Structural Misassignment Research Articles

Observation of untoward 3 Jcc correlations in 1,1-ADEQUATE spectra of pyrimidine analogs: Avoiding potential interpretation pitfalls.

Recently, it has been reported that large n JCC correlations can sometimes be observed in 1,1-ADEQUATE spectra with significant intensity, which opens the possibility of structural misassignment. In this work, we have focused on pyrimidine-based compounds, which exhibit multiple bond correlations in the 1,1-ADEQUATE experiment as a consequence of 3 JCC coupling constants greater than 10Hz. Results are supported by both the experimental measurement of 3 JCC coupling constants in question using J-modulated-ADEQUATE and density functional theory calculations.

HUG and SQUEEZE: using CRYSTALS to incorporate resonant scattering in the SQUEEZE structure-factor contributions to determine absolute structure.

The resonant-scattering contributions to single-crystal X-ray diffraction data enable the absolute structure of crystalline materials to be determined. Crystal structures can be determined even if they contain considerably disordered regions because a correction is available via a discrete Fourier transform of the residual electron density to approximate the X-ray scattering from the disordered region. However, the corrected model cannot normally account for resonant scattering from atoms in the disordered region. Straightforward determination of absolute structure from crystals where the strongly resonantly scattering atoms are not resolved has therefore not been possible. Using an approximate resonant-scattering correction to the X-ray scattering from the disordered regions, we have developed and tested a procedure (HUG) to recover the absolute structure using conventional Flack x refinement or other post-refinement determination methods. Results show that in favourable cases the HUG method works well and the absolute structure can be correctly determined. It offers no useful improvement in cases where the original correction for the disordered region scattering density is problematic, for example, when a large fraction of the scattering density in the crystal is disordered, or when voids are not occupied equally by the disordered species. Crucially, however, if the approach does not work for a given structure, the statistics for the absolute structure measures are not improved, meaning it is unlikely to lead to misassignment of absolute structure.

Biomimetic Synthesis of Macahydantoins A and B from Lepidium meyenii, and Structure Revision of Macahydantoin B as a Class of Thiohydantoin with a 4-Methyl-hexahydropyrrolo[1,2-c]imidazole Skeleton.

Phytochemical investigation on Lepidium meyenii led to the discovery of macahydantoin C (3), a new thiohydantoin with a 1,3-diazabicyclo[3.3.1]nonane core, the spectral properties of which indicate a potential structural misassignment of its previously reported analogue, macahydantoin B (2a). To probe this hypothesis, a concise, scalable, and biomimetic synthesis of the originally proposed 2a and its revised structure (2b) was efficiently accomplished using the modified Edman degradation as the key step from commercially available materials in 65% (three steps) and 52% (three steps) overall yields, respectively. These synthetic endeavors undoubtedly reassigned the structure of macahydantoin B as an unreported type of thiohydantoin featuring a 4-methyl-hexahydropyrrolo[1,2-c]imidazole scaffold.

Application of Computational Chemical Shift Prediction Techniques to the Cereoanhydride Structure Problem-Carboxylate Complications.

Despite the vast array of techniques available to modern-day chemists, structural misassignments still occur. These misassignments are often only realized upon attempted synthesis, when the spectra of synthesized products do not match previously reported spectra. This was the case with marine natural product cereoanhydride. The originally proposed 7-membered ring anhydride (1) was shown to be incorrect, although a likely precursor to the correct structure (2) in both its laboratory synthesis and biosynthesis. Herein, in addition to showing how NMR computations could have been used to arrive at the correct structure, we show that the conversion of 1 to 2 is indeed energetically viable, and we highlight complications in predicting NMR chemical shifts for molecules with acidic protons.

First total synthesis of glabramycin B and revision of its relative configuration

Structural revision of glabramycin B, which is an antibacterial 10-membered lactone isolated from a fermentation broth of Neosartorya glabra, was achieved by enantioselective synthesis of our proposed structure. The correct structure of glabramycin B was presumed on comparison with related compounds, and synthesis of it was succeeded via dianion alkylation, Shiina's lactonization and Stille cross-coupling. By this synthesis, we were able to correct the reported structural misassignment, and to confirm the relative configuration of glabramycin B to be 10S*,11S*,15R*,20S*.

Total Synthesis and Structural Revision of the Cytotoxin Aruncin B.

The sodium salts E-15 and Z-15 of the originally proposed dihydropyran acid structure of aruncin B (1) were prepared through ring-closing alkene metathesis (RCM) and ethoxyselenation-selenoxide elimination, but acid sensitivity of these salts, together with inconsistencies in the spectral data, suggested a significant structural misassignment. A β-iodo Morita-Baylis-Hillman reaction to give Z-iodo ester 24, followed by Sonogashira cross-coupling-5-exo-dig lactonization, provided concise access to a Z-γ-alkylidenebutenolide 18, which possessed data corresponding to those originally reported for aruncin B.

Selecting the Most Appropriate NMR Experiment to Access Weak and/or Very Long-Range Heteronuclear Correlations.

Heteronuclear long-range NMR experiments are well established as essential NMR techniques for the structure elucidation of unknown natural products and small molecules. It is generally accepted that the absence of a given (n)JXH correlation in an HMBC or HSQMBC spectrum would automatically place the proton at least four bonds away from the carbon in question. This assumption can, however, be misleading in the case of a mismatch between the actual coupling constant and the delay used to optimize the experiment, which can lead to structural misassignments. Another scenario arises when an investigator, for whatever reason, needs to have access to very long-range correlations to confirm or refute a structure. In such cases, a conventional HMBC experiment will most likely fail to provide the requisite correlation, regardless of the delay optimization. Two recent methods for visualizing extremely weak or very long-range connectivities are the LR-HSQMBC and the HSQMBC-TOCSY experiments. Although they are intended to provide similar structural information, they utilize different transfer mechanisms, which differentiates the experiments, making each better suited for specific classes of compounds. In this report we have sought to examine the considerations implicit in choosing the best experiment to access weak or very long-range correlations for different types of molecules.

Toward Structural Correctness: Aquatolide and the Importance of 1D Proton NMR FID Archiving.

The revision of the structure of the sesquiterpene aquatolide from a bicyclo[2.2.0]hexane to a bicyclo[2.1.1]hexane structure using compelling NMR data, X-ray crystallography, and the recent confirmation via full synthesis exemplify that the achievement of “structural correctness” depends on the completeness of the experimental evidence. Archived FIDs and newly acquired aquatolide spectra demonstrate that archiving and rigorous interpretation of 1D 1H NMR data may enhance the reproducibility of (bio)chemical research and curb the growing trend of structural misassignments. Despite being the most accessible NMR experiment, 1D 1H spectra encode a wealth of information about bonds and molecular geometry that may be fully mined by 1H iterative full spin analysis (HiFSA). Fully characterized 1D 1H spectra are unideterminant for a given structure. The corresponding FIDs may be readily submitted with publications and collected in databases. Proton NMR spectra are indispensable for structural characterization even in conjunction with 2D data. Quantum interaction and linkage tables (QuILTs) are introduced for a more intuitive visualization of 1D J-coupling relationships, NOESY correlations, and heteronuclear experiments. Overall, this study represents a significant contribution to best practices in NMR-based structural analysis and dereplication.

NMR Structure Elucidation of Small Organic Molecules and Natural Products: Choosing ADEQUATE vs HMBC

Long-range heteronuclear shift correlation methods have served as the cornerstone of modern structure elucidation protocols for several decades. The (1)H-(13)C HMBC experiment provides a versatile and relatively sensitive means of establishing predominantly (3)J(CH) connectivity with the occasional (2)J(CH) or (4)J(CH) correlation being observed. The two-bond and four-bond outliers must be identified specifically to avoid spectral and/or structural misassignment. Despite the versatility and extensive applications of the HMBC experiment, it can still fail to elucidate structures of molecules that are highly proton-deficient, e.g., those that fall under the so-called "Crews rule". In such cases, recourse to the ADEQUATE experiments should be considered. Thus, a study was undertaken to facilitate better investigator understanding of situations where it might be beneficial to apply 1,1- or 1,n-ADEQUATE to proton-rich or proton-deficient molecules. Equipped with a better understanding of when a given experiment might be more likely to provide the necessary correlation data, investigators can make better decisions on when it might be advisible to employ one experiment over the other. Strychnine (1) and cervinomycin A2 (2) were employed as model compounds to represent proton-rich and proton-deficient classes of molecules, respectively. DFT methods were employed to calculate the relevant (n)J(CH) heteronuclear proton-carbon and (n)J(CC) homonuclear carbon-carbon coupling constants for this study.

Enantioselective Syntheses of the Proposed Structures of Kopeolin and Kopeolone

The first total syntheses of the proposed structures of kopeolin (1) and kopeolone (3) have been achieved from a common enantiopure chiral building block obtained by a chemoenzymatic enantioconvergent methodology. The syntheses feature two key steps: a one-pot reduction/diastereoselective protonation followed by a highly diastereoselective addition of an organocerate. The synthetic structures were fully characterized and all stereocenters were confirmed. The results show that the two previously reported structures were not assigned correctly, and suggest an initial structural misassignment during the isolation of the natural products. Thus, two revised structures, 1' for kopeolin and 3' for kopeolone, are proposed.

Synthesis of (-)-Muricatacin from Tri-O-acetyl-d-glucal

The total synthesis of (–)-muricatacin is achieved using commercially available tri-O-acetyl- d -glucal as the starting material. The structure of the intermediate chiral butenolide is established unambiguously by X-ray crystallographic analysis, which consequently leads to correction of a previous structural misassignment.

Successful combination of computationally inexpensive GIAO 13C NMR calculations and artificial neural network pattern recognition: a new strategy for simple and rapid detection of structural misassignments

GIAO NMR chemical shift calculations coupled with trained artificial neural networks (ANNs) have been shown to provide a powerful strategy for simple, rapid and reliable identification of structural misassignments of organic compounds using only one set of both computational and experimental data. The geometry optimization, usually the most time-consuming step in the overall procedure, was carried out using computationally inexpensive methods (MM+, AM1 or HF/3-21G) and the NMR shielding constants at the affordable mPW1PW91/6-31G(d) level of theory. As low quality NMR prediction is typically obtained with such protocols, the decision making was foreseen as a problem of pattern recognition. Thus, given a set of statistical parameters computed after correlation between experimental and calculated chemical shifts the classification was done using the knowledge derived from trained ANNs. The training process was carried out with a set of 200 molecules chosen to provide a wide array of chemical functionalities and molecular complexity, and the results were validated with a set of 26 natural products that had been incorrectly assigned along with their 26 revised structures. The high prediction effectiveness observed makes this method a suitable test for rapid identification of structural misassignments, preventing not only the publication of wrong structures but also avoiding the consequences of such a mistake.

Regio- and Stereoselective Synthesis of Cyclic Imidates via Electrophilic Cyclization of 2-(1-Alkynyl)benzamides. A Correction

The electrophilic cyclization of 2-(1-alkynyl)benzamides affords high yields of cyclic imidates, instead of the previously reported isoindolin-1-ones, where cyclization proceeds on the oxygen of the carbonyl group rather than the nitrogen of the amide functionality. X-ray crystallography and spectroscopic techniques have been used to characterize the products. A correction is hereby provided in order to rectify the previous misassignment of structure.

An Ester Enolate–Claisen Rearrangement Route to Substituted 4-Alkylideneprolines. Studies toward a Definitive Structural Revision of Lucentamycin A

Substituted 4-alkylideneprolines represent a rare class of naturally occurring amino acids with promising biological activities. Lucentamycin A is a cytotoxic, marine-derived tripeptide that harbors a 4-ethylidine-3-methylproline (Emp) residue unique among known peptide natural products. In this paper, we examine the synthesis of Emp and related 4-alkylideneprolines employing a versatile ester enolate-Claisen rearrangement. The scope and selectivity of the key rearrangement reaction are described with a number of diversely substituted glycine ester substrates. Treatment of the allyl esters with excess NaHMDS at ambient temperature gives rise to highly substituted α-allylglycine products with good to excellent diastereoselectivities. Resolution of dipeptide diastereomers and cyclization to form the pyrrolidine rings provide rapid access to stereopure prolyl dipeptides. We have applied this strategy to the synthesis of four Emp-containing isomers of lucentamycin A in pursuit of a definitive stereochemical revision of the natural product. Our studies indicate that the Emp stereogenic centers are not the source of structural misassignment. The current strategy should find broad utility in the synthesis of additional natural product analogues and related 3-alkyl-4-alkylidene prolines.

Survey of marine natural product structure revisions: A synergy of spectroscopy and chemical synthesis

The structural assignment of new natural product molecules supports research in a multitude of disciplines that may lead to new therapeutic agents and or new understanding of disease biology. However, reports of numerous structural revisions, even of recently elucidated natural products, inspired the present survey of techniques used in structural misassignments and subsequent revisions in the context of constitutional or configurational errors. Given the comparatively recent development of marine natural products chemistry, coincident with modern spectroscopy, it is of interest to consider the relative roles of spectroscopy and chemical synthesis in the structure elucidation and revision of those marine natural products that were initially misassigned. Thus, a tabulated review of all marine natural product structural revisions from 2005 to 2010 is organized according to structural motif revised. Misassignments of constitution are more frequent than perhaps anticipated by reliance on HMBC and other advanced NMR experiments, especially when considering the full complement of all natural products. However, these techniques also feature prominently in structural revisions, specifically of marine natural products. Nevertheless, as is the case for revision of relative and absolute configuration, total synthesis is a proven partner for marine, as well as terrestrial, natural products structure elucidation. It also becomes apparent that considerable ‘detective work’ remains in structure elucidation, in spite of the spectacular advances in spectroscopic techniques.

It All Began with an Error: The Nomofungin/Communesin Story

The communesin/nomofungin/perophoramidine story is an impressive example of how biogenetic considerations can lead to the correction of structural misassignments and inspire synthetic chemists with new, fruitful ideas. Intensive studies by a number of research groups culminated in the total synthesis of perophoramidine by the Funk research group in 2004. In 2007, Qin and co-workers completed the first total synthesis of a communesin.

Studies Relating to the Structure of Bruceoside C: Total Synthesis of the Alleged Aglycon of Bruceoside C

The structures assigned to bruceoside C (1) and the derived aglycon (2) have been shown to be incorrect. The structural misassignments were made clear by an unambiguous total synthesis of racemic 2 whose structure rests on spectral data and a single-crystal X-ray analysis of intermediate 22.

Total Synthesis of Cryptophycins. Revision of the Structures of Cryptophycins A and C

The convergent total synthesis of cryptophycins C and D is described. It has been shown that in both natural products the absolute configuration of the a-amino acid corresponds to the D-series. The structural assignment for cryptophycin C has been corrected to reflect this fact. Since the structure of cryptophycin A has been correlated to cryptophycin C, the chloro-0-methyltyrosine unit in cryptophycin A has the D-configuration. Cryptophycins are potent tumor-selective cytotoxins associated with the terrestrial blue-green algae Nostoc sp. GSV 224' and Nostoc sp. ATCC 53789.2 The major cytotoxin in each alga, cryptophycin A, shows excellent activity against solid tumors implanted in mice, including a drug-resistant tumor. Over 20 related cytotoxins are present in the GSV 224 strain as minor constituent^,'^^ and some of these compounds, e.g., cryptophycins B and C, have been isolated in sufficient amounts for in vivo e~aluation.~ In order to acquire adequate quantities of selected naturally-occurring cryptophycins and synthetic analogs for structure-activity relationship (SAR) studies, preclinical evaluation, and human clinical trials, we have designed a general synthesis. Cryptophycins C and D, as described in the original paper, were chosen to be the initial targets as they represented examples from both of the alleged Land D-tyrosine series. We report here the total syntheses of cryptophycins C and D which (1) revise the structures of cryptophycins A and C to reflect the D-configuration for the a-amino acid unit as depicted in the structural drawings in this paper and (2) confirm the structures of cryptophycins B and D. Retrosynthetic analysis of the cryptophycins was straightforward: the structure is composed of four units (A-D, Figure 1); consequently several convergent approaches could be envisioned. The combination of two pairs of units (e.g., A-B and C-D) appeared to be optimally convergent. Since the success of the synthesis depended on the formation of a 16membered depsipeptide from an acyclic precursor, a macrolactamization involving the amino group of unit C and the carboxylate of unit B appeared to be the best choice. The acyclic precursor to cryptophycin D would therefore be 1. This, in turn, suggested a disconnection into two fragments, one represented by 2 and composed of (S)-( -)-2-hydroxy-4-methylvaleric (L-leucic) acid (D) and (R)-3-amino-2-methylpropanoic acid (C) units, and the other by 3 and composed of O-methylD-tyrosine (B) and (2E,7E,5S,6R)-5-hydroxy-6-methyl-8-phenyloctadienoic acid (A) units. In the direction of the synthesis, @ Abstract published in Advance ACS Absfracts, February 15, 1995. (1) Trimurtulu, G.; Ohtani, I.; Patterson, G. M. L.; Moore, R. E.; Corbett, T. H.; Valeriote, F. A.; Demchik, L. J. Am. Chem. SOC. 1994, 116, 47294731. (2) Schwartz, R. E.; Hirsch, C. F.; Sesin, D. F.; Flor, J. E.; Chartrain, M.; Fromtling, R. E.; Harris, G. H.; Salvatore, M. J.; Liesch, J. M.; Yudin, K. J. Ind. Microbiol. 1990, 5, 113-24. (3) Trimurtulu, G.; Ogino, J.; Heltzel, C. E.; Patterson, G. M. L.; Moore, R. E. Manuscript in preparation. An explanation of the structural misassignment for cryptophycins A and C is presented. (4) Heltzel, C. E.; Ogino, J.; Trimurtulu, G.; Mooberry, S. L.; Patterson, G. M. L.; Moore, R. E.; Corbett, T. H.; Valeriote, F. A,; Demchik, L. Manuscript in preparation. A Figure 1. Numbering system for each of the units of cryptophycins C and D. This numbering system is used for the NMR data.