Determination of heteronuclear coupling constants from 3D HSQC-TOCSY experiment with optimized random sampling of evolution time space

A general strategy for the structural determination of carbohydrates by multi-dimensional NMR spectroscopies

Two-dimensional NMR spectroscopies are one of the most frequently used techniques for the structural determination of carbohydrates. However, the data analysis is challenging because of the signal overlap in the ¹H homonuclear correlation spectra. We attempted to explore a general strategy for the structural determination of carbohydrates by combined multi-dimensional spectroscopies. The strategy was applied to a human milk oligosaccharide lacto-N-difucohexaose I, that has been previously studied by conventional two-dimensional NMR spectroscopy. Assignment of the intra-residue resonances of the hexasaccharide using the three-dimensional spectrum was straightforward. Consequently, data analysis of the multi-dimensional spectra was significantly simplified, leading to a quicker determination of the intra- and inter-residue connections in the hexasaccharide. Application of the NMR strategy to chondroitin sulfate from bovine cartilage revealed two repeating disaccharide regions of the A and C units of chondroitin sulfate, indicating the high potential of this technique for the structural determination of complex polysaccharides.

Structural analysis of 25-hydroxycholesterol stereoisomers differing in configuration in position 17 and 20, by three-dimensional NMR spectra

The application of 3D NMR experiments and DFT calculations enabled the structure investigation of C-17 epimer of 3-(25-hydroxycholest-5-enyl) acetate is presented. The H-17 and H-20 protons features the same values of ¹H chemical shift, what causes that the structure elucidation require additional resolution enabled by 3D NMR experiments. The NMR experiments and theoretical calculations allowed for: the resonance assignment (3D COSY-HMBC and 3D TOCSY-HSQC techniques), the prediction of spatial structure (3D NOESY-HSQC and 3D ROESY-HSQC experiments), and the precise measurement of heteronuclear coupling constants (3D HSQC-TOCSY spectra with E.COSY-type multiplets).

Identification of Unknown Metabolomics Mixture Compounds by Combining NMR, MS, and Cheminformatics

Metabolomics aims at the comprehensive identification of metabolites in complex mixtures to characterize the state of a biological system and elucidate their roles in biochemical pathways. For many biological samples, a large number of spectral features observed by NMR spectroscopy and mass spectrometry (MS) belong to unknowns, i.e., these features do not belong to metabolites that have been previously identified, and their spectral information is not available in databases. By combining NMR, MS, and combinatorial cheminformatics, the analysis of unknowns can be pursued in complex mixtures requiring minimal purification. This chapter describes the SUMMIT MS/NMR approach covering sample preparation, NMR and MS data collection and processing, and the identification of likely unknowns with the use of cheminformatics tools and the prediction of NMR spectral properties.

Multiplicity-edited 1 H-1 H TOCSY experiment

A ¹ H-¹ H total correlation spectroscopy (TOCSY) experiment incorporating ¹³ C multiplicity information is proposed. In addition, broadband ¹ H homodecoupling in the indirect dimension can be implemented using a perfect BIRD module that affords exclusive ¹ H chemical shift evolution with full decoupling of all heteronuclear and homonuclear (including ² J_HH ) coupling constants. As a complement to the normal TOCSY and the recent PSYCHE-TOCSY experiments, this novel multiplicity-edited TOCSY experiment distinguishes between CH/CH₃ (phased up) and CH₂ (phased down) cross-peaks, which facilitates resonance analysis and assignment.

Accurate Identification of Unknown and Known Metabolic Mixture Components by Combining 3D NMR with Fourier Transform Ion Cyclotron Resonance Tandem Mass Spectrometry

Metabolite identification in metabolomics samples is a key step that critically impacts downstream analysis. We recently introduced the SUMMIT NMR/mass spectrometry (MS) hybrid approach for the identification of the molecular structure of unknown metabolites based on the combination of NMR, MS, and combinatorial cheminformatics. Here, we demonstrate the feasibility of the approach for an untargeted analysis of both a model mixture and E. coli cell lysate based on 2D/3D NMR experiments in combination with Fourier transform ion cyclotron resonance MS and MS/MS data. For 19 of the 25 model metabolites, SUMMIT yielded complete structures that matched those in the mixture independent of database information. Of those, seven top-ranked structures matched those in the mixture, and four of those were further validated by positive ion MS/MS. For five metabolites, not part of the 19 metabolites, correct molecular structural motifs could be identified. For E. coli, SUMMIT MS/NMR identified 20 previously known metabolites with three or more ¹H spins independent of database information. Moreover, for 15 unknown metabolites, molecular structural fragments were determined consistent with their spin systems and chemical shifts. By providing structural information for entire metabolites or molecular fragments, SUMMIT MS/NMR greatly assists the targeted or untargeted analysis of complex mixtures of unknown compounds.

Extending long-range heteronuclear NMR connectivities by HSQMBC-COSY and HSQMBC-TOCSY experiments

The detection of long-range heteronuclear correlations presenting J(CH) coupling values smaller than 1-2Hz is a challenge in the structural analysis of small molecules and natural products. HSQMBC-COSY and HSQMBC-TOCSY pulse schemes are evaluated as complementary NMR methods to standard HMBC/HSQMBC experiments. Incorporation of an additional J(HH) transfer step in the basic HSQMBC pulse scheme can favor the sensitive observation of traditionally missing or very weak correlations and, in addition, facilitates the detection of a significant number of still longer-range connectivities to both protonated and non-protonated carbons under optimum sensitivity conditions. A comparative (1)H-(13)C study is performed using strychnine as a model compound and several examples are also provided including (1)H-(15)N applications.

Straightforward measurement of individual (1)J(CH) and (2)J(HH) in diastereotopic CH(2) groups

The C-H(A) cross-peak corresponding to a diastereotopic CHAHB methylene spin system exhibits a characteristic 1:0:1 multiplet pattern along the indirect dimension of a ω1-coupled HSQC spectrum. It is shown here that the use of the initial (13)C Boltzmann polarization instead of the regular INEPT-based (1)H Boltzmann polarization makes visible the central lines of this multiplet pattern. A spin-state-selective method is proposed for the efficient measurement of both (1)J(CHA) and (1)J(CHB) along the indirect dimension of a 2D spectrum as well as to the magnitude and the sign of the geminal (2)J(HAHB) coupling constant from the straightforward analysis of a single four-component E.COSY cross-peak. Additionally, the extraction of (1)J(CH) values for CH and CH3 multiplicities can be also performed from the same spectrum. The success of the method is also illustrated for the determination of residual dipolar (1)D(CH) and (2)D(HH) coupling constants in a small molecule weakly aligned in a PMMA swollen gel.

Long-range proton-carbon coupling constants: NMR methods and applications

A general review of novel NMR methods to measure heteronuclear long-range proton-carbon coupling constants ((n)JCH; n>1) in small molecules is made. NMR experiments are classified in terms of NMR pulse scheme and cross-peak nature. A discussion about simplicity, general applicability and accuracy for each particular NMR experiment is presented and exemplified. Important aspects such as the sign determination and measurement of very small coupling values involving protonated and non-protonated carbons as well as the complementarity between different experiments are also discussed. Finally, a compilation of applications in structural and conformational analysis of different types of molecules since 2000 is surveyed.

Simultaneous measurement of J(HH) and two different (n)J(CH) coupling constants from a single multiply edited 2D cross-peak

Three different J-editing methods (IPAP, E.COSY and J-resolved) are implemented in a single NMR experiment to provide spin-state-edited 2D cross-peaks from which a simultaneous measurement of different homonuclear and heteronuclear coupling constants can be performed. A new J-selHSQMBC-IPAP experiment is proposed for the independent measurement of two different (n)J(CH) coupling constants along the F2 and F1 dimensions of the same 2D cross-peak. In addition, the E.COSY pattern provides additional information about the magnitude and relative sign between J(HH) and (n)J(CH) coupling constants.

Study of near-symmetric cyclodextrins by compressed sensing 2D NMR

The compressed sensing NMR (CS-NMR) is an approach to processing of nonuniformly sampled NMR data. Its idea is to introduce minimal l(p) -norm (0 < p ≤ 1) constraint to a penalty function used in a reconstruction algorithm. Here, we demonstrate that 2D CS-NMR spectra allow the full spectral assignment of near-symmetric β-cyclodextrin derivatives (mono-modified at the C6 position). The application of CS-NMR ensures experimental time saving and the resolution improvement, necessary because of very low chemical shift dispersion. In the overnight experimental time, the set of properly resolved 2D NMR spectra required for the unambiguous assignment of mono(6-deoxy-6-(1-1,2,3-triazo-4-yl)-1-propane-3-O-(phenyl)) β-cyclodextrin was obtained. The highly resolved HSQC spectrum was reconstructed from 5.12% of the data. Moreover, reconstructed 2D HSQC-TOCSY spectrum yielded information about the correlations within one sugar unit, and 2D HSQC-NOESY technique allowed the sequential assignment of the glucosidic units.

Speeding up the measurement of one-bond scalar (1J) and residual dipolar couplings (1D) by using non-uniform sampling (NUS)

The accurate and precise measurement of one-bond scalar and residual dipolar coupling (RDC) constants is of prime importance to be able to use RDCs for structure determination. If coupling constants are to be extracted from the indirect dimension of HSQC spectra a significant saving of measurement time can be achieved by non-uniform sampling (NUS). Coupling constants can either be obtained with the same precision as in traditionally acquired spectra in a fraction of the measurement time or the precision can be significantly improved if the same amount of measurement time as for traditionally acquired spectra is invested. The application of NUS for the measurement of (1)J (scalar coupling constants) and (1)T (total couplings constants) from different kinds of ω(1)-coupled spectra (including also J-scaled ones) is examined in detail and the possible gains in time or resolution are discussed. When using the newly proposed compressed sensing (CS) algorithm for processing, the quality of the spectra is comparable to the traditionally sampled ones.

Measurement and applications of long-range heteronuclear scalar couplings: recent experimental and theoretical developments

The use of long-range heteronuclear couplings, in association with (1)H-(1)H scalar couplings and NOE restraints, has acquired growing importance for the determination of the relative stereochemistry, and structural and conformational information of organic and biological molecules. However, the routine use of such couplings is hindered by the inherent difficulties in their measurement. Prior to the advancement in experimental techniques, both long-range homo- and heteronuclear scalar couplings were not easily accessible, especially for very large molecules. The development of a large number of multidimensional NMR experimental methodologies has alleviated the complications associated with the measurement of couplings of smaller strengths. Subsequent application of these methods and the utilization of determined J-couplings for structure calculations have revolutionized this area of research. Problems in organic, inorganic and biophysical chemistry have also been solved by utilizing the short- and long-range heteronuclear couplings. In this minireview, we discuss the advantages and limitations of a number of experimental techniques reported in recent times for the measurement of long-range heteronuclear couplings and a few selected applications of such couplings. This includes the study of medium- to larger-sized molecules in a variety of applications, especially in the study of hydrogen bonding in biological systems. The utilization of these couplings in conjunction with theoretical calculations to arrive at conclusions on the hyperconjugation, configurational analysis and the effect of the electronegativity of the substituents is also discussed.

Using indirect covariance processing for structure elucidation of small molecules in cases of spectral crowding

Indirect and unsymmetrical indirect covariance NMR provide powerful tools to compute and visualize correlation information by transforming component spectra into combined spectral data matrices. Sensitive component spectra such as TOCSY, HSQC and NOESY can be quickly converted into experimentally insensitive or time-consuming correlation spectra such as HSQC-NOESY. The comparison of illustrative series of spectra from four steroids, dexamethasone, testosterone, allylestrenol and tibolone, renders the effects of resonance overlap on the ease of interpretation visible. The compounds are selected such that signal overlap increases systematically in the proton and carbon domain. Spectra are defined as light, moderate and heavy signal overlap, based on signal density. The investigation suggests that moderate spectral congestion in either proton or carbon domain leads to a number of artifacts that does not hamper signal assignment but lowers the level of confidence on de novo structure elucidation. Since the number of correlations usually increases through covariance processing, component spectra with severe spectral congestion in both dimensions are not suitable for covariance processing and the resulting spectra do not support structure confirmation or structure elucidation. The calculated spectra are compared with the corresponding experimental spectra with respect to their application in structure elucidation laboratory environments.

IPAP-HSQMBC: measurement of long-range heteronuclear coupling constants from spin-state selective multiplets

A new NMR approach is proposed for the measurement of long-range heteronuclear coupling constants ((n)J(XH), n>1) in natural abundance molecules. Two complementary in-phase (IP) and anti-phase (AP) data are separately recorded from a modified HSQMBC experiment and then added/subtracted to provide spin-state-selective α/β-HSQMBC spectra. The magnitude of (n)J(XH) can be directly determined by simple analysis of the relative displacement between α- and β-cross-peaks. The robustness of this IPAP-HSQMBC experiment is evaluated experimentally and by simulation using a variety of different conditions. Important aspects such as signal intensity dependence and presence of unwanted cross-talk effects are discussed and examples on the measurement of small proton-carbon ((n)J(CH)) and proton-nitrogen ((n)J(NH)) coupling constants are provided.

Complete (1)H and (13)C signal assignment of prenol-10 with 3D NMR spectroscopy

The complete assignment of (1)H and (13)C chemical shifts of natural abundance prenol-10 is reported for the first time. It was achieved using 3D NMR experiments, which were based on random sampling of the evolution time space followed by multidimensional Fourier transform. This approach makes it possible to acquire 3D NMR spectra in a reasonable time and preserves high resolution in indirectly detected dimensions. It is shown that the interpretation of 3D COSY-HMBC and 3D TOCSY-HSQC spectra is crucial in the structural analysis of prenol-10.