Fast determination of 13C NMR chemical shifts using artificial neural networks

Nine different artificial neural networks were trained with the spherically encoded chemical environments of more than 500000 carbon atoms to predict their 13C NMR chemical shifts. Based on these results the PC-program "C_shift" was developed which allows the calculation of the 13C NMR spectra of any proposed molecular structure consisting of the covalently bonded elements C, H, N, O, P, S and the halogens. Results were obtained with a mean deviation as low as 1.8 ppm; this accuracy is equivalent to a determination on the basis of a large database but, in a time as short as known from increment calculations, was demonstrated exemplary using the natural agent epothilone A. The artificial neural networks allow simultaneously a precise and fast prediction of a large number of 13C NMR spectra, as needed for high throughput NMR and screening of a substance or spectra libraries.     

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.     

Automated structure elucidation of organic molecules from (13)c NMR spectra using genetic algorithms and neural networks.

The automated structure elucidation of organic molecules from experimentally obtained properties is extended by an entirely new approach. A genetic algorithm is implemented that uses molecular constitution structures as individuals. With this approach, the structure of organic molecules can be optimized to meet experimental criteria, if in addition a fast and accurate method for the prediction of the used physical or chemical features is available. This is demonstrated using (13)C NMR spectrum as readily obtainable information. (13)C NMR chemical shift, intensity, and multiplicity information is available from (13)C NMR DEPT spectra. By means of artificial neural networks a fast and accurate method for calculating the (13)C NMR spectrum of the generated structures exists. The approach is limited by the size of the constitutional space that has to be searched and by the accuracy of the shift prediction for the unknown substance. The method is implemented and tested successfully for organic molecules with up to 20 non-hydrogen atoms.     

Application of Artificial Neural Networks for Analysis of 13C NMR Spectra of Fucoidans

A new approach for structure determination of native and O-desulfated fucoidans by the analysis of their ¹³C NMR spectra by artificial neural networks (ANNs) is described. Two ANN models were studied: the simple three-layer feed-forward network, which employs supervised learning, and the adaptive resonance theory (ART) network with unsupervised learning. Training sets for the networks were constructed using chemical shifts of synthetic oligofucosides. The results obtained demonstrate that both models worked better in the case of desulfated fucoidans, while the ART-type networks gave better results in sulfated (native) fucoidan structure elucidation.     

Automatic assignment of absolute configuration from 1D NMR data

[reaction: see text] Opposite enantiomers exhibit different NMR properties in the presence of an external common chiral element, and a chiral molecule exhibits different NMR properties in the presence of external enantiomeric chiral elements. Automatic prediction of such differences, and comparison with experimental values, leads to the assignment of the absolute configuration. Here two cases are reported, one using a dataset of 80 chiral secondary alcohols esterified with (R)-MTPA and the corresponding (1)H NMR chemical shifts and the other with 94 (13)C NMR chemical shifts of chiral secondary alcohols in two enantiomeric chiral solvents. For the first application, counterpropagation neural networks were trained to predict the sign of the difference between chemical shifts of opposite stereoisomers. The neural networks were trained to process the chirality code of the alcohol as the input, and to give the NMR property as the output. In the second application, similar neural networks were employed, but the property to predict was the difference of chemical shifts in the two enantiomeric solvents. For independent test sets of 20 objects, 100% correct predictions were obtained in both applications concerning the sign of the chemical shifts differences. Additionally, with the second dataset, the difference of chemical shifts in the two enantiomeric solvents was quantitatively predicted, yielding r(2) 0.936 for the test set between the predicted and experimental values.     

Interpretation of substituent effects on 13C and 15N NMR chemical shifts in 6-substituted purines

A range of purine derivatives modified at position 6 of the basic purine skeleton exhibit a variety of biological activities. Several derivatives are used or tested nowadays for pharmacological treatments. The present work aims to analyze the effects of substituents on the electron distribution in the purine core as reflected by NMR chemical shifts. We collected a comprehensive set of experimental NMR data for a variety of 6-substituted purines (-NH(2), -NHMe, -NMe(2), -OMe, -Me, -CCH, and -CN) and determined the molecular and crystal structures of three derivatives (-NHMe, -CCH, and -CN) by X-ray diffraction. The density-functional methods calibrated in our recent study (Phys. Chem. Chem. Phys., 2010, 12, 5126) have been employed to enable understanding of the substituent-induced changes in the NMR chemical shifts of the atoms in the purine skeleton. Analyses of the nuclear shielding using localized molecular orbitals (LMOs), specifically the natural LMOs (NLMOs) and Pipek-Mezey LMOs, were used to break down the values of the isotropic (13)C and (15)N NMR chemical shifts and the chemical shift tensors into the contributions of the individual LMOs. The experimental and calculated trends in the chemical shift of the N-3 atom correlate nicely with the Hammett constants (σ(para)) and the calculated natural charges on N-3, whereas the contributions of the LMOs to the N-1 and C-6 chemical shifts are found to be more complex.     

Selective separation of structure-related alkaloids in Rhizoma coptidis with "click" binaphthyl stationary phase and their structural elucidation with liquid chromatography-mass spectrometry

It is a new task to separate structure-related compounds into a fraction according to their structural characteristics in a complex traditional Chinese medicine (TCM). This method makes separation of the components of the sample simple and structural elucidation easy. In this study, selective separation of alkaloids in Rhizoma coptidis was realized on a "click" binaphthyl column possessing a planar conjugate structure. Three kinds of alkaloids, aporphine, tetrahydroprotoberberine and protoberberine in Rhizoma coptidis showed better retention than other compounds by virtue of π-π interactions with the stationary phase. Moreover, the "click" binaphthyl column could distinguish the aporphine and tetrahydroprotoberberine alkaloids possessing two benzene rings from the protoberberine alkaloids possessing three benzene rings. After separating on the "click" binaphthyl column, the fractions containing the alkaloids were collected and then analyzed with liquid chromatography-mass spectrometry (LC-MS). Totally, 23 alkaloids were identified, and among these alkaloids, three tetrahydroprotoberberine, two aporphine and seven protoberberine alkaloids were first found in Rhizoma coptidis. These newly found alkaloids are minor compounds, and they are always neglected without eliminating the interference of compounds in large amounts by pre-separation on the "click" binaphthyl column. The typical fragmentation pathways of each class of alkaloids were summarized to illustrate their structures. In the MS(2) spectrum, the loss of a molecule of dimethylamine ((CH(3))(2)NH) was observed as the characteristic loss of aporphine alkaloids. All the tetrahydroprotoberberine alkaloids would undergo the Retro-Diels-Alder (RDA) fragmentation reaction in the MS(2) fragmentation. For protoberberine alkaloids, different characteristic fragmentations were observed with different skeleton structures.     

Density functional theory study of 13C NMR chemical shift of chlorinated compounds

The use of the standard density functional theory (DFT) leads to an overestimation of the paramagnetic contribution and underestimation of the shielding constants, especially for chlorinated carbon nuclei. For that reason, the predictions of chlorinated compounds often yield too high chemical shift values. In this study, the WC04 functional is shown to be capable of reducing the overestimation of the chemical shift of Cl‐bonded carbons in standard DFT functionals and to show a good performance in the prediction of ¹³C NMR chemical shifts of chlorinated organic compounds. The capability is attributed to the minimization of the contributions that intensively increase the chemical shift in the WC04. Extensive computations and analyses were performed to search for the optimal procedure for WC04. The B3LYP and mPW1PW91 standard functionals were also used to evaluate the performance. Through detailed comparisons between the basis set effects and the solvent effects on the results, the gas‐phase GIAO/WC04/6‐311+G(2d,p)//B3LYP/6‐31+G(d,p) was found to be specifically suitable for the prediction of ¹³C NMR chemical shifts of chlorides in both chlorinated and non‐chlorinated carbons. Further tests with eight molecules in the probe set sufficiently confirmed that WC04 was undoubtedly effective for accurately predicting ¹³C NMR chemical shifts of chlorinated organic compounds. Copyright © 2012 John Wiley & Sons, Ltd.     

The 1H and 13C NMR chemical shifts of Strychnos alkaloids revisited at the DFT level

The density functional theory calculation of ¹H and ¹³C NMR chemical shifts in a series of ten 10 classically known Strychnos alkaloids with a strychnine skeleton was performed at the PBE0/pcSseg-2//pcseg-2 level. It was found that calculated ¹H and ¹³C NMR chemical shifts provided a markedly good correlation with experiment characterized by a mean absolute error of 0.08 ppm in the range of 7 ppm for protons and 1.67 ppm in the range of 150 ppm for carbons, so that a mean absolute percentage error was as small as ~1% in both cases.     

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.     

Application of the multi-standard methodology for calculating 1H NMR chemical shifts

Gauge including atomic orbitals (GIAO) (1)H NMR chemical shift calculations have been performed for 66 organic compounds at 72 different levels of theory using the multi-standard approach (MSTD) previously developed for (13)C NMR. This straightforward computational technique involves the combination of methanol and benzene as standards. The studied methodology has been shown to predict (1)H NMR chemical shifts efficiently at different levels of theory.     

Isolation and Structural Characterization of New,Highly Functionalized Diterpenes from Euphorbia serrulata

Five new diterpene polyesters, 1 – 5 , with jatrophane skeletons were isolated from the fresh whole plants of Euphorbia serrulata. The structure elucidation was performed by means of UV/VIS spectroscopy, HR‐ESI‐MS, and advanced two‐dimensional NMR methods, including ¹H‐NMR, JMOD, ¹H,¹H‐COSY, NOESY, HMQC, and HMBC experiments. The relative configurations of 1 – 5 and their conformations in solution were analyzed on the basis of NOESY measurements. As a result of detailed NMR studies, complete ¹H and ¹³C chemical‐shift assignments of the compounds were possible. The isolated compounds differ stereochemically and do not comprise a uniform series regarding the configurations at C(2), C(6), and C(13). Compound 5 possesses the new structural feature of a double bond with (Z)‐configuration in the macrocyclic ring of the jatrophane skeleton, while compound 2 has a C?C bond in the five‐membered ring, this being the first observation of this structural feature in the type of macrocyclic Euphorbiaceae diterpenes.     

二萜生物碱的~(13)C核磁共振谱

本文通过对186个二萜生物碱及其衍生物的~(13)C NMR谱数据的分析比较,就以下几方面作了归纳总结:①信号归属的方法;②常见取代基OCH_3、NCH_3、、NCH_2CH_3、OCOCH_3、的化学位移范围;③季碳和某些特定碳的化学位移规律。某些特定结构,如C_(20)二萜生物碱中的噁唑烷环以及C_(20)差向异构体等的~(13)C NMR谱特征;④C_(19)二萜生物碱中不同位置上取代基(H→OH、H→OMe、OH→OAc、OH→OMe、OH→C=O)效应和立体化学效应。这些归纳总结有助于此类化合物结构的阐明。     

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.     

Chemistry of the SO Bond. 8—A stereochemical investigation of some methyl-substituted trimethylene sulphites (1,3,2-Dioxathian 2-Oxides) via 13C nuclear magnetic resonance

¹³C NMR chemical shifts for trimethylene sulphite and 35 derivatives are presented. From the magnitudes of the β shifts it has been possible to establish chemical shift additivity relationships for a series of compounds. The results are discussed in terms of probable conformations in solution.     

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.     

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.