Structure validation of natural products by quantum-mechanical GIAO calculations of 13C NMR chemical shifts

Geometry optimization and GIAO (gauge including atomic orbitals) (13)C NMR chemical shift calculations at Hartree-Fock level, using the 6-31G(d) basis set, are proposed as a tool to be applied in the structural characterization of new organic compounds, thus providing useful support in the interpretation of experimental NMR data. Parameters related to linear correlation plots of computed versus experimental (13)C NMR chemical shifts for fourteen low-polar natural products, containing 10-20 carbon atoms, were employed to assess the reliability of the proposed structures. A comparison with the hybrid B3LYP method was carried out to evaluate electron correlation contributions to the calculation of (13)C NMR chemical shifts and, eventually, to extend the applicability of such computational methods to the interpretation of NMR spectra in apolar solutions. The method was tested by studying three examples of revised structure assignments, analyzing how the theoretical (13)C chemical shifts of both correct and incorrect structures matched the experimental data.     

Molecular structure, IR and NMR spectra of 2,6 distyrylpyridine by density functional theory and ab initio Hartree-Fock calculations

Vibrational frequencies and gauge including atomic orbital (GIAO) 13C NMR and 1H NMR chemical shift values of 2,6 distyrylpyridine (C21H17N) in the ground state have been calculated by using the Hartree-Fock (HF) and density functional method (B3LYP) with 6-31G(d) basis set. These methods are proposed as a tool to be applied in the structural characterization of 2,6 distyrylpyridine (C21H17N). The title compound has C2v point group, thus providing useful support in the interpretation of experimental IR data. In addition, obtained results were related to the linear correlation plot of experimental 13C NMR, 1H NMR chemical shifts values and IR data.     

Simple method for identification of skeletons of aporphine alkaloids from 13C NMR data using artificial neural networks

This paper describes the use of artificial neural networks as a theoretical tool in the structural determination of alkaloids from (13)C NMR chemical shift data, aiming to identify skeletal types of those compounds. For that, 162 aporphine alkaloids belonging to 12 different skeletons were codified with their respective (13)C NMR chemical shifts. Each skeleton pertaining to aporphine alkaloid type was used as output, and the (13)C NMR chemical shifts were used as input data of the net. Analyzing the obtained results, one can then affirm the skeleton to which each one of these compounds belongs with high degree of confidence (over 97%). The relation between the correlation coefficient and the number of epochs and the architecture of net (3-layer MLP or 4-layer MLP) were analyzed, too. The analysis showed that the results predicted by the 3-layer MLP networks trained with a number of the epochs higher than 900 epochs are the best ones. The artificial neural nets were shown to be a simple and efficient tool to solve structural elucidation problems making use of (13)C NMR chemical shift data, even when a similarity between the searched skeletons occurs, offering fast and accurate results to identification of skeletons of organic compounds.     

非对映异构体~（13）C NMR化学位移不等性研究

合成了８对非对映异构体酰胺，测定了它们的~（１３）Ｃ　ＮＭＲ化学位移值和相应的非对映异构体基团的化学位移差。根据实验数据提出一种分子优势构象与~（１３）Ｃ　ＮＭＲ化学位移不等性的相关模型。     

Determining valine side-chain rotamer conformations in proteins from methyl 13C chemical shifts: application to the 360 kDa half-proteasome

A method is presented for determining Val side-chain χ(1) rotamer distributions in proteins based exclusively on measured (13)C(γ1) and (13)C(γ2) chemical shifts. The approach selects an ensemble of 20 χ(1) values, calculates average methyl (13)C(γ1,γ2) chemical shifts via theoretical quantum chemical calculations and maximizes the agreement with the experimentally measured shifts using a genetic algorithm. The methodology is validated with an application involving six proteins for which (13)C(γ) chemical shifts and three-bond methyl-backbone scalar couplings are available. The utility of the methodology is demonstrated with an application to the 360 kDa 'half-proteasome' where the χ(1) rotameric distributions of Val residues are calculated on the basis of chemical shifts. For the most part the χ(1) profiles so obtained compare very well with those generated from the high-resolution (2.3 ?) X-ray structure of the proteasome. Both NMR and X-ray distributions are cross-validated by comparing calculated (1)H-(13)C methyl residual dipolar couplings with measured values, and the level of agreement is at least as good for the NMR derived χ(1) values. Notably, as the resolution of the X-ray data improves (rotamer distributions from 3.4 and 2.3 ? X-ray structures are compared with the NMR data), the agreement with the NMR gets significantly better. This emphasizes the importance of NMR approaches for the study of high molecular weight complexes that can be recalcitrant to high resolution X-ray analysis.     

Solid-state NMR yields structural constraints on the V3 loop from HIV-1 Gp120 bound to the 447-52D antibody Fv fragment

Solid-state NMR measurements were performed on the complex of an 18-residue peptide derived from the V3 loop sequence of the gp120 envelope glycoprotein of the HIV-1 MN strain with Fv fragments of the human anti-gp120 monoclonal antibody 447-52D in a frozen glycerol/water solution. The peptide was uniformly (15)N- and (13)C-labeled in a 7-residue segment containing the conserved GPGR motif in the epitope. (15)N and (13)C NMR chemical shift assignments for the labeled segment were obtained from two-dimensional (13)C-(13)C and (15)N-(13)C magic-angle spinning NMR spectra. Reductions in (13)C NMR line widths and changes in chemical shifts upon complex formation indicate the adoption of a well-defined, antibody-dependent structure. Intramolecular (13)C-(13)C distances in the complex, which constrain the peptide backbone and side chain conformations in the GPGR motif, were determined from an analysis of rotational resonance (RR) data. Structural constraints from chemical shifts and RR measurements are in good agreement with recent solution NMR and crystallographic studies of this system, although differences regarding structural ordering of certain peptide side chains are noted. These experiments explore and help delineate the utility of solid state NMR techniques as structural probes of peptide/protein complexes in general, potentially including membrane-associated hormone/receptor complexes.     

Complete assignments of (1)H and (13)C NMR spectroscopic data for two new triterpenoid saponins from Ilex pernyi

Ilexpernoside A and ilexpernoside B, two new pentacyclic C(4)-nortriterpenoid saponins, were isolated from the leaves of Ilex pernyi Franch. Their chemical structures were determined by MS, NMR spectroscopy and chemical analysis. Complete assignments of the (1)H and (13)C NMR spectroscopic data were achieved by 1D and 2D NMR experiments (HSQC, HMBC, (1)H-(1)H COSY and NOESY).     

Conformational state of benzilidene aniline derivatives from ab initio calculation and NMR spectroscopy data

Quantum chemical calculations of the structure and conformational state of a number of Shiff bases have been performed. ¹³C NMR spectra of investigated molecules were calculated and compared with experimental data to test verification of the used calculation model. The effect of terminal substituents on the conformation of azomethines and a relation between the conformation and ¹³C NMR chemical shift were examined.     

1H and 13C NMR chemical shift assignments of spiro-cycloalkylidenehomo- and methanofullerenes by the DFT-GIAO method

The (1)H and (13)C NMR chemical shifts of spiro-cycloalkylidene[60]fullerenes were assigned using experimental NMR data and the Density Functional Theory (DFT)-Gauge Independence Of Atomic Orbitals method (GAIO) calculation method in the Perdew Burke Ernzerhof (PBE)/3z approach. The calculated values of the (13)C NMR chemical shifts adequately reproduce the experimental values at this quantum chemistry approach. Similar assignments will be helpful for (13)C NMR spectral analysis of homo- and methano[60]fullerene derivatives for structure elucidation and to determine the influence of fullerene frames on substituents and the influence of substituents on fullerene cores.     

1H and 13C NMR spectral assignment of androstane derivatives

(1)H and (13)C NMR spectroscopic data for 5alpha-androstanes and halo-5alpha-androstanes with different substituents at positions C-3, C-9, C-11 and C-17 were examined and assigned by a combination of 1D and 2D NMR experiments. The substituent effects on the (13)C chemical shifts were compared with those of epi-androsterone, used as a reference compound. The coupling constants (n)J((19)F,(13)C) were measured for compounds 6, 8, 11 and 14.     

Use of 13C NMR spectrometric data to produce a predictive model of estrogen receptor binding activity

We have developed a spectroscopic data-activity relationship (SDAR) model based on 13C NMR spectral data for 30 estrogenic chemicals whose relative binding affinities (RBA) are available for the alpha (ERalpha) and beta (ERbeta) estrogen receptors. The SDAR models segregated the 30 compounds into strong and medium binding affinities. The SDAR model gave a leave-one-out (LOO) cross-validation of 90%. Two compounds that were classified incorrectly in the SDAR model were in the transition zone between classifications. Real and predicted 13C NMR chemical shifts were used with test compounds to evaluate the predictive behavior of the SDAR model. The 13C NMR SDAR model using predicted 13C NMR data for the test compounds provides a rapid, reliable, and simple way to screen whether a compound binds to the estrogen receptors.     

X-ray photoelectron spectra and structure of 2-(2-phenylhydrazono) acetoacetanilide

2-(2-Phenylhydrazono)acetoacetanilide, itsN-methyl derivatives, and model compounds were studied by X-ray photoelectron spectroscopy. The chemical shifts were obtained from the¹³C NMR spectra. A correlation between the calculated charges, the binding energies on N atoms, and the¹³C NMR chemical shifts was found. The analysis of the XPS data and the¹³C NMR chemical shifts led to the conclusion that crystalline 2-(2-phenylhydrazono)acetoacetanilide exists mainly in the oxo hydrazone form. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 3, pp. 488–491, March, 1999.     

The alkali cation effect on the 1H NMR chemical shifts of the indenyl carbanion

The complex character of the temperature dependence of the ¹H NMR chemical shifts of indenyl-lithium and -sodium in dimethoxyethane is explained. It is shown that the cation causes a polarisation of the C? H bonds and thus influences the proton shifts of the anion, both directly by its electric field along the bonds (the direct effect) and indirectly via its effect on the π-electron distribution (the indirect effect). The indirect effect is inferred from ¹³C NMR chemical shift data. By subtracting the temperature dependent contribution of the indirect effect from the experimental ¹H data, the direct effect is visualised. It appears that information on ion paris obtained by ¹H and ¹³C NMR on the one hand and optical spectroscopy on the other hand is complementary. Apparently, aggregation of ion pairs does not seriously affect the chemical shift data.     

1H and 13C NMR assignments for two new angular furanocoumarin glycosides from Peucedanum praeruptorum

Two novel angular-type furanocoumarin glycosides, peucedanoside A (1) and peucedanoside B (2), along with a known compound apterin (3), were isolated from the roots of Peucedanum praeruptorum Dunn. Their chemical structures were determined by MS, NMR spectroscopy and chemical analysis. Complete assignments of the 1H and 13C NMR spectroscopic data were achieved by 1D and 2D NMR experiments including DEPT, HSQC, HMBC and ROESY.     

Determination of the relative stereochemistry of flexible organic compounds by Ab initio methods: conformational analysis and Boltzmann-averaged GIAO 13C NMR chemical shifts

Ab initio calculations at the Hartree-Fock level with full-geometry optimization using the 6-31G(d) basis set, and GIAO (gauge including atomic orbitals) (13)C NMR chemical shifts, are presented here as a support in the study of the stereochemistry of low-polar organic compounds having an open-chain structure. Four linear stereoisomers, fragments of a natural product previously characterized by experimental (13)C NMR spectra, which possesses three stereogenic centers, 11 carbon atoms, and 38 atoms in total, were considered. Conformational searches, by empirical force-field molecular dynamics, pointed out the existence of 8-13 relevant conformers per stereoisomer. Thermochemical calculations at the ab initio level in the harmonic approximation of the vibrational modes, allowed the evaluation, at 298.15 K, of the standard Gibbs free energy of the conformers. The (13)C NMR chemical shift of a given carbon atom in each stereoisomer was considered as the average chemical shift value of the same atom in the different conformers. The averages were obtained by the Boltzmann distribution, using the relative standard free energies as weighting factors. Computed parameters related to linear correlation plots of experimental (13)C chemical shifts versus the corresponding computed average data allowed us to distinguish among the four stereoisomers.     

Calculation of the 13C magnetic shielding in cyclopentadienyl complexes by eliminating effects due to charge

A method for estimating the contributions of different factors to the ¹³C NMR chemical shifts of a ligand has been proposed which is based on elimination of the charge effect and a determination of the combined effect of the remaining factors (the coordination effect). This enabled the authors to establish a relationship between the ¹³C NMR data and the chemical properties of cyclopentadienyl metal compounds.     

Complete assignments of 1H and 13C NMR spectroscopic data for two new triterpenoid saponins from Ilex hainanensis

Two novel unsaturated E-ring pentacyclic triterpenoid saponins, ilexhainanoside A and ilexhainanoside B, were isolated from the leaves of Ilex hainanensis. Their chemical structures were determined by MS, NMR spectroscopy and chemical analysis. Complete assignments of the 1H and 13C NMR spectroscopic data were achieved by 1D and 2D NMR experiments (HSQC, HMBC, ROESY and 1H-1H COSY).     

Frequency dependence of nuclear magnetic resonance parameters in poly(methyl methacrylate)

Using 26 NMR spectrometers, the Research Group on NMR, the Society of Polymer Science, Japan observed the ¹H NMR chemical shift, resolution, and signal intensity; ¹³C NMR chemical shift, resolution, and signal intensity; the effect from initiator fragment signal; ¹H spin-lattice relaxation times; ¹³C spin-lattice relaxation times; and ¹³C nuclear Overhauser enhancement of radically polymerized poly(methyl methacrylate). Excellent reliability was found after comparison between the data from different spectrometers. Molecular motion of this polymer was analyzed with a term of 3τ model.     

(s)-多沙唑嗪的核磁共振理论和实验研究

报道了(s)-多沙唑嗪的1H、13C、DEPT、1H-1H COSY等的NMR波谱数据, 并对1H、13C NMR信号进行了指认. (s)-多沙唑嗪分子中含有9个季碳原子, 其中绝大部分通过常规实验的方法难以指认. 应用量子化学规范不变原子轨道(GIAO)的Becke-3-Lee-Yang-Parr(B3LYP)和Hartree-Fock(HF)方法, 分别在6-21G基组下计算了标题化合物的13C NMR化学位移值. 计算结果表明, 理论计算数据与实验结果吻合较好, 可以帮助对(s)-多沙唑嗪季碳原子NMR位移信号进行指认.     

Novel methods of automated structure elucidation based on 13C NMR spectroscopy

Three new approaches for automated structure elucidations of organic molecules using NMR spectroscopic data were introduced recently. These approaches apply a neural network 13C NMR chemical shift prediction method to rank the results of structure generators by their agreement of the predicted and experimental chemical shifts. These three existing implementations are compared using realistic example molecules. The applicability and reliability of such approaches is addressed.