Dihedral Angle Research Articles

Molecular Dynamics Simulation for the Acidic Compounds Retention Mechanism Study on Octyl-Quaternary Ammonium Mixed-Mode Stationary Phase.

With the widespread application of mixed-mode chromatography in separation analysis, it is becoming increasingly important to study its retention mechanism. The retention behavior of acidic compounds on mixed-mode octyl-quaternary ammonium (Sil-C8-QA) columns was investigated by computer simulation. Firstly, the benzoic acid homologues were used as the analytes, and the simulation model was constructed by the Materials Studio. Geometric optimization, annealing and molecular dynamics (MD) simulation of these complexes resulted in optimized conformations. The binding energy, mean square displacement (MSD) and torsion angle distribution generated by MD simulation were then analyzed. The results showed that the more negative binding energy, the greater the MSD and the narrower the torsion angle distribution, indicating that the stationary phase behaves with stronger interaction and retention. The retention behavior of five acidic drugs on the Sil-C8-QA column was then successfully explained by simulation. Acidic drugs are more retentive on the mixed-mode column due to the more substantial interaction brought by the reversed-phase/ion-exchange mixed-mode mechanism compared to other single-mode columns. This simulation method is expected to provide ideas for studying the separation mechanism and predicting the retention behavior of more complex samples.

Aromaticity in Semi-Condensed Figure-Eight Molecules.

Electron delocalization and aromaticity was comparatively evaluated in recently synthesized figure-eight molecules made of two condensed U-shaped polycyclic aromatic hydrocarbon moieties connected either by two single bonds or by two para-phenylene groups. The selected examples include molecules that incorporate eight-membered and sixteen-membered rings, as well as a doubly [5]helicene-bridged (1,4)cyclophane. We probe whether some electron delocalization could occur through the stereogenic single bonds in these molecules: Is aromaticity purely (semi-)local, or possibly also global in these molecules? It was concluded that the situation can go from a purely (semi-)local character when the dihedral angle at the connecting single bonds is large, such as in biphenyl, to a predominantly (semi-)local character with a minor global contribution when the dihedral angle is small, such as in the para-phenylene connectors of the [5] helicene-bridged cyclophane.

Comparing ANI-2x, ANI-1ccx neural networks, force field, and DFT methods for predicting conformational potential energy of organic molecules

In this study, the conformational potential energy surfaces of Amylmetacresol, Benzocaine, Dopamine, Betazole, and Betahistine molecules were scanned and analyzed using the neural network architecture ANI-2 × and ANI-1ccx, the force field method OPLS, and density functional theory with the exchange-correlation functional B3LYP and the basis set 6-31G(d). The ANI-1ccx and ANI-2 × methods demonstrated the highest accuracy in predicting torsional energy profiles, effectively capturing the minimum and maximum values of these profiles. Conformational potential energy values calculated by B3LYP and the OPLS force field method differ from those calculated by ANI-1ccx and ANI-2x, which account for non-bonded intramolecular interactions, since the B3LYP functional and OPLS force field weakly consider van der Waals and other intramolecular forces in torsional energy profiles. For a more comprehensive analysis, electronic parameters such as dipole moment, HOMO, and LUMO energies for different torsional angles were calculated at two levels of theory, B3LYP/6-31G(d) and ωB97X/6-31G(d). These calculations confirmed that ANI predictions are more accurate than density functional theory calculations with B3LYP functional and OPLS force field for determining potential energy surfaces. This research successfully addressed the challenges in determining conformational potential energy levels and shows how machine learning and deep neural networks offer a more accurate, cost-effective, and rapid alternative for predicting torsional energy profiles.

Analysis of load carrying performance for glass fiber reinforced thermoplastic composite pipe under different in-service conditions

Fiber reinforced thermoplastic composite pipe (FRTP) has advantages over traditional metallic counterparts for oil and gas transportation. During in-service the pipe is subjected to different mechanical loads including internal pressure, torsion, and bending. In this work, a special type of continuous glass fiber reinforced thermoplastic composite pipe (DN150-6.4 MPa) is analyzed by finite element method (FEM) under various complex service-in conditions. Stress and strain are investigated for different layers of FRTP to determine the extreme load capacity. Experimental analysis is conducted to validate proposed method. Combining the results from FEM and test, it is concluded that the ultimate internal pressure (burst pressure) of FRTP is 61.7 MPa, the ultimate axial tensile displacement is 66.4 mm, the maximum torsion angle is 71.5°, and the minimum bending radius 978.9 mm. Under different working conditions, the mechanical properties of the FRTP are still surplus under the given load. For the good agreement with experimental data, the FEM modeling can be guide for practical application of FRTP.

Unraveling the Nature of Spin Coupling in a Metal-Free Diradical: Theoretical Distinction of Ferromagnetic and Antiferromagnetic Interactions.

Metal-free diradicals based on polycyclic aromatic hydrocarbons are promising candidates for organic spintronics due to their stable magnetism and tunable spin coupling. However, distinguishing and elucidating the origins of ferromagnetic and antiferromagnetic interactions in these systems remain challenging. Here, we investigate the 2-OS diradical molecule sandwiched between gold electrodes using a combined density functional theory and hierarchical equations of motion approach. We find that the dihedral angle between the radical moieties controls the nature and strength of the intramolecular spin coupling, transitioning smoothly from antiferromagnetic to ferromagnetic as the angle increases. Distinct features in the inelastic electron tunneling spectra are identified that can discern the two coupling regimes, including spin excitation steps whose energies directly reveal the exchange coupling constant. Mechanical stretching of the junction is predicted to modulate the spectral line shapes by adjusting the hybridization of the molecular radicals with the electrodes. Our work elucidates the electronic origin of tunable spin interactions in 2-OS and provides spectroscopic fingerprints for characterizing magnetism in metal-free diradicals.

On the geometry dependence of the nuclear magnetic resonance chemical shift of mercury in thiolate complexes: A relativistic density functional theory study.

Thiolate containing mercury(II) complexes of the general formula [Hg(SR) ] have been of great interest since the toxicity of mercury was recognized. 199Hg nuclear magnetic resonance spectroscopy (NMR) is a powerful tool for characterization of mercury complexes. In this work, the Hg shielding constants in a series of [Hg(SR) ] complexes are therefore investigated computationally with particular emphasis on their geometry dependence. Geometry optimizations and NMR chemical shift calculations are performed at the density functional theory (DFT) level with both the zeroth-order regular approximation (ZORA) and four-component relativistic methods. The four exchange-correlation (XC) functionals PBE0, PBE, B3LYP, and BLYP are used in combination with either Dyall's Gaussian-type (GTO) or Slater-type orbitals (STOs) basis sets. Comparing ZORA and four-component calculations, one observes that the calculated shielding constants for a given molecular geometry have a constant difference of 1070 ppm. This confirms that ZORA is an acceptable relativistic method to compute NMR chemical shifts. The combinations of four-component/PBE0/v3z and ZORA/PBE0/QZ4P are applied to explore the geometry dependence of the isotropic shielding. For a given coordination number, the distance between mercury and sulfur is the key factor affecting the shielding constant, while changes in bond and dihedral angles and even different side groups have relatively little impact.

Accurate and Efficient Conformer Sampling of Cyclic Drug-Like Molecules with Inverse Kinematics.

Identification of all of the influential conformers of biomolecules is a crucial step in many tasks of computational biochemistry. Specifically, molecular docking, a key component of in silico drug development, requires a comprehensive set of conformations for potential candidates in order to generate the optimal ligand-receptor poses and, ultimately, find the best drug candidates. However, the presence of flexible cycles in a molecule complicates the initial search for conformers since exhaustive sampling algorithms via torsional random and systematic searches become very inefficient. The devised inverse-kinematics-based Monte Carlo with refinement (MCR) algorithm identifies independently rotatable dihedral angles in (poly)cyclic molecules and uses them to perform global conformational sampling, outperforming popular alternatives (MacroModel, CREST, and RDKit) in terms of speed and diversity of the resulting conformer ensembles. Moreover, MCR quickly and accurately recovers naturally occurring macrocycle conformations for most of the considered molecules.

Regulating the photoisomerization pathway to achieve efficient E → Z isomerization of azobenzene-embedded molecular cages

Achieving efficient E → Z photoconversion of Azobenzene is now still a challenge. Based on our previously reported cage C1, which exhibits an E → Z photoisomerization efficiency of up to 94%, two additional cages C2 and C3 were synthesized with more rigid and longer units replacing the flexible diphenyl ether motifs in C1. It was found that, when the diphenyl ether rims were changed to biphenyl groups (C2), or to diphenylacetylene motifs (C3), the dihedral angles of the two benzene rings of the azobenzene rim in these cages decreased correspondingly from 48.86° to 42.96°, and finally to 30.13°. The E → Z photoisomerization quantum yields measurements indicate that, with the decreasing of the dihedral angles, the role of the inversion pathway in the E → Z processes of these cages gradually decreases, while the role of the rotation pathway becomes increasingly greater, accompanied by the decreasing in the E → Z photoconversions from 94% to 87%, and to 72%. These results validate our new strategy of promoting inversion pathway/inhibiting rotation pathway to achieve efficient E → Z photoconversion of azobenzene.

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.

ЭЛЕКТРОННЫЕ ПАРАМЕТРЫ КОНФОРМАЦИОННЫХ СОСТОЯНИЙ БЕТА-АМИЛОИДНОГО ПЕПТИДА (25-35)

The electronic characteristics of stable conformational states of beta-amyloid peptide (25-35) have been studied by molecular modeling methods. Beta-amyloid peptide (Aβ) is the main component of senile plaques found in the brains of patients with Alzheimer's disease. Aβ (25-35) fragment of a molecule with the amino acid sequence Gly-Ser-Asn-Lys-Gly-Ala-Ile-Ile-Gly-Leu-Met. It has been shown that the conformational features of a molecule are largely determined by its environment; therefore, the aim of this work was to study the differences in the conformations of amyloid beta-peptide (25-35) in vacuum and in a low-polarity medium using the methods of molecular mechanics and quantum chemical calculations. The studies were carried out in two stages: 1) the geometric and energy parameters of the low-energy conformational states of the indicated peptide were determined, 2) the electronic characteristics of the established low-energy conformations of these molecule were calculated. Calculations showed that the conformational behavior of this peptide can be described by a set of similar low-energy conformations with structure on the C-terminal sequence. It has also been shown that the low-energy structures of the amyloid beta-peptide (25-35) have the most favorable dispersion contacts and, therefore, it can be expected that they will become most preferable in a low-polarity environment, when electrostatic interactions do not play a significant role. Permissible changes in the dihedral angles of the amyloid beta-peptide (25-35) in the energetically preferred conformation and the stability of secondary structure elements were also investigated. The distribution of electron density and equipotential surfaces in the energetically preferred conformations of the beta-amyloid peptide were obtained and compared (25-35). Quantum chemical calculations showed that the largest negative charges in the peptide are concentrated precisely on the oxygen atoms of the carbonyl groups and the nitrogen atoms of the amino group. The distribution of electron density and equipotential surfaces in the energetically preferred conformations of the beta-amyloid peptide (25-35) were obtained and compared.

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

Discovery of a new bimetallic borate with strong optical anisotropy activated by π-conjugated [B2O5] units.

Birefringent materials with high optical anisotropy have been identified as a research hotspot owing to their significant scientific and technological significance in modern optoelectronics for manipulating light polarization. Researchers studying borate systems have discovered that adding π-conjugated units placed in parallel can significantly increase the birefringence of crystalline solids; some examples include [BO3] units, [B2O5] units, and [B3O6] units. However, there are not many borates with strictly parallel configurations of π-conjugated [B2O5] units. In this study, a new bimetallic borate Sr2Cd4(B2O5)3 with near-parallel arrangement of π-conjugated [B2O5] units was discovered. Sr2Cd4(B2O5)3 possesses the maximum number density of [B2O5] units, shortest dihedral angle of [B2O5] units (between the two [BO3]), and largest degree of [CdO6] octahedral distortion among all the currently known Sr-Cd-B-O tetragonal system borates, making it demonstrate a large birefringence of 0.102 at 532 nm. Theoretical analysis proves that π-conjugated [B2O5] anions are the primary source of the large birefringence of Sr2Cd4(B2O5)3.

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.

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.