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.

Vibrational Optical Activity Study of Four Antibiotic (Lipo)glycopeptides: Vancomycin, Oritavancin, Dalbavancin, and Teicoplanin.

The antibiotic glycopeptide class, of which vancomycin is the original compound, has received due attention over the past few decades in search of antibiotics to overcome resistances developed by bacteria. Crucial for the understanding and further development of glycopeptides that possess desired antibacterial effects is the determination of their conformational behavior, as this sheds light on the mechanism of action of the compound. Among others, vibrational optical activity (VOA) techniques (vibrational circular dichroism and Raman optical activity) can be deployed for this, but the question remains to what extent these spectroscopic techniques can provide information concerning the molecular class under investigation. This contribution takes the last hurdle in the search for the capabilities of the VOA techniques in the conformational analysis of the antibiotic glycopeptide class by extending research that was previously conducted for vancomycin toward its three derivatives: oritavancin, dalbavancin, and teicoplanin. The principal information that can be drawn from VOA spectra is the conformation of the rigid cyclic parts of the glycopeptides and the aromatic rings that are part hereof. The addition or removal of carbohydrates does not induce noticeable VOA spectral responses, preventing the determination of the conformation they adopt.

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.

Comparative Study of the Vibrational Optical Activity Techniques in Structure Elucidation: The Case of Galantamine.

The absolute configuration of the alkaloid galantamine was studied using a range of solution-state techniques; nuclear magnetic resonance (NMR), vibrational circular dichroism (VCD), and Raman optical activity (ROA). While the combined use of NMR and VCD does provide a fast, high-resolution methodology for determining the absolute configuration of galantamine, both techniques were needed in concert to achieve this goal. ROA, on the other hand, proved to be sensitive enough to assign the full absolute configuration without relying on other techniques. In both cases, statistical validation was applied to aid the determination of absolute configuration. In the case of galantamine, ROA combined with statistical validation is shown to be a powerful stand-alone tool for absolute configuration determination.

Carbamate Synthesis Using a Shelf-Stable and Renewable C1 Reactant.

4-Propylcatechol carbonate is a shelf-stable, renewable C1 reactant. It is easily prepared from renewable 4-propylcatechol (derived from wood) and dimethyl carbonate (derived from CO2 ) using a reactive distillation system. In this work, the 4-propylcatechol carbonate is used for the two-step synthesis of carbamates under mild reaction conditions. In the first step, 4-propylcatechol carbonate is treated with an alcohol at 50-80 °C in the presence of a Lewis acid catalyst, such as Zn(OAc)2 ⋅2 H2 O. With liquid alcohols, no solvent is used and with solid alcohols 2-methyltetrahydrofuran is used as solvent. In the second step, the alkyl 2-hydroxy-propylphenyl carbonate intermediates obtained react with amines at room temperature in 2-methyltetrahydrofuran, forming the target carbamates and the byproduct 4-propylcatechol, which can be recycled into a carbonate reactant.

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.

Effect of Fluorination on the Competition of Halogen Bonding and Hydrogen Bonding: Complexes of Fluoroiodomethane with Dimethyl Ether and Trimethylamine.

To further rationalize the competition between halogen and hydrogen bonding, a combined experimental and theoretical study on the weakly bound molecular complexes formed between the combined halogen bond/hydrogen bond donor fluoroiodomethane and the Lewis bases dimethyl ether and trimethylamine (in standard and fully deuterated form) is presented. The experimental data are obtained by recording infrared and Raman spectra of mixtures of the compounds in liquid krypton, at temperatures between 120 and 156 K. The experiments are supported by ab initio calculations at the MP2/aug-cc-pVDZ-PP level, statistical thermodynamics and Monte Carlo free energy perturbation calculations. For the mixtures containing fluoroiodomethane and dimethyl ether a hydrogen-bonded complex with an experimental complexation enthalpy of -7.0(2) kJ mol-1 is identified. Only a single weak spectral feature is observed which can be tentatively assigned to the halogen-bonded complex. For the mixtures involving trimethylamine, both halogen- and hydrogen-bonded complexes are observed, the experimental complexation enthalpies being -12.5(1) and -9.6(2) kJ mol-1 respectively. To evaluate the influence of fluorination on the competition between halogen and hydrogen bonding, the results obtained for fluoroiodomethane are compared with those of a previous study involving difluoroiodomethane.

Taking the halogen bonding-hydrogen bonding competition one step further: complexes of difluoroiodomethane with trimethylphosphine, dimethyl sulfide and chloromethane.

To rationalize the driving factors in the competition of halogen bonding and hydrogen bonding, the complexes of the combined halogen-/hydrogen-bond donor difluoroiodomethane with the Lewis bases trimethylphosphine, dimethyl sulfide and chloromethane are studied. For all Lewis bases, ab initio calculations lead to halogen- and hydrogen-bonded complexes. Fourier transform-IR experiments involving solutions of mixtures of difluoroiodomethane with trimethylphosphine(-d9) or dimethyl sulfide(-d6) in liquid krypton confirm the coexistence of a halogen-bonded and hydrogen-bonded complex. Also for solutions containing chloromethane, evidence of the formation of binary associations is found, but no definitive assignment of the multiple complex bands could be made. Using van't Hoff plots, the experimental complexation enthalpies for the halogen- and hydrogen-bonded complex of difluoroiodomethane with trimethylphosphine are determined to be -15.4 (4) and -10.5 (3) kJ mol-1, respectively, while for the halogen- and hydrogen-bonded complexes with dimethyl sulfide, the values are -11.3 (5) and -7.7 (6) kJ mol-1, respectively. The experimental observation that for both trimethylphospine and dimethyl sulfide the halogen-bonded complex is more stable than the hydrogen-bonded complex supports the finding that softer Lewis bases tend to favor iodine halogen bonding over hydrogen bonding.

Dimers or trimers? A characterization of the halogen bonded complexes of CF3X (X=I or Br) with dimethyl ether and acetone in cryosolutions.

Acetone molecules dissolved in liquid krypton are inclined to self-associate into dimers. This behavior affects its use as a prototype Lewis base in studies of weak intermolecular interactions. In this study infrared spectra of mixed solutions of dimethyl ether and CF3X and of acetone and CF3X (with X=I or Br) dissolved in liquid argon and liquid krypton are recorded at constant temperature. The dataset for dimethyl ether is used to validate a numerical method based on least-squares fitting of a model including contributions of both monomers and a heterodimer with 1:1 stoichiometry. The resulting monomer and dimer spectra show excellent agreement with previous studies found in literature. The analysis of the dataset for acetone requires an extension of the model with contributions for the acetone homodimer and for (acetone)2·CF3X and acetone·(CF3X)2 trimers. The results show that many signals for acetone·CF3I and (acetone)2·CF3I are observed, while only a few bands due to acetone·(CF3I)2 occur. The use of numerical approaches adjusted to the specificities of a mixture of two compounds allows to reliably resolve overlapping spectra of monomers and heterocomplexes and characterizing heterocomplex features that could not be deduced using earlier methods. To support the assignments made, ab initio calculations predicting geometries, relative stabilities and harmonic vibrational frequencies for the species envisaged are performed.

Combining density functional theory (DFT) and collision cross-section (CCS) calculations to analyze the gas-phase behaviour of small molecules and their protonation site isomers.

Electrospray ion mobility-mass spectrometry (IM-MS) data show that for some small molecules, two (or even more) ions with identical sum formula and mass, but distinct drift times are observed. In spite of showing their own unique and characteristic fragmentation spectra in MS/MS, no configurational or constitutional isomers are found to be present in solution. Instead the observation and separation of such ions appears to be inherent to their gas-phase behaviour during ion mobility experiments. The origin of multiple drift times is thought to be the result of protonation site isomers ('protomers'). Although some important properties of protomers have been highlighted by other studies, correlating the experimental collision cross-sections (CCSs) with calculated values has proven to be a major difficulty. As a model, this study uses the pharmaceutical compound melphalan and a number of related molecules with alternative (gas-phase) protonation sites. Our study combines density functional theory (DFT) calculations with modified MobCal methods (e.g. nitrogen-based Trajectory Method algorithm) for the calculation of theoretical CCS values. Calculated structures can be linked to experimentally observed signals, and a strong correlation is found between the difference of the calculated dipole moments of the protomer pairs and their experimental CCS separation.

Rotational Study of Dimethyl Ether-Chlorotrifluoroethylene: Lone Pair···π Interaction Links the Two Subunits.

The rotational spectra of two isotopologues of chlorotrifluoroethylene-dimethyl ether show that the two constituent molecules are held together by a lone pair···π interaction. The ether oxygen is linked to the (CF2) carbon atom, with a C-O distance of 2.908 Å.

Self-Associating Behavior of Acetone in Liquid Krypton.

Acetone molecules are inclined to self-associate through dipole-dipole interactions because of their large dipole moment. Infrared spectroscopy of compounds dissolved in liquid noble gases supported by high level ab initio calculations allows investigating the self-associating behavior and determining the thermodynamical properties. In this study, infrared spectra of various concentrations of acetone dissolved in liquid krypton are recorded at constant temperature. Overlapping monomer and dimer spectra are separated by analyzing the obtained data sets with numerical methods based on least-squares fitting. Although acetone is known to self-associate, only a few spectral features have been presented in literature before. In this study, the application of new numerical approaches succeeds in resolving overlapping spectra and allows observing isolated acetone dimer absorption bands for the complete mid infrared spectrum. By use of data sets of spectra recorded at temperatures between 134 and 142 K, the experimental standard dimerization enthalpy was determined to be -10.8 kJ mol(-1). MP2/aug-cc-pVDZ calculations predicted a stacked and planar dimer geometry of which the stacked geometry is more stable. Combining MP2 energies and single point corrections involving CCSD(T) calculations and complete basis set extrapolations based on the MP2/aug-cc-pVDZ equilibrium geometry lead to complexation energy of -28.4 kJ mol(-1) for the stacked geometry and -15.1 kJ mol(-1) for the planar geometry. The corresponding values for the complexation enthalpies in solution, obtained by combining these values with corrections for thermal and solvent influences are -13.7 and -5.8 kJ mol(-1).

Exploring the limits of cryospectroscopy: Least-squares based approaches for analyzing the self-association of HCl.

To rationalize the concentration dependent behavior observed for a large spectral data set of HCl recorded in liquid argon, least-squares based numerical methods are developed and validated. In these methods, for each wavenumber a polynomial is used to mimic the relation between monomer concentrations and measured absorbances. Least-squares fitting of higher degree polynomials tends to overfit and thus leads to compensation effects where a contribution due to one species is compensated for by a negative contribution of another. The compensation effects are corrected for by carefully analyzing, using AIC and BIC information criteria, the differences observed between consecutive fittings when the degree of the polynomial model is systematically increased, and by introducing constraints prohibiting negative absorbances to occur for the monomer or for one of the oligomers. The method developed should allow other, more complicated self-associating systems to be analyzed with a much higher accuracy than before.

Mechanism of the CuII-catalyzed benzylic oxygenation of (aryl)(heteroaryl)methanes with oxygen.

A mechanistic study of the copper-catalyzed oxidation of the methylene group of aryl(di)azinylmethanes was performed. Initial reaction rates were measured making use of in situ IR reaction monitoring and a kinetic analysis of the reaction was executed. The reaction proved to be first order in oxygen concentration. For substrate and acid concentration, saturation kinetics due to O2 mass transfer limitation were observed. The occurrence of mass transfer limitation was further confirmed by examining the effect of the stirring rate on the initial reaction rate. Interestingly, the effect of the concentration of the catalyst on the rate shows that higher loadings result in a maximal initial rate, followed initially by a steady decrease and subsequently a rate plateau when the concentration is increased further. Mass transfer limitation and increased concentration of dinuclear catalytically active species rationalizes this hitherto unprecedented rate behavior. Continuous-wave and pulsed electron paramagnetic resonance methods were used to characterize the catalytic species present in the solution during the reaction and confirmed the presence of both mono- and dinuclear copper species. Analysis of a diverse substrate scope points towards imine-enamine tautomerization as a crucial process in the oxidation reaction. DFT calculations of these equilibrium constants (pKeq) provided us with a qualitative tool to predict whether or not a substrate is viable for oxidation under the reaction conditions developed.

Microwave, r0 Structural Parameters, Conformational Stability, and Vibrational Assignment of (Chloromethyl)fluorosilane.

The FT-microwave spectrum (6.5-26 GHz) of (chloromethyl)fluorosilane (ClCH2-SiH2F) has been recorded and 250 transitions for the parent species along with (13)C, (37)Cl, (29)Si, and (30)Si isotopologues have been assigned for trans conformer. Infrared spectra (3100 to 400 cm(-1)) of gas, solid, and the variable temperature (-100 to -60 °C) studies of the infrared spectra of the sample dissolved in xenon have been recorded. Additionally, the variable temperature (-153 to -133 °C) studies of the Raman spectra of the sample dissolved in krypton have been recorded. The enthalpy difference between the trans and gauche conformers in xenon solutions has been determined to be 109 ± 15 cm(-1) (1.47 ± 0.16 kJ mol(-1)), and in krypton solution, the enthalpy difference has been determined to be 97 ± 16 cm(-1) (1.16 ± 0.19 kJ mol(-1)) with the trans conformer as the more stable form. Approximately 46 ± 2% of the trans form is present at ambient temperature. By utilizing the microwave rotational constants of five isotopologues for trans and the structural parameters predicted from MP2(full)/6-311+G(d,p) calculations, adjusted r0 parameters have been obtained for trans conformer. The r0 structural parameter values for the trans form are for the heavy atom distances (Å): Si-F = 1.608 (3); C-Cl = 1.771 (3); Si-C = 1.884 (3); and angles (deg): ∠FSiC = 108.9 (5); ∠ClCSi = 104.9 (5). The results are discussed and compared to some related molecules.

Expanding Lone Pair···π Interactions to Nonaromatic Systems and Nitrogen Bases: Complexes of C2F3X (X = F, Cl, Br, I) and TMA-d9.

The molecular electrostatic potential surface of unsaturated, locally electron-deficient molecules shows a positive region perpendicular to (a part of) the molecular framework. In recent years it has been shown both theoretically and experimentally that molecules are able to form noncovalent interactions with Lewis bases through this π-hole. When studying unsaturated perfluorohalogenated molecules containing a higher halogen atom, a second electropositive region is also observed near the halogen atom. This region, often denoted as a σ-hole, allows the molecules to interact with Lewis bases and form a halogen bond. To experimentally characterize the competition between both these noncovalent interactions, Fourier transform infrared and Raman spectra of liquefied noble gas solutions containing perfluorohalogenated ethylene derivatives (C2F3X; X = F, Cl, Br, or I) and trimethylamine(-d9) were investigated. Analysis of the spectra shows that in mixed solutions of trimethylamine(-d9) and C2F4 or C2F3Cl lone pair···π complex is present, while evidence for halogen-bonded complex is found in solutions containing trimethylamine(-d9) and C2F3Cl, C2F3Br, or C2F3I. For all species observed, complexation enthalpies were determined, the values varying between -4.9(1) and -24.4 kJ mol(-1).

Chiroptical studies on brevianamide B: vibrational and electronic circular dichroism confronted.

Chiroptical spectroscopies, such as electronic circular dichroism (ECD) and vibrational circular dichroism (VCD), are highly sensitive techniques to probe molecular conformation, configuration, solvation, and aggregation. Here we report the application of these techniques to study the fungal metabolite brevianamide B. Comparison of the experimental ECD and VCD spectra with the density functional theory simulated counterparts establishes that VCD is the more reliable technique to assign absolute configuration due to the larger functional and dispersion dependence of computed ECD spectra. Despite a low amount of available material and a relatively unusual example of using VCD carbonyl multiplets, the absolute configuration could be reliably predicted, strengthening the case for application of VCD in the study of complex natural products. Spectral and crystallographic evidence for or against the formation of a dimeric aggregate is discussed; in solution, the VCD spectra strongly suggest only monomeric species are present.

Competition of C(sp²)-X···O halogen bonding and lone pair···π interactions: cryospectroscopic study of the complexes of C2F3X (X = F, Cl, Br, and I) and dimethyl ether.

Inspection of the electrostatic potential of C2F3X (X = F, Cl, Br, and I) revealed a second electropositive region in the immediate vicinity of the C═C double bond apart from the σ hole of chlorine, bromine, and iodine, leading to C(sp(2))-X···Y halogen bonding, through which complexes stabilized by so-called lone pair···π interactions can be formed. Consequently, the experimental studies for the complexes of dimethyl ether with C2F3X (X = F, Cl, Br, and I) not only allowed one to experimentally characterize and rationalize the effects of hybridization on halogen bonding but, for the first time, also allowed the competition of C-X···Y halogen bonding and lone pair···π interactions to be studied at thermodynamic equilibrium. Analysis of the infrared and Raman spectra reveals that in the cryosolutions of dimethyl ether and C2F3I, solely the halogen-bonded complex is present, whereas C2F3Br and C2F3Cl give rise to a lone pair···π bonded complex as well as a halogen-bonded complex. Mixtures of dimethyl ether with C2F4 solely yield a lone pair···π bonded complex. The experimentally derived complexation enthalpies for the halogen bonded complexes are found to be -14.2(5) kJ mol(-1) for C2F3I·DME and -9.3(5) kJ mol(-1) for C2F3Br·DME. For the complexes of C2F3Cl with dimethyl ether, no experimental complexation enthalpy could be obtained, whereas the C2F4·DME complex has a complexation enthalpy of -5.5(3) kJ mol(-1). The observed trends have been rationalized with the aid of an interaction energy decomposition analysis (EDA) coupled to a Natural Orbital for Chemical Valence (NOCV) analysis and also using the noncovalent interaction index method.

N lone-pair···π interaction: a rotational study of chlorotrifluoroethylene···ammonia.

The rotational spectra of four isotopologues of the adduct C2F3Cl-NH3 show that NH3 is bound to the partner molecule through a (N)lone-pair···π interaction. Ammonia is located in proximity to the C2 atom (the one linked to two fluorine atoms), with the C2···N distance = 2.987(2) Å. The nuclear hyperfine structure due to the quadrupole coupling effects of (35)Cl/(37)Cl and (14)N nuclei has been fully resolved. The (14)N quadrupole coupling constants allow estimating the effective orientation of NH3 in the complex.