Automated structure verification based on a combination of 1D (1)H NMR and 2D (1)H - (13)C HSQC spectra

A method for structure validation based on the simultaneous analysis of a 1D (1)H NMR and 2D (1)H - (13)C single-bond correlation spectrum such as HSQC or HMQC is presented here. When compared with the validation of a structure by a 1D (1)H NMR spectrum alone, the advantage of including a 2D HSQC spectrum in structure validation is that it adds not only the information of (13)C shifts, but also which proton shifts they are directly coupled to, and an indication of which methylene protons are diastereotopic. The lack of corresponding peaks in the 2D spectrum that appear in the 1D (1)H spectrum, also gives a clear picture of which protons are attached to heteroatoms. For all these benefits, combined NMR verification was expected and found by all metrics to be superior to validation by 1D (1)H NMR alone. Using multiple real-life data sets of chemical structures and the corresponding 1D and 2D data, it was possible to unambiguously identify at least 90% of the correct structures. As part of this test, challenging incorrect structures, mostly regioisomers, were also matched with each spectrum set. For these incorrect structures, the false positive rate was observed as low as 6%.     

Automated compound verification using 2D-NMR HSQC data in an open-access environment

Since the introduction of NMR prediction software, medicinal chemists have imagined submitting their compounds to corporate compound registration systems that would ultimately display a simplified pass/fail result. We initially implemented such a system based on HPLC and liquid chromatography mass spectrometry (LCMS) data that is embedded within our industry standard sample submission and registration process. By using gradient-heteronuclear single quantum coherence (HSQC) experiments, we have extended this concept to NMR data through a comparison of experimentally acquired data against predicted (1)H and (13)C NMR data. Integration of our compound registration system with our analytical instruments now provides our chemists unattended and automated NMR verification for collections of submitted compounds. The benefits achieved from automated processing and interpretation of results produced enhanced confidence in our compound library and released the chemists from the tedium of manipulating large amounts of data. This allows scientists to focus more of their attention to the drug discovery process.     

Automated structure verification based on 1H NMR prediction

A unique opportunity exists when an experimental NMR spectrum is obtained for which a specific chemical structure is anticipated. A process of Verification--the confirmation of a postulated structure--is now possible, as opposed to Elucidation-the de novo determination of a structure. A method for automated structure verification is suggested, which compares the chemical shifts, intensities and multiplicities of signals in an experimental 1H NMR spectrum with those from a predicted spectrum for the proposed structure. A match factor (MF) is produced and used to classify the spectrum-structure match into one of three categories, correct, ambiguous, or incorrect. The verification result is also augmented by the spectrum assignment obtained as part of the verification process. This method was tested on a set of synthetic spectra and several sets of experimental spectra, all of which were automatically prepared from raw data. Taking into account even the most problematic structures, with many labile protons present and poor prediction accuracy, 50% of all spectra can still be automatically verified without any false positives or negatives. In a blind test on a typical set of data, it is shown that fewer than 31% of the structures would need manual evaluation. This means that a system is possible whereby 69% of the spectra are prepared and evaluated automatically, and never need to be seen or evaluated by a human.     

Automatic compatibility tests of HSQC NMR spectra with proposed structures of chemical compounds

A recently introduced similarity measure is extended here for comparing two-dimensional spectra. Its applicability is demonstrated with heteronuclear single-quantum correlation (HSQC) NMR spectra. For testing the compatibility of a spectrum with the proposed chemical structure, first, the spectrum is predicted on the basis of that structure and then, the proposed comparison algorithm is applied. In this context, the topics of optimization are peak picking, signal intensity measures, and optimizing the parameters of the two-dimensional comparison method. The performance is analyzed with a test set of 289 structures of organic compounds and their HSQC and ¹H NMR spectra. The results obtained with HSQC spectra are better than those achieved using the previously described one-dimensional similarity test with ¹H NMR spectra alone.     

Application of Hadamard spectroscopy to automated structure verification in high‐throughput NMR

Combined verification using 1‐D proton and HSQC has been proved to be quite successful; the acquisition time of HSQC spectra, however, can be limiting in its high‐throughput applications. The replacement with Hadamard HSQC can significantly enhance the throughput. We hereby propose a protocol to optimize the grouping of the predicted carbon chemical shifts from the proposed structure and the associated Hadamard frequencies and bandwidths. The resulting Hadamard HSQC spectra compare favorably with their Fourier‐transformed counterparts, and have demonstrated to perform equivalently in terms of combined verification, but with several fold enhancement in throughput, as illustrated for 21 commercial available molecules and 16 prototypical drug compounds. Further improvement of the verification accuracy can be achieved by the cross validation from Hadamard TOCSY, which can be acquired without much sacrifice in throughput. Copyright © 2009 John Wiley & Sons, Ltd.     

Towards the automatic analysis of NMR spectra: part 6. Confirmation of chemical structure employing both 1H and 13C NMR spectra

A method of comparing predicted and experimental chemical shifts was used to confirm or refute postulated structures. 1H NMR spectra returned all true positives with a false positive rate of 4%. When an analogous procedure was adopted for 13C NMR spectra, the false positive rate dropped to 1%, whereas the more practical HSQC data yielded a false positive rate of 2%. If the HSQC results were combined with 1H results, a false positive rate of 1% resulted, 4 times more accurate than 1H alone.     

Structural determination of two new steroidal saponins from Smilax china

Two new steroidal saponins (1 and 2) were isolated from the BuOH fraction of the 70% EtOH extract of the tubes of Smilax china, together with four known analogues, 3–6. The structures of the new compounds were elucidated by means of chemical evidence and spectroscopic analyses, including HR‐MS, IR, ¹H‐ and ¹³C‐NMR, and 2D experiments (¹H–¹H COSY, HSQC and HMBC). Copyright © 2009 John Wiley & Sons, Ltd.     

Cucurbitane Glycosides from Siraitia grosvenorii

Systematic phytochemical studies of the extract of Luo Han Go (Siraitia grosvenorii) furnished six known cucurbitane glycosides, namely, mogrosides IVa, mogrosides V and VI, isomogroside V, 11-oxomogroside V, and siamenoside I. The structures of all the isolated compounds were characterized on the basis of extensive spectral and chemical studies. Though the partial NMR spectral data has been reported for some of the isolated compounds previously, the complete ¹H and ¹³C NMR spectral assignments of all the isolated compounds are reported herewith for the first time based on COSY, HSQC, HMBC, and NOESY spectroscopic data.     

Branched polyphenylenes and phenylene dendrimers: NMR and optical studies

Two branched polyphenylenes with 1,3,5-triphenylbenzene as branching centers were synthesized together with a family of phenylene cyclotrimers as model compounds. On the basis of the NMR analysis, specifically ¹H NMR, ¹³C NMR and 2D heteronuclear correlation experiments (HSQC and HMBC) of model compounds, the huge number of overlapping signals in the polymer spectra are attributed to aromatic protons and carbon atoms of the branched phenylene structure. The comparison with absorption spectra of linear model compounds clearly shows that the polymer optical properties depend on the length of the segments between the branching cores. This result strongly supports the proposed NMR assignment proving that the combination of the two techniques is a powerful tool for unveiling complex branched structures.     

1H, 13C and 15N NMR spectroscopic characterization of unexpected degradation products of the nifedipine analogue bis(2‐cyanoethyl) 2,6‐dimethyl‐4‐(2‐nitrophenyl)‐1,4‐dihydro‐3,5‐pyridinedicarboxylate

In the course of saponification experiments with bis(2‐cyanoethyl) 2,6‐dimethyl‐4‐(2‐nitrophenyl)‐1,4‐dihydro‐3,5‐pyridinedicarboxylate ( 1 ), an analogue of the calcium channel blocker nifedipine, three unexpected degradation products were isolated. The compounds were identified as 3‐(2‐acetamido‐1‐carboxy‐1‐propenyl)‐1‐hydroxy‐2‐indolecarboxylic acid ( 3 ), 9‐hydroxy‐1,3‐dimethyl‐β‐carboline‐4‐carboxylic acid ( 4 ) and 6‐hydroxy‐2,4‐dimethyl‐5‐oxo‐5,6‐dihydrobenzo[c][2,7]naphthyridine‐1‐carboxylic acid ( 6 ). The structures of these compounds were deduced from one‐ and two‐dimensional ¹H, ¹³C and natural abundance ¹⁵N NMR experiments (¹H,¹H‐COSY, gs‐HSQC, gs‐HMBC, ¹⁵N gs‐HMBC), and corroborated by comparison of their NMR data with the respective data for structurally similar compounds. Copyright © 2002 John Wiley & Sons, Ltd.     

Micromelosides A–D,four new coumarins from the stem bark of Micromelum falcatum

Four new coumarins, micromelosides A–D, together with four known coumarins were isolated from the stem bark of Micromelum falcatum. The complete assignments of the ¹H and ¹³C NMR chemical shifts for these new compounds were achieved by means of 1D and 2D NMR techniques, including ¹H‐¹H COSY, HSQC, HMBC and NOE difference. Copyright © 2009 John Wiley & Sons, Ltd.     

Complete assignment of the 1H and 13C NMR spectra of antimicrobial 4‐arylamino‐ 3‐nitrocoumarin derivatives

Herein, we describe the synthesis and complete assignment of the ¹H and ¹³C NMR chemical shifts of a series of antimicrobial 4‐arylamino‐3‐nitrocoumarin derivatives based on a combination of ¹H and ¹³C NMR, ¹H‐¹H‐COSY, NOESY, HSQC and HMBC experiments. Conformational effects upon the chemical shifts of the coumarin moiety arising from the anisotropy of the aryl side group are briefly discussed. This study provides the first complete and fully assigned NMR data for this important group of antimicrobial compounds and bridges the gap existing in the literature with regard to NMR structural data for 4‐arylamino‐3‐nitrocoumarins. Copyright © 2010 John Wiley & Sons, Ltd.     

Structure determination of selaginellins G and H from Selaginella pulvinata by NMR spectroscopy

Selaginellins G ( 1 ) and H ( 2 ), two new selaginellin derivatives, were isolated from the whole plant of Selaginella pulvinata. Their structures were elucidated, and complete assignments of the ¹H and ¹³C NMR spectroscopic data were achieved by 1D and 2D NMR experiments (HSQC, HMBC, COSY and ROESY). Compound 1 displayed good antifungal activity against Candida albicans with an IC₅₀ value of 5.3 µg/ml. Copyright © 2010 John Wiley & Sons, Ltd.     

Unequivocal total assignment of 13C and 1H NMR spectra of some pyrido[1,2‐a]pyrimidine derivatives by 2D‐NMR

We report the total assignments of the ¹³C and ¹H NMR spectra of some 4‐methyl‐2‐oxo‐(2H)‐pyrido[1,2‐a]pyrimidine and 2‐methyl‐4‐oxo‐(4H)‐pyrido[1,2‐a]pyrimidine derivatives. The products were characterized by ¹H and ¹³C NMR and reported data for similar compounds. No comparative data for the two sets of isomeric compounds with respect to ¹³C and ¹H NMR have been reported to date. We made some detailed studies of the 2D NMR spectra of these compounds and observed that assignments made for non‐protonated carbon atoms by us and those reported in the literature for similar compounds need correction. The revised assignments were made on the basis of heteronuclear single quantum correlation (HSQC) and heteronuclear multiple bond correlation (HMBC) techniques. Copyright © 2003 John Wiley & Sons, Ltd.     

Complete assignments of 1H and 13C NMR data for two new sesquiterpenes from Cyperus rotundus L.

Two new sesquiterpenes, epi‐guaidiol A (1) and sugebiol (3), together with four known sesquiterpenes, guaidiol A(2), sugetriol triacetate (4), cyperenoic acid (5), and cyperotundone (6) were isolated from the rhizomes of Cyperus rotundus L. Their structures were identified by MS and NMR experiments, and the complete assignments of ¹H and ¹³C NMR data for two new sesquiterpenes were obtained by the aid of two‐dimensional (2D) NMR techniques, including HSQC, HMBC, ¹H‐¹HCOSY and nuclear overhauser enhancement spectroscopy(NOESY). Copyright © 2009 John Wiley & Sons, Ltd.     

Synthesis of novel steroids bearing a spirochromene side chain by BF3·Et2O catalyzed aldol condensation of spirostane sapogenins and salicylaldehyde

Treatment of a CH₂Cl₂ solution of sarsasapogenin acetate with salicylaldehyde and BF₃·Et₂O afforded a mixture of two C-22 epimeric steroids bearing a spirochromene moiety in the side chain. The elucidation of the structures of the new compounds were carried out employing a combination of 1D and 2D NMR techniques that includes ¹H, ¹³C, HSQC, HMBC, COSY and NOESY.     

Isolation and structure elucidation of two new compounds from artemisia Ordosica Krasch

Abstract

Two new compounds, namely arteordoyn A (1) and arteordoyn B (2), together with four known compounds, were isolated from the petroleum ether extract of Artemisia ordosica Krasch. The structures elucidation of 1 and 2 were carried out by 1D-NMR (¹H and ¹³C NMR), 2D-NMR (COSY, HSQC, HMBC and NOESY) and HR-ESI-MS spectral analysis.     

Complete assignments of 1H and 13C NMR data of three new dihydrophenanthrofurans from Pleione yunnanensis

Three new dihydrophenanthrofurans, pleionesins A–C (1–3), together with two known dihydrophenanthrenes (4–5) were isolated from the tubers of Pleione yunnanensis (Rolfe). The complete ¹H and ¹³C NMR spectra assignments of these compounds were carried out using 1D and 2D NMR experiments (¹H, ¹³C, selective 1D NOE, HSQC and HMBC). Copyright © 2010 John Wiley & Sons, Ltd.     

NMR Studies of a Series of Shikimic Acid Derivatives

The investigations of the ¹H and ¹³C resonances of a series of 9 shikimic acid derivatives were carried out using one‐ and two‐dimensional methods. ¹H and ¹³C spectral data were assigned by DEPT, ¹H‐¹H COSY, HSQC, HMBC, and the stereo configuration was confirmed by 1D selective NOESY experiments.     

New Flavanol Glucosides from Abacopteris aspera (Presl) Ching

Three new flavanol glycosides, 1 – 3 , and eight known compounds, 4 – 11 , were isolated from a MeOH extract of the fern Abacopteris aspera (Presl ) Ching . Their structures were elucidated on the basis of extensive spectroscopic analysis, including HSQC, HMBC, ¹H,¹H‐COSY, and NOESY experiments, acid hydrolysis, and by the comparison of their NMR data with those of related compounds.