the conductor-like polarizable continuum model, CPCM, at the B3LYP/6-311++G(d,p) level of theory, with the UAKS cavity model. The pK(a) value of H(2)ONO(+) was calculated using two different schemes: the direct method and the proton exchange method. The calculated pK(a) values at different levels of theory range from -9.4 to -15.6, showing that H(2)ONO(+) is a strong acid (i.e., HONO is only a weak base). The equilibrium constant, K(R), for protonation of nitrous acid followed by dissociation to give NO(+) and H(2)O has also been calculated using the same methodologies. The pK(R) value calculated by the G3 and CBS-QB3 methods is in best (and satisfactory) agreement with experimental results, which allows us to narrow down the likely value of the pK(a) of H(2)ONO(+) to about -10, a value appreciably more acidic than literature values.