A new method to determine the absolute configuration of organic compounds is described. It is a modern variation of Mosher's method and is designated 'modified Mosher's method'. The method uses MTPA moiety as a chiral auxiliary, the phenyl group of which affects the chemical shifts of the protons in the molecule. The compound possessing a secondary alcohol moiety is esterified with (R) and (S) -MTPA acids, and the respective diastereomers are subjected to NMR analyses to assign the signals of as many protons as possible. The pattern of arrangement of Δδ values defined as Δδ=δS-δR for each proton leads to the absolute configuration of the compound in question. Versatility and limitation of this new method are discussed.
This article deals with how modern and advanced NMR techniques (mainly various 2 D ones) are manipulated for the structure elucidation of natural organic compounds by giving the examples which the author has been involved in. Examples shown here are a) urochordamines A and B, larval settlement/metamorphosis-promoting alkaloids from some ascidians, b) a novel kind of bile acid in chronic subdural hematoma, as an example for application of a very small amount of sample (ca. 70 μg), c) 2-isocyanoallopupukeanane, a new sesquiterpene with a novel tricylic skeleton from nudibranchs, d) a skeletally rearranged product from a derivative of terrecyclic acid A, as an example for utilization of 13C-labelled compounds and 2 D-INADEQUATE experiment, and e) orbiculamide A, a novel cytotoxic cyclic peptide from a marine sponge. Several new NMR techniques not mentioned in the examples are also listed.
Application of NMR techniques, especially a spin saturation transfer technique, to several organometallic compounds are reported with emphasis on compounds undergoing fluxional behavior with two-electron-threecentered bonds such as a M-H-C bond, i.e. agostic interaction, and a M-H-H bond, i.e. a molecular hydrogen ligand. 13C spin saturation transfer experiments on the tautomers of H2Os3(CO)10(μ-CH2) and HOs(CO)10(μ-CH3) show intramolecular hydrogen exchange to convert all of the four isomers. 1H spin saturation tranfer experiments on [RuH(diop)2] PF6 show intramolecular hydrogen exchange between the hydride ligand and an aliphatic proton, presumably involving an agostic interaction, of the phosphine ligand. 1H spin saturation transfer experiments on [RuH(η2-H2)(dppp)2]PF6 show intramolecular hydrogen exchange between the molecular hydrogen and the hydride ligand. Application of isotopic perturbation of resonance to agostic interaction is mentioned as a method to show the presence of a proton of an agostic interaction undergoing a rapid exchange.
Two-dimensional (2 D) nuclear magnetic resonance (NMR) spectroscopy is a useful tool for the structure elucidation of proteins with a molecular weight of up to ca. 10 kDa. This molecular size limitation is caused by resonance overlap in 2 D NMR spectra and the low sensitivity due to large linewidth associated with the increased size of proteins. Recent progress of recombinant DNA technology allowed one to obtain 13C- and/or 15N-labelled proteins in large quantities. Development of multi-dimensional NMR technique using such labelled proteins has made it possible to determine solution structures of larger proteins up to ca. 30 kDa by increasing spectral resolution and utilizing large one-bond J couplings for transfer magnetization. This novel NMR technique may open great possibilities for us to understand important problems in the fields of protein chemistry and protein engineering.
Identification of sugar components and sugar linkages is required for structural determination of oligosaccharide chains. Several magnetization transfer methods, such as multiple relayed COSY and homonuclear Hartmann-Hahn methods are useful to extract subspectra of constituent monosaccharides. Individual monosaccharides give characteristic cross peak patterns due to their chemical shifts and spin-spin couplings so that we can identify the sugar types. The linkages of each sugar residue can be subsequently determined by the analysis of NOESY spectra. Thus, the chemical structure of oligosaccharide chains can be elucidated by non-empirical manner. We have applied this method to determine the chemical structure of oligosaccharide chains of a novel glycolipid from a sea urchin.
Principle and recent advances of automated structure elucidation system for organic compound, CHEMICS will be reviewed, CHEMICS has been designed to generate all possible candidate structures compatible with input data. However, a large number of candidates were more often generated. In order to cope with this problem, recently, several useful functions (2 D-NMR analysis, 13C-NMR chemical shift prediction and assignment, and mass spectral prediction and evaluation) have been developed and introduced into CHEMICS. The effectiveness of these functions will be shown through execution of proper examples. Furthermore, complementary application of CHEMICS and spectral database, Speclnfo will be mentioned as one of the future styles for computer-assisted structure elucidation.
Mass spectrometric analyses of glycoconjugates are most commonly performed by fast atom bombardment (FAB) or liquid matrix-assisted secondary ion mass spectrometry (SIMS). However, more recent ionization methods, such as electrospray (ESI) and matrix-assisted laser desorption (MALD), have made mass spectrometric analyses applicable to even larger, thermally labile biomolecules. ESI often produces multiply-charged ions, and a molecular weight is obtained by the deconvolution of those multiply-charged ions. On the other hand, MALD may produce intact molecular ions up to half a million daltons. Combination of high performance liquid chromatography with mass spectrometry (HPLC-MS) is often a strategy of choice for biological samples in which contamination of other chemical species is usually unavoidable. Tandem mass spectrometry (MS/MS) with collision-induced dissociation (CID) often provides structural information for unknown sample molecules. In particular, charge-remote fragmentation applying a high-energy collision sometimes gives detailed information about the locations of unsaturation and branchings of metal-cationated molecules.
X-Ray crystal structure analysis has become very easy and an enormous number of crystal structures have been determined. Although such a development is partly brought about by the four-circle diffractometer, recent developments in technique of crystal structure analysis and computation require another diffractometer for quick data collection. Two methods are proposed; the synchrotron radiation to obtain more intense X-rays, and the Imaging-plate as a two-dimensional detector. Several types of diffractometer using the Imaging-plate have been made, for example, IPD-WAS, R-AXIS IIc, DIP-320 W and FIXD. The three-dimensional intensity data can be collected within 35 hours whereas about 23 days are necessary for the four-circle diffractometer. The data will be collected more quickly at photon Factory, using the synchrotron radiation. Recently an unstable intermediate structure has been observed by the step-wise structure analysis for the crystalline-state racemization of the cobaloxime complex crystal using the above IPD-WAS. A desolvation process has been observed for another cobaloxime complex crystal. Such a dynamical process observed in crystals should make clear the reaction mechanism more precisely. A new type of diffractometer is now designed to analyze the crystal structure within a submillisecond at SPring-8. Some structures at the excited states will be analyzed in near future.
During the last decade, we have witnessed significant advances in various technological aspects of a discipline called “protein crystallography” which is a branch of the technique of X-ray crystal structure analyses specifically aimed at solving the crystal structures (and thus the molecular structures) of biological macromolecules. After the introductory sections dealing with 1) the relationship of the present field with organic chemistry and 2) the rationale for further promotion of the technique of protein crystallography, the advances in various technological aspects are summarized in the form of Table 1. Finally more detaild accounts are given for 1) the method and prospect of time-resolved X-ray crystal structure analysis using the Laue method and 2) the present situation of the Brookhaven Protein Data Bank.
The CD exciton chirality method, a powerful chiroptical tool for determination of absolute stereochemistry of organic compounds on the basis of the exciton theory, has been extensively applied to various natural products and synthetic chiral compounds. The concept, mechanism, and applications of this method are briefly outlined below. The CD exciton chirality method is also applicable to acyclic 1, 2- and 1, 3-dibenzoates, and the sign of their observed Cotton effects was explained on the basis of the results of conformational analysis. Recently, the theoretical calculation of the CD spectra by the π-electron SCF-CI-DV MO method has become an important tool in the absolute configurational study of a variety of twisted and conjugated π-electron systems. In fact, the absolute stereochemistry of (+) -1, 8a-dihydro-3, 8-dimethylazulene, was theoretically determined by application of this method. We have also succeeded in the experimental verification of the absolute configuration theoretically determined, by comparison of the CD spectra of the natural product with those of synthetic chiral model compounds. We also clarified that the π-electron SCF-CI-DV MO method was powerful for nonempirical determination of the absolute configuration of more complicated natural products, new marine natural products of halenaquinol family isolated from tropical marine sponges. We achieved the first total synthesis of these chiral halenaquinol and halenaquinone with twisted π-electron systems. By the total synthesis we experimentally proved that the absolute stereochemistry of halenaquinol family theoretically determined was correct. The absolute stereochemistry of a biflavone, a natural atropisomer, was also theoretically determined by this method.