NMR spectra, GIAO and charge density calculations of five-membered aromatic heterocycles

The B3LYP/6-31+G(d) molecular geometry optimized structures of 17 five-membered heterocycles were employed together with the gauge including atomic orbitals (GIAO) density functional theory (DFT) method at the B3LYP/6-31+G(d,p), B3LYP/6-311++G(d,p) and B3LYP/6-311+G(2d,p) levels of theory for the calculation of proton and carbon chemicals shifts and coupling constants. The method of geometry optimization for pyrrole (1), N-methylpyrrole (2) and thiophene (7) using the larger 6-311++G(d,p) basis sets at the B3LYP/6-31+G(d,p), B3LYP/6-311++G(d,p), B3LYP/6-31+G(2d,p) and B3LYP/cc-pVTZ levels of theory gave little difference between calculated and experimental values of coupling constants. In general, the (1)H and 13C chemical shifts for all compounds are in good agreement with theoretical calculations using the smaller 6-31 basis set. The values of nJHH(n=3, 4, 5) and rmnJ(CH)(n=1, 2, 3, 4) were predicted well using the larger 6-31+G(d,p) and 6-311++G(d,p) basis sets and at the B3LYP/6-31+G(d,p), B3LYP/6-311++G(d,p), B3LYP/6-31+G(2d,2p) levels of theory. The computed atomic charges [Mülliken; Natural Bond Orbital Analysis (NBO); Merz-Kollman (MK); CHELP and CHELPG] for the B3LYP/6-311++G(d,p) geometry optimized structures of 1-17 were used to explore correlations with the experimental proton and carbon chemical shifts.     

GIAO DFT 13C/15N chemical shifts in regioisomeric structure determination of fused pyrazoles

The combined use of two‐dimensional NMR correlation experiments and gauge including atomic orbital density functional theory in ¹³C NMR chemical shift (CS) calculations allowed reliable and simple structural determination of regioisomeric heterocyclic systems that originate from the reactions of acylquinolinones with substituted hydrazines. Moreover, the results of differential analysis between the calculated ¹⁵N NMR CSs for hypothetical structures and the experimental data of the title azaheterocyclic systems were even more advantageous with respect to ¹³C because there was no need for correlational analysis: structures of the regioisomeric compounds could be determined just by direct comparison. Copyright © 2010 John Wiley & Sons, Ltd.     

Determination of substitution sites in monosubstituted five-membered aromatic heterocycles

Similar magnitudes of proton-proton couplings across three, four, and five bonds and proton-carbon couplings across two and three bonds combined with difficult to predict substituent effects make the results of an indiscriminate use of routine (COSY, HSQC, HMBC, etc.) techniques for substitution site determination in C-monosubstituted five-membered heteroaromatics suspect. As demonstrated on two examples of natural products, the use of 1,1-ADEQUATE leads to unambiguous substitution site determination lending thus further support to suggested inclusion of 1,1-ADEQUATE data into computer-assisted structure elucidation (CASE) protocols.     

Structural studies on aryl‐substituted enaminoketones and their thio analogues. Part I. Analysis of high‐resolution 1H, 13C NMR and 13C CP MAS spectra combined with GIAO‐DFT calculations

A series of aryl‐substituted enaminoketones and their thio analogues in CDCl₃ solution and in the solid state were studied by the use of high‐resolution ¹H and ¹³C as well as ¹³C cross polarization magic angle spinning (CP MAS) NMR spectra in combination with gauge including atomic orbitals‐density functional theory (GIAO‐DFT) calculations performed at the B3PW91/6–311 + + G(d,p) level of theory using the B3PW91/6‐311 + + G(d,p)‐optimized geometries. The analysis of the ¹³C NMR spectra in solution was done by using the Incredible Natural Abundance DoublE QUAntum Transfer Experiment (INADEQUATE) technique, whereas trends observed in the ¹³C shielding constants, calculated for the compounds studied, were a great help in assigning most of the signals in the ¹³C CP MAS NMR spectra. It was established on the basis of the experimental and theoretical NMR data that both groups of compounds exist in the form of Z‐s‐Z‐s‐E isomers in CDCl₃ solution as well as in the solid state, with the NH hydrogen atom involved in intramolecular hydrogen bonding. This conclusion is in agreement with the fact that some of the compounds studied reveal liquid‐crystalline properties. Three‐bond H, H and C, H coupling constants measured in solution played a crucial role in the structure elucidation. Copyright © 2009 John Wiley & Sons, Ltd.     

On the configuration of five-membered rings: a spin-spin coupling constant approach

Five-membered rings are clearly among the most common structural motifs found in chemistry and biology. Nevertheless, the configuration of conformationally mobile five-membered rings is often difficult to assign from nuclear magnetic resonance (NMR) data. A simple, reliable, and efficient approach for the stereochemical analysis of five-membered rings based on the measurement of NMR coupling constants is presented. Density functional theory calculations using representative conformations of the full conformational space available to rings with different substitution patterns were used to identify differences between the accessible coupling constant values for cis and trans relative orientations of the substituents. The calculations were assessed experimentally using NMR data obtained from a number of models. This approach can be easily used to analyze different five-membered rings, such as oxolanes, cyclopentanes, furanosides and pyrrolidines, and their relative configuration can be determined without the need for making further conformational considerations.     

Structural elucidation of dioxa‐cage compounds from tetrahydroisobenzofuran‐1(3H)‐one: analysis of NMR data and GIAO chemical shifts calculations

The polycyclic compounds, especially the dioxa‐cages, have attracted considerable attention in recent years. In our work, a series of 9β‐substituted 3‐oxo‐4,11‐dioxatetracyclo[5.2.1.1^5,8.0^2,6]undecane compounds were unexpectedly isolated during bromination, chlorination and epoxidation reactions of the 3‐hydroxy‐3a,4,7,7a‐tetrahydro‐4,7‐methanoisobenzofuran‐1(3H)‐one. After careful analysis of the NMR data, the chemical shifts of the isolated and the expected products were predicted by theoretical calculations using density functional theory and gauge including atomic orbitals. The best correlation between calculated and experimental data was evaluated by comparing mean absolute errors and applying DP4 probability methodology. Results from both approaches indicated a correct structural elucidation. Copyright © 2016 John Wiley & Sons, Ltd.     

Substituent effects on 13C chemical shifts of ketenimines: a GIAO/HF and DFT study

GIAO/HF and DFT methods were utilized to predict the ¹³C chemical shifts of substituted ketenimines. GIAO HF/6–311+G(2d,p) and B3LYP/6–311+G(2d,p) methods were applied on the optimized B3LYP/6–31G(d) geometries and ¹³C chemical shifts of C_α and C_β of substituted ketenimines were correlated with group electronegativities. HF and DFT calculations indicated that increasing substituent group electronegativity leads to increasing chemical shift of C_β of substituted ketenimines, whereas the C_α values decrease. Copyright © 2003 John Wiley & Sons, Ltd.     

Pronounced stereospecificity of 1H, 13C, 15N and 77Se shielding constants in the selenophenyl oximes as shown by NMR spectroscopy and GIAO calculations

In the ¹H and ¹³C NMR spectra of 1‐(2‐selenophenyl)‐1‐alkanone oximes, the ¹H, the ¹³C‐3 and ¹³C‐5 signals of the selenophene ring are shifted by 0.1–0.4, 2.5–3.0 and 5.5–6.0 ppm, respectively, to higher frequencies, whereas those of the ¹³C‐1, ¹³C‐2 and ¹³C‐4 carbons are shifted by 4–5, ～11 and ～1.7 ppm to lower frequencies on going from the E to Z isomer. The ¹⁵N chemical shift of the oximic nitrogen is larger by 13–16 ppm in the E isomer relative to the Z isomer. An extraordinarily large difference (above 90 ppm) between the ⁷⁷Se resonance positions is revealed in the studied oxime isomers, the ⁷⁷Se peak being shifted to higher frequencies in the Z isomer. The trends in the changes of the measured chemical shifts are well reproduced by the GIAO calculations of the ¹H, ¹³C, ¹⁵N and ⁷⁷Se shielding constants in the energy‐favorable conformation with the syn orientation of the? C?N? O? H group relative to the selenophene ring. Copyright © 2009 John Wiley & Sons, Ltd.     

GIAO/DFT evaluation of 13C NMR chemical shifts of selected acetals based on DFT optimized geometries

DFT/B3LYP calculations of the ground-state conformation of eight cyclic and acyclic acetals are presented and compared with experimental data. Results of single-point GIAO/DFT calculations at five different levels of theory show that isotropic shieldings need to be empirically scaled to achieve agreement with experimental chemical shifts. Statistical evaluation of data indicates that the most accurate prediction of 13C chemical shifts is achieved at the MPW1PW91/6-311G** level of theory. An empirical equation describing the relationship between delta values and shielding constants is postulated. This equation has been applied to the non-chair ground-state conformation of the six-membered acetonide and to the conformationally flexible benzodioxonine derivative. The agreement observed between the experimental and predicted chemical shifts shows that calculations at the MPW1PW91/6-311G** level of theory are adequate for addressing questions of conformation.     

Solid-state NMR studies and DFT calculations of flavonoids: baicalein, baicalin and wogonoside

Three flavonoids of pharmaceutical importance-baicalein, baicalin, and wogonoside-were isolated from a Chinese medicinal plant Scutellaria baicalensis Georgi and studied by 13C NMR in solution and solid state. Two-dimensional (2D) NMR spectroscopy in the liquid phase and dipolar dephasing (DD) experiments in magic-angle spinning (MAS) spectra enabled the assignment of 13C resonances. The cross-polarization (CP) time constants T(CH) and relaxation times T(H) (1rho) were obtained from the variable-contact time experiments. The principal elements of the 13C chemical shift tensor were determined in the spectra recorded under slow sample spinning (2 kHz) using phase-adjusted spinning sideband (PASS)-2D NMR technique, and were verified by density functional theory gauge-independent atomic orbital (DFT GIAO) calculations of shielding constants. Analysis of the 13C delta(ii) and comparison with shielding parameters calculated for different conformers of compounds 1-3 enabled the selection of the most reliable geometry in the solid phase. In all three compounds, an intramolecular hydrogen bond C5--OH...=C4 is formed; the existence of baicalein and baicalin with 'anticlockwise' orientation of OH groups is more probable.     

Structural study of oxalamide compounds: H, C, and DFT calculations

The conformational properties of some N-alkyl, N,N′-dialky, and tetraalkyloxalamides have been investigated, in vacuo and in solvent using DFT methods at the B3LYP/6-31G^∗∗ computational level. Special emphasis has been given on oxalamides with substituents of the type -CH₂CH₂OH. In oxalamides with the N-H group (N-alkyl and N,N′-dialky), the most stable conformations are those in which the oxalamide moiety adopts a planar s-trans arrangement and the amide bonds are trans. A different situation appears in the case of tetraalkyloxalamides, in which the oxalamide moiety always adopts a skewed arrangement and there are conformations with similar energy. A careful study of ¹³C and ¹H NMR spectra together with theoretical calculations (GIAO method) allowed the assignment of the signals of these conformers. The presence of the -CH₂CH₂OH chain produces numerous rotamers. The most stable rotamers, in vacuo, are those with strong intramolecular hydrogen bonds, however in solvent, hydrogen bonds are not crucial to establish the most stable specie and depend on the solvent used.     

Comparative analysis of 13C shielding constants stereospecificity in the silicon and germanium derivatives of acetylenic aldehyde and ketone oximes based on the 13C NMR spectroscopy and GIAO calculations

In the acetylenic aldehyde oximes with substituents containing silicon and germanium, the ¹³C NMR signal of the C‐2 carbon of triple bond is shifted by 3.5 ppm to lower frequency and that of the C‐3 carbon is moved by 7 ppm to higher frequency on going from E to Z isomer. A greater low‐frequency effect of 5.5 ppm on the C‐2 carbon signal and a greater high‐frequency effect of 11 ppm on the C‐3 carbon signal are observed in the analogous acetylenic ketone oximes. The carbon chemical shift of the C?N bond is larger by 4 ppm in E isomer relative to Z isomer for the aldehyde and ketone oximes. The ²⁹Si chemical shifts in the silicon containing acetylenic aldehyde and ketone oximes are almost the same for the diverse isomers. The trends in changes of the measured chemical shifts are well reproduced by the gauge‐including atomic orbital (GIAO) calculations of the ¹³C and ²⁹Si shielding constants. Copyright © 2009 John Wiley & Sons, Ltd.     

GIAO/DFT studies on 1,2,4‐triazole‐5‐thiones and their propargyl derivatives

Density functional theory (DFT)/Becke–Lee–Yang–Parr (B3LYP) and gauge‐including atomic orbital (GIAO) calculations were performed on a number of 1,2,4‐triazole derivatives, and the optimized structural parameters were employed to ascertain the nature of their predominant tautomers. ¹³C and ¹⁵N NMR chemical shifts of 3‐substituted 1,2,4‐triazole‐5‐thiones and their propargylated derivatives were calculated via GIAO/DFT approach at the B3LYP level of theory with geometry optimization using a 6‐311++G** basis set. A good agreement between theoretical and experimental ¹³C and ¹⁵N NMR chemical shifts could be found for the systems investigated. The data generated were useful in predicting ¹⁵N chemical shifts of all the nitrogen atoms of the triazole ring, some of which could not be obtained in solution state ¹⁵N HMBC/HSQC NMR measurements. The energy profile computed for the dipropargylated derivatives was found to follow the product distribution profile of regioisomers formed during propargylation of 1,2,4‐triazole thiones. Copyright © 2013 John Wiley & Sons, Ltd.     

Conformational analysis of cis‐3, 5‐dioxa‐bicyclo[5.4.0]undecane and its 4‐substituted derivatives by DNMR,molecular modeling,and GIAO/DFT methods

Temperature‐dependent ¹H and ¹³C‐NMR spectra of the title compounds are presented. Coalescence effects are discussed and assigned to dynamic process—the interconversion of bicyclic system. The free energies of activation covered the range 39–52 kJ/mol. The dioxepane ring adopts twist‐chair (TC) conformation. GIAO/DFT calculation of isotropic shieldings for the set of low‐energy conformations showed that only one conformer is present at 298 K in solution that matched well with experimental data. Copyright © 2010 John Wiley & Sons, Ltd.     

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.     

3D Heteronuclear long‐range 1H–13C scalar correlation at natural abundance: application to oligosaccharide analysis

A 3D ¹H–¹³C–¹H refocused INEPT transfer experiment is proposed in which the initial coherence transfer of ¹H longitudinal to ¹³C transverse magnetization is tuned to the long‐range ¹H, ¹³C couplings while the reverse INEPT component transfers the magnetization to the directly bonded ¹H. Integration of a constant time ¹H evolution period into the long‐range coherence transfer interval provides absorption mode signals for each dimension. A ¹³C purge component at the beginning of the sequence selects for ¹²C‐bound ¹H magnetization that is then transferred to a ¹³C‐bound hydrogen, thus strongly suppressing the diagonal signals. This experiment is expected to be of particular value for situations in which resonance overlap in the ¹³C dimension renders 2D long‐range heteronuclear correlation data ambiguous. In combination with a diagonal‐suppressed 3D ¹H–¹³C–¹H TOCSY‐HSQC experiment, complete assignment of the ring resonances of the Lewis‐b hexasaccharide was obtained on a 4.2 mM sample using a conventional 500 MHz probe (0.1% ethylbenzene signal‐to‐noise ratio of 600), suggesting its applicability to sub‐millimolar samples using cryoprobe technology. Copyright © 2002 John Wiley & Sons, Ltd.     

Configurational analysis of the natural product passifloricin A by quantum mechanical C NMR GIAO chemical shift calculations

Quantum chemical calculations at mPW1PW91 level, with full geometry optimization, using the 6-31g(d) basis set, and GIAO (gauge including atomic orbitals) ¹³C NMR chemical shifts using the 6-31g(d,p) basis set, are here utilized as a support to define the configurational features of the natural product passifloricin A, whose previously proposed relative configuration has been recently shown, by synthetic studies, to be incorrect. This study suggests that the relative stereostructure for passifloricin A corresponds to the δ-lactone of the (5R,7R,9S,11R)-tetrahydroxyhexacos-2-enoic acid.     

DFT and NMR parameterized conformation of valeranone

A Monte Carlo random search using molecular mechanics, followed by geometry optimization of each minimum energy structure employing density functional theory (DFT) calculations at the B3LYP/6-31G* level and a Boltzmann analysis of the total energies, generated accurate molecular models which describe the conformational behavior of the antispasmodic bicyclic sesquiterpene valeranone (1). The theoretical H-C-C-H dihedral angles gave the corresponding 1H, 1H vicinal coupling constants using a generalized Karplus-type equation. In turn, the 3J(H,H) values were used as initial input data for the spectral simulation of 1, which after iteration provided an excellent correlation with the experimental 1H NMR spectrum. The calculated 3J(H,H) values closely predicted the experimental values, excepting the coupling constant between the axial hydrogen alpha to the carbonyl group and the equatorial hydrogen beta to the carbonyl group (J(2beta, 3beta)). The difference is explained in terms of the electron density distribution found in the highest occupied molecular orbital (HOMO) of 1. The simulated spectrum, together with 2D NMR experiments, allowed the total assignment of the 1H and 13C NMR spectra of 1.     

DFT/NMR integrated approach: a valid support to the total synthesis of chiral molecules

The analysis of the configuration of kedarcidin chromophore and palau'amine through quantum chemical calculation of Js and chemical shifts suggests a fast and convenient quantum chemical approach that can be applied prior to proceeding to the total synthesis of complex natural compounds in order to avoid loss of time and resources employed in the total synthesis of wrong diastereoisomers.