1H and 13C NMR spectra of Strychnos alkaloids: Selected NMR updates

The PBE0/pcSseg-2//pcseg-2 calculations of ¹H and ¹³C NMR chemical shifts were performed for a classical series of 12 Strychnos alkaloids (except for the earlier studied parent strychnine), namely akuammicine, isostrychnine, rosibiline, tsilanine, spermostrychnine, diaboline, cyclostrychnine, henningsamide, strychnosilidine, strychnobrasiline, holstiine, and icajine. It was found that the calculated ¹H and ¹³C NMR chemical shifts show markedly good correlations with available experimental data, as characterized by a mean absolute error of 0.22 ppm for the range of 8 ppm for protons and 1.97 ppm for the range of 180 ppm for carbons. Complementarily, the present results provide essential NMR update and fill a gap in the NMR data of this distinguished group of vitally important natural products.     

Computational NMR of natural products: On the way to super large molecules exemplified with alasmontamine A

¹H and ¹³C nuclear magnetic resonance (NMR) chemical shifts of a tetrakis monoterpene indole alkaloid alasmontamine A with a molecular formula of C₈₄H₉₁N₈O₁₂ have been calculated at the PBE0/pcSseg-2//pcseg-2 level of theory on M06-2X/aug-cc-pVDZ geometry. In the course of the preliminary conformational search, six true minimum energy conformers were identified that can contribute to the actual conformation of this huge alkaloid. Calculated chemical shifts generally demonstrated a good agreement with available experimental data characterized with a corrected mean absolute error of 0.10 ppm for the range of about 7 ppm for protons and 1.1 ppm for the range of about 160 ppm for carbons.     

DFT computational schemes for 1H and 13C NMR chemical shifts of natural products,exemplified by strychnine

A number of computational schemes based on different Density Functional Theory (DFT) functionals in combination with a number of basis sets were tested in the calculation of ¹H and ¹³C NMR chemical shifts of strychnine, as a typical representative of the vitally important natural products, and used as a challenging benchmark and a rigorous test for such calculations. It was found that the most accurate computational scheme, as compared with experiment, was PBE0/pcSseg-4//pcseg-3 characterized by a mean absolute error of 0.07 ppm for the range of about 7 ppm for ¹H NMR chemical shifts and that of only 1.13 ppm for ¹³C NMR chemical shifts spread over the range of about 150 ppm. For more practical purposes, including investigation of larger molecules from this series, a much more economical computational scheme, PBE0/pcSseg-2//pcseg-2, characterized by almost the same accuracy and much less computational demand, was recommended.     

Relativistic effect of iodine in <Superscript>13</Superscript>C NMR chemical shifts of iodomethanes from quantum chemical calculations within the framework of the full four-component relativistic Dirac—Coulomb scheme

¹³C NMR shielding constants (chemical shifts) of iodomethanes were calculated within the framework of the full four-component relativistic Dirac—Coulomb scheme. As the number of iodine atoms in the molecule increases, the relativistic counterpart of the ¹³C NMR chemical shift increases from a few tens to several hundreds of ppm. Calculations of ¹³C NMR chemical shifts of organoiodine compounds should be performed at the relativistic level using relativistic Dyall’s basis sets dyall.vXz and dyall.xvXz (x = a, c, ac, ae; X = 2, 3, 4) of at least triple-zeta quality or at the correlated non-relativistic level taking into account relativistic corrections. Solvent effects are not of prime importance; however, taking into account the solvent corrections causes the mean absolute error of determination of the ¹³C NMR chemical shifts to decrease by 1—2 ppm.     

Stereochemical dependence of substituent γ-effects in the 19F NMR shielding constants

The substituent α-, β-, and γ-effects of the elements of the second and third periods on ¹⁹F NMR chemical shifts are evaluated including the establishment of stereochemical dependence of γ-effect, the latter particularly important in stereochemical studies of fluorine-containing compounds. Benchmark calculations performed for a series of 32 simple inorganic fluorine-containing molecules demonstrated a markedly good correlation between calculated and experimental fluorine chemical shifts characterized by a mean absolute error of 22.5 ppm in the range of about 900 ppm, which corresponds to a 2.5% error in the percentage terms.     

Are there reliable DFT approaches for 13C NMR chemical shift predictions of fullerene C60 derivatives?

The relationships between experimental and theoretical ¹³C NMR chemical shifts of a pristine fullerene C₆₀, monoadducts from [2 + n] cycloaddition (n = 1–3), and one [2 + 1] bis‐adduct are systematically analyzed for the first time by using diverse quantum‐chemical levels of theory. These levels involved B3LYP, B3PW91, B97‐2, mPW1PW91, PBE1PBE, and X3LYP hybrid functionals combined with 3‐21G, 6‐31G, 6‐31G(d), 6‐31G(d,p), 6‐31G(d,2p), LanL2DZ, and SDDAll basis sets. X3LYP/6‐31G approach is determined to have the lowest deviations from the ¹³C NMR experimental data compared to the other methods for all the fullerene compounds (mean absolute error value is 0.856 ppm and root mean squared error value is 1.197 ppm). The highest deviations are characteristic for α (sp² C2/C5/C8/C10) and β (sp² C6/C7/C11/C12) carbon atoms relative to a functionalization site and for those (sp³ C1/C9) directly attached with a side fragment in the [2 + n] monoadducts (n = 1–3). A probable reason of such deviation is that the approaches do not take into account a contribution of paramagnetic ring currents to ¹³C NMR chemical shifts. The results will be useful in design of novel fullerene derivatives and in performing unambiguous ¹³C NMR chemical shift assignments with modern quantum chemistry calculations.     

DFT computational schemes for 15N NMR chemical shifts of the condensed nitrogen-containing heterocycles

A systematic density functional theory (DFT) study of the accuracy factors (functionals, basis sets, and solvent effects) for the computation of ¹⁵N NMR chemical shifts has been performed in the series of condensed nitrogen-containing heterocycles. The behavior of the most representative functionals was examined based on the benchmark calculations of ¹⁵N NMR chemical shifts in the reference set of compounds. It was found that the best agreement with experiment was achieved with OLYP functional in combination with aug-pcS-3(N)//pc-2 locally dense basis set scheme providing mean absolute error of 5.2 ppm in the range of about 300 ppm. Taking into account solvent effects was performed within a general Tomasi's polarizable continuum model scheme. It was also found that computationally demanding supermolecular solvation model computations essentially improved some “difficult” cases, as was illustrated with phenanthroline dissolved in methanol. Based on the performed calculations, some 200 unknown ¹⁵N NMR chemical shifts were predicted with a high level of confidence for about 50 real-life condensed nitrogen-containing heterocycles, which could serve as a practical guide in structural elucidation of this class of compounds.     

MP2 calculation of 77Se NMR chemical shifts taking into account relativistic corrections

The main factors affecting the accuracy and computational cost of the Second‐order Möller‐Plesset perturbation theory (MP2) calculation of ⁷⁷Se NMR chemical shifts (methods and basis sets, relativistic corrections, and solvent effects) are addressed with a special emphasis on relativistic effects. For the latter, paramagnetic contribution (390–466 ppm) dominates over diamagnetic term (192–198 ppm) resulting in a total shielding relativistic correction of about 230–260 ppm (some 15% of the total values of selenium absolute shielding constants). Diamagnetic term is practically constant, while paramagnetic contribution spans over 70–80 ppm. In the ⁷⁷Se NMR chemical shifts scale, relativistic corrections are about 20–30 ppm (some 5% of the total values of selenium chemical shifts). Solvent effects evaluated within the polarizable continuum solvation model are of the same order of magnitude as relativistic corrections (about 5%). For the practical calculations of ⁷⁷Se NMR chemical shifts of the medium‐sized organoselenium compounds, the most efficient computational protocols employing relativistic Dyall's basis sets and taking into account relativistic and solvent corrections are suggested. The best result is characterized by a mean absolute error of 17 ppm for the span of ⁷⁷Se NMR chemical shifts reaching 2500 ppm resulting in a mean absolute percentage error of 0.7%. Copyright © 2015 John Wiley & Sons, Ltd.     

GIAO‐DFT calculation of 15N NMR chemical shifts of Schiff bases: Accuracy factors and protonation effects

¹⁵N NMR chemical shifts in the representative series of Schiff bases together with their protonated forms have been calculated at the density functional theory level in comparison with available experiment. A number of functionals and basis sets have been tested in terms of a better agreement with experiment. Complimentary to gas phase results, 2 solvation models, namely, a classical Tomasi's polarizable continuum model (PCM) and that in combination with an explicit inclusion of one molecule of solvent into calculation space to form supermolecule 1:1 (SM + PCM), were examined. Best results are achieved with PCM and SM + PCM models resulting in mean absolute errors of calculated ¹⁵N NMR chemical shifts in the whole series of neutral and protonated Schiff bases of accordingly 5.2 and 5.8 ppm as compared with 15.2 ppm in gas phase for the range of about 200 ppm. Noticeable protonation effects (exceeding 100 ppm) in protonated Schiff bases are rationalized in terms of a general natural bond orbital approach.     

Towards the versatile DFT and MP2 computational schemes for 31P NMR chemical shifts taking into account relativistic corrections

The main factors affecting the accuracy and computational cost of the calculation of ³¹P NMR chemical shifts in the representative series of organophosphorous compounds are examined at the density functional theory (DFT) and second‐order Møller–Plesset perturbation theory (MP2) levels. At the DFT level, the best functionals for the calculation of ³¹P NMR chemical shifts are those of Keal and Tozer, KT2 and KT3. Both at the DFT and MP2 levels, the most reliable basis sets are those of Jensen, pcS‐2 or larger, and those of Pople, 6‐311G(d,p) or larger. The reliable basis sets of Dunning's family are those of at least penta‐zeta quality that precludes their practical consideration. An encouraging finding is that basically, the locally dense basis set approach resulting in a dramatic decrease in computational cost is justified in the calculation of ³¹P NMR chemical shifts within the 1–2‐ppm error. Relativistic corrections to ³¹P NMR absolute shielding constants are of major importance reaching about 20–30 ppm (ca 7%) improving (not worsening!) the agreement of calculation with experiment. Further better agreement with the experiment by 1–2 ppm can be obtained by taking into account solvent effects within the integral equation formalism polarizable continuum model solvation scheme. We recommend the GIAO‐DFT‐KT2/pcS‐3//pcS‐2 scheme with relativistic corrections and solvent effects taken into account as the most versatile computational scheme for the calculation of ³¹P NMR chemical shifts characterized by a mean absolute error of ca 9 ppm in the range of 550 ppm. Copyright © 2014 John Wiley & Sons, Ltd.     

NMR-Spectroscopic Investigations of Potentially Planarized Nonafulvenes

¹H- and ¹³C-NMR spectra of nonafulvene 1e and nonafulvenes 2 and 3 have been assigned, high-resolution ¹H-NMR spectra of 2 (600 MHz, Fig. 3) and of 3 (400 MHz, Fig. 2) have been analyzed, and the data are compared with those of other nonafulvenes (Tables 1–6). Generally speaking, according to their spectroscopic behavior, four classes of nonafulvenes (A–D) may be distinguished (Fig. 1). The investigation shows that compounds 1e and 3 belong to class A, being characterized by ¹H-chemical shifts around 6 ppm, strongly alternating ³J(H,H) and ¹³C chemical shifts in the range of 123 to 130 ppm, thus existing in the olefinic form with a non-planar nine-membered ring. On the other hand, 2 is the first nonafulvene of class D, being characterized by ¹H chemical shifts in the aromatic range, large ³J(H,H) values of the same size, and ¹³C chemical shifts around 110 ppm. Since NMR parameters are virtually not influenced by temperature (?50° to 50°) or solvents, it is concluded that 2 exclusively exists in the dipolar structure 2 ^± with a planarized nine-membered ring. According to Fig. 4, these classes (and their spectroscopic data) are linked by 10,10-bis(dimethylamino)nonafulvene ( 1c ; and its temperature-dependent NMR parameters): for 1c , a temperature-dependent equilibrium 1c?1c ^± had earlier been established.     

On the accuracy of the GIAO‐DFT calculation of 15N NMR chemical shifts of the nitrogen‐containing heterocycles – a gateway to better agreement with experiment at lower computational cost

The main factors affecting the accuracy and computational cost of the gauge‐independent atomic orbital density functional theory (GIAO‐DFT) calculation of ¹⁵N NMR chemical shifts in the representative series of key nitrogen‐containing heterocycles – azoles and azines – have been systematically analyzed. In the calculation of ¹⁵N NMR chemical shifts, the best result has been achieved with the KT3 functional used in combination with Jensen's pcS‐3 basis set (GIAO‐DFT‐KT3/pcS‐3) resulting in the value of mean absolute error as small as 5 ppm for a range exceeding 270 ppm in a benchmark series of 23 compounds with an overall number of 41 different ¹⁵N NMR chemical shifts. Another essential finding is that basically, the application of the locally dense basis set approach is justified in the calculation of ¹⁵N NMR chemical shifts within the 3–4 ppm error that results in a dramatic decrease in computational cost. Based on the present data, we recommend GIAO‐DFT‐KT3/pcS‐3//pc‐2 as one of the most effective locally dense basis set schemes for the calculation of ¹⁵N NMR chemical shifts. Copyright © 2014 John Wiley & Sons, Ltd.     

The crystal and molecular structure of potassium aquapentachloroiridate(III) and the H, C, N NMR coordination shifts in iridium(III) chloride complexes with 2,2′-bipyridine or 1,10-phenanthroline

The crystal and molecular structure of potassium aquapentachloroiridate(III) (K₂[Ir(H₂O)Cl₅]) was reported. The [Ir(H₂O)Cl₅]²⁻ anions are nearly octahedral, the axial Ir–Cl bond (2.322(2) Å) being shorter than the equatorial ones (2.346(2)–2.360(2) Å); the Ir–O bond length is 2.090(4) Å. Ir(III) chloride complexes with 2,2′-bipyridine (LL = bpy) or 1,10-phenanthroline (LL = phen), of the general formulae K[Ir(LL)Cl₄] and cis-[Ir(LL)₂Cl₂]Cl, were studied by far-IR and ¹H–¹³C, ¹H–¹⁵N HMBC/HMQC/HSQC–NMR. High-frequency ¹H NMR coordination shifts (Δ^1H_coord = δ^1H_complex − δ^1H_ligand; max. ca. +1 ppm) were noted for [Ir(LL)Cl₄]⁻ anions, while for cis-[Ir(LL)₂Cl₂]⁺ cations they had variable sign and magnitude (max. ca. ±1 ppm); they were dependent on the proton position, being mostly expressed for the nitrogen-adjacent hydrogens (H(6) for bpy, H(2) for phen). ¹³C NMR signals were high-frequency shifted (by max. ca. 8 ppm), whereas all ¹⁵N nuclei were shifted to the lower frequency (by ca. 105–120 ppm). The experimental ¹H, ¹³C, ¹⁵N NMR chemical shifts were reproduced by semi-empirical quantum-chemical calculations (B3LYP/LanL2DZ+6-31G^**//B3LYP/LanL2DZ+6-31G*).     

Computation and structural elucidation of compounds formed via epoxide alcoholysis

Isobenzofuranones are known for their wide range of biological activities such as fungicide, insecticide, and anticancer. The search for novel bioactive compounds was performed by reaction of epoxide 2 with methanol, ethanol, propan-1-ol, propan-2-ol, and butan-1-ol. The mechanism for the stereoselective and stereospecific epoxide opening with methanol was reasoned by calculating the transition states for the two putative structures (rac)-3a and (rac)-3b. The compound (rac)-3a is the kinetic product as inferred from the lower energies of its transition state (TS1). The ¹H and ¹³C nuclear magnetic resonance (NMR) chemical shifts for these two candidate structures were calculated and compared with the experimental data using mean absolute error (MAE) and DP4 analyses. Therefore, the relative stereochemistry of (rac)-3a was established by the mechanism, MAE, and DP4 approaches. The hydroxyl group was acetylated to surpass the problem of signal overlapping of H5 and H6 in the ¹H NMR. The relative stereochemistry of the corresponding ester determined by NMR interpretation was in agreement with the structure of (rac)-3a.     

A direct hydrogen-1, carbon-13, and nitrogen-15 NMR study of lutetium(III)-isothiocyanate complexation in aqueous solvent mixtures

A direct, low-temperature hydrogen-1, carbon-13, and nitrogen-15 nuclear magnetic resonance study of lutetium(III)-isothiocyanate complex formation in aqueous solvent mixtures has been completed. At –100°C to –120°C in water-acetone-Freon mixtures, ligand exchange is slowed sufficiently to permit the observation of separate¹H,¹³C, and¹⁵N NMR signals for coordinated and free water and isothiocyanate ions. In the¹³C and¹⁵N spectra of NCS^–, resonance signals for five complexes are observed over the range of concentrations studied. The¹³C chemical shifts of complexed NCS^– varied from –0.5 ppm to –3 ppm from that of free anion. For the same complexes, the¹⁵N chemical shifts from free anion were about –11 ppm to –15 ppm. The magnitude and sign of the¹⁵N chemical shifts identified the nitrogen atom as the binding site in NCS^–. The concentration dependence of the¹³C and¹⁵N signal areas, and estimates of the fraction of anion bound at each NCS^–:Lu³⁺ mole ratio, were consistent with the formation of [(H₂O)₅Lu(NCS)]²⁺ through [(H₂O)Lu(NCS)₅]^2–. Although proton and/or ligand exchange and the resulting bulk-coordinated signal overlap prevented accurate hydration number measurements, a good qualitative correlation of the water¹H NMR spectral results with those of¹³C and¹⁵N was possible.     

NMR of heparin API: investigation of unidentified signals in the USP-specified range of 2.12–3.00 ppm

This article addresses the identification and quantification of the chemical species resulting in resonances at 2.17 and 2.25 ppm in the ¹H nuclear magnetic resonance (NMR) spectrum of pharmaceutical-grade heparin sodium. The NMR signals in question were first confirmed to arise from chemical moieties covalently attached to the heparin molecule through NMR diffusion experiments as well as chemical treatment of heparin active pharmaceutical ingredient (API) containing the resonances. The material responsible for the extra NMR signals was then demonstrated by NMR spiking studies to be something other than oversulfated chondroitin sulfate and was finally identified as an O-acetylation product of heparin through ¹³C labeling experiments with subsequent NMR analysis. The extent of O-acetylation was quantified using three orthogonal techniques: ¹H NMR, ion chromatography, and headspace gas chromatography/mass spectrometry. The results of this work showed good agreement between the three quantitative methods developed to analyze the signals in the United States Pharmacopeia-specified region of 2.12–3.00 ppm for heparin API.     

Synthesis and structural elucidation of a phthalide analog using NMR analysis and DFT calculations

Phtalides are secondary metabolites found in several fungi with a wide range of biological activities. A novel phthalide analog was synthesized by Diels–Alder reaction between cyclopentadiene and 3,4-dichlorofuran-2(5H)-one. Quantum mechanical calculations were used in conjunction with the spectrometric methods to determine the structure of the title compound. The calculated NMR chemical shifts for eight candidate pairs of enantiomers were compared with the experimental NMR chemical shifts applying the DP4 probability and mean absolute errors methodology. DP4 analysis using ¹H and ¹³C NMR chemical shifts without assignment of the signals presented 100% probability for the correct candidate structure 3d , proving the consistency of the method even without spectra interpretation. Results from theoretical calculation and NMR spectra interpretation were in agreement to the structure of rac-(3aR,4S,4aS,5R,8S,8aR,9R,9aS)-3a,9a-dichloro-3a,4,4a,5,8,8a,9,9a-octahydro-4,9:5,8-dimethanonaphtho[2,3-c]furan-1(3H)-one.     

QSAR studies of phenylhydrazine-substituted tetronic acid derivatives based on the 1H NMR and 13C NMR chemical shifts

The quantitative structure–activity relationship models of 40 phenylhydrazine-substituted tetronic acid derivatives were established between the ¹H nuclear magnetic resonance (NMR) and ¹³C NMR chemical shifts and the antifungal activity against Fusarium graminearum, Botrytis cinerea, Rhizoctonia cerealis, and Colletotrichum capsici. The models were validated by R, R², R_A², variance inflation factor, F, and P values testing and residual analysis. It was concluded from the models that the ¹³C NMR chemical shifts of C8, C10, C7, and the ¹H NMR chemical shifts of Ha contributed positively to the activity against Fusarium graminearum, Botrytis cinerea, Colletotrichum capsici, and Rhizoctonia cerealis, respectively. The models indicated that decreasing the election cloud density of specific nucleuses in compounds, for example, by the substituting of electron withdrawing groups, would improve the antifungal activity. These models demonstrated the practical application meaning of chemical shifts in the quantitative structure–activity relationship study. Furthermore, a practical guide was provided for further structural optimization of the antifungal phenylhydrazine-substituted tetronic acid derivatives based on the ¹H NMR and ¹³C NMR chemical shifts.