Dihedral Angle Research Articles

Synthesis, crystal structure and Hirshfeld surface analysis of 1-[3-(2-oxo-3-phenyl-1,2-dihydroquinoxalin-1-yl)propyl]-3-phenyl-1,2-dihydroquinoxalin-2-one

In the title compound, C31H24N4O2, the dihydroquinoxaline units are both essentially planar with the dihedral angle between their mean planes being 64.82 (4)°. The attached phenyl rings differ significantly in their rotational orientations with respect to the dihydroquinoxaline planes. In the crystal, one set of C—H...O hydrogen bonds form chains along the b-axis direction, which are connected in pairs by a second set of C—H...O hydrogen bonds. Two sets of π-stacking interactions and C—H...π(ring) interactions join the double chains into the final three-dimensional structure.

Crystal structure of a three-coordinate lithium complex with monodentate phenyloxazoline and hexamethyldisilylamide ligands

The reaction of lithium hexamethyldisilylamide, [Li{N(Si(CH3)3)2}] (LiHMDS), with 4,4-dimethyl-2-phenyl-2-oxazoline (Phox, C11H13NO) in hexane produced colourless crystals of bis(4,4-dimethyl-2-phenyl-2-oxazoline-κN)(hexamethyldisilylamido-κN)lithium, [Li(C6H18NSi2)(C11H13NO)2] or [Li{N(Si(CH3)3)2}(Phox)2] in high yield (89%). Despite the 1:1 proportion of the starting materials in the reaction mixture, the product formed with a 1:2 amide:oxazoline ratio. In the unit cell of the C2/c space group, the neutral molecules lie on twofold rotation axes coinciding with the Li—N(amide) bonds. The lithium(I) centre adopts a trigonal–planar coordination geometry with three nitrogen donor atoms, one from the HMDS anion and two from the oxazolines. All ligands are monodentate. In the phenyloxazoline units, the dihedral angle defined by the five-membered heterocyclic rings is 35.81 (5)°, while the phenyl substituents are approximately face-to-face, separated by 3.908 (5) Å. In the amide, the methyl groups assume a nearly eclipsed arrangement to minimize steric repulsion with the analogous substituents on the oxazoline rings. The non-covalent interactions in the solid-state structure of [Li{N(Si(CH3)3)2}(Phox)2] were assessed by Hirshfeld surface analysis and fingerprint plots. This new compound is attractive for catalysis due to its unique structural features.

СТРУКТУРНАЯ ОРГАНИЗАЦИЯ ГЛИПРОЛИНОВОЙ ГЕКСАПЕПТИДНОЙ МОЛЕКУЛЫ

Computer modeling based on the use of the method of theoretical conformational analysis and programs that allow obtaining a graphic image of the spatial structures of biomolecules was performed for a hexapeptide molecule – glyproline H-Phe-Gly-Gly-Phe-Gly-Pro-OH. Glyprolines are short peptides whose amino acid sequences contain glycine and proline residues. Their mechanisms of action are currently poorly understood. Using the method of molecular mechanics, the spatial structure and conformational possibilities of this hexapeptide molecule were determined. Its potential energy was estimated as the sum of non-valente, electrostatic, torsion interactions and the energy of hydrogen bonds. 9 low-energy structures were found for the glyproline hexapeptide, the values of the dihedral angles of the main and side chains of the amino acids included in the molecule. The energy of intra- and interresidual interactions was estimated. The calculation showed that the folded forms of the main chain are low-energy for the hexapeptide. In them, the side chains of amino acids phenylalanine and proline, which are conformationally rigid, carry out effective interactions with all parts of the hexapeptide molecule.

КОНФОРМАЦИОННЫЕ СВОЙСТВА И ЭЛЕКТРОННАЯ СТРУКТУРА ПРОТИВООПУХОЛЕВОГО АГЕНТА TYR-SER-LEU

Molecular modeling methods were used to study the features of the spatial and electronic structure of the antitumor tripeptide YSL (Tyr-Ser-Leu), developed by Chinese scientists. The conformational analysis of the molecule revealed a limited set of its energetically preferable conformational states in a certain range of relative energy. The nature of the forces stabilizing the low-energy conformations of the tripeptide molecule was determined. As a result of the study, the energetically preferable ranges of dihedral angles, the energy contributions of interresidual interactions and hydrogen bonds, as well as the mutual arrangement of residues and their side chains in low-energy conformations of the tripeptide were also determined. Using the methods of molecular mechanics, the energy contributions of intramolecular interactions in low-energy conformational states of the molecule were obtained. Based on quantum-chemical calculations, the distribution of electron density and the values of dipole moments of the most optimal spatial structures of the YSL tripeptide molecule were determined. The reactivity of the tripeptide was also studied by quantum chemical calculations based on the obtained electronic characteristics of each low-energy conformation of the molecule. Using the calculated coordinates of the atoms of the energetically preferable structures of the molecule, their molecular models were built, the comparison of which makes it possible to identify the structural criteria necessary to create a drug suitable for clinical use.

One-Dimensional Covalent Organic Framework with Improved Charge Transfer for Enhanced Electrochemiluminescence.

We present a dimensional regulating charge transfer strategy to achieve an enhanced electrochemiluminescence (ECL) by constructing a one-dimensional pyrene-based covalent organic framework (1D-COF). The dual-chain-like edge architecture in 1D-COF facilitates the stabilization of aromatic backbones, the enhancement of electronic conjugations, and the decrease of energy loss. The 1D-COF generates enhanced anodic (92.5-fold) and cathodic (3.2-fold) signals with tripropylamine (TPrA) and K2S2O8 as the anodic and cathodic coreactants, respectively, compared with 2D-COF. The anodic and cathodic ECL efficiencies of 1D-COF are 2.08- and 3.08-fold higher than those of 2D-COF, respectively. According to density functional theory (DFT), the rotational barrier energy (ΔE) of 1D-COF enhances sharply with the increase of dihedral angle, suggesting that the architecture in 1D-COF restrains the intramolecular spin of aromatic chains, which facilitates the decrease of nonradiative transitions and the enhancement of ECL. Furthermore, 1D-COF can be used to construct an ECL biosensor for sensitive detection of dopamine.

ELECTRONIC PARAMETERS OF CONFORMATIONAL STATES OF ABETA-AMYLOID PEPTIDE (25-35)

ELECTRONIC PARAMETERS OF CONFORMATIONAL STATES OF ABETA-AMYLOID PEPTIDE (25-35)

СТРУКТУРНАЯ ОРГАНИЗАЦИЯ МОЛЕКУЛ СОЙМОРФИНОВ

The conformational capabilities of soymorphine-5 (Thr1-Pro2-Phe3-Val4-Val5-NH2), soymorphine-6 (Tyr1-Pro2-Phe3-Val4-Val5-Asn6-NH2) and soymorphine-7 (Tyr1- Pro2-Tyr3-Val4-Val5-Asn6-Ala7-NH2) molecules have been studied by the method of theoretical conformational analysis. The potential function of the system is chosen as the sum of non-valence, electrostatic and torsion interactions and the energy of hydrogen bonds. The low-energy conformations of soymorphine-5, soymorphine-6 and soymorphine-7 molecules were found, the dihedral angles of the main and side chains of amino acid residues that make up the molecule were found, and the energy of intra- and interresidual interactions was estimated. Thus, the spatial structure of soymorphine-5, soymorphine-6 and soymorphine-7 molecules can be represented by eight structural types. It can be assumed that the molecules perform their physiological functions in these structures. Comparison of the low-energy structures of soymorphins shows that in all molecules the first four low-energy conformations are representatives of the structural types efef, efee, efff, effe for soymorphine-5, effff, efeff, efffe, effee for soymorphine-6, efffff, efeffe, efffef, effeee for soymorphine-6. soymorphine-7. On the basis of these structures, it is possible to propose their artificial analogues for synthesis. It was shown that the spatial structure of soymorphine-5, soymorphine-6 and soymorphine-7 molecules is represented by the conformations of eight shapes of the peptide skeleton. The results obtained can be used to elucidate the structural and structural-functional organization of soymorphine molecules.

High-precision comparison method of right dihedral angle using differential wavefront sensing

High-precision comparison method of right dihedral angle using differential wavefront sensing

ASCC1 structures and bioinformatics reveal a novel helix-clasp-helix RNA-binding motif linked to a two-histidine phosphodiesterase

Activating signal co-integrator complex 1 (ASCC1) acts with ASCC-ALKBH3 complex in alkylation damage responses. ASCC1 uniquely combines two evolutionarily ancient domains: nucleotide-binding K-Homology (KH) (associated with regulating splicing, transcriptional, and translation) and two-histidine phosphodiesterase (PDE) (associated with hydrolysis of cyclic nucleotide phosphate bonds). Germline mutations link loss of ASCC1 function to spinal muscular atrophy with congenital bone fractures 2 (SMABF2). Herein analysis of The Cancer Genome Atlas (TCGA) suggests ASCC1 RNA overexpression in certain tumors correlates with poor survival, Signatures 29 and 3 mutations, and genetic instability markers. We determined crystal structures of Alvinella pompejana (Ap) ASCC1 and Human (Hs) PDE domain revealing high resolution details and features conserved over 500 million years of evolution. Extending understanding of the KH domain Gly-X-X-Gly sequence motif, we define a novel structural Helix-Clasp-Helix (HCH) nucleotide binding motif and show ASCC1 sequence–specific binding to CGCG-containing RNA. The V-shaped PDE nucleotide binding channel has two His-Φ-Ser/Thr-Φ (HXT) motifs (Φ being hydrophobic) positioned to initiate cyclic phosphate bond hydrolysis. A conserved atypical active-site histidine torsion angle implies a novel PDE substrate. Flexible active site loop and arginine-rich domain linker appear regulatory. Small angle X-ray scattering (SAXS) revealed aligned KH-PDE RNA binding sites with limited flexibility in solution. Quantitative evolutionary bioinformatic analyses of disease and cancer-associated mutations support implied functional roles for RNA binding, phosphodiesterase activity, and regulation. Collective results inform ASCC1 roles in transactivation and alkylation damage responses, its targeting by structure-based inhibitors, and how ASCC1 mutations may impact inherited disease and cancer.

Orthogonal effect of exchange and correlation parameters in density functional theory to compute geometric and spectroscopic quantities.

The influence of the composition of the functional used for density functional theory computations on one structural parameter (a dihedral angle) and a spectroscopic parameter (absorption wavelength) is assessed in this study on the basis of two molecules (flavonols). In this kind of molecules, these two parameters should be correlated according to the nature of the electronic transition involved. However, it is shown herein that by varying the proportion of true exchange and correlation while building a functional, it is possible to obtain independently a large range of values for these parameters without any relation with the underlying real values. Therefore, it is concluded that the choice of a functional after a benchmark, especially using user-defined functionals, should be carried out with great care to avoid such effects.

Analysis of <i>cis</i>-isomer-enriched dihydroquercetin sample by 1D and 2D NMR spectroscopy

Introduction. The structure of dihydroquercetin (DHQ) is characterized by two chiral centers at positions 2 and 3 of the benzopyran cycle, resulting in possible diastereomers: trans- and cis-isomers. Therefore, the development of methods for qualitative and quantitative control of DHQ diastereomers in analyzed samples is essential for patient safety management. Nuclear magnetic resonance (NMR) spectroscopy is one of the physicochemical methods that can be used for this purpose.Aim. The study objective was to accumulate the analytical and structural characteristics of cis-DHQ by NMR spectroscopy of the spheroidal form of this flavonoid (DHQs).Materials and Methods. 1D 1H, 1H,1H-COSY, 1H,1H-NOESY, and 1H,13C-HSQC NMR spectra were acquired at 298 K on an 800 MHz NMR spectrometer equipped with a TXI triple resonance probe. The number of scans was 32. The mixing time in the NOESY experiment was 400 ms. The 1H and 13C were analyzed using CcpNmr software. The dihedral angles were calculated by applying the Karplus equation.Results and discussion. In trans-DHQ, the chemical shift values for H2 and H3 are 4.93 ppm and 4.52 ppm, respectively, and in cis-DHQ they are 5.31 ppm and 4.20 ppm, respectively. The spin-spin coupling constants between H2 and H3 of trans- and cis-DHQ are 12.00 Hz and 2.40 Hz, respectively. Thus, the dihedral angles for the trans- and cis-isomers are 154° and 64°, respectively. We found that DHQs contains 12.5 % of the cis-isomer.Conclusion. Our experiments confirmed that NMR spectroscopy can discriminate between trans- and cis-DHQ based on the chemical shift values for the cross-peaks of H2 and H3. The second major finding was that this method can be considered as a more selective quantitative analysis than HPLC with UV detection without reference. One of the most important results of this study for drug development is the updated information on the structural parameters of DHQ diastereomers in the liquid phase.

On the Validation of Protein Force Fields Based on Structural Criteria.

Molecular dynamics simulations depend critically on the quality of the force field used to describe the interatomic interactions and the extent to which it has been validated for use in a specific application. Using a curated test set of 52 high-resolution structures, 39 derived from X-ray diffraction and 13 solved using NMR, we consider the extent to which different parameter sets of the GROMOS protein force field can be distinguished based on comparing a range of structural criteria, including the number of backbone hydrogen bonds, the number of native hydrogen bonds, polar and nonpolar solvent-accessible surface area, radius of gyration, the prevalence of secondary structure elements, J-coupling constants, nuclear Overhauser effect (NOE) intensities, positional root-mean-square deviations (RMSD), and the distribution of backbone ϕ and ψ dihedral angles. It is shown that while statistically significant differences between the average values of individual metrics could be detected, these were in general small. Furthermore, improvements in agreement in one metric were often offset by loss of agreement in another. The work establishes a framework and test set against which protein force fields can be validated. It also highlights the danger of inferring the relative quality of a given force field based on a small range of structural properties or small number of proteins.

Synthesis of Macrolactone Core of ent-Formosalide A via Regioselective Ether Cyclization.

Formosalide A is a cytotoxic macrolide isolated from the dinoflagellate Prorocentrum sp, whose structure is characterized by functionalized 5- and 6-membered ether rings embedded in the macrolactone and an all cis-tetraene side chain. Here, we report the synthesis of the macrolactone core of ent-formosalide A. Our approach is highlighted by the Au-mediated 6-exo-dig cyclization for the synthesis of the 6-membered ether ring, which proceeded in a highly regioselective manner. Control experiments demonstrated that the acyclic protecting group of the C9,C10-diol was crucial for the desired 6-exo-dig cyclization. Theoretical studies were performed focusing on structural component analysis, which suggested that the C8-C9-C10-C11 dihedral angle induced by the protecting group controlled the regioselectivity. An additional 6 steps including Shiina macrolactone formation from the 6-membered ether ring completed the synthesis of the macrolactone core of ent-formosalide A.

Magnetic Anisotropy and Relaxation in Four-Coordinate Cobalt(II) Single-Ion Magnets with a [CoIIO4] Core.

A mononuclear four-coordinate Co(II) complex with a [CoIIO4] core, namely, PPN[Li(MeOH)4][Co(L)2] (1) (PPN = bis(phosphoranediyl)iminium; H2L = perfluoropinacol), has been studied by X-ray crystallography, magnetic characterization, and theoretical calculations. This complex presents a severely distorted coordination geometry. The O-Co-O bite angle is 83.42°/83.65°, and the dihedral twist angle between the O-Co-O chelate planes is 55.6°. The structural distortion results in a large easy-axis magnetic anisotropy with D = -104(1) cm-1 and a transverse component with |E| = +4(2) cm-1. Alternating current (ac) susceptibility measurements demonstrate that 1 exhibits slow relaxation of magnetization at zero static field. However, the frequency-dependent out-of-phase (χ"M) susceptibilities of 1 at 0 Oe do not show a characteristic maximum. Upon the application of a dc field or the dilution with a diamagnetic Zn matrix, the quantum tunneling of magnetization (QTM) process can be successfully suppressed. Notably, after dilution with the Zn matrix, the obtained sample exhibits a structure different from that of the pristine complex. In this altered sample, the asymmetric unit does not contain the Li(MeOH)4+ cation, resulting in an O-Co-O bite angle of 86.05° and a dihedral twist angle of 75.84°, thereby leading to an approximate D2d symmetry. Although such differences are not desirable for magnetic studies, this study still gives some insights. Theoretical calculations reveal that the D parameter is governed by the O-Co-O bite angle, in line with our previous report for other tetrahedral Co(II) complex with a [CoIIN4] core. On the other hand, the rhombic component is found to increase as the dihedral angle deviates from 90°. These findings provide valuable guidelines for fine-tuning the magnetic properties of Co(II) complexes.

A visual and sensitive sensor for colorimetric and fluorescent recognition of Fe3+/2+, theoretical calculation and strip applications in wine

Total iron ions (Fe3+/2+) are a critical factor influencing wine quality and stability. A novel “turn-on” fluorescent probe (E)-2-((4-(5-methyl-1H-benzo[d]imidazol-2-yl)benzylidene)amino)phenol (probe MBBP) for monitoring Fe3+/2+ in wine was developed. It was designed with benzimidazole as the fluorophore and o-aminophenol as the Fe3+/2+ recognition site, simple and easy to prepare. The probe itself in EtOH/H2O (v: v, 49:1) emitted weak fluorescence and produced strong blue fluorescence after adding Fe3+/2+. The sensing of Fe3+/2+ was performed via the nucleophilic attack of Fe3+/2+ to imine groups of the probe with a 1:1 binding stoichiometry, and the fluorescence enhancement of the sensor was mainly due to the generation of compound 3 with the ICT effect. Results demonstrated that the probe exhibited high selectivity and sensitivity with a lower detection limit of 0.054 nM than previously reported Fe3+/2+ probes. In addition, based on the TD-DFT method and CAM-B3LYP and PBE0 functional theory, the significant changes in the dihedral angle stemmed from the isomerisation and rotation of the C = N bond. Probe MBBP was successfully applied to detect Fe2+/3+ in wine by intelligent software and the rapid detection of Fe3+/2+ using strips was also conducted.

Tunable circularly polarized luminescence behaviors caused by the structural symmetry of achiral pyrene-based emitters in chiral co-assembled systems

The regulation of circularly polarized luminescence (CPL) behavior is of great significance for practical applications. Herein, we deliberately designed three achiral pyrene derivatives (Py-1, Py-2, and Py-3) with different butoxy-phenyl substituents and the chiral binaphthyl-based inducer (R/S-B) with anchored dihedral angle to construct chiral co-assemblies, and explored their induced CPL behaviors. Interestingly, the resulting co-assemblies demonstrate tunable CPL emission behaviors caused by the structural symmetry effect of achiral pyrene-based emitters during the chiral co-assembly process. And in spin-coated films, the dissymmetry factor (gem) values were 9.1 × 10-3 for (R/S-B)1-(Py-1)10, 5.6 × 10-2 for (R/S-B)1-(Py-2)7, and 8.6 × 10-4 for (R/S-B)1-(Py-3)1, respectively. The strongest CPL emission (|gem| = 5.6 × 10-2, λem = 423 nm, QY = 34.8 %) was detected on (R/S-B)1-(Py-2)7 due to the formation of regular and ordered helical nanofibers through the strong π-π stacking interaction between the R/S-B and the achiral Py-2 emitter. The strategy presented here provides a creative approach for progressively regulating CPL emission behaviors in the chiral co-assembly process.

Analysis and optimization of the coupling effect for duct-rotor based on aerodynamic performance

The duct has the potential to provide additional thrust, which can enhance the overall aerodynamic performance of the system. Nonetheless, since the duct and the rotor interact with each other, it is crucial to consider their interaction while optimizing the system for improved performance. This paper presents a parameterization approach for the duct and rotor. Primarily, a rotor space characterization and parameter modeling method that utilizes Bezier curves, class functions/shape functions, and Bernstein polynomials is proposed. Next, the aerodynamic performance of different key factors of the duct-rotor system is calculated and analyzed using a numerical calculation method. The study found that the coupling effect of camber yf and chord length parameter Bc3 had a significant impact on the thrust coefficient, with a contribution rate of 7.3 %. Correspondingly, the coupling effect of camber yf and torsion angle parameter Ba3 had a great influence on the Figure of Merit (FM), with a contribution rate of 7.1 %. The thrust coefficient and FM of the rotor-duct system were optimized by taking the coupling effect into consideration, and the optimized ducted rotor was verified by experimental measurement. The test results shows that the high thrust case achieves a 25.60 % increase in thrust coefficient, while the high-FM case establishes an 8.89 % increase in the FM. This implies that the collaborative optimization based on the coupling effect of duct and rotor shape parameters can effectively improve the system's performance, such as thrust coefficient and Figure of Merit.

Characterization of torsion plate energy-absorbing members and multi-objective optimization of mechanical properties

In order to prevent damage to the support equipment caused by rock burst, a torsion plate energy absorption member is designed to be used with hydraulic columns. Explicit dynamic simulation is used and compared with the tests. The equations of structural parameters to the mean value of the reaction force (Fmean), specific energy absorption (SEA), and mean squared deviation (σ) are constructed based on the response surface method. The structural parameters are optimized using MOPSO. The results indicate that the torsion plate exhibits excellent energy absorption characteristics. The error rate of the simulation compared to the test is less than 5%, indicating a high level of simulation accuracy. All three sets of response fitted equations have R2 above 0.97, indicating a good fit. The three evaluation indexes demonstrate a trend of increasing then decreasing as the torsion angle increases. The wall thickness is positively correlated with the influence of each parameter index, while the effect of fillet radius is reversed. The maximum relative error of the predicted value is 9.50%. After optimization, the Fmean is effectively increased by more than 78%, the SEA is increased by more than 24.72%. The σ is increased by 8.31%, the optimization effect is remarkable.

Square-planar nickel/copper(II) complexes of (E)-2-(((2-ethylphenyl)imino)(phenyl)methyl)phenol: Supramolecular analysis, keto-enol tautomerism, polymorphism and antibacterial activities

A new Schiff base proligand, (E)-2-(((2-ethylphenyl)imino)(phenyl)methyl)phenol (HL), was synthesized from 2-hydroxybenzophenone and 2-ethylaniline and its coordination chemistry with nickel(II) and copper(II) acetate explored. In solution, the proligand HL undergoes ketoimine-enolimine tautomerism which settles exclusively into an enolimine form in the solid-state. Interestingly, while a single crystalline habit was obtained for the nickel complex 1 (block-shaped single crystals), the copper species 2 was found to solidify in two detectable polymorphs: block-shaped crystals (2a, monoclinic space group P21/c) and rhombic crystals (2b, triclinic space group P-1). Single-crystal X-ray diffraction studies reveal that the N,O Schiff base ligand chelates the divalent metal ions with square-planar geometry in the isostructural 1 and 2a and in a distorted square-planar geometry with a dihedral chelate-plane angle of 27.9° in 2b. The copper complex 2 exhibits significant antibacterial activity against the E. coli and medium activity against S. aureus bacteria. The physical properties of the complexes were further probed using thermal techniques, while their electronic structure was investigated by electrochemistry and electronic absorption spectroscopy.

Unveiling interatomic distances influencing the reaction coordinates in alanine dipeptide isomerization: An explainable deep learning approach.

The present work shows that the free energy landscape associated with alanine dipeptide isomerization can be effectively represented by specific interatomic distances without explicit reference to dihedral angles. Conventionally, two stable states of alanine dipeptide in vacuum, i.e., C7eq (β-sheet structure) and C7ax (left handed α-helix structure), have been primarily characterized using the main chain dihedral angles, φ (C-N-Cα-C) and ψ (N-Cα-C-N). However, our recent deep learning combined with the "Explainable AI" (XAI) framework has shown that the transition state can be adequately captured by a free energy landscape using φ and θ (O-C-N-Cα) [Kikutsuji et al., J. Chem. Phys. 156, 154108 (2022)]. In the perspective of extending these insights to other collective variables, a more detailed characterization of the transition state is required. In this work, we employ interatomic distances and bond angles as input variables for deep learning rather than the conventional and more elaborate dihedral angles. Our approach utilizes deep learning to investigate whether changes in the main chain dihedral angle can be expressed in terms of interatomic distances and bond angles. Furthermore, by incorporating XAI into our predictive analysis, we quantified the importance of each input variable and succeeded in clarifying the specific interatomic distance that affects the transition state. The results indicate that constructing a free energy landscape based on the identified interatomic distance can clearly distinguish between the two stable states and provide a comprehensive explanation for the energy barrier crossing.