Molecular Dynamics of Steroidal Rotors Probed by Theoretical, Spectroscopic and Dielectric Methods

Our study focuses on molecular rotors with fast-moving rotators and their potential applications in the development of new amphidynamic crystals. Steroidal molecular rotors with a dipolar fluorine-substituted phenyl group as the rotator were synthesized and characterized. Three different rotors were investigated with varying numbers of fluorine atoms. A comprehensive analysis was performed using vibrational spectroscopy (Raman, FT-IR), electronic circular dichroism (ECD), and dielectric response to understand the behavior of the investigated model rotors. The results were supported by theoretical calculations using Density Functional Theory (DFT) methods. The angle-dependent polarized Raman spectra confirmed the crystallinity of the samples. Nearly frequency and temperature-independent permittivity suggest low-frequency librational motion of stators. An in-depth analysis of ECD spectra revealed high conformational flexibility in solution, resulting in low ECD effects, while in the solid-state with restricted rotation, significant ECD effects were observed. These findings shed light on the conformational behavior and potential applications of the studied steroidal molecular rotors.

Impact of conformation and intramolecular interactions on vibrational circular dichroism spectra identified with machine learning

Vibrational Circular Dichroism (VCD) spectra often differ strongly from one conformer to another, even within the same absolute configuration of a molecule. Simulated molecular VCD spectra typically require expensive quantum chemical calculations for all conformers to generate a Boltzmann averaged total spectrum. This paper reports whether machine learning (ML) can partly replace these quantum chemical calculations by capturing the intricate connection between a conformer geometry and its VCD spectrum. Three hypotheses concerning the added value of ML are tested. First, it is shown that for a single stereoisomer, ML can predict the VCD spectrum of a conformer from solely the conformer geometry. Second, it is found that the ML approach results in important time savings. Third, the ML model produced is unfortunately hardly transferable from one stereoisomer to another.

Behaviours of antiviral Oseltamivir in different media: DFT and SQMFF calculations

The synthetic cyclohexenecarboxylate ester antiviral Oseltamivir (O) have been theoretically studied by B3LYP/6–311 +  + G** calculations to estimate its reactivity and behaviour in gas and aqueous media. The most stable structure obtained in above media is consistent with that reported experimental for Oseltamivir phosphate. The solvation energy value of (O) in aqueous media is between the predicted for antiviral Idoxuridine and Ribavirin. Besides, (O) containing a NH₂ group and NH group reveals lower solvation energy compared with other antiviral agents with an NH₂ group, such as Ribavirin, Cidofovir, and Brincidofovir. Atomic charges on N and O atoms in acceptors and donor groups reveal different behaviours in both media, while the natural bond orbital (NBO) studies show a raised stability of (O) in aqueous solution. This latter resulted is in concordance with the lower reactivity evidenced in water. Frontier orbital studies have revealed that (O) in gas phase has a very similar gap value to antiviral Cidofovir used against the ebola disease, while Chloroquine in the two media are more reactive than (O). This study will allow to identify (O) by using vibrational spectroscopy because the 144 vibration modes expected have been assigned using the harmonic force fields calculated from the scaled mechanical force field methodology (SQMFF). Scaled force constants for (O) in the mentioned media are also reported for first time. Due to hydration of the C = O and NH₂ groups by solvent molecules, the calculations in solution produce variations not only in the IR wavenumbers bands, but also in their intensities.

Base-Catalyzed, Solvent-Free Synthesis of Rigid V-Shaped Epoxydibenzo[b,f][1,5]diazocines

A novel method for the synthesis of epoxydibenzo[b,f][1,5]diazocines exhibiting a V-shaped molecular architecture is reported. The unique approach is based on unprecedented base-catalyzed, solvent-free autocondensation and cross-condensation of fluorinated o-aminophenones. The structure of the newly synthesized diazocines was confirmed independently by X-ray analysis and chiroptical methods. The rigidity of the diazocine scaffold allowed for the separation of the racemate into single enantiomers that proved to be thermally stable up to 140 °C. Furthermore, the inertness of the diazocine scaffold was demonstrated by performing a series of typical transformations, including transition metal-catalyzed reactions, proceeding without affecting the bis-hemiaminal subunit.

Fluorescent Molecular Cages with Sucrose and Cyclotriveratrylene Units for the Selective Recognition of Choline and Acetylcholine

The synthesis of four fluorescent diastereoisomeric molecular cages containing cyclotriveratrylene and sucrose moieties connected via the naphthalene linkers is reported. These diastereoisomers were found to be selective and efficient receptors for acetylcholine and choline. Compound P-5a has a better affinity for choline over acetylcholine, while cage M-5a exhibits a higher association constant for acetylcholine over choline. The highest selectivity value was observed for compound M-5a (K_ACh/K_Ch = 3.1). Cages P-5a, P-5b, M-5a, and M-5b were fully characterized by the advanced NMR techniques, and ECD spectroscopy was supported by DFT calculations. The binding constants K_a of these receptors were determined by fluorescence titration experiments in acetonitrile.

Vibrational Circular Dichroism Absolute Configuration of Natural Products From 2015 to 2019

Although demonstrated in 1975, vibrational circular dichroism (VCD) finally started to popularize during this century as a reliable tool to determine the absolute configuration (AC) of organic molecules. This research field continues to be a very dynamic one, in particular for the study of natural products which are a unlimited source of chiral molecules. It therefore turns of interest to summarize the accomplishments published in recent years and to comment on some eventual difficulties that emerged in rare cases to complete the AC determination task. Therefore the aim of this review is to update VCD results for the AC assignment of natural products published from 2015 to 2019, a period in which VCD was reported in some 126 publications involving almost 300 molecules. They are organized according the type of studied metabolite allowing an easily search. The molecules correspond to 28 monoterpenes concerning 17 papers, to 42 sesquiterpenes in 14 papers, to 51 diterpenes in 19 publications, to 5 other terpenoids in three papers, to 48 aromatic molecules in 15 reports, to 20 polyketides in 10 publications, to 27 miscellaneous formulas also in 10 papers, and to 76 nitrogen containing compounds, which include alkaloids and their synthetic analogs, in 38 articles. The landscape of reviewed molecules is quite wide as it goes from simple monoterpenes, like borneol or camphor, to very relevant biological molecules like the alkaloid cocaine or tadalafil samples to distinguish genuine and counterfeit Cialis®. In addition, 5 natural products and a simple derivative published outside the reviewed period, were used to illustrate some aspects of density functional theory calculations.

Solution Structure of Mannobioses Unravelled by Means of Raman Optical Activity

Structural analysis of carbohydrates is a complicated endeavour, due to the complexity and diversity of the samples at hand. Herein, we apply a combined computational and experimental approach, employing molecular dynamics (MD) and density functional theory (DFT) calculations together with NMR and Raman optical activity (ROA) measurements, in the structural study of three mannobiose disaccharides, consisting of two mannoses with varying glycosidic linkages. The disaccharide structures make up the scaffold of high mannose glycans and are therefore important targets for structural analysis. Based on the MD population analysis and NMR, the major conformers of each mannobiose were identified and used as input for DFT analysis. By systematically varying the solvent models used to describe water interacting with the molecules and applying overlap integral analysis to the resulting calculational ROA spectra, we found that a full quantum mechanical/molecular mechanical approach is required for an optimal calculation of the ROA parameters. Subsequent normal mode analysis of the predicted vibrational modes was attempted in order to identify possible marker bands for glycosidic linkages. However, the normal mode vibrations of the mannobioses are completely delocalised, presumably due to conformational flexibility in these compounds, rendering the identification of isolated marker bands unfeasible.

Isolation and Structure Elucidation of Cembranoids from a Dongsha Atoll Soft Coral Sarcophyton stellatum

Six new polyoxygenated cembrane-based diterpenoids, stellatumolides A–C (1–3), stellatumonins A and B (4 and 5), and stellatumonone (6), were isolated together with ten known related compounds (7–16) from the ethyl acetate (EtOAc) extract of soft coral Sarcophyton stellatum. The structures of the new compounds were established by extensive spectroscopic analyses, including 1D and 2D nuclear magnetic resonance (NMR) spectroscopy and data comparison with related structures. Compounds 8 and 14 were isolated from a natural source for the first time. The isolated metabolites were shown to be not cytotoxic against a limited panel of cancer cells. Compound 9 showed anti-inflammatory activity by reducing the expression of proinflammatory cyclooxygenase-2 (COX-2) and inducible nitric oxide synthase (iNOS) proteins in lipopolysaccharide (LPS)-stimulated mouse leukaemic monocyte macrophage (RAW 264.7) cells.

Chirality sensing of bioactive compounds with amino alcohol unit via circular dichroism

The aim of the present work was to test various chiroptical techniques, including in particular the in situ dirhodium methodology, to assign the absolute configuration of 1,2- and 1,3-amino alcohols. As models, we selected mainly compounds that have both an additional strongly absorbing and interfering chromophoric system and application in medicinal chemistry. Determination of the absolute configuration (AC) of the tested molecules such as cinchona alkaloids, Tamiflu, and others was carried out using a combination of electronic and vibrational circular dichroism (ECD, VCD) spectroscopy. It has been demonstrated that both 1,2- and 1,3-aminol moieties are subject to the same sector rule correlating stereostructure of formed Rh₂ -complex with chiroptical properties, and that the changes in the position of the stereogenic center do not affect its proper use.

The role of chirality in a set of key intermediates of pharmaceutical interest, 3-aryl-substituted-γ-butyrolactones, evidenced by chiral HPLC separation and by chiroptical spectroscopies

The enantiomers of four chiral 3-aryl-substituted-γ-butyrolactones, key intermediates for the preparation of compounds of pharmaceutical interest, were successfully isolated by enantioselective chromatography, employing the Chiralpak AD-H chiral stationary phase. For all compounds the same elution order was observed, as monitored by a full set of chiroptical methods that we employed, namely ORD (optical rotatory dispersion), ECD (electronic circular dichroism, or CD in the UV range), and VCD (vibrational circular dichroism, or CD in the IR range). By density functional theory (DFT) calculations we were able to determine that the first eluted enantiomer has (S) absolute configuration in all four cases. We were able to justify the elution order by molecular docking calculations for all four enantiomeric pairs and suitable modeling of the stationary and mobile phases of the employed columns. The optimal performance of the chiroptical spectroscopies and of the DFT calculations allows us to formulate a lactone chirality rule out of the CO stretching region of the VCD spectra.

Stereoisomers of oseltamivir – synthesis, in silico prediction and biological evaluation

Three diastereoisomers of oseltamivir were synthesized, their properties predicted by quantum-chemical calculations and their antiviral activities evaluated.

Reassignment of the absolute configuration of plakinidone from the sponge consortium Plakortis halichondrioides-Xestospongia deweerdtae using a combination of synthesis and a chiroptical approach

Recent work by Wu et al. in connection with the first synthesis of the marine natural product plakinidone revealed that the most salient feature of its purported structure, a six-membered perlactone moiety, was in fact a five-membered lactone, i.e. a 3-methyl-4-hydroxy-2(5H)-furanone or tetronic acid ring. With the planar structure of plakinidone confidently revised, we undertook a new investigation to unambiguously establish its absolute configuration. Upon preparing two stable derivatives 1 and 5 from a sample of naturally occurring plakinidone extracted from the sponge association Plakortis halichondriodes-Xetospongia deweerdtae, the absolute configuration was assigned by synthesis and vibrational and electronic circular dichroism (VCD and ECD) measurements in combination with density functional theory calculations at the B3LYP/aug-cc-pVDZ/PCM(CH3CN) level of theory. Our combined efforts and the agreement between the experimental and calculated VCD/ECD spectra of 1 revealed that the absolute configuration of plakinidone was in fact (11S,17R) and not the formerly reported (11S,17S) diastereomer assigned by Wu et al.. Therefore, we propose that natural plakinidone is accurately represented by structure 12.

The Raman optical activity of β-D-xylose: where experiment and computation meet

Besides its applications in bioenergy and biosynthesis, β-d-xylose is a very simple monosaccharide that exhibits relatively high rigidity. As such, it provides the best basis to study the impact of different solvation shell radii on the computation of its Raman optical activity (ROA) spectrum. Indeed, this chiroptical spectroscopic technique provides exquisite sensitivity to stereochemistry, and benefits much from theoretical support for interpretation. Our simulation approach combines density functional theory (DFT) and molecular dynamics (MD) in order to efficiently account for the crucial hydration effects in the simulation of carbohydrates and their spectroscopic response predictions. Excellent agreement between the simulated spectrum and the experiment was obtained with a solvation radius of 10 Å. Vibrational bands have been resolved from the computed ROA data, and compared with previous results on different monosaccharides in order to identify specific structure-spectrum relationships and to investigate the effect of the solvation environment on the conformational dynamics of small sugars. From the comparison with ROA analytical results, a shortcoming of the classical force field used for the MD simulations has been identified and overcome, again highlighting the complementary role of experiment and theory in the structural characterisation of complex biomolecules. Indeed, due to unphysical puckering, a spurious ring conformation initially led to erroneous conformer ratios, which are used as weights for the averaging of the spectral average, and only by removing this contribution was near perfect comparison between theory and experiment achieved.