Search Results (168)

Aqueous solutions are not homogeneous and could be considered supramolecular systems. They can emit electromagnetic waves. Electromagnetic emission from one supramolecular system (“source”) can be received by another supramolecular system (“receiver”) without direct contact (distantly). This process represents a transfer of a “molecular signal” and causes changes in conformation and symmetry of the “receiver”. The aim of the current work is to theoretically describe such changes primarily using a solution of the chiral protein interferon-gamma (IFNγ) as an example. We provide theoretical evidence that supramolecular systems of highly diluted (HD) aqueous solutions formed by self-assembly after mechanical activation generate a stronger molecular signal compared to non-activated solutions, due to their higher energy-saturated state. Additionally, molecular signals cause supramolecular systems with complex (including chiral) structures to undergo easier changes in conformation and symmetry compared to simpler systems, enhancing their biological activity. Using statistical physics, we obtained the parameter Ic, characterizing the magnitude of conformational and symmetry changes in supramolecular (including chiral) systems caused by molecular signals. In quantum information science, there is an analogue of the parameter Ic, which characterizes the entanglement depth of quantum systems. This study contributes to the understanding of the physico-chemical basis of distant molecular interactions and opens up new possibilities for controlling the properties of complex biological and chemical systems. Full article

(−)-Patagonic acid (1) is a clerodane diterpene isolated from several plants from the Alismataceae, Asteraceae, Euphorbiaceae, Fabaceae, Lamiaceae, Salicaceae, Sapindaceae, and Velloziaceae families, and its biological potential as an inhibitor of butyrylcholinesterase (BChE) and acetylcholinesterase (AChE) and as an anti-inflammatory compound has been described. Furthermore, the enantiomer (+)-1 is also described in Fabaceae and Verbenaceae. A lack of formal studies about the absolute configuration (AC) determination of 1 is emphasized. Thus, the present manuscript describes the AC determination of patagonic acid (1). The chemical correlation of (−)-1 from (−)-hardwickiic acid (2) was achieved by a simplistic oxidative process. The specific rotation value and electronic circular dichroism (ECD) analysis allowed for the AC determination of (−)-1 as (5R,8R,9S,10R)-(−)-patagonic acid. ECD revealed a positive exciton chirality (EC) phenomenon in both (−)-1 and (−)-2, which is directly associated with their configuration and conformational preferences, which were assessed by DFT calculations at the B3LYP/DGDZVP level of theory. Since the NMR data of (+)-1 are fully coincident with those from its enantiomer studied herein, the chirality of (5S,8S,9R,10S)-(+)-patagonic acid could also be determined. These experimental conclusions deeply complement the literature related to clerodane compounds biosynthesized in several families of plants of scientific interest. Full article

Sotolon is a chiral furanone derivative featuring three distinct oxygen atoms at carbonyl, hydroxyl, and cyclic ether groups that can serve as hydrogen-bond acceptor sites, making it an ideal model system for probing water’s preferential interactions with competing functional groups. In this study, the rotational spectrum of sotolon and its microsolvated complexes, representing the early stages of hydration, was investigated using chirped-pulse Fourier transform microwave (CP-FTMW) spectroscopy. The conformational landscape of sotolon is dominated by a single conformer stabilized by an intramolecular O–H···O=C hydrogen bond. During hydration, water molecules disrupt this interaction by forming closed hydrogen-bonded cycles, resulting in mono- and dihydrated complexes. High-level theoretical calculations underscore the central role of electrostatic interactions in stabilizing these hydrated structures. Furthermore, A/E splittings observed in the rotational spectrum, arising from the internal rotation of one of sotolon’s methyl groups, provide insight into how hydration modulates the methyl internal rotation barrier. Full article

The central objective of this study is to develop some different wave solutions and perform a qualitative analysis on the nonlinear dynamics of the time-fractional chiral nonlinear Schrodinger’s equation (NLSE) in the conformable sense. Combined with the semi-inverse method (SIM) and traveling wave transformation, we establish the variational principle (VP). Based on this, the corresponding Hamiltonian is constructed. Adopting the Galilean transformation, the planar dynamical system is derived. Then, the phase portraits are plotted and the bifurcation analysis is presented to expound the existence conditions of the various wave solutions with the different shapes. Furthermore, the chaotic phenomenon is probed and sensitivity analysis is given in detail. Finally, two powerful tools, namely the variational method (VM) which stems from the VP and Ritz method, as well as the Hamiltonian-based method (HBM) that is based on the energy conservation theory, are adopted to find the abundant wave solutions, which are the bell-shape soliton (bright soliton), W-shape soliton (double-bright solitons or double bell-shaped soliton) and periodic wave solutions. The shapes of the attained new diverse wave solutions are simulated graphically, and the impact of the fractional order $\delta$ on the behaviors of the extracted wave solutions are also elaborated. To the authors’ knowledge, the findings of this research have not been reported elsewhere and can enable us to gain a profound understanding of the dynamics characteristics of the investigative equation. Full article

Background/Objective: Avapritinib is an orally bioavailable tyrosine kinase inhibitor and was approved by the FDA in 2020 for gastrointestinal stromal tumor treatments. Although avapritinib is known to be chiral, its stereochemistry was initially established randomly. This study aims to develop a definitive method for determining avapritinib’s absolute configuration and propose a universal methodology for stereochemical characterization of flexible chiral drugs. Methods: The absolute configuration of avapritinib was determined through an integrated approach combining chiral resolution, chiroptical spectroscopy and synthetic validation. Enantiomeric separation was achieved via chiral liquid chromatography, followed by comprehensive chiroptical characterization including electronic circular dichroism (ECD), specific optical rotation and optical rotatory dispersion. Conformational analysis and density functional theory (DFT) calculations correlated experimental spectra with theoretical predictions, facilitating definitive configurational assignment. The stereochemical determination were further verified through ECD derivatization and chemical synthesis. Finally, the enantiomers’ kinase inhibition profiles against c-KIT D816V were quantitatively assessed. Results: Two enantiomers of avapritinib were resolved via chiral HPLC and a Chiralpak IG column. Through combined experimental ECD spectra and time-dependent DFT calculations employing the core extraction method, the levo-isomer was unambiguously determined as S configuration. This stereochemical assignment was confirmed by p-cyanobenzaldehyde derivatization and de novo synthesis. Biological evaluation revealed (S)-(−)-avapritinib exhibited superior c-KIT D816V inhibitory activity compared to its (R)-(+)-counterpart, a finding corroborated by molecular docking studies elucidating their differential target interactions. Conclusions: This study advances avapritinib stereochemical understanding and establishes a definitive protocol for its absolute configuration assignment, serving as a paradigm for flexible chiral drug characterization. Full article

The regulation of superhelical stress, mediated by the combined action of topoisomerases and fork rotation, is crucial for DNA replication. The conformational changes during DNA replication are still experimentally challenging, mainly due to the rapid kinetics of the replication process. Here, we present the first molecular dynamics simulations of partially replicated circular DNA molecules, with stalled replication forks at both early and late stages of DNA replication. These simulations allowed us to map the distribution of superhelical stress after deproteinization. We propose a five-component model that determines the linking number difference of replication intermediates. At a thermodynamic equilibrium, the contribution of these five components was correlated to the progress of the replication forks. Additionally, we identified four types of segment collision events in replication intermediates, characterized by their geometric properties, including chirality and topological sign. The distribution of these collision events between the early and late stages of DNA replication provides new insights into the coordinated function of topoisomerases, warranting further discussion. Full article

Novel peptides based on common amino acid building blocks may serve as possible drug candidates; however, their flexible structures may require stabilization via the incorporation of conformational constraints. The insertion of unusual amino acids is a feasible option that may provide improved pharmacokinetic and pharmacodynamic properties of such peptide-type drugs. The stereochemical purity of these kinds of building blocks must be verified by an efficient separation technique, such as high-performance liquid chromatography. Here, we present and discuss the results of the stereoselective separation mechanism of ß-methylated phenylalanine (ß-MePhe), tyrosine (ß-MeTyr), 1,2,3,4-tetrahydroisoquinoline-3-carboxylic acid (ß-MeTic), and cyclohexylalanine (ß-MeCha) together with non-methylated Phe, Tyr, Tic, and Cha applying Cinchona alkaloid-based chiral stationary phases (CSPs). The studied zwitterionic CSPs acting as ion exchangers provided optimal performance in the polar ionic mode when methanol or a mixture of methanol and acetonitrile was utilized as the mobile phase together with organic acid and base additives. It was found that the basicity of small amines applied as mobile phase additives did not directly influence the chromatographic ion exchange concept. However, the size of the amines and their concentration led to a reduced retention time following the principles of ion exchange chromatography. On the basis of a systematic study of the effects of the eluent composition on the chromatographic behavior, important structure–retention and enantioselectivity relationships could be revealed. Through a temperature study, it has become evident that the composition of the eluent and the structure of analytes markedly affect the thermodynamic properties. Full article

Several D-amino acid residue-containing peptides (DAACPs) with antimicrobial, cardio-excitatory, and neuronal activities have been identified in various species. The L-Asn-D-Trp-L-Phe-NH₂ (N(dW)F) tripeptide, derived from Aplysia kurodai, exhibits cardiac activity in invertebrates. The chirality of the tryptophan residue at the second position in N(dW)F influences its conformation and biological characteristics. We demonstrated the chiral separation of N(dW)F and its diastereomer NWF using (S)-3,3′-diphenyl-1,1′-binaphthyl-20-crown-6-ether columns (CR-I(+)). A reduction in the ratio of acetonitrile and methanol in the mobile phase allowed the complete separation of N(dW)F and its diastereomer, improving the separation factor (α) from 0.96 to 6.28. Molecular dynamics simulations revealed that the interaction of N(dW)F with CR-I(−) was more favorable than with CR-I(+). These findings indicate that the structure of the CR-I column stereoselectively recognizes peptides and facilitates the separation of naturally occurring D-amino acid residue-containing tripeptides. Full article

Midazolam is a benzodiazepine that is utilized for the induction of anesthesia and the facilitation of procedural sedation. Despite the absence of stereogenic centers, the non-planar seven-membered ring devoid of reflection symmetry elements confers planar stereogenicity to the molecule. Due to the rapid conformational inversion of the Rp and Sp enantiomers, which occurs via a simple ring flip, high-performance liquid chromatography (HPLC) enantiomeric separation is restricted to sub-room temperature conditions. In this study, the energy barriers for the racemization of midazolam at five distinct temperatures and in acetonitrile/water mixtures were determined by monitoring the decay of the circular dichroism signal at a specific wavelength over time. The kinetic and thermodynamic data obtained were compared with those determined by dynamic enantioselective high-performance liquid chromatography using the Chiralpak IG-3 chiral stationary phase, which contains the amylose tris(3-chloro-5-methylphenylcarbamate) as the selector. The temperature-dependent dynamic HPLC of midazolam was carried out at the same temperatures and with the same aqueous mixtures used in parallel kinetic off-column experiments. To simulate dynamic chromatographic profiles, a lab-made computer program based on a stochastic model was utilized. The results indicated that the moderate influence of the stationary phase resulted in a slight increase in the activation barriers, which was more pronounced as the time spent in the column increased. This phenomenon was found to be mitigated when switching from a 250 mm × 4.6 mm, 3 µm, Chiralpak IG-3 column to a 50 mm × 4.6 mm, 1.6 µm, Chiralpak IG-U UHPLC column. The outcomes obtained under UHPLC conditions were found to be more closely aligned with those obtained through the ECD technique, with a discrepancy of only 0.1 kcal/mol or less, indicating a high degree of concordance between the two methods. Full article

This is a review/research paper on anomalies applied in a bottom–up approach to standard model and gravity. It is divided into two parts. The first consists of a proper review of anomalies in quantum field theories. Anomalies are analyzed according to three different methods: a perturbative one based on a Feynman diagram, a non-perturbative one relying on the Schwinger–DeWitt approach, and, third, one hinging on the Atiyah–Singer family’s index theorem. The three methods are applied both to chiral gauge anomalies and trace anomalies. The fundamental distinction, which our presentation leads to, is between obstructive (O) and non-obstructive (NO) anomalies. The former is tied to the non-existence of fermion propagators, which fatally maim the corresponding theory. In the second part, we apply this analysis to the SM and a variety of its extensions, which are immersed in a gravitational background, and we find that they are all plagued by a residual chiral trace anomaly. To completely eliminate all kinds of dangerous anomalies in SM-like theories, we propose a somewhat unconventional scheme and exemplify it by means of an explicit model. The latter is a left–right symmetric model. We embed it in a Weyl geometry to render it a conformal invariant. We then deal with some of its quantum aspects, particularly its even (NO) trace anomalies and the means to preserve its conformal invariance at the quantum level. We briefly review renormalization and unitarity in the framework of similar models discussed in the existing literature. Finally, we present a possible (conjectural) application of the model to describe the junction between cosmology and quantum field theory. Full article

Vibrational circular dichroism (VCD) enhancement by low-lying electronic states (LLESs) is a fascinating phenomenon, but accounting for it theoretically remains a challenge despite significant research efforts over the past 20 years. In this article, we synthesized two transition metal complexes using the tetradentate Schiff base ligands (R,R)- and (S,S)-N,N′-Bis(3,5-di-tert-butylsalicylidene)-1,2-cyclohexanediamine with Co(II) and Mn(III), referred to as Co(II)-salen-chxn and Mn(III)-Cl-salen-chxn, respectively. Their stereochemical properties were explored through a combined experimental chiroptical spectroscopic and theoretical approach, with a focus on Co(II)-salen-chxn. Extensive conformational searches in CDCl₃ for both high- and low-spin states were carried out and the associated infrared (IR), VCD, ultraviolet-visible (UV-Vis) absorption, and electronic circular dichroism (ECD) spectra were simulated. A good agreement between experimental and simulated data was achieved for IR, VCD, UV-Vis, and ECD, except in the case of VCD of Co(II)-salen-chxn which exhibits significant intensity enhancement and monosignate VCD bands, attributed to the LLESs. Interestingly, detailed comparisons with Mn(III)-Cl-salen-chxn and previously reported Ni(II)-salen-chxn and Cu(II)-salen-chxn complexes suggest that the enhancement factor is predicted by the current density functional theory simulations. However, the monosignate signatures observed in the experimental Co(II) VCD spectrum were not captured theoretically. Based on the experiment and theoretical VCD and ECD comparison, it is tentatively suggested that Co(II)-salen-chxn exists in both low- and high-spin states, with the former being dominant, while Mn(III)-Cl-salen-chxn in the high-spin state. The study indicates that VCD enhancement by LLESs is at least partially captured by the existing theoretical simulation, while the symmetry consideration in vibronic coupling provides further insight into the mechanisms behind the VCD sign-flip. Full article

Enantiopure turbo chirality in small organic molecules, without other chiral elements, is a fascinating topic that has garnered significant interest within the chemical and materials science community. However, further research into and application of this concept have been severely limited by the lack of effective asymmetric tools. To date, only a few enantiomers of turbo chiral targets have been isolated, and these were obtained through physical separation using chiral HPLC, typically on milligram scales. In this work, we report the first asymmetric approach to enantiopure turbo chirality in the absence of other chiral elements such as central and axial chirality. This is demonstrated by assembling aromatic phosphine oxides, where three propeller-like groups are anchored to a P(O) center via three axes. Asymmetric induction was successfully carried out using a chiral sulfonimine auxiliary, with absolute configurations and conformations unambiguously determined by X-ray diffraction analysis. The resulting turbo frameworks exhibit three propellers arranged in either a clockwise (P,P,P) or counterclockwise (M,M,M) configuration. In these arrangements, the bulkier sides of the aromatic rings are oriented toward the oxygen atom of the P=O bond rather than in the opposite direction. Additionally, the orientational configuration is controlled by the sulfonimine auxiliary as well, showing that one of the Naph rings is pushed away from the auxiliary group (-CH₂-NHSO₂-tBu) of the phenyl ring. Computational studies were conducted on relative energies for the rotational barriers of a turbo target along the P=O axis and the transition pathway between two enantiomers, meeting our expectations. This work is expected to have a significant impact on the fields of chemistry, biomedicine, and materials science in the future. Full article

This publication reports a facile and convenient preparation of tri-O-acetyl-glucopyranoses, derived from the corresponding 2-deoxyaminosugar, where the vicinal anomeric and C2 positions are decorated by azido and (thio)ureido groups, respectively. This double functionalization leads to an inherently chiral core incorporating the versatile azido and (thio)ureido linkages prone to further manipulation. The latter also provides a structural element for hydrogen-bonded donor-acceptor (HB-DA) sites, which are of immense value in organocatalytic pursuits. A computation-aided conformational analysis unveils the landscape of available conformers and their relative stability. N-aryl (thio)ureas bearing substituents at ortho positions exist as mixtures of M- and P-atropisomeric conformers. Full article

The star matter composed of nucleons deep inside compact stars, such as neutron stars, is believed to be very dense, such that various types of new concepts and physical phenomena are naturally expected due to the nontrivial strong correlations between hadrons. The possibility of revealing the hidden scale symmetry in dense baryonic matter has been discussed recently, to uncover the pseudo-conformal phase in dense star matter. In the pseudo-conformal phase, the trace of the energy–momentum tensor becomes density-independent, and the speed of sound approaches the conformal velocity in scale symmetric matter. Interestingly, it is also observed that the effective nucleon mass becomes a density-independent finite quantity, which can be identified as the chiral invariant mass of the parity doublet model, indicating that the parity doubling is an emergent phenomenon. In this paper, we will discuss how parity-doubling symmetry emerges inside the core of a compact star as a consequence of the interplays between $\omega$ vector mesons and nucleons (or dilaton, $\chi$, equivalently) and between the chiral symmetry and the scale symmetry. Full article

The antimicrobial properties of a series of anionic bis(carbene) silver complexes Na₃[Ag(NHC^R)₂] were investigated (2a–2g and 2c′, where NHC^R is a 2,2′-(imidazol-2-ylidene)dicarboxylate-type N-heterocyclic carbene). The complexes were synthesized by the interaction of imidazolium dicarboxylate compounds with silver oxide in the presence of aqueous sodium hydroxide. Complexes 2f,g were characterized analytically and spectroscopically, and the ligand precursor 1f and complexes 2c and 2g were structurally identified by X-ray diffraction methods. The anions of 2c and 2g, [Ag(NHC^R)₂]³⁻, showed a typical linear disposition of C_carbene-Ag-C_carbene atoms and an uncommonly eclipsed conformation of carbene ligands. The antimicrobial properties of complexes 2a–g, which contains chiral (2b–2e and 2c′) and non-chiral derivatives (2a,f,g), were evaluated against Gram-negative bacteria, Escherichia coli and Pseudomonas aeruginosa, and a Gram-positive bacterium, Staphylococcus aureus. From the observed values of the minimal inhibitory concentration and minimal bactericidal concentration, complexes 2a and 2b showed the best antimicrobial activity against all strains. An interesting chirality–antimicrobial relationship was found, and eutomer 2c′ showed better activity than its enantiomer 2c against the three bacteria. Furthermore, these complexes were investigated experimentally and theoretically by ¹⁰⁹Ag nuclear magnetic resonance, and the electronic and steric characteristics of the dianionic carbene ligands were also examined. Full article