Antimicrobial Dihydroflavonols and Isoflavans Isolated from the Root Bark of Dalbergia gloveri.

Three new dihydroflavonols, gloverinols A-C (1-3), a new flavon-3-ol, gloverinol D (4), two new isoflavans, gloveriflavan A (5) and B (6), and seven known compounds were isolated from the root bark of Dalbergia gloveri. The structures of the isolates were elucidated by using NMR, ECD, and HRESIMS data analyses. Among the isolated compounds, gloverinol B (2), gloveriflavan B (6), and 1-(2,4-dihydroxyphenyl)-3-hydroxy-3-(4-hydroxyphenyl)-1-propanone (10) were the most active against Staphylococcus aureus, with MIC values of 9.2, 18.4, and 14.2 µM, respectively.

Antiviral Rotenoids and Isoflavones Isolated from Millettia oblata ssp. teitensis.

Three new (1-3) and six known rotenoids (5-10), along with three known isoflavones (11-13), were isolated from the leaves of Millettia oblata ssp. teitensis. A new glycosylated isoflavone (4), four known isoflavones (14-18), and one known chalcone (19) were isolated from the root wood extract of the same plant. The structures were elucidated by NMR and mass spectrometric analyses. The absolute configuration of the chiral compounds was established by a comparison of experimental ECD and VCD data with those calculated for the possible stereoisomers. This is the first report on the use of VCD to assign the absolute configuration of rotenoids. The crude leaves and root wood extracts displayed anti-RSV (human respiratory syncytial virus) activity with IC50 values of 0.7 and 3.4 µg/mL, respectively. Compounds 6, 8, 10, 11, and 14 showed anti-RSV activity with IC50 values of 0.4-10 µM, while compound 3 exhibited anti-HRV-2 (human rhinovirus 2) activity with an IC50 of 4.2 µM. Most of the compounds showed low cytotoxicity for laryngeal carcinoma (HEp-2) cells; however compounds 3, 11, and 14 exhibited low cytotoxicity also in primary lung fibroblasts. This is the first report on rotenoids showing antiviral activity against RSV and HRV viruses.

Improving the IR spectra alignment algorithm with spectra deconvolution and combination with Raman or VCD spectroscopy.

The relative stereochemistry of organic molecules can be determined by comparing theoretical and experimental infrared (IR) spectra of all isomers and assessing the best match. For this purpose, we have recently developed the IR spectra alignment (IRSA) algorithm for automated optimal alignment. IRSA provides a set of quantitative metrics to identify the candidate structure that agrees best with the experimental spectrum. While the correct diastereomer could be determined for the tested sets of rigid and flexible molecules, two issues were identified with more complex compounds that triggered further development. First, strongly overlapping peaks in the IR spectrum are not treated adequately in the current IRSA implementation. Second, the alignment of multiple spectra from different sources (e.g. IR and VCD or Raman) can be improved. In this study, we present an in-depth discussion of these points, followed by the description of modifications to the IRSA algorithm to address them. In particular, we introduce the concept of deconvolution of the experimental and theoretical spectra with a set of pseudo-Voigt bands. The pseudo-Voigt bands have a set of parameters, which can be employed in the alignment algorithm, leading to improved scoring functions. We test the modified algorithm on two data sets. The first set contains compounds with IR and Raman spectra measured in this study, and the second set contains compounds with IR and VCD spectra available in the literature. We show that the algorithm is able to determine the correct diastereomer in all cases. The results highlight that vibrational spectroscopy can be a valuable alternative or complementary method to inform about the stereochemistry of compounds, and the performance of the updated IRSA algorithm suggests that it is a powerful tool for quantitative-based spectral assignments in academia and industry.

Pushing the boundaries of VCD spectroscopy in natural product chemistry.

Vibrational circular dichroism (VCD) is one of the most powerful techniques to assess the stereochemistry of chiral molecules in solution state. The need for quantum chemical calculations to interpret experimental data, however, has precluded its widespread use by non-experts. Herein, we propose the search and validation of IR and VCD spectral markers to circumvent the requirement of DFT calculations allowing for absolute configuration assignments even in complex mixtures. To that end, a combination of visual inspection and machine learning based methods is used. Monoterpene mixtures are selected for this proof-of-concept study.

Correction: Monaco et al. Chiral Phase Transfer Catalysis in the Asymmetric Synthesis of a 3,3-Disubstituted Isoindolinone and Determination of Its Absolute Configuration by VCD Spectroscopy. Molecules 2020, 25, 2272.

In this note, we report a correction to the published article, Molecules2020, 25, 2272 [...].

The Halogen Bond in Weakly Bonded Complexes and the Consequences for Aromaticity and Spin-Orbit Coupling.

The halogen bond complexes CF3X⋯Y and C2F3X⋯Y, with Y = furan, thiophene, selenophene and X = Cl, Br, I, have been studied by using DFT and CCSD(T) in order to understand which factors govern the interaction between the halogen atom X and the aromatic ring. We found that PBE0-dDsC/QZ4P gives an adequate description of the interaction energies in these complexes, compared to CCSD(T) and experimental results. The interaction between the halogen atom X and the π-bonds in perpendicular orientation is stronger than the interaction with the in-plane lone pairs of the heteroatom of the aromatic cycle. The strength of the interaction follows the trend Cl < Br < I; the chalcogenide in the aromatic ring nor the hybridization of the C−X bond play a decisive role. The energy decomposition analysis shows that the interaction energy is dominated by all three contributions, viz., the electrostatic, orbital, and dispersion interactions: not one factor dominates the interaction energy. The aromaticity of the ring is undisturbed upon halogen bond formation: the π-ring current remains equally strong and diatropic in the complex as it is for the free aromatic ring. However, the spin-orbit coupling between the singlet and triplet π→π* states is increased upon halogen bond formation and a faster intersystem crossing between these states is therefore expected.

Anti-SARS-CoV-2 Activity and Cytotoxicity of Amaryllidaceae Alkaloids from Hymenocallis littoralis.

The Amaryllidaceae species are well-known as a rich source of bioactive compounds in nature. Although Hymenocallis littoralis has been studied for decades, its polar components were rarely explored. The current phytochemical investigation of Amaryllidaceae alkaloids from H. littoralis led to the identification of three previously undescribed compounds: O-demethyl-norlycoramine (1), (-)-2-epi-pseudolycorine (2) and (+)-2-epi-pseudolycorine (3), together with eight known compounds: 6α-hydroxyhippeastidine (4), 6ß-hydroxyhippeastidine (5), lycorine (6), 2-epi-lycorine (7), zephyranthine (8), ungeremine (9), pancratistatin (10) and 9-O-demethyl-7-O-methyllycorenine (11). Among the eight previously reported compounds, five were isolated from H. littoralis for the first time (compounds 4, 5, 7, 8, and 9). Compounds 1, 4, 5, 7, 8, and 11 exhibited weak anti-SARS-CoV-2 activity (EC50 = 40-77 µM) at non-cytotoxic concentrations. Assessment of cytotoxicity on the Vero-E6 cell line revealed lycorine and pancratistatin as cytotoxic substances with CC50 values of 1.2 µM and 0.13 µM, respectively. The preliminary structure-activity relationship for the lycorine-type alkaloids in this study was further investigated, and as a result ring C appears to play a crucial role in their anti-SARS-CoV-2 activity.

Insights in the vibrational optical activity spectra of the antibiotic vancomycin in DMSO.

Vibrational circular dichroism (VCD) and Raman optical activity (ROA) are two spectroscopic techniques that are sensitive towards the conformational behaviour of molecules, and are often complementary herein. In this work we pursue the determination of the conformational ensemble of the antibiotic glycopeptide vancomycin in DMSO through comparison of experimental and computational spectra, both for VCD and ROA. ROA is found to be highly suitable for the task, identifying an ensemble that strongly resembles the NMR conformation. In the case of VCD, however, a too high sensitivity of the intensities with respect to minor conformational changes hampers a reliable conformational analysis. Whence attempting to improve the match between the VCD experiment and calculations by any means - e.g., by inducing minor conformational changes or including solvent effects in the calculations - we show that there is the risk of going down the rabbit hole. In conclusion, this work contributes to the broader understanding of where, when and how VCD and ROA can be deployed as techniques for conformational analysis.

Epimeric Mixture Analysis and Absolute Configuration Determination Using an Integrated Spectroscopic and Computational Approach-A Case Study of Two Epimers of 6-Hydroxyhippeastidine.

Structural elucidation has always been challenging, and misassignment remains a stringent issue in the field of natural products. The growing interest in discovering unknown, complex natural structures accompanies the increasing awareness concerning misassignments in the community. The combination of various spectroscopic methods with molecular modeling has gained popularity in recent years. In this work, we demonstrated, for the first time, its power to fully elucidate the 2-dimensional and 3-dimensional structures of two epimers in an epimeric mixture of 6-hydroxyhippeastidine. DFT calculation of chemical shifts was first performed to assist the assignment of planar structures. Furthermore, relative and absolute configurations were established by three different ways of computer-assisted structure elucidation (CASE) coupled with ORD/ECD/VCD spectroscopies. In addition, the significant added value of OR/ORD computations to relative and absolute configuration determination was also revealed. Remarkably, the differentiation of two enantiomeric scaffolds (crinine and haemanthamine) was accomplished via OR/ORD calculations with cross-validation by ECD and VCD.

Synthesis, Structure and Photophysical Properties of a New Class of Inherently Chiral Boron(III) Chelates-The tert-Leucine Complexes.

A new family of boron(III) chelates is introduced whereby molecular chirality, confirmed by circular dichroism, is imported during synthesis such that isolation of the diastereoisomers does not require separation procedures. The photophysical properties of two members of the family have been examined: the N,O,O-salicylaldehyde-based derivative shows pronounced intramolecular charge-transfer character in fluid solution and is weakly fluorescent, with a large Stokes shift. The corresponding 2-methylamino-benzaldehyde-derived N,N,O-chelate absorbs and fluoresces in the visible region with a much smaller Stokes shift. Orange fluorescence is also observed for this compound as a cast film. Temperature-dependence studies show that decay of the fluorescent state is weakly activated but emission is less than quantitative at 77 K. Quite rare for boron(III)-based chelates, this derivative undergoes intersystem crossing to form a meta-stable triplet-excited state. X-ray crystal structures are reported for both compounds, along with simulated ECD spectra.

Exploring machine learning methods for absolute configuration determination with vibrational circular dichroism.

The added value of supervised Machine Learning (ML) methods to determine the Absolute Configuration (AC) of compounds from their Vibrational Circular Dichroism (VCD) spectra was explored. Among all ML methods considered, Random Forest (RF) and Feedforward Neural Network (FNN) yield the best performance for identification of the AC. At its best, FNN allows near-perfect AC determination, with accuracy of prediction up to 0.995, while RF combines good predictive accuracy (up to 0.940) with the ability to identify the spectral areas important for the identification of the AC. No loss in performance of either model is observed as long as the spectral sampling interval used does not exceed the spectral bandwidth. Increasing the sampling interval proves to be the best method to lower the dimensionality of the input data, thereby decreasing the computational cost associated with the training of the models.

Antiplasmodial Oleanane Triterpenoids from Terminalia albida Root Bark.

Phytochemical investigation of the n-BuOH extract of the roots of Terminalia albida Sc. Elliot (Combretaceae) led to the isolation and identification of 10 oleanane triterpenoids (1-10), among which six new compounds, i.e., albidanoside A (2), albidic acid A (4), albidinolic acid (5), albidienic acid (8), albidolic acid (9), and albidiolic acid (10), and two triterpenoid aglycones, i.e., albidic acid B (6) and albidic acid C (7), were isolated here for the first time from a natural source, along with two known compounds. The structures of these constituents were established by means of 1D and 2D NMR spectroscopy and ESI mass spectrometry. The isolated compounds were evaluated for their antiplasmodial and antimicrobial activity against the chloroquine-resistant strain Plasmodium falciparum K1, Candida albicans, and Staphylococcus aureus. Compounds 1-4, 6, 7, and 8 showed moderate antiplasmodial activity with IC50 values between 5 and 15 µM. None of the tested compounds were active against C. albicans or S. aureus. These findings emphasize the potential of T. albida as a source for discovery of new antiplasmodial compounds.

A Combined Experimental/Quantum-Chemical Study of Tetrel, Pnictogen, and Chalcogen Bonds of Linear Triatomic Molecules.

Linear triatomic molecules (CO2, N2O, and OCS) are scrutinized for their propensity to form perpendicular tetrel (CO2 and OCS) or pnictogen (N2O) bonds with Lewis bases (dimethyl ether and trimethyl amine) as compared with their tendency to form end-on chalcogen bonds. Comparison of the IR spectra of the complexes with the corresponding monomers in cryogenic solutions in liquid argon enables to determine the stoichiometry and the nature of the complexes. In the present cases, perpendicular tetrel and pnictogen 1:1 complexes are identified mainly on the basis of the lifting of the degenerate ν 2 bending mode with the appearance of both a blue and a red shift. Van 't Hoff plots of equilibrium constants as a function of temperature lead to complexation enthalpies that, when converted to complexation energies, form the first series of experimental complexation energies on sp1 tetrel bonds in the literature, directly comparable to quantum-chemically obtained values. Their order of magnitude corresponds with what can be expected on the basis of experimental work on halogen and chalcogen bonds and previous computational work on tetrel bonds. Both the order of magnitude and sequence are in fair agreement with both CCSD(T) and DFA calculations, certainly when taking into account the small differences in complexation energies of the different complexes (often not more than a few kJ mol-1) and the experimental error. It should, however, be noted that the OCS chalcogen complexes are not identified experimentally, most probably owing to entropic effects. For a given Lewis base, the stability sequence of the complexes is first successfully interpreted via a classical electrostatic quadrupole-dipole moment model, highlighting the importance of the magnitude and sign of the quadrupole moment of the Lewis acid. This approach is validated by a subsequent analysis of the molecular electrostatic potential, scrutinizing the σ and π holes, as well as the evolution in preference for chalcogen versus tetrel bonds when passing to "higher" chalcogens in agreement with the evolution of the quadrupole moment. The energy decomposition analysis gives further support to the importance/dominance of electrostatic effects, as it turns out to be the largest attractive term in all cases considered, followed by the orbital interaction and the dispersion term. The natural orbitals for chemical valence highlight the sequence of charge transfer in the orbital interaction term, which is dominated by an electron-donating effect of the N or O lone-pair(s) of the base to the central atom of the triatomics, with its value being lower than in the case of comparable halogen bonding situations. The effect is appreciably larger for TMA, in line with its much higher basicity than DME, explaining the comparable complexation energies for DME and TMA despite the much larger dipole moment for DME.

Nonhydrolyzable Heptose Bis- and Monophosphate Analogues Modulate Pro-inflammatory TIFA-NF-κB Signaling.

d-Glycero-d-manno-heptose-1ß,7-bisphosphate (HBP) and d-glycero-d-manno-heptose-1ß-phosphate (H1P) are bacterial metabolites that were recently shown to stimulate inflammatory responses in host cells through the activation of the TIFA-dependent NF-κB pathway. To better understand structure-based activity in relation to this process, a family of nonhydrolyzable phosphonate analogues of HBP and H1P was synthesized. The inflammation modulation by which these molecules induce the TIFA-NF-κB signal axis was evaluated in vivo at a low-nanomolar concentration (6 nM) and compared to that of the natural metabolites. Our data showed that three phosphonate analogues had similar stimulatory activity to HBP, whereas two phosphonates antagonized HBP-induced TIFA-NF-κB signaling. These results open new horizons for the design of pro-inflammatory and innate immune modulators that could be used as vaccine adjuvant.

A combined Raman optical activity and vibrational circular dichroism study on artemisinin-type products.

Artemisinin and two of its derivatives, dihydroartemisinin and artesunate, which are front line drugs against malaria, were investigated using Raman optical activity (ROA) and vibrational circular dichroism (VCD) experiments, both supported by density functional theory (DFT) level calculations. The experimental techniques combined with DFT calculations could show that dihydroartemisinin was present as an epimeric mixture in solution. In addition, an approximation of the epimeric ratio could be extracted which was in agreement with the ratio obtained by 1H-NMR spectroscopy. The current study also demonstrates that both ROA and VCD are able to assign the correct absolute configuration (AC) of artemisinin and artesunate out of all their possible diastereomers without any explicit knowledge on their correct stereochemistry and accentuates the synergetic effect between ROA and VCD in AC determination.

Chiral Phase Transfer Catalysis in the Asymmetric Synthesis of a 3,3-Disubstituted Isoindolinone and Determination of Its Absolute Configuration by VCD Spectroscopy.

In this work we report our endeavors toward the development of an asymmetric synthesis of a 3,3-disubstituted isoindolinone, dimethyl 2-(1-methyl-3-oxoisoindolin-1-yl)malonate, via asymmetric cascade reaction of 2-acetylbenzonitrile with dimethylmalonate and the determination of its absolute configuration (AC) by vibrational circular dichroism (VCD). Bifunctional ammonium salts, derived from trans-1,2-cyclohexanediamine in combination with inorganic bases under phase transfer conditions, were the most effective catalytic systems, leading to the target in high yields and moderate enantioselectivity. An efficient process of heterochiral crystallization allowed the increase of the enantiopurity up to 96% ee and in an acceptable overall yield. An important aim of the present work is the comparison of different VCD methodologies for AC determination of the target compound.

Tracking Conformational Changes in Phosvitin throughout a Crowding-Agent-Based Titration.

The sensitivity of Raman optical activity (ROA) towards small conformational changes is explored by tracking the structural changes in an intrinsically disordered protein-phosvitin-induced by different concentrations of crowding agent. It is shown that ROA is capable of tracking small conformational changes involving ß-sheet and α-helical secondary structural properties of the protein. Furthermore, it is indicated that the influences of the crowding agents employed, Ficoll 70 and dextran 70, on the structural properties of phosvitin differ significantly, with the structural changes induced by the presence of Ficoll 70 being more pronounced and already being visible at a lower concentration. The data also suggest that some spectral changes do not arise from a change in the secondary structure of the protein, but are related to differences in interaction between the phosphorylated residues of the protein and the sugar-based crowding agent.

Absolute configuration and biological profile of pyrazoline enantiomers as MAO inhibitory activity.

A new racemic pyrazoline derivative was synthesized and resolved to its enantiomers using analytic and semipreparative high-pressure liquid chromatography. The absolute configuration of both fractions was established using vibrational circular dichroism. The in vitro monoamine oxidase (MAO) inhibitory profiles were evaluated for the racemate and both enantiomers separately for the two isoforms of the enzyme. The racemic compound and both enantiomers were found to inhibit hMAO-A selectively and competitively. In particular, the R enantiomer was detected as an exceptionally potent and a selective MAO-A inhibitor (Ki  = 0.85 × 10-3  ± 0.05 × 10-3  µM and SI: 2.35 × 10-5 ), whereas S was determined as poorer compound than R in terms of Ki and SI (0.184 ± 0.007 and 0.001). The selectivity of the enantiomers was explained by molecular modeling docking studies based on the PDB enzymatic models of MAO isoforms.

Vibrational Circular Dichroism Sheds New Light on the Competitive Effects of Crowding and ß-Synuclein on the Fibrillation Process of α-Synuclein.

The effects of crowding, using the crowding agent Ficoll 70, and the presence of ß-synuclein on the fibrillation process of α-synuclein were studied by spectroscopic techniques, transmission electron microscopy, and thioflavin T assays. This combined approach, in which all techniques were applied to the same original sample, generated an unprecedented understanding of the effects of these modifying agents on the morphological properties of the fibrils. Separately, crowding gives rise to shorter mutually aligned fibrils, while ß-synuclein leads to branched, short fibrils. The combination of both effects leads to short, branched, mutually aligned fibrils. Moreover, it is shown that the nondestructive technique of vibrational circular dichroism is extremely sensitive to the length and the higher-order morphology of the fibrils.

Exploiting the σ-Hole Concept: An Infrared and Raman-Based Characterization of the S⋠⋠⋠O Chalcogen Bond between 2,2,4,4-Tetrafluoro-1,3-dithiethane and Dimethyl Ether.

In the last decade, halogen bonds, noncovalent interactions formed between positive regions in the electrostatic potential on halogen atoms, often referred to as σ-holes, and electron-rich sites, have gained a lot of interest. Recently, this interest has been expanded towards interactions with Group V and Group VI elements, giving rise to pnicogen and chalcogen bonds. Although chalcogen bonds have already shown some promising results for applications in crystallography and catalysis, experimental results characterising these noncovalent interactions remain scarce. In this combined experimental and theoretical study, original data allowing the characterization of S⋅⋅⋅O chalcogen bonds is obtained by studying the 1:1 molecular complexes between 2,2,4,4-tetrafluoro-1,3-dithiethane (C2 F4 S2 ) and dimethyl ether (DME). Ab initio calculations of the C2 F4 S2 ⋅DME dimer yield two stable chalcogen-bonded isomers, the difference being the presence or absence of secondary F⋅⋅⋅H interactions. Liquid-krypton solutions containing C2 F4 S2 and DME were studied using FTIR and Raman spectroscopy. Upon subtraction of rescaled monomer spectra, clear complex bands are observed. The observed complexation shifts agree favourably with the ab initio calculated shifts of the chalcogen-bonded complexes. The 1:1 stoichiometry of the complex is confirmed and a complexation enthalpy of -13.5(1) kJ mol-1 is found, which is in good agreement with the calculated values. A Ziegler-Rauk energy decomposition analysis revealed that electrostatic interactions prominently dominate over orbital interactions. Nevertheless, significant charge transfer occurs from the oxygen in DME to one of the sulfur atoms in C2 F4 S2 and the carbon along the extension of the chalcogen bond.