Conformational Isomers Research Articles

On the Use of Strong Proton Donors as a Tool for Overcoming Line Broadening in NMR: A Comment.

Overcoming line broadening of labile protons and achieving high-resolution NMR spectra is crucial for the structural and conformational analysis of organic molecules. Recently, Ma etal. (Magn. Reson. Chem. 2024, 62, 198-207) demonstrated the effectiveness of 2,2,2-trifluoroacetic acid (TFA) in sharpening NMR signals for nitrogen-containing compounds which exhibit prototropic tautomerization or conformational isomerism using high molar ratio of [acids]/[solute] ~ 5 to 200. In this commentary, we provide an overview of earlier publications and highlight the extensive applications of TFA in enhancing NMR resolution across a variety of organic functional groups, with the use of very small ratios of [acids]/[solute] ~ 10-3 to 10-2. The prospects for the unequivocal structure analysis using labile protons as the starting point will be analyzed.

Coordination geometry flexibility driving supramolecular isomerism of Cu/Mo pillared-layer hybrid networks.

Hydrothermal synthesis led to four novel 3D pillared-layer metal-organic frameworks: [Cu4(4,4'-bipy)4(MoO4)4·0.3H2O]n (1), [Cu(4,4'-bipy)0.5(MoO4)·0.25H2O]n (2), [Cu(4,4'-bipy)(MoO4)·0.1H2O]n (3), and [{Cu(4,4'-bipy)}2(Mo8O26)0.5]n (4). These compounds exhibit diverse supramolecular isomerism within their 3D coordination networks, each incorporating bimetallic {CuMoO} layers linked by 4,4'-bipyridine, demonstrating a remarkable structural diversity. Compound 1 features a 3D network derived from conformational supramolecular isomerism. Its bimetallic layer comprises fused 16-membered {Cu4Mo4O8} and eight-membered {Cu2Mo2O4} rings, with varying O-Cu-O bond angles affecting the network puckering and Cu-Cu distances. In contrast, the coordination networks observed in 2, 3, and 4 correspond to structural supramolecular isomers from the earlier stated networks. In 2, centrosymmetric Cu2+ dimers with distorted square-pyramidal geometry are linked along the c axis by 4,4'-bipyridine, forming 1D {Cu2(4,4'-bipy)}n chains with a Cu-Cu distance of 2.95 Å. Its oxide substructure comprises bilayers of fused 12-membered {Cu3Mo3O6} rings. Crystal structures 3 and 4 are particularly notable for their construction at the Cu+ centers. In compound 4, this isomerism is further influenced by the interplay between the distortion of the coordination geometry of both the Cu and Mo ions. The propensity to form these supramolecular isomers primarily stems from the flexible coordination environment of copper ions. Electron paramagnetic resonance measurements corroborated the structural descriptions of the paramagnetic compounds 1 and 2.

Ultra-high pressure slalom chromatography: Application to the characterization of large DNA and RNA samples relevant in cell and gene therapy

Slalom chromatography (SC), initially co-discovered by Boyes and Kasai in the late 1980s, has recently re-emerged as a breakthrough technique to rapidly analyze DNA samples. With the development of cutting-edge ultra-high pressure liquid chromatography (UHPLC) systems and columns, SC now offers enhanced resolution and sensitivity for analyzing large DNA samples. By revisiting the fundamentals of the SC retention mechanism (non-equilibrium separation mode) and considering the physicochemical properties of DNA biopolymers (contour length, extension under shear flow, relaxation time), we provide analytical chemists with a general strategy and framework for selecting the most relevant applications in the expanding field of cell and gene therapy. We then present proof-of-concept data demonstrating the rapid separation (under 2 min) of plasmid digest samples containing linear double-stranded (ds) DNA macromolecules starting from 2 kbp to 25 kbp, as well as the accurate size determination (±6%) of linear dsDNAs. Additionally, we show rapid baseline separation and quantification of extensible linear dsDNAs, along with the more rigid plasmid dsDNA (supercoiled/circular/nicked circular). We also quantify dsRNA impurities present in vitro transcription (IVT) media used for producing new mRNA therapeutics and assess dsRNA structural heterogeneity (conformational isomers). These findings aim to support in a near future application chemists in addressing emerging bioanalytical challenges in cell and gene therapy by offering advanced SC columns and methods.

Exploring rotational isomerism of fluorescent diarylethenes comprising 2-naphthyl and regioisomeric oxazoyl groups. A combined experimental and computational study

In the paper a phenomenon of rotational (conformational) isomerism within 1,2-diarylethenic compounds (DAE) comprising heteroarene ring of oxazole is explored on the example of the fluorescent naphthyl-vinyl-oxazole framework. In this regard three regioisomers of a n-(2-(naphthalen-2-yl)vinyl)oxazole molecule (nNVOx), differing in the oxazole substitution pattern (n = 2, 4, 5), are synthesized and methodically investigated by means of electronic UV–Vis spectroscopy combined with chemometric methods for spectral data analysis. Design of the experiments and interpretation of their output is additionally supported by quantum-chemical simulations based on the (TD) DFT methodology. As the result, all the studied nNVOx compounds are unveiled to simultaneously occur in form of at least two non-equivalent rotational isomers, varying in the conformation taken by the arene moieties with respect to the central vinyl fragment. The individual rotamers are then demonstrated to exhibit non-identical spectroscopic properties expressed by differences in corresponding absorption and fluorescence profiles, thereby ultimately confirming the impact of rotamerism onto the investigated molecular systems.

Structural dynamics of human deoxyuridine 5’-triphosphate nucleotidohydrolase (dUTPase)

Structural- and functional heterogeneity, as well as allosteric regulation, in homo-monomeric enzymes is a highly active area of research. One such enzyme is human nuclear-associated deoxyuridine 5’-triphosphate nucleotidohydrolase (dUTPase), which has emerged as an interesting drug target in combination therapy with traditional nucleotide analogue treatment of cancer. We report, for the first time, a full structural dynamics study of human dUTPase by NMR. dUTPase has been investigated in terms of structural dynamics in its apo form, in complex with the modified substrate resistant to hydrolysis, 2’-deoxyuridine 5’-α,β-imido-triphosphate (dUpNHpp), as well as the product, 2’-deoxy-uridine-monophosphate (dUMP). The apo form of the enzyme displayed slow dynamics in the milli- to microsecond regime in relaxation dispersion experiments, which was further slowed down to observable heterogeneity upon substrate-analogue binding. The results suggest that the non-hydrolysable substrate-analogue traps the enzyme in the conformational isomerization step that has been previously suggested to be part of the enzyme catalysis kinetics cycle. The observed heterogeneity fits well with the pattern expected to emerge from the suggested kinetic model, and no evidence for homotropic allosterism was found. The heatmaps of the slow dynamics, chemical shift perturbation upon substrate binding and conserved regions of the enzyme sequence all displayed a similar pattern, which suggests that the structural dynamics is finely tuned and important for the biological function of the enzyme for binding, conformational shift, catalysis and substrate release.

Conformational isomerism breaks the electrolyte solubility limit and stabilizes 4.9 V Ni-rich layered cathodes

By simply increasing the concentration of electrolytes, both aqueous and non-aqueous batteries deliver technical superiority in various properties such as high-voltage operation, electrode stability and safety performance. However, the development of this strategy has encountered a bottleneck due to the limitation of the intrinsic solubility, and its comprehensive performance has reached its limit. Here we demonstrate that the conformational isomerism of the solvent would significantly affect the solubility of electrolytes. By transforming the configuration of solvent from cis-cis to cis-trans upon thermal triggering, we successfully break the solubility limit, and a beyond concentrated electrolyte with the lowest solvent-to-salt molar ratio of 0.70 is constructed. Transitions between cis-cis and cis-trans conformers are observed through Nuclear Magnetic Resonance (NMR) testing. The electrolyte consists entirely of anion-mediated solvation structures and promotes the formation of robust inorganic-dominated cathode electrolyte interphase. As a result, it enables stable cycling of 4.9 V-class LiNi0.8Co0.1Mn0.1O2 positive electrodes. Moreover, a high capacity of 151.2 mAh g−1 can be maintained after 1000 cycles at cut-off voltage of 4.8 V. This work provides a chemical pathway to build new concept electrolytes working under harsh conditions.

‘Invisible’ Molecular Dynamics Revealed for a Conformationally Chiral π‐Stacked Perylene Bisimide Foldamer

Whilst energetic and kinetic aspects of folding processes are meanwhile well understood for natural biomacromolecules, the folding dynamics in so far studied artificial foldamer counterparts remain largely unexplored. This is due to the low energy barriers between their conformational isomers that make the dynamic processes undetectable with conventional methods such as UV/vis absorption, fluorescence, and NMR spectroscopy, making such processes ‘invisible’. Here we present an asymmetric perylene bisimide dimer (bis‐PBI 1) that possesses conformational chirality in its folded state. Owing to the large interconversion barrier (≥ 116 kJ mol–1), four stereoisomers could be separated and isolated. Since the interconversion between these stereoisomers requires the foldamer to first open and then to re‐fold, the transformation of one stereoisomer into others allowed us to ‘visualize’ the dynamics of folding with time and determine its lifetimes and the energetic barriers associated with the folding process. Supported by quantum chemical calculations, we identified the open structure to be only a fleeting metastable state of higher energy. Our experimental observation of the kinetics associated with the molecular dynamics in the PBI foldamer advances the fundamental understanding of folding in synthetic foldamers and paves the way for the design of smart functional materials.

'Invisible' Molecular Dynamics Revealed for a Conformationally Chiral π-Stacked Perylene Bisimide Foldamer.

Whilst energetic and kinetic aspects of folding processes are meanwhile well understood for natural biomacromolecules, the folding dynamics in so far studied artificial foldamer counterparts remain largely unexplored. This is due to the low energy barriers between their conformational isomers that make the dynamic processes undetectable with conventional methods such as UV/Vis absorption, fluorescence, and NMR spectroscopy, making such processes 'invisible'. Here we present an asymmetric perylene bisimide dimer (bis-PBI1) that possesses conformational chirality in its folded state. Owing to the large interconversion barrier (≥116 kJ mol-1), four stereoisomers could be separated and isolated. Since the interconversion between these stereoisomers requires the foldamer to first open and then to re-fold, the transformation of one stereoisomer into others allowed us to 'visualize' the dynamics of folding with time and determine its lifetimes and the energetic barriers associated with the folding process. Supported by quantum chemical calculations, we identified the open structure to be only a fleetingly metastable state of higher energy. Our experimental observation of the kinetics associated with the molecular dynamics in the PBI foldamer advances the fundamental understanding of folding in synthetic foldamers and paves the way for the design of smart functional materials.

Kinetic and Mechanistic Studies of Human Oligoadenylate Synthetase 1.

Oligoadenylate synthetase 1 (OAS1) catalyzes the dsRNA-dependent polymerization of ATP to form oligoadenylate, a second messenger of the innate immunity system. This paper reports kinetic and mechanistic studies of OAS1-catalyzed dimerization of ATP to form 2'-5'-diadenylate and pyrophosphate (PPi), the first step in ATP polymerization. Major findings include the following: (1) Reaction progress curves for the production of PPi are biphasic, characterized by a presteady-state lag followed by the linear, steady-state production of PPi. (2) The dependence of steady-state velocity on ATP concentration is sigmoidal and can be described by a rate law derived for a mechanism involving enzyme-catalyzed substrate dimerization. (3) Steady-state velocities were determined as a function of ATP concentration at fixed concentrations of poly(I:C), a synthetic dsRNA activator of OAS1. The data suggest a random mechanism in which either ATP or poly(I:C) can add first to the enzyme. (4) The dependence of klag on poly(I:C) and ATP concentration requires expansion of this mechanism to include slow conformational isomerization of various poly(I:C)- and ATP-bound complexes of inactive OAS1 to form complexes comprising an active enzyme, to ultimately form the reactive Michaelis complex of active OAS1, poly(I:C), and two molecules of ATP. Finally, within this complex, the two molecules of ATP dimerize to form 2'-5'-diadenylate and pyrophosphate. (5) The pH dependence and solvent deuterium isotope effect for kcat suggests that proton transfer occurs in the rate-limiting transition state, which likely involves proton abstraction from the 2'-hydroxyl of the adenylate acceptor ATP as the oxygen of this hydroxyl attacks the a-phosphate of the adenylate donor ATP in an SN2 fashion.

Single-Molecule White Circularly Polarized Photoluminescence and Electroluminescence from Dual-Emission Enantiomers.

The strategy of integrating conformational isomerization donors and chiral acceptors in a single molecule was proposed to construct white circularly polarized luminescence (WCPL) materials in this work. Consequently, a pair of dual-emission enantiomers, namely (R/S)-DO-PTZ, were designed and synthesized, which displayed white emission with blue and yellow dual-emission bands in solution and solid films with Commission Internationale de l'Eclairage (CIE) coordinates of (0.30, 0.33) and (0.33, 0.35), respectively. Meanwhile, (R/S)-DO-PTZ exhibited a high PLQY of up to 67 % in doped films and clear mirror-image WCPL signals with a |glum| value of 3.0×10-3. Moreover, white circularly polarized electroluminescence (WCPEL) based on organic light-emitting diodes (OLEDs) with (R/S)-DO-PTZ as emitters were also achieved with CIE coordinates of (0.32, 0.37) and EQEmax of 4.7 %, representing the state-of-the-art level of white OLEDs based on single-molecule purely organic emitters. By optimizing the device structure, warm WCPEL devices were further obtained with a |gEL| value of 2.8×10-3, CIE coordinates of (0.37, 0.48) and EQEmax of up to 15.6 %. To our knowledge, this is the first report of CP-WOLEDs based on single-molecule purely organic emitters.

Unveiling the Influence of Linkers on Conformations of Oligomeric Acceptors for High-Performance Polymer Solar Cells.

Conformational isomerism of organic photovoltaic materials has a profound impact on their molecular packing and therefore performance of polymer solar cells (PSCs). However, the conformations of oligomeric acceptors (OAs) are mostly predicted by simulations rather than experimental determinations. Herein, the stereochemical S-shaped structure of two dimeric-type acceptor molecules, V-DYIC and V-DYIC-4F, is first confirmed with different end groups (IC for V-DYIC and IC-2F for V-DYIC-4F), incorporating vinylene linkage for connecting the distinct state-of-the-art small molecule acceptor Y-segments. Through the synthetic control of fluorination sites adjacent to the vinyl-linker, S-shaped the conformation by NMR experiments is validated. Compared to the O-shaped dimer, S-shaped conformation results in enhanced lamellar order and reduced nonradiative recombination losses. The optimal acceptor, V-DYIC-4F, achieved a champion efficiency of 18.10% with the lowest energy loss of 0.556eV in its devices paired with PM6 due to their efficient carrier transport, and suppressed recombination compared to other devices, being attributed to the synergistic effect of conformation and end group fluorination. The insights gained in this work contribute valuable knowledge of both synthetic control and structural determination of OAs, providing strategic design guidelines for the future development of dimeric acceptors toward high-efficiency PSCs.

Diphenylacetylene-Incorporating Octaphyrin: A Rigid Macrocycle with Readily Separable Conformational Isomers.

An expanded carbaporphyrinoid analogue, octaphyrin(2,1,1,1,2,1,1,1), containing two rigid diphenylacetylene moieties is reported. In contrast to traditional pyrrolic macrocycles where flexible conformers coexist in dynamic equilibrium, this macrocycle exists as two separable, conformationally stable stereoisomers, denoted as 1A and 1B. The conformational effect of both conformers, as well as their protonated forms, were thoroughly studied using NMR spectroscopy, UV-Vis, and single crystal X-ray diffraction analyses. Importantly, heating conformer 1B leads to its irreversible conversion to 1A, whereas in its protonated form, 1A·2MSA undergoes irreversible transformation to 1B·2MSA at lower temperatures. These temperature-dependent features establish a foundation for developing new accumulated heat sensors, as demonstrated by the use of the present octaphyrins as a customized thermochromic indicator in steam sterilization. The present study thus underscores how the conformational rigidity of these new polypyrrolic macrocycles imparts properties that are distinct from historically flexible expanded porphyrinoids.

TPE-embedded butterfly bis-crown ether with controllable conformation and supramolecular chiroptical property

Understanding how subtle structural differences between macrocyclic conformational isomers impact their properties and separation has garnered increasing attention in the field of supramolecular synthetic chemistry. In this work, a series of tetraphenylene (TPE)-embedded butterfly bis-crown ether macrocycles (BCE[n], n = 4–7), comprising two crown ether side rings and a TPE core, are synthesized through intramolecular McMurry coupling. Unexpectedly, the presence of flexible oligoethylene chains with varying lengths are found to influence molecular conformation via multiple intramolecular interactions, resulting in the formation of two stabilized conformers with specific semi-rigid symmetric/asymmetric structures (sym-BCE[n] and asym-BCE[n], n = 5, 6). Moreover, it is noteworthy that neither symmetric nor asymmetric conformers are present in the more rigid BCE[4] or the more flexible BCE[7]. Interestingly, these conformers display distinct fluorescence properties and host-guest binding abilities, and only sym-BCE[5] can serve as a host for chiral polymer binding, resulting in the formation of chiral supramolecular assemblies through host-guest interaction induced chirality. Moreover, both circular dichroism and circularly polarized luminescence signals of the obtained assemblies can be switched off by the addition of sodium ion, suggesting potential applications in the field of dynamic chiral materials.

Conformational Isomerization Promotes Balanced Ambipolar Transport for Efficient Narrowband Near-Ultraviolet Fluorophore and Non-doped Device with Low Efficiency Roll-Off

Conformational Isomerization Promotes Balanced Ambipolar Transport for Efficient Narrowband Near-Ultraviolet Fluorophore and Non-doped Device with Low Efficiency Roll-Off

Inverse mapping of quantum properties to structures for chemical space of small organic molecules

Computer-driven molecular design combines the principles of chemistry, physics, and artificial intelligence to identify chemical compounds with tailored properties. While quantum-mechanical (QM) methods, coupled with machine learning, already offer a direct mapping from 3D molecular structures to their properties, effective methodologies for the inverse mapping in chemical space remain elusive. We address this challenge by demonstrating the possibility of parametrizing a chemical space with a finite set of QM properties. Our proof-of-concept implementation achieves an approximate property-to-structure mapping, the QIM model (which stands for “Quantum Inverse Mapping”), by forcing a variational auto-encoder with a property encoder to obtain a common internal representation for both structures and properties. After validating this mapping for small drug-like molecules, we illustrate its capabilities with an explainability study as well as by the generation of de novo molecular structures with targeted properties and transition pathways between conformational isomers. Our findings thus provide a proof-of-principle demonstration aiming to enable the inverse property-to-structure design in diverse chemical spaces.

Structural basis of NEAT1 lncRNA maturation and menRNA instability.

NEAT1 long noncoding RNA orchestrates paraspeckle assembly and impacts tumorigenesis, fertility and immunity. Its maturation requires RNase P cleavage yielding an unstable transfer RNA-like multiple endocrine neoplasia-β tRNA-like transcript (menRNA) due to CCACCA addition. Here we report the crystal structure of human menRNA, which partially mimics tRNAs to drive RNase P and ELAC2 processing. Biophysical analyses uncover an RNA-centric, riboswitch-like mechanism whereby the nascent CCA reshapes the RNA folding landscape and propels a spontaneous conformational isomerization that directs repeat CCA addition, marking the menRNA and defective tRNAs for degradation.

Atroposelective Formal [2 + 5] Macrocyclization Synthesis for a Novel All-Hydrocarbon Cyclo[7] Meta-Benzene Macrocycle.

A novel axially chiral all-hydrocarbon cyclo[7] (1,3-(4,6-dimethyl)benzene (CDMB-7) was designed and synthesized using atroposelective[2 + 5] cyclization through Suzuki-Miyaura coupling. CDMB-7 adopts an irregular bowl-like shape with C2 symmetry and exhibits two diastereoisomers in its crystallographic structure. The conformational isomers of CDMB-7 racemates remain stable at high temperatures (393 K). High-performance liquid chromatography (HPLC) confirmed that a single chiral isomer will spontaneously undergo racemization within 30 min at room temperature. This finding opens up possibilities for achieving adaptive chirality in all-hydrocarbon cyclo[7] m-benzene macrocycles.

Conformation-Selective Ultraviolet-Ultraviolet Hole Burning Spectra of Ubiquitin Ions in a Cryogenic Ion Trap.

Understanding the structural variations of conformational isomers in proteins is crucial for elucidating protein folding mechanisms. Here, we present a novel method for obtaining conformation-selective ultraviolet (UV)-UV hole burning (HB) spectra of ubiquitin ions ((Ubi+zH)+z, z = 7-10) produced via electrospray ionization. Our approach involves binding multiple N2 molecules to ubiquitin ions ((Ubi+zH)+z(N2)m, m = 1-55) within a cryogenic ion trap. Upon exposure to UV irradiation, efficient fragmentation of (Ubi+zH)+z(N2)m occurs, primarily yielding bare (Ubi+zH)+z ions as fragments. The significant mass difference between the parent and fragment ions facilitates the acquisition of UV-UV HB spectra, which reveal the presence of at least two distinct conformers. Molecular dynamics simulations suggest that these conformers correspond to A-state structures, differing only in the interactions of a tyrosine residue with neighboring residues. Our findings underscore UV-UV HB spectroscopy of protein ions as a powerful tool for exploring diverse protein isomers.

Screening and Identification of High-Yielding Strains of Conjugated Linoleic Acid and Optimization of Conditions for the Conversion of CLA.

Conjugated linoleic acid (CLA) is a class of naturally occurring octadecadienoic acid in humans and animals and is a general term for a group of conformational and positional isomers of linoleic acid. In order to obtain the development of excellent lactic acid strains with a high production of conjugated linoleic acid, 32 strains with a possible CLA conversion ability were obtained by initial screening using UV spectrophotometry, and then the strains were re-screened by gas chromatography, and finally, the strain with the highest CLA content was obtained. The strains were optimized for cultivation by changing the amount of substrate addition, inoculum amount, and fermentation time. The results showed that the yield of the experimentally optimized strain for the conversion of conjugated linoleic acid could reach 94.68 ± 3.57 μg/mL, which was 74.4% higher than the initial yield of 54.28 ± 2.12 μg/mL of the strain. The results of this study can provide some basis for the application of conjugated linoleic acid production by Lactobacillus paracasei in the fermentation of lactic acid bacteria.

Mechanistic Investigation on the Regioselectivity of Electrochemical Co(II)-Catalyzed [2 + 2 + 2] Cycloaddition of Terminal Acetylenes.

In this paper, the regioselectivity of electrochemical Co(II)-catalyzed [2 + 2 + 2] cycloaddition of terminal alkynes was investigated using density functional theory. We explored in detail the energy profiles for both 1,2,4- and 1,3,5-regioselectivity pathways and revealed the origin of the regioselectivity. Two kinds of conformational isomers derived from the different coordination modes of alkynes with cobaltacyclopentadiene have been found, which were formed through electrochemically mediated redox processes. The regioselectivity of the reaction depends on the two coordination modes. When the Co(II) center attacks α-C of the third alkyne, while β2-C in cyclopentadiene bonds to β-C of the alkyne, the reaction favors the formation of 1,2,4-products. In contrast, when the Co(II) center connects to β-C of the alkyne, it forms only the 1,3,5-products via [4 + 2] cycloaddition because of the steric repulsion between the bulky ligand on Co(II) and the phenyl group in the alkyne.