Rotational Conformers Research Articles

Polymorphism in oxyresveratrol studied by 3D ED.

The polymorphism of oxyresveratrol, a natural extract widely used in traditional Asian medicine, was investigated by means of the most recent structure characterization techniques. A previously unknown anhydrate oxyresveratrol crystal structure was identified for the first time from a submicrometric polyphasic mixture using 3D electron diffraction (3D ED). Additionally, a new polymorph of the dihydrate form of oxyresveratrol was also discovered and structurally studied. Detailed thermal and calorimetry studies revealed their thermal behavior and dehydration path. DFT calculations were also employed to investigate the stability of the rotational conformers involved in the hydrated phases (in both new and already known phases). This research exemplifies how 3D ED combined with cryo-plunging and routine solid-state analysis can elucidate the polymorphism scenario of a nanocrystalline natural compound.

The Liebeskind-Srogl Cross-Coupling Reaction as a Crucial Step in the Synthesis of New Squaramide-Based Antituberculosis Agents.

The synthesis of an extensive series of new squaramides with high potential in treating drug-resistant tuberculosis employing the Liebeskind-Srogl cross-coupling reaction is presented. Using the protocol given and various substrates, we assessed the scope and limitations of our methodology and prepared an extensive range of desired compounds. Moreover, 1H NMR spectra in solution show the presence of two rotational conformers (rotamers) in special cases. The results of antimycobacterial activity demonstrate the highly selective substrate specificity of the tested squaramides, requiring an efficient and widely applicable synthetic approach needed for the discovery of lead compounds. Our synthetic strategy confirms the versatility of squaramides that can be easily transformed into diverse functionalized molecules.

Synthesis and Structure of Protonated Propiolic Acid.

Propiolic acid was investigated in the superacidic system XF/SbF5 (X = H, D). The salts of the monoprotonated species of propiolic acid were characterized by vibrational and NMR spectroscopy as well as single-crystal analyses. The rotational conformers of the protonated species can be distinguished by NMR spectroscopy via the temperature-dependent rotational barrier. In the solid state, they can be detected by H/D exchange and packing effects due to different anions. The experimental results are discussed together with an IRC calculation of the rotational barrier. After acetic acid and formic acid, this is the third protonated carboxylic acid for which the energy differences between the conformers have been determined.

Bis(Dicarbollide) Complexes of Transition Metals: How Substituents in Dicarbollide Ligands Affect the Geometry and Properties of the Complexes.

The interaction between different types of substituents in dicarbollide ligands and their influence on the stabilization of various rotational conformers (rotamers) of transition metal bis(dicarbollide) complexes [3,3'-M(1,2-C2B9H11)2]- are considered. It has been shown that the formation of intramolecular CH···X hydrogen bonds between dicarbollide ligands is determined by the size of the proton acceptor atom X rather than its electronegativity. Due to the stabilization of rotamers with different dipole moments, intramolecular hydrogen bonds between ligands in transition metal bis(dicarbollide) complexes can have a significant impact on the biological properties of their derivatives. In the presence of external complexing metals, weak intramolecular CH···X hydrogen bonds can be broken to form stronger X->M donor-acceptor bonds. This process is accompanied by the mutual rotation of dicarbollide ligands and can be used in sensors and molecular switches based on transition metal bis(dicarbollide) complexes.

Structural basis of directional switching by the bacterial flagellum.

The bacterial flagellum is a macromolecular protein complex that harvests energy from uni-directional ion flow across the inner membrane to power bacterial swimming via rotation of the flagellar filament. Rotation is bi-directional, with binding of a cytoplasmic chemotactic response regulator controlling reversal, though the structural and mechanistic bases for rotational switching are not well understood. Here we present cryoelectron microscopy structures of intact Salmonella flagellar basal bodies (3.2-5.5 Å), including the cytoplasmic C-ring complexes required for power transmission, in both counter-clockwise and clockwise rotational conformations. These reveal 180° movements of both the N- and C-terminal domains of the FliG protein, which, when combined with a high-resolution cryoelectron microscopy structure of the MotA5B2 stator, show that the stator shifts from the outside to the inside of the C-ring. This enables rotational switching and reveals how uni-directional ion flow across the inner membrane is used to accomplish bi-directional rotation of the flagellum.

Rotational conformers and nuclear spin isomers of carbonyl diisothiocyanate.

Nuclear spin isomers of molecules play a pivotal role in our understanding of quantum mechanics and can have significant implications for various fields. In this work, we report the isolation and characterization of stable nuclear spin isomers as well as conformational isomers of a reactive compound, namely carbonyl diisothiocyanate. It can exist as three rotational conformers, two of which, the syn-syn and syn-anti, were observed in a pulsed supersonic jet by chirped pulse Fourier transform microwave spectroscopy in the 2-12 GHz frequency region. The rotational spectra of two distinct nuclear spin isomers of syn-syn-carbonyl diisothiocyanate, ortho and para, were recorded and analyzed. Experimental molecular rotational parameters for the identified rotational and nuclear spin isomers were determined, including rotational constants, centrifugal distortion constants, and nuclear quadrupole coupling constants. The two nuclear spin isomers are distinguished by unique hyperfine splitting signatures in their rotational spectra as an outcome of their different nuclear spin states. The relative abundances of the two observed conformers in the gas phase were estimated from the intensity of their rotational transitions. Following detection of singly substituted rare isotopologues of the syn-syn conformer, a partial substitution (rs) structure was determined.

Dual phosphorescent emissions from conformers of iridium complex rotors.

The chiral iridium rotors Ir(ppy)2(pyX)Cl (X = CC-SiR3, R = alkyl) remarkably contain two distinct rotational conformers in the ground (S0) and excited (T1) states that can be detected by NMR and emission measurements respectively at variable temperatures. The observed phosphorescent emissions, vibronic (involving L = ppy) and broad (L = pyX), arise from different triplet ligand to metal charge transfers from the two rotational conformers at distinct 3MLCT excited states. Both conformers exist in these Ir(ppy)2(pyX)Cl rotors due to the electron-withdrawing, conjugated substituent X.

Unveiling the chemical kinetics of aminomethanol (NH2CH2OH): insights into H and O2 photo-oxidation reactions and formamide dominance.

Aminomethanol is released into the atmosphere through various sources, including biomass burning. In this study, we have expounded the chemical kinetics of aminomethanol in the reaction pathways initiated by the hydroxyl radical ( H) with the aid of ab initio//density functional theory (DFT) i.e., coupled-cluster theory (CCSD(T))//hybrid-DFT (M06-2X/6-311++G (3df, 3pd). We have explored various possible directions of the H radical on aminomethanol, as well as the formation of distinct pre-reactive complexes. Our computational findings reveal that the H transfer necessitates activation energies ranging from 4.1 to 6.5kcal/mol from the -CH2 group, 3.5-6.5kcal/mol from the -NH2 group and 7-9.3kcal/mol from the -OH group of three rotational conformers. The H transfer from -CH2, -NH2 and -OH exhibits an estimated total rate constant (k OH) of approximately 1.97 × 10-11cm3 molecule-1s-1 at 300K. The branching fraction analysis indicates a pronounced dominance of C-centered NH2 HOH radicals with a favorability of 77%, surpassing the N-centered HCH2OH (20%) and O-centered NH2CH2 (3%) radicals. Moreover, our investigation delves into the oxidation of the prominently favored carbon-centered NH2 HOH radical through its interaction with atmospheric oxygen molecules. Intriguingly, our findings reveal that formamide (NH2CHO) emerges as the predominant product in the NH2 HOH + 3O2 reaction, eclipsing alternative outcomes such as amino formic acid (NH2COOH) and formimidic acid (HN = C(H)-OH). At atmospheric conditions pertinent to the troposphere, the branching fraction value for the formation of formamide is about 99%, coupled with a rate constant of 5.5 × 10-12cm3 molecule-1 s-1. Finally, we have scrutinized the detrimental impact of formamide on the atmosphere. Interaction of formamide with atmospheric hydroxyl radicals could give rise to the production of potentially perilous compounds such as HNCO. Further, unreacted HCH2OH radicals may initiate the formation of carcinogenic nitrosamines when reacting with trace N-oxides (namely, NO and NO2). This, in turn, escalates the environmental risk factors.

"Gear-driven"-type chirality transfer of tetraphenylethene-based supramolecular organic frameworks for peptides in water.

Chirality transfer for natural chiral biomolecules can reveal the indispensable role of chiral structures in life and can be used to develop the chirality-sensing biomolecular recognition. Here, we report the synthesis and characterization of a series of achiral supramolecular organic frameworks (SOF-1, SOF-2, and SOF-3), constructed from cucurbit[8]uril (CB[8]) and tetraphenylethene (TPE) derivatives (1, 2, and 3), respectively, as chirality-sensing platforms to explore their chirality transfer mechanism for peptides in water. Given the right-handed (P) and left-handed (M) rotational conformation of TPE units and the selective binding of CB[8] to aromatic amino acids, these achiral SOFs can be selectively triggered in water by peptides containing N-terminal tryptophan (W) and phenylalanine (F) residues into their P- or M-rotational conformation, exhibiting significantly different circular dichroism (CD) spectra. Although various peptides have the same l-type chiral configuration, they can induce positive CD signals of SOF-1 and negative CD signals of SOF-2 and SOF-3, respectively. Based on the structural analysis of the linkage units between CB[8] and TPE units in these SOFs, a "gear-driven"-type chirality transfer mechanism has been proposed to visually illustrate the multiple-step chirality transfer process from the recognition site in the CB[8]'s cavity to TPE units. Furthermore, by utilizing the characteristic CD signals generated through the "gear-driven"-type chirality transfer, these SOFs can serve as chiroptical sensor arrays to effectively recognize and distinguish various peptides based on their distinctive CD spectra.

Influence of the substitution position on spin communication in photoexcited perylene-nitroxide dyads.

By virtue of the modularity of their structures, their tunable optical and magnetic properties, and versatile applications, photogenerated triplet-radical systems provide an ideal platform for the study of the factors controlling spin communication in molecular frameworks. Typically, these compounds consist of an organic chromophore covalently attached to a stable radical. After formation of the chromophore triplet state by photoexcitation, two spin centres are present in the molecule that will interact. The nature of their interaction is governed by the magnitude of the exchange interaction between them and can be studied by making use of transient electron paramagnetic resonance (EPR) techniques. Here, we investigate three perylene-nitroxide dyads that only differ with respect to the position where the nitroxide radical is attached to the perylene core. The comparison of the results from transient UV-vis and EPR experiments reveals major differences in the excited state properties of the three dyads, notably their triplet state formation yield, excited state deactivation kinetics, and spin coherence times. Spectral simulations and quantum chemical calculations are used to rationalise these findings and demonstrate the importance of considering the structural flexibility and the contribution of rotational conformers for an accurate interpretation of the data.

C-Cl Bond Activation at Rotated vs Unrotated Dinuclear Site Related to [FeFe]-Hydrogenases.

The novel dinuclear complex related to the [FeFe]-hydrogenases active site, [Fe2(μ-pdt)(κ2-dmpe)2(CO)2] (1), is highly reactive toward chlorinated compounds CHxCl4-x (x = 1, 2) affording selectively terminal or bridging chloro diiron isomers through a C-Cl bond activation. DFT calculations suggest a cooperative mechanism involving a formal concerted regioselective chloronium transfer depending on the unrotated or rotated conformation of two isomers of 1.

Construction of fluorescent sensor array and three-dimensional microfluidic paper based analytical device for specific identification and visual determination of antibiotics in food.

For antibiotics misuse since the global outbreak of COVID 19, a novel strategy for discriminating and detecting antibiotics is proposed based on the graphene quantum dots with multi-doped heteroatoms including F, N and P (M-GQDs), which exhibit blue emission (419.0nm) under the excitation of 336.0nm. Specifically, the fluorescence of M-GQDs is quenched by tetracyclines (TCs) owing to inner filter effect (IFE) and enhanced by alkane-modified fluoroquinolones (AFQs), which is attributed to restricted conformational rotation based on π-π stacking, hydrogen-bonding and electrostatic interactions. Meanwhile, the electron-accepting property of oxazine ring in oxazine-modified fluoroquinolones (OFQs) increases emission peak at 498.0nm and decreases emission peak at 419.0nm as the color changes from blue to cyan. Moreover, a cascade system integrated with 3D microfluidic paper-based analytical device (3D-μPAD) is applied successfully for visually distinguishing three antibiotics, which shows great potential and versatility of M-GQDs for food safety monitoring.

Partial spontaneous intersubunit rotations in pretranslocation ribosomes

The two main steps of translation, peptidyl transfer, and translocation are accompanied by counterclockwise and clockwise rotations of the large and small ribosomal subunits with respect to each other. Upon peptidyl transfer, the small ribosomal subunit rotates counterclockwise relative to the large subunit, placing the ribosome into the rotated conformation. Simultaneously, tRNAs move into the hybrid conformation, and the L1 stalk moves inward toward the P-site tRNA. The conformational dynamics of pretranslocation ribosomes were extensively studied by ensemble and single-molecule methods. Different experimental modalities tracking ribosomal subunits, tRNAs, and the L1 stalk showed that pretranslocation ribosomes undergo spontaneous conformational transitions. Thus, peptidyl transfer unlocks the ribosome and decreases an energy barrier for the reverse ribosome rotation during translocation. However, the tracking of translation with ribosomes labeled at rRNA helices h44 and H101 showed a lack of spontaneous rotations in pretranslocation complexes. Therefore, reverse intersubunit rotations occur during EF-G catalyzed translocation. To reconcile these views, we used high-speed single-molecule microscopy to follow translation in real time. We showed spontaneous rotations in puromycin-released h44-H101 dye-labeled ribosomes. During elongation, the h44-H101 ribosomes undergo partial spontaneous rotations. Spontaneous rotations in h44-H101-labeled ribosomes are restricted prior to aminoacyl-tRNA binding. The pretranslocation h44-H101 ribosomes spontaneously exchanged between three different rotational states. This demonstrates that peptidyl transfer unlocks spontaneous rotations and pretranslocation ribosomes can adopt several thermally accessible conformations, thus supporting the Brownian model of translocation.

Insights into Entropy Change of β2 Relaxation in Retraction of Uniaxially Stretched Polyimide Films

AbstractStretching has been extensively applied for decades in the production of polyimide (PI) materials with improved mechanical, electrical, and thermal properties. Meanwhile, a detailed understanding of the molecular motions during stretching is still limited. Herein, the thermomechanical behaviors of uniaxially stretched PI films prepared from 3,3′,4,4′‐biphenyl tetracarboxylic dianhydride (BPDA) and 2,2′‐bis (trifluoromethyl) benzidine (TFDB) are studied, and the possible molecular motions responsible for the sub‐glass transition temperature (Tg) stretchability and retraction after stretching are systematically investigated. Based on X‐ray diffraction and dynamic mechanical analysis, it is revealed that both the sub‐Tg stretchability and retraction correlates with β2 relaxation, which originates from the highly cooperative molecular motions of conformational rotations involving segmented BPDA units. A thermodynamic model is established and applied for the analysis of the retraction behaviors of stretched BPDA‐TFDB PI films. It is found that the increase of entropy under stretching plays a significant role in most retraction cases. However, as the stretching temperature increases, the α relaxation‐correlated large‐scale molecular motions emerge. Such motions partially counterbalance the conformational rotations of BPDA segments, leading to an enhanced contribution of enthalpy decrease during the retraction of BPDA‐TFDB PI films.

A smart Zn-MOF-based ratiometric fluorescence sensor for accurate distinguish and optosmart sensing of different types of tetracyclines

Tetracyclines misuse has brought enormous pressure on the environment, and it is significant to develop sensitive and selective methods for detecting tetracyclines. A ratiometric fluorescence-enhanced sensor with Zn-based metal-organic framework (HNU-55) as detection signal and rhodamine B (RhB) as reference signal is constructed for differentiation and optosmart detection of tetracyclines. Sensor specifically recognizes tetracyclines through chelation between Zn2+ of sensor and –OH of tetracyclines and sensitizes tetracyclines to induce fluorescence enhancement. The π–π stacking interactions between sensor and tetracyclines induce aggregation of tetracyclines. Intermolecular hydrogen bonding enhances sensor rigidity and limits its conformational rotation, further strengthening the fluorescence. Different fluorescence emission of sensor achieves discrimination of four tetracyclines. Fluorescent sensing array based on sensor distinguishes four tetracyclines precisely by principal component analysis. Binding energies and bond angles calculated from density functional theory are attributed to distinguish tetracyclines. Detection limits of sensor for doxycycline, tetracycline, oxytetracycline and chlortetracycline are 4.6, 2.6, 4.7 and 7.5 nmol/L, respectively. Applying sensor for tetracyclines detection in lake water obtains satisfactory recoveries. The portable optosmart sensing system is developed for on-site visual quantification of tetracyclines. An effective strategy for accurate identification and optosmart sensing of tetracyclines offers a wide range of applications in environmental monitoring.

Combination of deep XLMS with deep learning reveals an ordered rearrangement and assembly of a major protein component of the vaccinia virion.

An outstanding problem in the understanding of poxvirus biology is the molecular structure of the mature virion. Via deep learning methods combined with chemical cross-linking mass spectrometry, we have addressed the structure and assembly pathway of P4a, a key poxvirus virion core component.

Chiral Adaptive Induction of an Achiral Cucurbit[8]uril-Based Supramolecular Organic Framework by Dipeptides in Water.

Chiral induction by natural biomolecules can reveal the indispensable role of chiral structures in life and can be used to develop the chirality-sensing biomolecular recognition. Here, we present the synthesis and characterization of an achiral supramolecular organic framework (SOF-1) constructed from cucurbit[8]uril (CB[8]) and hexaphenylbenzene (HPB) derivative (1) in water. Due to the propeller-like rotational chiral conformation of HPB units and the specific recognition properties of CB[8], SOF-1 demonstrates chiral adaptive induction in water when interacting with the N-terminal Trp-/Phe-containing dipeptides including L-TrpX and L-PheX (X is an amino acid residue), respectively, exhibiting contrasting circular dichroism (CD) and circularly polarized luminescence (CPL) spectra. Consequently, SOF-1 has been developed as a supramolecular host and chiroptical sensor capable of recognizing and distinguishing the sequence-opposite Trp-/Phe-containing dipeptide pairs including L-TrpX/L-XTrp and L-PheX/L-XPhe based on the sequence-selective CD responses.

Chiral Adaptive Induction of an Achiral Cucurbit[8]uril‐Based Supramolecular Organic Framework by Dipeptides in Water

AbstractChiral induction by natural biomolecules can reveal the indispensable role of chiral structures in life and can be used to develop the chirality‐sensing biomolecular recognition. Here, we present the synthesis and characterization of an achiral supramolecular organic framework (SOF‐1) constructed from cucurbit[8]uril (CB[8]) and hexaphenylbenzene (HPB) derivative (1) in water. Due to the propeller‐like rotational chiral conformation of HPB units and the specific recognition properties of CB[8], SOF‐1 demonstrates chiral adaptive induction in water when interacting with the N‐terminal Trp‐/Phe‐containing dipeptides including L‐TrpX and L‐PheX (X is an amino acid residue), respectively, exhibiting contrasting circular dichroism (CD) and circularly polarized luminescence (CPL) spectra. Consequently, SOF‐1 has been developed as a supramolecular host and chiroptical sensor capable of recognizing and distinguishing the sequence‐opposite Trp‐/Phe‐containing dipeptide pairs including L‐TrpX/L‐XTrp and L‐PheX/L‐XPhe based on the sequence‐selective CD responses.

Fluxionality Modulating the Magnetic Anisotropy in Lanthanoarene [(ηCnRn)2Ln(II/III)] (n = 4-8) Single-Ion Magnets.

Lanthanoarenes have emerged as the best bet for the futuristic application of single-ion magnets in information storage devices. While dysprosocenium molecules with various substituents at the arene ring exhibit a very large blocking temperature, the corresponding Er(III) analogues do not, and this is reversed if the size of the arene ring is eight. Using a combination of ab initio CASSCF and DFT-based molecular dynamics (MD) study, we have explored 25 Dy(III)/Er(III)/Ho(II)/Tb(II)/Dy(II) arene complexes with the ring size varying from 4 to 8 to understand the differences observed and decipher the correlation of structure to the spin dynamics behavior. Among the oxidation state of +2 complexes studied, Tb(II) exhibits the highest barrier, with the Cp-Tb-Cp angle being linear. Further, one of the four-membered arene model studied exhibits a very large barrier of 1442 cm-1, suggesting a potential high-blocking SIM. While bulky substituents at the arene ring help increase the axiality and the CR-Ln-CR angle, this also fetches several agostic C-H···Ln interactions, which injects transverse anisotropy. Furthermore, MD coupled with the CASSCF study reveals that the fluxional behavior of the arene ring generates several rotational conformers that are even accessible at lower temperatures offering a shortcut to the magnetization relaxation process. The importance of structural fluctuations in controlling the magnetic anisotropy by choosing apt metal-ion/ring partners and the corresponding substituents has been highlighted to offer clues to the futuristic SIM design.

Sequential Two-Photon Delayed Fluorescence Anisotropy for Macromolecular Size Determination

Time-resolved fluorescence anisotropy (FA) uses the fluorophore depolarization rate to report on rotational diffusion, conformation changes, and intermolecular interactions in solution. Although FA is a rapid, sensitive, and nondestructive tool for biomolecular interaction studies, the short (∼ns) fluorescence lifetime of typical dyes largely prevents the application of FA on larger macromolecular species and complexes. By using triplet shelving and recovery of optical excitation, we introduce optically activated delayed fluorescence anisotropy (OADFA) measurements using sequential two-photon excitation, effectively stretching fluorescence anisotropy measurement times from the nanosecond scale to hundreds of microseconds. We demonstrate this scheme for measuring slow depolarization processes of large macromolecular complexes, derive a quantitative rate model, and perform Monte Carlo simulations to describe the depolarization process of OADFA at the molecular level. This setup has great potential to enable future biomacromolecular and colloidal studies.