Summary of DFT calculations coupled with current statistical and/or artificial neural network (ANN) methods to assist experimental NMR data in identifying diastereomeric structures

Iriomoteolide-1a and -1b: Structure Elucidation by Integrating NMR Spectroscopic Analysis, Theoretical Calculation, and Total Synthesis

The structure of iriomoteolide-1a, a marine macrolide with potent cytotoxic activity against human cancer cells, has been under scrutiny for more than a decade since the first total synthesis of the proposed structure was achieved by Horne. Here we disclose the correct structure of iriomoteolide-1a. Given a huge number of possible stereoisomers, we adopted an integrated strategy toward the structure elucidation of iriomoteolide-1a: (1) NMR spectroscopic analysis/molecular mechanics-based conformational analysis for configurational reassignment of the macrolactone domain; (2) model synthesis for validating the reassigned configuration of the macrolactone domain; (3) GIAO NMR calculation/DP4+ analysis of side chain stereoisomers; and (4) total synthesis of the most likely structure. Moreover, the correct structure of iriomoteolide-1b, a natural congener, was also determined by an integration of NMR spectroscopic analysis, GIAO NMR calculation/DP4+ analysis, and total synthesis.

Highly Functionalized Spirobisnaphthalenes from Roussoella sp. KT4147

Highly functionalized spirobisnaphthalenes, preussomerins N (1) and O (2), and simpler compounds, such as 2,3-α-epoxypalmarumycin CP18 (3), 3α-hydroxy-CJ-12,372 (4), and 16 known structurally related congeners, were isolated from a culture broth of Roussoella sp. KT4147. Structural analysis revealed that 1 was a dimer of preussomerin G (6), connected by a nitrogen atom, and 2 was a derivative of 6 with a macommelin substructure. Preussomerin N (1) was considered to be biosynthetically derived via the Michael-type 1,4-addition of ammonia to 6, followed by another Michael addition to another molecule of 6. Contrarily, 2 was suggested to be derived through an endo-Diels-Alder cycloaddition between a diene derived from the (E)-enol form of macommelinal via an ene-reaction and dienophile 6. Compounds 1 and 2 exhibited potent cytotoxicity against COLO-201 human colorectal cancer cells.

Utilization of 13C NMR Carbon Shifts for the Attribution of Diastereomers in Methyl-Substituted Cyclohexanes

In this report, we address the challenge of assigning diastereomers for methyl cyclohexanes, particularly those with quaternary centers, which remains nontrivial despite modern NMR techniques. By utilizing a HSQC NMR experiment to identify methyl-carbons coupled with a simple conformational analysis, we identified an effective and quite general method for assigning stereochemistry, even in cases where diastereomeric mixtures are inseparable.

Relative stereochemical determination of the C61-C83 fragment of symbiodinolide using a stereodivergent synthetic approach

Structural determination is required in the use of marine natural products to create novel drugs and drug leads in medicinal chemistry. Symbiodinolide, which is a polyol marine natural product with a molecular weight of 2860, increases the intracellular Ca2+ concentration and exhibits inhibitory activity against cyclooxygenase-1. Seventy percent of the structure of symbiodinolide has been stereochemically clarified. Herein, we report the elucidation of the relative configuration of the C61-C83 fragment, which is among the remaining thirty percent, using a stereodivergent synthetic strategy. We first assigned the relative configuration of the C61-C74 fragment. Two candidate diastereomers of the C61-C74 fragment were synthesized, and their NMR data were compared with those of the natural product, revealing the relative stereochemistry of this component. We then narrowed down the candidate compounds for the C69-C83 fragment from 16 possible diastereomers by analyzing the NMR data of the natural product, and we thus selected eight candidate diastereomers. Stereodivergent synthesis of the candidates for this fragment and comparison of the NMR data of the natural product and the eight synthetic products resulted in the relative stereostructural clarification of the C69-C83 fragment. These individually determined relative stereochemistries of the C61-C74 and C69-C83 fragments were connected via the common C69-C73 tetrahydropyran moiety of the fragments. Finally, the relative configuration of the C61-C83 fragment of symbiodinolide was determined. The stereodivergent synthetic approach used in this study can be extended to the stereochemical determination of other fragments of symbiodinolide.

On the Use of Deuterated Organic Solvents without TMS to Report 1H/13C NMR Spectral Data of Organic Compounds: Current State of the Method, Its Pitfalls and Benefits, and Related Issues

The quite popular, simple but imperfect method of referencing NMR spectra to residual 1H and 13C signals of TMS-free deuterated organic solvents (referred to as Method A) is critically discussed for six commonly used NMR solvents with respect to their δH and δC values that exist in the literature. Taking into account the most reliable data, it was possible to recommend 'best' δX values for such secondary internal standards. The position of these reference points on the δ scale strongly depends on the concentration and type of analyte under study and the solvent medium used. For some solvents, chemically induced shifts (CISs) of residual 1H lines were considered, also taking into account the formation of 1:1 molecular complexes (for CDCl3). Typical potential errors that can occur as a result of improper application of Method A are considered in detail. An overview of all found δX values adopted by users of this method revealed a discrepancy of up to 1.9 ppm in δC reported for CDCl3, most likely caused by the CIS mentioned above. The drawbacks of Method A are discussed in relation to the classical use of an internal standard (Method B), two 'instrumental' schemes in which Method A is often implicitly applied, that is, the default Method C using 2H lock frequencies and Method D based on Ξ values, recommended by the IUPAC but only occasionally used for 1H/13C spectra, and external referencing (Method E). Analysis of current needs and opportunities for NMR spectrometers led to the conclusion that, for the most accurate application of Method A, it is necessary to (a) use dilute solutions in a single NMR solvent and (b) to report δX data applied for the reference 1H/13C signals to the nearest 0.001/0.01 ppm to ensure the precise characterization of new synthesized or isolated organic systems, especially those with complex or unexpected structures. However, the use of TMS in Method B is strongly recommended in all such cases.

Simple, accurate, adjustable-parameter-free prediction of NMR shifts for molecules in solution

Accurate prediction of NMR shifts is invaluable for interpreting and assigning NMR spectra, especially for complex applications such as determining the identity of unknown substances or resolving stereochemical assignments. Statistical linear regression models have proven effective for accurately correlating density functional theory predictions of chemical shieldings with experimentally-measured shifts, but lack transferability - they must be reparameterised using a reasonably extensive training set at each level of theory and for each choice of NMR solvent. We have previously introduced a novel two-point "shift-and-scale" correction procedure for gas phase shieldings that overcomes these limitations without significant loss of accuracy. In this work, we demonstrate that this approach is equally applicable for predicting solution-phase shifts from computed gas phase shieldings, using acetaldehyde as an experimentally and computationally convenient reference system. We also present all of the required experimental reference data to enable this approach to be used for any target analyte in a range of commonly used NMR solvents (chloroform, dichloromethane, acetonitrile, methanol, acetone, DMSO, D2O, benzene, pyridine).

Glycosylated and Succinylated Macrocyclic Lactones with Amyloid-β-Aggregation-Regulating Activity from a Marine Bacillus sp

Two new glycosylated and succinylated macrocyclic lactones, succinyl glyco-oxydifficidin (1) and succinyl macrolactin O (2), were isolated from a Bacillus strain collected from an intertidal mudflat on Anmyeon Island in Korea. The planar structures of 1 and 2 were proposed using mass spectrometric analysis and NMR spectroscopic data. The absolute configurations of 1 and 2 were determined by optical rotation, J-based configuration analysis, chemical derivatizations, including the modified Mosher's method, and quantum-mechanics-based calculation. Biological evaluation of 1 and 2 revealed that succinyl glyco-oxydifficidin (1) inhibited/dissociated amyloid β (Aβ) aggregation, whereas succinyl macrolactin O (2) inhibited Aβ aggregation, indicating their therapeutic potential for disassembling and removing Aβ aggregation.

Electron Correlation or Basis Set Quality: How to Obtain Converged and Accurate NMR Shieldings for the Third-Row Elements?

The quality of theoretical NMR shieldings calculated at the quantum-chemical level depends on various theoretical aspects, of which the basis set type and size are among the most important factors. Nevertheless, not much information is available on the basis set effect on theoretical shieldings of the NMR-active nuclei of the third row. Here, we report on the importance of proper basis set selection to obtain accurate and reliable NMR shielding parameters for nuclei from the third row of the periodic table. All calculations were performed on a set of eleven compounds containing the elements Na, Mg, Al, Si, P, S, or Cl. NMR shielding tensors were calculated using the SCF-HF, DFT-B3LYP, and CCSD(T) methods, combined with the Dunning valence aug-cc-pVXZ, core-valence aug-cc-pCVXZ, Jensen polarized-convergent aug-pcSseg-n and Karlsruhe x2c-Def2 basis set families. We also estimated the complete basis set limit (CBS) values of the NMR parameters. Widely scattered nuclear shieldings were observed for the Dunning polarized-valence basis set, which provides irregular convergence. We show that the use of Dunning core-valence or Jensen basis sets effectively reduces the scatter of theoretical NMR results and leads to their exponential-like convergence to CBS. We also assessed the effect of vibrational, temperature, and relativistic corrections on the predicted shieldings. For systems with single bonds, all corrections are relatively small, amounting to less than 4% of the CCSD(T)/CBS value. Vibrational and temperature corrections were less reliable for H3PO and HSiCH due to the high anharmonicity of the molecules. An abnormally high relativistic correction was observed for phosphorus in PN, reaching ~20% of the CCSD(T)/CBS value, while the correction was less than 7% for other tested molecules.

Structural Revision of the Stemona Alkaloids Tuberostemonine O, Dehydrocroomines A and B, and Dehydrocroomine

The structural revision of four Stemona alkaloids from Stemona tuberosa is reported. The misassignment of the tuberostemonine O structure (1) was recognized when a new alkaloid, tuberostemonine P, was isolated and unambiguously assigned structure 1 in this work. Reinvestigation of the spectroscopic data and NMR calculations led to the revised structure 1a for tuberostemonine O. The structural misassignment of dehydrocroomine A as 2 was corrected by reinterpreting the X-ray crystal structure, which was consistent with 2a. The structural reassignments of dehydrocroomine B (3 to 3a) and dehydrocroomine (4 to 4a) were confirmed by X-ray crystallography and NMR calculations, respectively.

Aplydactylonins A-C, three new sesquiterpenes from the Vietnamese sea hare Aplysia dactylomela and their cytotoxicity

Aplydactylonins A-C (1-3), three new sesquiterpenes, were isolated from the Vietnamese sea hare Aplysia dactylomela. Their structures and absolute configurations were elucidated based on spectroscopic analysis, X-ray crystallography, and density functional theory (DFT) calculations of NMR and ECD data. Compound 2 exhibited cytotoxicity against HepG2, DU145 and A549 cells with respective IC₅₀ values of 4.08 ± 0.63, 38.64 ± 1.04 and 12.33 ± 0.95 µM. In addition, HepG2 cells treated with 5 μM compound 2 for 48 h showed a significant increase in early apoptotic cells (P < 0.05) and increased caspase 3 activity (P < 0.01). Moreover, compound 2 induced sub-G1 phase arrest in HepG2 cells.