Determination of absolute configuration using density functional theory calculation of optical rotation: chiral alkanes

Discovery of pyranonaphthoquinones and an eighteen-membered ring macrolide from the rhizospheric soil-derived fungus Phialocephala sp. YUD18001 by OSMAC strategy

Two new pyranonaphthoquinones, phialoyxinones A (1) and B (2), a new eighteen-membered ring lactone, phialoyxtone (3), and five known pyranonaphthoquinone derivatives were identified from the fungus Phialocephala sp. YUD18001, which was isolated from the rhizospheric soil associated with Gastrodia elata. Their structures were unequivocally established by a comprehensive interpretation of the spectroscopic data, with the stereochemistry for 1-3 was defined by a combination of TDDFT calculations, and the DP4+ probability analysis based on NMR chemical shift calculations. All of the new compounds 1-3 were evaluated for cytotoxicity and acetylcholinesterase inhibitory, compound 2 exhibited in vitro cytotoxic activities against five human cancer cell lines (HL-60, SMMC-7721, A549, MCF-7 and SW480) with IC50 values ranging from 11.80 to 19.32 μM. Compounds 2 and 3 exhibited moderate AChE inhibitory activities. A putative biosynthetic pathway for the pyranonaphthoquinones was proposed.

Novel Kinetic Resolution of Thiazolo-Benzimidazolines Using MAO Enzymes

The kinetic resolution of racemic 1H,3H-thiazolo[3,4-a]benzimidazoline (TBIM) heterocycles was achieved using E. coli whole cells expressing the MAO-N D11 enzyme. Several cosolvents were screened using TBIM 2a as the substrate. DMF was the best cosolvent, affording the pure enantiomer (+)-2a in 44% yield, 94% ee. The stereochemistry of TBIM was predicted by means of ab initio calculations of optical rotation and circular dichroism spectra. The reaction scope was investigated for 11 substituted (±) TBIM using an optimized protocol. The best yield and % ee were obtained for the nonsubstituted 2a. Among the substituted compounds, the 5-substituted-TBIM showed better % ee than the 4-substituted one. The small electron donor group (Me) led to better % ee than the electron-withdrawing groups (-NO2 and -CO2Et), and the bulky naphthyl group was detrimental for the kinetic resolution. Docking experiments and molecular dynamics (MD) simulations were employed to further understand the interactions between MAO-N D11 and the thiazolo-benzimidazoline substrates. For 2a, the MD showed favorable positioning and binding energy for both enantiomers, thus suggesting that this kinetic resolution is influenced not only by the active site but also by the entry tunnel. This work constitutes the first report of the enzymatic kinetic resolution applied to TBIM heterocycles.

Photoelectron Circular Dichroism as a Probe of Chiral Hydrocarbons

The sensitivity of Photoelectron Circular Dichroism (PECD) in the angular distribution of photoelectrons, a recent chiral technique, to detect chirality in pure hydrocarbons is investigated in a number of benchmark molecules. It is found that a very large chiral signal is expected, surpassing most current examples, giving a sure fingerprint of absolute configuration. On the other hand, the sensitivity to specific isomers or closely related molecules is relatively modest.

Optical Activity in Saturated Cyclic Amines: Untangling the Roles of Nitrogen-Inversion and Ring-Puckering Dynamics

The dispersive optical activity of two saturated cyclic amines, (R)-2-methylpyrrolidine (R-2MPY) and (S)-2-methylpiperidine (S-2MPI), has been interrogated under isolated and solvated conditions to elucidate the roles of large-amplitude motion associated with nitrogen-center inversion and ring-puckering dynamics. Experimental optical rotatory dispersion profiles were almost mirror images of one another and displayed parallel solvent dependencies. Quantum-chemical analyses built on density-functional and coupled-cluster methods revealed four low-lying conformers for each molecule, which are distinguished by axial/equatorial orientations of their amino hydrogens and methyl substituents. Chiroptical signatures predicted for these species were combined through an independent-conformer ansatz to simulate the ensemble-averaged response, with a polarizable continuum model (PCM) being used to treat implicit solute-solvent interactions. The intrinsic behavior observed for isolated (gaseous) R-2MPY and S-2MPI was reproduced best by merging coupled-cluster (CCSD) estimates of rotatory powers with thermal population fractions deduced from complete basis set (CBS-APNO) free-energy calculations. Although prior claims of sizable chiroptical contributions arising from helically twisted (chiral) heterocyclic frameworks could be discounted, less satisfactory agreement between experiment and theory was realized for solution phases. Response properties sustained modest isomer-dependent changes in the presence of PCM solvation, but the corresponding energy metrics showed systematic trends, whereby structures having larger electric-dipole moments were stabilized preferentially in media of high polarity. Despite the fact that R-2MPY conformations were predicted to undergo a progressive reordering of their relative energies across the six solvents of interest, S-2MPI was found to exhibit more pronounced solvent-induced perturbations at long wavelengths (viz., in regions far removed from electronic resonances). Experimental results are discussed in terms of the distinct ring-puckering mechanisms for R-2MPY and S-2MPI, which are expected to be dominated by hindered pseudorotation among envelope/twist motifs and semi-inversion between chairlike antipodes, respectively.

Chemical Constituents from Roots of Sophora davidii (Franch.) Skeels and Their Glucose Transporter 4 Translocation Activities

Sophora davidii (Franch.) Skeels is a multi-purpose traditional medicine that has long been used for the treatment of various diseases. To discover the potential bioactive composition of S. davidii, a chemical investigation was thus performed. In this research, two new stilbene oligomers, Davidiol E–F (1–2), one new 4-aryl-substituted isoflavan Davidinin A (3), and one new 2-arylbenzofuran dimer, Shandougenine C (4), as well as six known compounds (5–10) were obtained from the ethyl acetate fraction of Sophora davidii (Franch.) Skeels. The structures of new compounds were established by extensive 1D and 2D nuclear magnetic resonance (NMR) spectra with mass spectroscopy data. The absolute configuration of 1–3 was assigned by comparing its experimental and calculated electronic circular dichroism (ECD) spectra. Compounds 1–10 promoted glucose transporter 4 (GLUT-4) translocations by the range of 1.28–2.60 folds, respectively. Compound 9 showed the most potent glucose transporter 4 translocations with 1.60 fold enhancement. The result attained in this study indicated that the separation and characterization of these compounds plays an important role in the research and development of new anti-diabetic drugs and pharmaceutical industry.

Highly Potent Antiausterity Agents from Callistemon citrinus and Their Mechanism of Action against the PANC-1 Human Pancreatic Cancer Cell Line

Human pancreatic cancer cells display remarkable tolerance to nutrition starvation that help them to survive in a hypovascular tumor microenvironment, a phenomenon known as "austerity". The elucidation of agents countering this tolerance is an established antiausterity strategy in anticancer drug discovery. In this study, a Callistemon citrinus leaf extract inhibited the viability of PANC-1 human pancreatic cancer cells preferentially under nutrient-deprived medium (NDM) with a PC₅₀ value of 7.4 μg/mL. Workup of this extract resulted in the isolation of three new meroterpenoids, callistrilones L-N (1-3), together with 14 known compounds (4-17). The structure elucidation of the new compounds was achieved by HRFABMS and by NMR and ECD spectroscopic analysis. The new compounds showed highly potent preferential cytotoxicity against PANC-1 cells with PC₅₀ values ranging from 10 to 65 nM in NDM. Of these, callistrilone L (1) inhibited PANC-1 cell migration and colony formation in a normal nutrient-rich condition. Callistrilone L (1) also strongly suppressed the migration of PANC-1 cells in real time. Mechanistically, 1 was found to inhibit the Akt/mTOR and autophagy activation pathway. Callistrilone L (1) and related meroterpenoids are promising leads for anticancer drug development based on the antiausterity strategy used in this work.

Assigning the absolute configuration of single aliphatic molecules by visual inspection

Deciphering absolute configuration of a single molecule by direct visual inspection is the next step in compound identification, with far-reaching implications for medicinal chemistry, pharmacology, and natural product synthesis. We demonstrate the feasibility of this approach utilizing low temperature atomic force microscopy (AFM) with a CO-functionalized tip to determine the absolute configuration and orientation of a single, adsorbed [123]tetramantane molecule, the smallest chiral diamondoid. We differentiate between single enantiomers on Cu(111) by direct visual inspection, and furthermore identify molecular dimers and molecular clusters. The experimental results are confirmed by a computational study that allowed quantification of the corresponding intermolecular interactions. The unique toolset of absolute configuration determination combined with AFM tip manipulation opens a route for studying molecular nucleation, including chirality-driven assembly or reaction mechanisms.

Structures and Biological Evaluation of Monoterpenoid Glycosides from the Roots of Paeonia lactiflora

Fractionation of an aqueous extract of the air-dried roots of a traditional Chinese medicinal plant, Paeonia lactiflora, yielded the new monoterpenoid glycosides 1-10. Their structures were assigned via spectroscopic techniques, and the absolute configurations of 1, 4-6, and 8 were verified via chemical methods, specific rotation, and electronic circular dichroism data. Compounds 1-4 are rare compared to the reported cage-like paeoniflorin derivatives; that is, they comprised two monoterpenoidal moieties. In the in vitro assay, compounds 5, 8, and 9 showed weak inhibitions against lipopolysaccharide-induced nitric oxide production in RAW264.7 macrophages, with IC₅₀ values of 64.8, 60.1, and 97.5 μM, respectively.

Optical Rotation Calculations for a Set of Pyrrole Compounds

Optical rotation of 14 molecules containing the pyrrole group is calculated by employing both time-dependent density functional theory (TDDFT) with the CAM-B3LYP functional and the second-order approximate coupled-cluster singles and doubles (CC2) method. All optical rotations have been provided using the aug-cc-pVDZ basis set at λ = 589 nm. The two methods predict similar results for both sign and magnitude for the optical rotation of all molecules. The obtained signs are consistent with experiments as well, although several conformers for four molecules needed to be studied to reproduce the experimental sign. We have also calculated excitation energies and rotatory strengths for the six lowest lying electronic transitions for several conformers of the two smallest molecules and found that each rotatory strength has various contributions for each conformer which can cause different optical rotations for different conformers of a molecule. Our results illustrate that both methods are able to reproduce the experimental optical rotations, and that the CAM-B3LYP functional, the least computationally expensive method used here, is an applicable and reliable method to predict the optical rotation for these molecules in line with previous studies.

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.

Theoretical approaches to the calculation of Raman optical activity spectra

In this article, we will give a brief account of the different approaches that have been presented in the literature for calculating Raman optical activity (ROA) spectra by ab initio methods. We will also outline the general structure of a self-consistent-field-based approach for analytic calculations of ROA spectra, including also contributions from London orbitals. The use of London orbitals ensures that the relevant ROA parameters are gauge origin independent. We will also give an outlook on the future of ab initio calculations of Raman optical activity spectra.

Structural reassignment, absolute configuration, and conformation of hypurticin, a highly flexible polyacyloxy-6-heptenyl-5,6-dihydro-2H-pyran-2-one

The structural reassignment, absolute configuration, and conformational behavior of the highly flexible natural product hypurticin (pectinolide E), 6S-[3'S,5'R,6'S-triacetoxy-1Z-heptenyl]-5S-acetoxy-5,6-dihydro-2H-pyran-2-one (1), were ascertained by a molecular modeling protocol, which includes extensive conformational searching, geometry optimization by DFT B3LYP/DGDZVP calculations, and comparison between the theoretical (DFT) and experimental (1)H-(1)H NMR coupling constants. Hyptolide (2), a related cytotoxic 5,6-dihydro-2H-pyran-2-one that increased the S phase of the HeLa cell cycle, was employed as a reference substance to validate the theoretical protocol designed to characterize the 3D properties of compound 1. The related synthetic derivative, tri-O-acetyl-3,6-dideoxy-d-glucose diphenyldithioacetal (14), was prepared by a six-step reaction sequence starting from d-glucose and served as an enantiopure building block to reinforce the structural and configurational assignment of 1. This protocol proved to be an important tool for the structural characterization of highly flexible bioactive polyoxygenated natural products.

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.

Determination of the absolute configurations of natural products using TDDFT optical rotation calculations: the iridoid oruwacin

We report the determination of the absolute configuration (AC) of the iridoid natural product oruwacin by comparison of the optical rotations, [alpha] D, of its two enantiomers, calculated using time-dependent density functional theory (TDDFT), to the experimental [alpha] D value, +193. Conformational analysis of oruwacin using density functional theory (DFT) identifies eight conformations which are significantly populated at room temperature. [alpha] D values of these eight conformations are calculated using TDDFT at the B3LYP/aug-cc-pVDZ//B3LYP/6-31G* level, leading to the conformationally averaged [alpha] D values of -193 for the (1 R,5 S,8 S,9 S,10 S)-enantiomer and +193 for the (1 S,5 R,8 R,9 R,10 R)-enantiomer. Comparison of the calculated [alpha] D values to the value of the natural product proves that naturally occurring oruwacin has the AC 1 S,5 R,8 R,9 R,10 R. This AC is opposite to that assigned by Adesogan by comparison of the [alpha] D of oruwacin to that of the iridoid plumericin. Our results show that the assignment of the AC of a natural product by comparison of its [alpha] D to that of a chemically related molecule can be unreliable and should not be assumed to be definitive.

Determination of the absolute configurations of flexible molecules: synthesis and theoretical simulation of electronic circular dichroism/optical rotation of some pyrrolo[2,3-b]indoline alkaloids--a case study

The paper describes the synthesis and chiroptical properties of (-)-1,2,3,3a,8,8a,-hexahydro-1,3a-dimethyl-pyrrolo[2,3-b]indole, (-)-1, one of the monomeric units of many flexible polypyrroloindoline alkaloids and (-)-chimonanthine, (-)-2. The aim of this investigation is to show that, under certain circumstances, namely, with molecules for which the sign and order of magnitude of [alpha](D) are determined by the lowest-energy valence-shell transitions (referred to as class (a) molecules), a small basis set calculation of chiroptical properties provides reliable results, and that such a treatment can be employed for absolute configurational assignment of larger oligomers, for which the increased flexibility renders the analysis as formidable task. Actually, as the aforementioned two molecules belong to class (a) systems, a TDDFT/B3LYP/6-31G* calculation of the ECD and ORD spectra gives rise to a more than satisfactory simulation of these data, assuming the reported absolute configurations. In other words, the use of the TDDFT/B3LYP method with the small 6-31G* basis set enables one to treat large and flexible molecules such as (-)-2 (52 atoms and 6 conformers) by usage of a simple PC in about 2 weeks. This protocol demonstrates that an ab initio prediction of ECD/ORD spectra results in reliable assignments of absolute configuration of even relatively large natural products, thus economizing computation time.

Magnitude of zero-point vibrational corrections to optical rotation in rigid organic molecules: a time-dependent density functional study

The zero-point vibrational corrections (ZPVCs) to the optical rotation of 22 rigid organic molecules have been calculated using time-dependent density functional theory with the B3LYP hybrid functional. We outline an implementation for calculating ZPVCs that can be applied with a variety of quantum chemistry programs and methods. It is shown that the ZPVCs to optical rotation have a wide range of values and can be quite significant depending on the molecule. On average, it has been determined that vibrational corrections can account for about 20% of the optical rotation for the equilibrium value. It is also concluded that vibrational effects alone cannot be the only factor in improving the calculated values of optical rotation with respect to experimental data measured in solution.

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.

Quantum Chemical Study on the Circular Dichroism Spectra and Specific Rotation of Donor−Acceptor Cyclophanes

The structures of donor,acceptor-substituted cyclophanes were optimized by DFT and MP2 methods and compared with the X-ray crystallographic structures. The electronic circular dichroism (CD) spectra of these chiral cyclophanes were simulated by time dependent density functional theory (TD-DFT) with several functionals including different amounts of "exact" Hartree-Fock exchange. The experimental oscillator and rotatory strengths were best reproduced by the BH-LYP/TZV2P method. The specific rotation and vibrational circular dichroism (VCD) spectra were also calculated at the BH-LYP/aug-cc-pVDZ and B3-LYP/6-31G(d) levels, respectively, and compared with the experimental data. Better performance was obtained with the ECD, rather than the specific rotation or the VCD spectral calculations in view of the computation time and accuracy for the determination of absolute configuration (AC). The exciton coupling model can be applied only for the cyclophanes without CT-character. However, the split pattern found in the experiment does not appear to originate from a simple two-transition coupling, indicating that this method should be applied with caution to the AC determination. This conclusion was supported by the TD-DFT investigations of the transition moments and the roles of excited-state electronic configuration associated with these split bands. Cyclophanes with donor-acceptor interactions showed Cotton effects at the CT band and couplets at the 1La and 1Lb bands. Although the degree of charge transfer between the rings is very small, as revealed by a Mulliken-Hash analysis, the split Cotton effects are due to a large separation in energy of the donor and acceptor orbitals. The effect of the distance and angle between the donor and acceptor moieties in model (intermolecular) CT complexes on the calculated CD spectra was also studied and compared with those obtained for various paracyclophanes.

Absolute Configuration of Conformationally Flexiblecis-Dihydrodiol Metabolites by the Method of Confrontation of Experimental and Calculated Electronic CD Spectra and Optical Rotations

We have determined the absolute configurations of conformationally flexible cis-dihydrodiol metabolites (cis-1,2-dihydroxy-3,5-cyclohexadienes), bearing different substituents (e.g., Br, F, CF3, CN, Me) in 3- and 5-positions, by the method of confrontation of experimental and calculated electronic CD spectra and optical rotations. Convergent results were obtained by both methods in eight out of ten cases. For the difficult cases, where either conformer population and/or chiroptical properties (calculated rotational strengths of the long-wavelength Cotton effect or optical rotations) of contributing conformers remain inconclusive, the absolute configuration could still be correctly assigned based on one of the biased properties (either ECD or optical rotation). This approach appears well-suited for a broad spectrum of conformationally flexible chiral molecules.

Determination of the Absolute Configuration of a Chiral Oxadiazol-3-one Calcium Channel Blocker, Resolved Using Chiral Chromatography, via Concerted Density Functional Theory Calculations of Its Vibrational Circular Dichroism, Electronic Circular Dichroism, and Optical Rotation

The chiral oxadiazol-3-one 2 has recently been shown to exhibit myocardial calcium entry channel blocking activity, substantially higher than that of diltiazem. To determine the enantioselectivity of this activity, the enantiomers of 2 have been resolved using chiral chromatography. The absolute configuration (AC) of 2 has been determined by comparison of density functional theory (DFT) calculations of its vibrational circular dichroism (VCD) spectrum, electronic circular dichroism (ECD) spectrum, and optical rotation (OR) to experimental VCD, ECD, and OR data. All three chiroptical properties yield identical ACs; the AC of 2 is unambiguously determined to be S(+)/R(-).