Determination of Molecular Structure Using Vibrational Circular Dichroism Spectroscopy: The Keto-lactone Product of Baeyer−Villiger Oxidation of (+)-(1R,5S)-Bicyclo[3.3.1]nonane-2,7-dione

Different routes for the construction of biologically active diversely functionalized bicyclo[3.3.1]nonanes: an exploration of new perspectives for anticancer chemotherapeutics

Cancer is the second most high-morbidity disease throughout the world. From ancient days, natural products have been known to possess several biological activities, and research on natural products is one of the most enticing areas where scientists are engrossed in the extraction of valuable compounds from various plants to isolate many life-saving medicines, along with their other applications. It has been noticed that the bicyclo[3.3.1]nonane moiety is predominant in most biologically active natural products owing to its exceptional characteristics compared to others. Many derivatives of bicyclo[3.3.1]nonane are attractive to researchers for use in asymmetric catalysis or as potent anticancer entities along with their successful applications as ion receptors, metallocycles, and molecular tweezers. Therefore, this review article discusses several miscellaneous synthetic routes for the construction of bicyclo[3.3.1]nonanes and their heteroanalogues in association with the delineation of their anticancer activities with few selective compounds.

Liquid-liquid equilibrium experiment and mechanism analysis of menthol-based deep eutectic solvents extraction for separation of fuel additive tert-butanol

Deep eutectic solvents (DESs) were synthesized using menthol as hydrogen bond acceptor (HBA) and different carbon chain carboxylic acids as hydrogen bond donors (HBD). The liquid equilibrium (LLE) experiment was used to determine the distribution coefficient (β) and slectivity (S) at standard atmospheric pressure and temperature. The effect of DESs on the separation efficiency was discussed by changing the proportion. Non-random two fluid (NRTL) model was used to correlate the experimental data. The molecular dynamics (MD) simulation method was used to investigate the micro mechanism of the extraction process. The results show van der Waals force plays a leading role in the interaction between solvents and tert-butyl alcohol (TBA) and week force with water. Compared with experimental and simulation results, the interaction between DESs and TBA would also be affected by the change of the number of HBD carbon chains, and DESs with decanoic acid as HBD has the best separation effect, which verifies the feasibility of separating high alcohol compounds from water by DESs and then treating them by DESs.

Vibrational circular dichroism enantiomeric similarity index improvement for absolute configuration discrimination using individual infrared scaling factors

The use of IR individual scaling factors (ISF) for the correction of DFT-calculated frequencies, and its effect on IR and VCD similarity functions, has been evaluated using (+)-(R)-3-methylcyclopentanone as a probe molecule. Contrary to using a single scaling factor to improve spectra matching, this approach sequentially searches for the optimal scaling factor for each calculated transition using a computational search algorithm to maximize the overlap of the calculated and observed IR spectra expressed as the IR similarity (S_IR ) function. The obtained ISFs are then applied to the calculated frequencies, which are used to produce a scaled VCD spectrum for comparison with the observed trace, thereby yielding enantiomeric similarity index (ESI) values as a similarity measure. This procedure provides a significant improvement of the S_IR and ESI values when compared with the use of a single scale factor, showing 15.1% and 34.1% in average increments, respectively, and values as high as 0.98 and 0.94, respectively. When a set of manually found ISFs is used, most differences in S_IR and ESI performance disappear, and nearly perfect spectra matches are found throughout the levels of theory tested. This suggests that the observed differences in computed IR/VCD spectra with commonly used levels of theory are related to differences in frequency rather than to intensity accuracy. Finally, the use of ISFs is expected to enhance the ability to aide stereochemical assignments, particularly in cases where sufficiently accurate frequencies are difficult to obtain due to the system size or complexity.

Reconciliation of chemical, enzymatic, spectroscopic and computational data to assign the absolute configuration of the DNA base lesion spiroiminodihydantoin

The diastereomeric spiroiminodihydantoin-2'-deoxyribonucleoside (dSp) lesions resulting from 2'-deoxyguanosine (dG) or 8-oxo-7,8-dihydro-2'-deoxyguanosine (dOG) oxidation have generated much attention due to their highly mutagenic nature. Their propeller-like shape leads these molecules to display mutational profiles in vivo that are stereochemically dependent. However, there exist conflicting absolute configuration assignments arising from electronic circular dichroism (ECD) and NOESY-NMR experiments; thus, providing definitive assignments of the 3D structure of these molecules is of great interest. In the present body of work, we present data inconsistent with the reported ECD assignments for the dSp diastereomers in the nucleoside context, in which the first eluting isomer from a Hypercarb HPLC column was assigned to be the S configuration, and the second was assigned the R configuration. The following experiments were conducted: (1) determination of the diastereomer ratio of dSp products upon one-electron oxidation of dG in chiral hybrid or propeller G-quadruplexes that expose the re or si face to solvent, respectively; (2) absolute configuration analysis using vibrational circular dichroism (VCD) spectroscopy; (3) reinterpretation of the ECD experimental spectra using time-dependent density functional theory (TDDFT) with the inclusion of 12 explicit H-bonding waters around the Sp free bases; and (4) reevaluation of calculated specific rotations for the Sp enantiomers using the hydration model in the TDDFT calculations. These new insights provide a fresh look at the absolute configuration assignments of the dSp diastereomers in which the first eluting from a Hypercarb-HPLC column is (-)-(R)-dSp and the second is (+)-(S)-dSp. These assignments now provide the basis for understanding the biological significance of the stereochemical dependence of enzymes that process this form of DNA damage.

Determination of Absolute Configuration of Natural Products: Theoretical Calculation of Electronic Circular Dichroism as a Tool

Determination of absolute configuration (AC) is one of the most challenging features in the structure elucidation of chiral natural products, especially those with complex structures. With revolutionary advancements in the area of quantum chemical calculations of chiroptical spectroscopy over the past decade, the time dependent density functional theory (TDDFT) calculation of electronic circular dichroism (ECD) spectra has emerged as a very promising tool. The principle is simply based on the comparison of the calculated and experimental ECD spectra: the more closely they match, the more reliable conclusion for the AC assignment can be drawn. This review attempts to use several examples representing monomeric flavonoids, rotationally restricted biflavonoids, complex hexahydroxydiphenoyl-containing flavonoids, conformationally flexible and restrained sesquiterpenoids, cembrane-africanene terpenoids, dihydropyranocoumarins, alkaloids, and dihydroxanthones to illustrate the applicability of this approach in determining the AC of structurally diverse natural products. The findings clearly indicate that the TDDFT calculation of ECD spectra can quantify the contribution of individual conformers and the interaction of multiple chromophores, making it possible to determine the AC of complex chiral molecules. The calculated electronic transitions and molecular orbitals provide new insight into the interpretation of ECD spectra at the molecular level.

The determination of the absolute configurations of chiral molecules using vibrational circular dichroism (VCD) spectroscopy

The vibrational circular dichroism (VCD) spectra of the two enantiomers of a chiral molecule are of equal magnitude and opposite sign: i.e. mirror-image enantiomers give mirror-image VCD spectra. In principle, the absolute configuration (AC) of a chiral molecule can therefore be determined from its VCD spectrum. In practice, the determination of the AC of a chiral molecule from its experimental VCD spectrum requires a methodology which reliably predicts the VCD spectra of its enantiomers. The only reliable methodology developed to date uses the Stephens quantum-mechanical theory of the rotational strengths of fundamental vibrational transitions, developed in the early 1980s, implemented using ab initio density functional theory in the GAUSSIAN program in the mid 1990s. This methodology has by now been widely used in determining ACs from experimental VCD spectra. In this article we discuss the protocol for determining the ACs of chiral molecules with optimum reliability and its implementation for a variety of molecules, including the D3 symmetry perhydrotriphenylene, a thiazino-oxadiazolone recently shown to be a highly active calcium entry channel blocker, the alkaloid natural products schizozygine, iso-schizogaline, and iso-schizogamine, and the iridoid natural products plumericin, iso-plumericin, and prismatomerin. The power of VCD spectroscopy in determining ACs, even for large organic molecules and for substantially conformationally-flexible organic molecules is clearly documented.

Determination of the absolute configurations of natural products via density functional theory calculations of vibrational circular dichroism, electronic circular dichroism, and optical rotation: The iso-schizozygane alkaloids isoschizogaline and isoschizogamine

The development of density functional theory (DFT) methods for the calculation of vibrational circular dichroism (VCD), electronic circular dichroism (ECD), and transparent spectral region optical rotation (OR) has revolutionized the determination of the absolute configurations (ACs) of chiral molecules using these chiroptical properties. We report the concerted application of DFT calculations of VCD, ECD, and OR to the determination of the ACs of the isoschizozygane alkaloid natural products, isoschizogaline, and isochizogamine, whose ACs have not previously been determined. The ACs of naturally occurring (-)-isoschizogaline and (-)-isoschizogamine, are both determined definitively to be 2R, 7R, 20S, 21S.

Absolute Configuration of Natural Cyclohexene Oxides by Time Dependent Density Functional Theory Calculation of the Optical Rotation: The Absolute Configuration of (−)-Sphaeropsidone and (−)-Episphaeropsidone Revised

The optical rotatory power of some natural cyclohexene oxides, such as (+)-chaloxone, 1, (+)-epiepoformine, 2, (+)-epoformine, 3, (+)-epoxidone, 5, (-)-sphaeropsidone, 6, (-)-episphaeropsidone, 7, and the synthetic compound (+)-epitheobroxide, 4, has been calculated by means of the TDDFT/B3LYP method using the 6-31G(d) and aug-cc-pVDZ basis sets, both in the gas phase and in solution by means of the polarizable continuum model. For compounds 1 and 2, which possess high (about 300 units) optical rotations, gas-phase calculations with the smaller basis set are able to reproduce the experimental values both in sign and order of magnitude. By contrast, a larger basis set is required to satisfactorily simulate the OR values of 3 and 4, which show smaller (about 100 units or less) rotations. The inclusion of the solvent effects is different for different compounds; for 1 and 2, it leads to a better agreement between experiment and prediction, while for 3 and 4, the presence of hydrogen bonding groups makes the application of continuum solvation models less satisfactory. For the flexible system 5, the absolute configuration could not be determined using gas-phase calculations and the smaller basis set, but both inclusion of solvent and larger basis set effects are compulsory. It is noteworthy that calculations both in the gas phase and in the solvent lead to a positive rotatory power for the laevorotatory natural compounds 6 and 7 if the ACs reported in the literature are employed to do the theoretical prediction. This strongly indicates that the ACs previously assigned to these compounds in the literature are not correct and that the TDDFT prediction of OR values has become by now a practicable tool for AC assignments.

Absolute configuration of verticillane diterpenoids by vibrational circular dichroism

Good agreement between theoretical and experimental vibrational circular dichroism curves of (1S,11S,12S)-(+)-verticilla-3E,7E-dien-12-ol (1) established the absolute configuration of this natural diterpene isolated from Bursera suntui. Molecular modeling of 1 was carried out using the Monte Carlo protocol followed by geometry optimization at the B3LYP 6-31G(d,p) level of theory. The 12-membered ring of 1 was found in a single preferred chair-chair-chair-chair conformation. In the six-membered ring a chair prevails over a distorted boat, and the C-OH bond rotation generates three predominant rotamers. Validation of the minimum energy conformation for 1 was achieved by comparison of theoretical and experimental infrared frequencies, vicinal 1H NMR coupling constants, and X-ray diffraction data. This study confirms that (+)-verticillol 1 isolated from Bursera species has the 1S,11S,12S absolute configuration that corresponds to the same enantiomeric series as verticillanes from Sciadopitys and Taxus, while verticillanes from Jackiella and Jungermannia have antipodal structures.

Determination of the Absolute Configurations of Natural Products via Density Functional Theory Calculations of Vibrational Circular Dichroism, Electronic Circular Dichroism, and Optical Rotation: The Iridoids Plumericin and Isoplumericin

The absolute configurations (ACs) of the iridoid natural products, plumericin (1) and isoplumericin (2), have been re-investigated using vibrational circular dichroism (VCD) spectroscopy, electronic circular dichroism (ECD) spectroscopy, and optical rotatory dispersion (ORD). Comparison of DFT calculations of the VCD spectra of 1 and 2 to the experimental VCD spectra of the natural products, (+)-1 and (+)-2, leads unambiguously to the AC (1R,5S,8S,9S,10S)-(+) for both 1 and 2. In contrast, comparison of time-dependent DFT (TDDFT) calculations of the ECD spectra of 1 and 2 to the experimental spectra of (+)-1 and (+)-2 does not permit definitive assignment of their ACs. On the other hand, TDDFT calculations of the ORD of (1R,5S,8S,9S,10S)-1 and -2 over the range of 365-589 nm are in excellent agreement with the experimental data of (+)-1 and (+)-2, confirming the ACs derived from the VCD spectra. Thus, the ACs initially proposed by Albers-Schönberg and Schmid are shown to be correct, and the opposite ACs recently derived from the ECD spectra of 1 and 2 by Elsässer et al. are shown to be incorrect. As a result, the ACs of other iridoid natural products obtained by chemical correlation with 1 and 2 are not in need of revision.

Enantiomeric separation and determination of absolute stereochemistry of asymmetric molecules in drug discovery—Building chiral technology toolboxes

The application of Chiral Technology, or the (extensive) use of techniques or tools for the determination of absolute stereochemistry and the enantiomeric or chiral separation of racemic small molecule potential lead compounds, has been critical to successfully discovering and developing chiral drugs in the pharmaceutical industry. This has been due to the rapid increase over the past 10-15 years in potential drug candidates containing one or more asymmetric centers. Based on the experiences of one pharmaceutical company, a summary of the establishment of a Chiral Technology toolbox, including the implementation of known tools as well as the design, development, and implementation of new Chiral Technology tools, is provided.

Absolute configuration of natural diastereoisomers of 6beta-hydroxyhyoscyamine by vibrational circular dichroism

The absolute configuration of the two natural diastereoisomers of 6beta-hydroxyhyoscyamine has been determined using vibrational circular dichroism (VCD) spectroscopy. The predicted VCD and IR spectra of (3R,6R,2'S)-6beta-hydroxyhyoscyamine (1) and (3S,6S,2'S)-6beta-hydroxyhyoscyamine (2) were calculated using density functional theory (DFT) with the B3LYP functional and 6-31G(d) basis set and considering the eight lower energy conformations of each diastereoisomer. In both cases, the first four conformers showed the N-Me group in the syn orientation, permitting the formation of a hydrogen bond between the hydroxy group at the tropane ring and the tertiary nitrogen atom. In addition the eight conformers showed an intramolecular hydrogen bond between the hydroxy and carbonyl groups of the tropic ester moiety. The calculated IR spectra of both molecules showed good agreement with the experimental spectra, while comparison of the experimental and calculated VCD spectra showed that the absolute configuration of dextrorotatory 6beta-hydroxyhyoscyamine is (3R,6R,2'S), while the levorotatory isomer is (3S,6S,2'S).

Determination of Absolute Configuration Using Density Functional Theory Calculations of Optical Rotation and Electronic Circular Dichroism: Chiral Alkenes

In principle, the absolute configuration (AC) of a chiral molecule can be deduced from its optical rotation (OR) and/or its electronic circular dichroism (ECD). In practice, this requires reliable methodologies for predicting OR and ECD. The recent application of ab initio time-dependent density functional theory (TDDFT) to the calculation of transparent spectral region OR and ECD has greatly enhanced the reliability with which these phenomena can be predicted. TDDFT calculations of OR and ECD are being increasingly utilized in determining ACs. Nevertheless, such calculations are not perfect, and as a result, ACs determined are not 100% reliable. In this paper, we examine the reliability of the TDDFT methods in the case of chiral alkenes. Sodium d line specific rotations, [alpha]D, are predicted for 26 conformationally rigid alkenes of known AC, ranging in size from 5 to 20 C atoms, and with [alpha]D values in the range of 0-500. The mean absolute deviation of predicted [alpha]D values from experimental values is 28.7. With one exception, beta-pinene, the signs of [alpha]D are correctly predicted. Errors in calculated [alpha]D values are approximately random. Our results define a "zone of indeterminacy" within which calculated [alpha]D values cannot be used to determine ACs with >95% confidence. TDDFT ECD spectra are predicted for eight of the alkenes and compared to experimental spectra. Agreement ranges from modestly good to poor, leading to the conclusion that TDDFT calculations of ECD spectra are not yet of sufficient accuracy to routinely provide highly reliable ACs. TDDFT OR calculations for two conformationally flexible alkenes, 3-tert-butylcyclohexene and trans-4-carene, are also reported. For the former, predicted rotations are incorrect in sign over the range 589-365 nm. It is possible that the AC of this molecule has been incorrectly assigned.

Determination of the absolute configurations of natural products via density functional theory calculations of optical rotation, electronic circular dichroism, and vibrational circular dichroism: the cytotoxic sesquiterpene natural products quadrone, suberosenone, suberosanone, and suberosenol A acetate

The determination of the absolute configurations (ACs) of chiral molecules using the chiroptical techniques of optical rotation (OR), electronic circular dichroism (ECD), and vibrational circular dichroism (VCD) has been revolutionized by the development of density functional theory (DFT) methods for the prediction of these properties. Here, we demonstrate the significance of these advances for the stereochemical characterization of natural products. Time-dependent DFT (TDDFT) calculations of the specific rotations, [alpha](D), of four cytotoxic natural products, quadrone (1), suberosenone (2), suberosanone (3), and suberosenol A acetate (4), are used to assign their ACs. TDDFT calculations of the ECD of 1 are used to assign its AC. The VCD spectrum of 1 is reported and also used, together with DFT calculations, to assign its AC. The ACs of 1 derived from its [alpha](D), ECD, and VCD are identical and in agreement with the AC previously determined via total synthesis. The previously undetermined ACs of 2-4, derived from their [alpha](D) values, have absolute configurations of their tricyclic cores identical to that of 1. Further studies of the ACs of these molecules using ECD and, especially, VCD are recommended to establish more definitively this finding. Our studies of the OR, ECD, and VCD of quadrone are the first to utilize DFT calculations of all three properties for the determination of the AC of a chiral natural product molecule.