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.

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.

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.

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.

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).

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.

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.

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.

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).

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.

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.

Tuning the halogen/hydrogen bond competition: a spectroscopic and conceptual DFT study of some model complexes involving CHF2I.

Insight into the key factors driving the competition of halogen and hydrogen bonds is obtained by studying the affinity of the Lewis bases trimethylamine (TMA), dimethyl ether (DME), and methyl fluoride (MF) towards difluoroiodomethane (CHF(2) I). Analysis of the infrared and Raman spectra of solutions in liquid krypton containing mixtures of TMA and CHF(2) I and of DME and CHF(2) I reveals that for these Lewis bases hydrogen and halogen-bonded complexes appear simultaneously. In contrast, only a hydrogen-bonded complex is formed for the mixtures of CHF(2) I and MF. The complexation enthalpies for the C-H⋅⋅⋅Y hydrogen-bonded complexes with TMA, DME, and MF are determined to be -14.7(2), -10.5(5) and -5.1(6) kJ mol(-1), respectively. The values for the C-I⋅⋅⋅Y halogen-bonded isomers are -19.0(3) kJ mol(-1) for TMA and -9.9(8) kJ mol(-1) for DME. Generalization of the observed trends suggests that, at least for the bases studied here, softer Lewis bases such as TMA favor halogen bonding, whereas harder bases such as MF show a substantial preference for hydrogen bonding.

Halogen bonding from a hard and soft acids and bases perspective: investigation by using density functional theory reactivity indices.

Halogen bonds between the trifluoromethyl halides CF(3)Cl, CF(3)Br and CF(3)I, and dimethyl ether, dimethyl sulfide, trimethylamine and trimethyl phosphine were investigated using Pearson's hard and soft acids and bases (HSAB) concept with conceptual DFT reactivity indices, the Ziegler-Rauk-type energy-decomposition analysis, the natural orbital for chemical valence (NOCV) framework and the non-covalent interaction (NCI) index. It is found that the relative importance of electrostatic and orbital (charge transfer) interactions varies as a function of both the donor and acceptor molecules. Hard and soft interactions were distinguished and characterised by atomic charges, electrophilicity and local softness indices. Dual-descriptor plots indicate an orbital σ hole on the halogen similar to the electrostatic σ hole manifested in the molecular electrostatic potential. The predicted high halogen-bond-acceptor affinity of N-heterocyclic carbenes was evidenced in the highest complexation energy for the hitherto unknown CF(3) I·NHC complex. The dominant NOCV orbital represents an electron-density deformation according to a n→σ*-type interaction. The characteristic signal found in the reduced density gradient versus electron-density diagram corresponds to the non-covalent interaction between contact atoms in the NCI plots, which is the manifestation of halogen bonding within the NCI theory. The unexpected C-X bond strengthening observed in several cases was rationalised within the molecular orbital framework.

Mechanistic and chiroptical studies on the desulfurization of epidithiodioxopiperazines reveal universal retention of configuration at the bridgehead carbon atoms.

The stereochemistry of the desulfurization products of chiral natural and synthetic 3,6-epidithiodiketopiperazines (ETPs) is specified inconsistently in the literature. Qualitative mechanisms have been put forward to explain apparently divergent stereochemical pathways, but the quantitative feasibility of such mechanistic pathways has not been assessed. We report a computational study revealing that desulfurization of ETPs should occur universally with retention of configuration. While the majority of stereochemically assigned and reassigned cases fit this model, until now desulfurization of the synthetic gliotoxin analogue shown has remained assigned as proceeding via inversion of configuration. Through detailed chiroptical studies comparing experimentally obtained optical rotation values, electronic circular dichroism spectra, and vibrational circular dichroism spectra to their computationally simulated counterparts as well as chemical derivatization studies, we have unambiguously demonstrated that contrary to its current assignment in the literature, the desulfurization of this synthetic ETP also proceeds with retention of configuration.

Experimental characterization of C-X···Y-C (X = Br, I; Y = F, Cl) halogen-halogen bonds.

Using FTIR and Raman spectroscopy, we investigated the formation of halogen bonded complexes of the trifluorohalomethanes CF3Cl, CF3Br, and CF3I with the halomethanes CH3F and CH3Cl and the haloethanes C2H5F and C2H5Cl dissolved in liquid krypton. For CF3Br and CF3I, evidence was found for the formation of C-X···F and C-X···Cl halogen bonded 1:1 complexes. Using spectra recorded at different temperatures, we determined the complexation enthalpies for the complexes to be -7.0(3) kJ mol(-1) for CF3Br·CH3F, -7.6(1) kJ mol(-1) for CF3I·CH3F, -5.9(2) kJ mol(-1) for CF3Br·CH3Cl, -8.3(3) kJ mol(-1) for CF3I·CH3Cl, -7.1(1) kJ mol(-1) for CF3Br·C2H5F, -8.7(2) kJ mol(-1) for CF3I·C2H5F, -6.5(2) kJ mol(-1) for CF3Br·C2H5Cl, and -8.8(3) kJ mol(-1) for CF3I·C2H5Cl. For all halogen bonded complexes with a fluorine-electron donor, a blue shift ranging from +0.6 to +1.5 cm(-1) was observed for the C-X stretching mode. The results from the cyrospectroscopic study are compared with ab initio calculations at the MP2/aug-cc-pVDZ(-PP) level.

Exploring the C-X π halogen bonding motif: an infrared and Raman study of the complexes of CF3X (X = Cl, Br and I) with the aromatic model compounds benzene and toluene.

The formation of halogen bonded complexes formed between the trifluorohalomethanes CF3Cl, CF3Br and CF3I and the Lewis bases benzene and toluene at temperatures below 150K was investigated using FTIR and Raman spectroscopy. Experiments using liquid krypton as solvent show that for both CF3Br and CF3I substantial fractions of the monomers can be involved in 1:1 complexes. In addition, weak absorptions illustrating the formation of 2:1 complexes between CF3I and benzene are observed. Using spectra recorded at temperatures between 120 and 140 K, observed information on the relative stability was obtained for all complexes by determining the complexation enthalpies in solution. The resulting values for CF3Br.benzene, CF3I.benzene and (CF3I)2.benzene are -6.5(3), -7.6(2) and -14.5(9) kJ mol⁻¹. The values for CF3Br.toluene and CF3I.toluene are -6.2(5) and -7.4(5) kJ mol⁻¹. The experimental complexation enthalpies are compared with theoretical data obtained by combining results from MP2/aug-cc-pVDZ(-PP) and MP2/aug-cc-pVTZ(-PP) ab initio calculations, from statistical thermodynamical calculations and from Monte Carlo Free Energy Perturbation simulations. The data are also compared with results derived for other C-X···π halogen bonded complexes involving unsaturated Lewis bases such as ethene and ethyne.

C-X···π halogen and C-H···π hydrogen bonding: interactions of CF3X (X = Cl, Br, I or H) with ethene and propene.

Using FTIR and Raman spectroscopy, the formation of halogen bonded complexes of the trifluorohalomethanes CF(3)Cl, CF(3)Br and CF(3)I with ethene and propene dissolved in liquid argon has been investigated. For CF(3)Br and CF(3)I, evidence was found for the formation of C-X···π halogen bonded 1:1 complexes. At a higher ratio of CF(3)I/propene, weak absorptions due to a 2:1 complex were also observed. Using spectra recorded at different temperatures, the complexation enthalpies for the complexes were determined to be -5.3(2) kJ mol(-1) for CF(3)Br·ethene, -7.5(2) kJ mol(-1) for CF(3)I·ethene, -5.6(1) kJ mol(-1) for CF(3)Br·propene, -8.8(1) kJ mol(-1) for CF(3)I·propene and -16.5(6) kJ mol(-1) for (CF(3)I·)(2)propene. The complexation enthalpies of the hydrogen bonded counterparts, with CF(3)H as the Lewis acid, were determined to be -4.6(4) kJ mol(-1) for CF(3)H·ethene and -5.1(2) kJ mol(-1) for CF(3)H·propene. For both hydrogen bonded complexes, a blue shift, by +4.8 and +4.0 cm(-1), respectively, was observed for the C-H stretching mode. The results from the cryospectroscopic study are compared with ab initio calculations at the MP2/aug-cc-pVDZ(-PP) level.

Solute-solvent interactions in cryosolutions: a study of halothane-ammonia complexes.

The formation of C-H···N bonded complexes of halothane with ammonia has been studied using infrared and Raman spectroscopy of solutions in the liquid rare gases argon, krypton and xenon, of supersonic jet expansions and of room temperature vapor phase mixtures. For the solutions and for the vapor phase experiments, the formation of complexes with 1:1 and 1:2 stoichiometry was observed. The complexation enthalpy for the 1:1 complex was determined to be -20 (1) kJ mol(-1) in the vapor phase, -17.0 (5) kJ mol(-1) in liquid xenon and -17.3 (6) kJ mol(-1) in liquid krypton. For the 1:2 complex in liquid xenon, the complexation enthalpy was determined to be -31.5 (12) kJ mol(-1). Using the complexation enthalpies for the vapor phase and for the solutions in liquid xenon and krypton, a critical assessment is made of the Monte Carlo Free Energy Perturbation approach to model solvent influences on the thermodynamical properties of the cryosolutions. The influences of temperature and solvent on the complexation shifts of the halothane C-H stretching mode are discussed.