Evaluating the accuracy of theoretical one-bond 13 C─13 C scalar couplings and their ability to predict structure in a natural product

One-Bond 13C-1H and 13C-13C Spin-Coupling Constants as Constraints in MA'AT Analysis of Saccharide Conformation

MA'AT analysis uses ensembles of redundant experimental NMR spin-coupling constants, parametrized J-coupling equations obtained from density functional theory (DFT) calculations, and circular statistics to produce probability distributions of molecular torsion angles in solution and information on librational motions about these angles (Meredith et al., J. Chem. Info. Model. 2022, 62, 3135-3141). Current DFT methods give nearly quantitative two- and three-bond J_HH, J_CH, and ¹J_CC values for use in MA'AT analysis of saccharides. In contrast, the accuracy of DFT-calculated one-bond ¹J_CH and ¹J_CC values is more difficult to determine, preventing their use in MA'AT modeling. This report describes experimental and computational studies that address this problem using two approaches (Strategies 1 and 2). Differences [¹J_CH^calc - ¹J_CH^exp] (Strategy 1) ranged from -1.2 to 2.5 Hz, giving an average difference of 0.8 ± 1.7 Hz. Percent differences ranged from -0.8% to 1.6%, giving an average % difference of 0.5 ± 1.1%. In comparison, [¹J_CH^MA'AT - ¹J_CH^exp] (Strategy 2) ranged from -1.8 to 0.2 Hz, giving an average difference of -1.2 ± 0.7 Hz. Percent differences ranged from -1.2% to 0.1%, giving an average % difference of -0.8 ± 0.5%. Strategy 1 gave an average difference of 2.1 Hz between calculated and experimental ¹J_CC values, with an average % difference of 5.1 ± 0.2%. Calculated ¹J_CC values were consistently larger than experimental values. Strategy 2 also gave calculated ¹J_CC values that were larger than the experimental values, with an average difference of 2.3 ± 0.6 Hz, and an average % difference of 5.6 ± 1.6%. The findings of both strategies are similar and indicate that ¹J_CH values in saccharides can be calculated nearly quantitatively, but ¹J_CC values appear to be consistently overestimated by ∼5% using current DFT methods.

Computational 1 H and 13 C NMR in structural and stereochemical studies

Present review outlines the advances and perspectives of computational ¹ H and ¹³ C NMR applied to the stereochemical studies of inorganic, organic, and bioorganic compounds, involving in particular natural products, carbohydrates, and carbonium ions. The first part of the review briefly outlines theoretical background of the modern computational methods applied to the calculation of chemical shifts and spin-spin coupling constants at the DFT and the non-empirical levels. The second part of the review deals with the achievements of the computational ¹ H and ¹³ C NMR in the stereochemical investigation of a variety of inorganic, organic, and bioorganic compounds, providing in an abridged form the material partly discussed by the author in a series of parent reviews. Major attention is focused herewith on the publications of the recent years, which were not reviewed elsewhere.

Computer Assisted Structure Elucidation (CASE): Current and future perspectives

The first efforts for the development of methods for Computer-Assisted Structure Elucidation (CASE) were published more than 50 years ago. CASE expert systems based on one-dimensional (1D) and two-dimensional (2D) Nuclear Magnetic Resonance (NMR) data have matured considerably by now. The structures of a great number of complex natural products have been elucidated and/or revised using such programs. In this article, we discuss the most likely directions in which CASE will evolve. We act on the premise that a synergistic interaction exists between CASE, new NMR experiments, and methods of computational chemistry, which are continuously being improved. The new developments in NMR experiments (long-range correlation experiments, pure-shift methods, coupling constants measurement and prediction, residual dipolar couplings [RDCs]), and residual chemical shift anisotropies [RCSAs], evolution of density functional theory (DFT), and machine learning algorithms will have an influence on CASE systems and vice versa. This is true also for new techniques for chemical analysis (Atomic Force Microscopy [AFM], "crystalline sponge" X-ray analysis, and micro-Electron Diffraction [micro-ED]), which will be used in combination with expert systems. We foresee that CASE will be utilized widely and become a routine tool for NMR spectroscopists and analysts in academic and industrial laboratories. We believe that the "golden age" of CASE is still in the future.

NMR structural characterization from one-bond 13 C13 C couplings: Complete assignment of a hydrogen-poor depsidone

The connectivity, conformation, tautomeric form, and dynamics of a new depsidone (perisalazinic acid) were characterized using one-bond ¹³ C¹³ C NMR scalar couplings (¹ J_CC ) obtained from the INADEQUATE experiment. Characterization of perisalazinic acid using more conventional NMR techniques is problematic due to the extremely limited number of CH protons present. In the present study, 81 candidate structures were considered and a best fit structure was selected by comparing computed ¹ J_CC values for each candidate to 15 experimental values. Of the six flexible moieties in perisalazinic acid, three are adequately represented by a single orientation stabilized by intramolecular hydrogen bonding. The three remaining groups are present as mixtures of conformers with two sites consisting of a pair of conformations and another disordered over six orientations. This study demonstrates the feasibility of complete three-dimensional structural characterization of an unknown using only theoretical and experimental ¹ J_CC values.

Application of INADEQUATE NMR techniques for directly tracing out the carbon skeleton of a natural product

INTRODUCTION

Nuclear magnetic resonance (NMR) measurement of ¹ J_CC coupling by two-dimensional (2D) INADEQUATE (incredible natural abundance double quantum transfer experiment), which is a special case of double-quantum (DQ) spectroscopy that offers unambiguous determination of ¹³ C-¹³ C spin-spin connectivities through the DQ transitions of the spin system, is especially suited to solving structures rich in quaternary carbons and poor in hydrogen content (Crews rule).

OBJECTIVE

To review published literature on the application of NMR methods to determine structure in the liquid-state, which specifically considers the interaction of a pair of carbon-13 (¹³ C) nuclei adjacent to one another, to allow direct tracing out of contiguous carbon connectivity using 2D INADEQUATE.

METHODOLOGY

A comprehensive literature search was implemented with various databases: Web of Knowledge, PubMed and SciFinder, and other relevant published materials including published monographs. The keywords used, in various combinations, with INADEQUATE being present in all combinations, in the search were 2D NMR, ¹ J_CC coupling, natural product, structure elucidation, ¹³ C-¹³ C connectivity, cryoprobe and CASE (computer-assisted structure elucidation)/PANACEA (protons and nitrogen and carbon et alia).

RESULTS

The 2D INADEQUATE continues to solve "intractable" problems in natural product chemistry, and using milligram quantities with cryoprobe techniques combined with CASE/PANACEA experiments can increase machine time efficiency. The ¹³ C-¹³ C-based structural elucidation by dissolution single-scan dynamic nuclear polarisation NMR can overcome disadvantages of ¹³ C insensitivity at natural abundance. Selected examples have demonstrated the trajectory of INADEQUATE spectroscopy from structural determination to clarification of metabolomics analysis and use of DFT (density functional theory) and coupling constants to clarify the connectivity, hybridisation and stereochemistry within natural products.

CONCLUSIONS

Somewhat neglected over the years because of perceived lack of sensitivity, the 2D INADEQUATE NMR technique has re-emerged as a useful tool for solving natural products structures, which are rich in quaternary carbons and poor in hydrogen content.

Characterization of a Bio-sourced, Fluorescent, Ratiometric pH Indicator with Alkaline pKa

Utilizing organisms as sources of fluorophores relieves the demand for petroleum feedstock in organic synthesis of fluorescent products, and endophytic fungi provide a promising vein for natural fluorescent products. We report the characterization of a pH-responsive fluorophore from an endophytic fungus isolated from sand pine. The endogenous fluorescence of the live organism was measured using fluorescence microscopy. Computational interpretation of the spectra was accomplished with time-dependent density functional theory methods. The combined use of experimental and theoretically predicted spectra revealed the pH equilibria and photoexcited tautomerization of the natural product, 5-methylmellein. This product shows promise both as a stand-alone pH-indicating fluorophore, with alkaline pK_a , and as "green" feedstock for synthesis of custom fluorophores.

Computational 1 H NMR: Part 3. Biochemical studies

This is the third and the last part of three closely interrelated reviews dealing with computation of ¹ H nuclear magnetic resonance chemical shifts and ¹ H-¹ H spin-spin coupling constants. Present review deals with the computation of these parameters in biologically active natural products, carbohydrates, and other molecules of biological origin focusing on stereochemical applications of computational ¹ H nuclear magnetic resonance to these objects.

13C NMR-Based Approaches for Solving Challenging Stereochemical Problems

Determining the configuration of proton-deficient molecules is challenging using conventional NMR methods including nuclear Overhauser effect (NOE) and the proton-dependent J-based configuration analysis (JBCA). The problem is exacerbated when only one stereoisomer is available. Alternative methods based on the utilization of ¹³C NMR chemical shifts, ¹³C-¹³C homonuclear couplings measured at natural abundance, and residual chemical shift anisotropy measurements in conjunction with density functional theory calculations are illustrated with a proton-deficient model compound.

Enhancing the utility of 1JCH coupling constants in structural studies through optimized DFT analysis

High accuracy for DFT-predicted ¹J_CH-couplings can be achieved without ad hoc corrections or empirical scaling by careful selection of the DFT method utilized for geometry optimization and J-coupling calculations.

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 J_CC 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 J_CC coupling constants greater than 10 Hz. Results are supported by both the experimental measurement of ³ J_CC coupling constants in question using J-modulated-ADEQUATE and density functional theory calculations.

Carbon-carbon spin-spin coupling constants: Practical applications of theoretical calculations

Practical applications of theoretical calculations of carbon-carbon spin-spin coupling constants in particular classes of organic and bioorganic molecules are reviewed, concentrating mainly on saturated, unsaturated, aromatic and heteroaromatic compounds and their functional derivatives as well as on carbohydrates and natural compounds.