Showing papers on "Molecular geometry published in 2023"

Exploring quantum computational, molecular docking, and molecular dynamics simulation with MMGBSA studies of ethyl-2-amino-4-methyl thiophene-3-carboxylate

Abstract: 2-aminothiophenes derivative, Ethyl-2-amino-4-methyl thiophene-3-carboxylate (EAMC) has been synthesized, characterized, and investigated quantum chemically. It was experimentally investigated by different spectroscopic methods like- NMR (1H-NMR and 13C-NMR), FT-IR, and UV-Visible. B3LYP method and 6-311++G(d,p) basis set were employed for optimization of molecular structure and calculation of wave numbers of normal modes of vibrations and various other important parameters. Calculated bond lengths and angles were compared with the experimental bond lengths and Bond Angle Parameters. Optimized bond parameters and experimental bond parameters were found in good agreement. Complete potential energy distribution assignments were done successfully by VEDA. The HOMO/LUMO energy gap emphasizes adequate charge transfer happening within the molecule. A study of donor-acceptor interconnections was done via NBO analysis. MEP surface analysis was done to demonstrate charge distribution and reactive areas qualitatively in the molecule. The degree of relative localization of electrons was analyzed via ELF Diagram. The Fukui function analysis showed possible sites for attacks by different substituents. By using the TD-DFT method and PCM solvent model, the UV–Vis spectrum (gas, methanol, DMSO) and the maximum absorption wavelength was computed and compared with experimental data. 3D and 2D intermolecular interactions in the crystal were analyzed via Hirshfeld surface analysis and fingerprint plots reveal that the EAMC crystal was stabilized by H–-H/H–-H/C–-H bond formation. The molecular docking was done with 7 different protein receptors on the molecule to find the best ligand-protein interactions. Molecular dynamic simulations and MMGBSA calculations were also carried out to find out the best binding of the ligand with the protein.Communicated by Ramaswamy H. Sarma

Crystal structures of (<i>Z</i>)-(ethene-1,2-diyl)bis(diphenylphosphine sulfide) and its complex with Pt^II dichloride

Abstract: The crystal structures of (Z)-(ethene-1,2-di-yl)bis-(di-phenyl-phosphine sulfide), C26H22P2S2 (I), along with its complex with PtII dichloride, di-chlorido[(Z)-(ethene-1,2-di-yl)bis-(di-phenyl-phosphine sulfide)-κ2S,S']platinum(II), [PtCl2(C26H22P2S2)] (II), are described here. Compound I features P=S bond lengths of 1.9571 (15) and 1.9529 (15) Å, with a torsion angle of 166.24 (7)° between the two phosphine sulfide groups. The crystal of compound I features both intra-molecular C-H⋯S hydrogen bonds and π-π inter-actions. Mol-ecules of compound I are held together with inter-molecular π-π and C-H⋯π inter-actions to form chains that run parallel to the z-axis. The inter-molecular C-H⋯π inter-action has a H⋯Cg distance of 2.63 Å, a D⋯Cg distance of 3.573 (5) Å and a D-H⋯Cg angle of 171° (where Cg refers to the centroid of one of the phenyl rings). These chains are linked by relatively long C-H⋯S hydrogen bonds with D⋯A distances of 3.367 (4) and 3.394 (4) Å with D-H⋯A angles of 113 and 115°. Compound II features Pt-Cl and Pt-S bond lengths of 2.3226 (19) and 2.2712 (19) Å, with a P=S bond length of 2.012 (3) Å. The PtII center adopts a square-planar geometry, with Cl-Pt-Cl and S-Pt-S bond angles of 90.34 (10) and 97.19 (10)°, respectively. Mol-ecules of compound II are linked in the crystal by inter-molecular C-H⋯Cl and C-H⋯S hydrogen bonds.

Characterization, biological evaluation and molecular docking of novel synthesised 2-arylamino-4-(naphth-2-yl)thiazoles

Abstract: The compounds 2-arylamino-4-(naphth-2-yl)thiazole are synthesised and characterized by FT-IR,1H NMR, 13C NMR and mass spectroscopy. The geometry of the molecule was optimised using the Gaussian 09 software and the B3LYP/6-31G density functional theory (DFT) approach. The 2-arylamino-4-(naphth-2-yl)thiazoles' bond lengths and bond angles have all been studied. Vibrational bands to distinct structural groups and their relevance were predicted using vibrational spectra analysis and were shown to be reliable when compared to experimental data and literature observations. The Mulliken atomic charges have been calculated. The charge transfer within the molecule is confirmed by the computed energy gap between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO).

Flux Crystal Growth of the Extended Structure Pu(V) Borate Na2(PuO2)(BO3).

Abstract: As part of our exploration of plutonium-containing materials as potential nuclear waste forms, we report the first extended structure Pu(V) material and the first Pu(V) borate. Crystals of Na2(PuO2)(BO3) were grown out of mixed hydroxide/boric acid flux and found to crystallize in the orthorhombic space group Cmcm with lattice parameters of a = 9.9067(4) Å, b = 6.5909(2) Å, and c = 6.9724(2) Å. Na2(PuO2)(BO3) adopts a layered structure in which layers of PuO2(BO3)2- are separated by sodium cations. Plutonium is found in a pentagonal bipyramidal coordination environment, with axial Pu(V)-O plutonyl bond lengths of 1.876(3) Å and equatorial Pu-O bond lengths ranging from 2.325(5) to 2.467(3) Å. We find that the Pu(V)-O plutonyl bond lengths are approximately 0.1 Å longer than the reported Pu(VI)-O plutonyl bond lengths and shorter by approximately 0.033 Å than the corresponding U(V) uranyl bond lengths. Raman spectroscopy on single crystals was used to determine the PuO2+ plutonyl stretching and the equatorial breathing mode frequencies of the pentagonal bipyramidal coordination environment around plutonium. Density functional theory calculations were used to calculate the Raman spectrum to help identify the Raman bands at 690 and 630 cm-1 as corresponding to the plutonyl(V) ν1 stretch and the equatorial PuO5 breathing mode, respectively. UV-vis measurements on single crystals indicate semiconducting behavior with a band gap of ∼2.60 eV.

Influence of C28H58 on the structure and phase change of C28H58/C22H46 n-alkane mixtures

Abstract: This study adopted molecular dynamics to investigate the influence of C28H58 mass fraction on the structure and phase change of C28H58/C22H46 n-alkane mixtures at different temperatures; systematically analyzed the C–H and C–C bond lengths, changes in the H–C–H bond angle and C–C–C–C torsion angle, and energy conversions within the mixture during heating of C28H58/C22H46 n-alkane mixtures; calculated the self-diffusion coefficient ( D) by combining the Einstein relation and mean squared displacement; and determined the phase change temperature of each mixture according to the relationship between D and temperature. The results show that, at 280 K, changing the mass fraction of C28H58 does not affect the C–H and C–C bond lengths and the H–C–H bond angle. At 350 K, the C–H bond length decreases with the increase in the mass fraction of C28H58, the C–C bond length increases slightly when the mass fraction is 65.2% and remains unchanged for other mass fractions, and the H–C–H bond angle slightly decreases. With an increase in temperature, the peak intensity of the stretched conformation at ±180° gradually decreases, while the peak of the twisted conformation appears around ±70°, and the degree of twist of the C–C–C–C dihedral angle in the mixture increases. The phase change temperature begins to increase slowly with the increase in the mass fraction of C28H58, and the phase change temperature increases rapidly when the mass fraction exceeds 65.2%. The kinetic and potential energies of the mixture tend to increase with the increasing mass fraction of C28H58.

Sequential bond dissociation energies of (Th(CO)x)+,x = 1-6: Quantum computational studies alternative approach. The capabilities of mass-spectrometry in the determination of molecule geometry

Abstract: The calculation problem of bond-dissociation energy BDE((CO)x-1Th+-CO), x = 1-6 was solved using the fundamental law of nature determining the dependence of chemical bond dissociation energy on its length. The recommended experimental values from literature are as follows bond dissociation energies BDE(Th+-CO)= 0.940.06 eV, BDE((CO)Th+-CO)=1.050.09 eV, BDE((CO)2Th+-CO)=1.090.05 eV, BDE((CO)3Th+-CO)=0.820.07 eV, BDE((CO)4Th+-CO)=0.630.05 eV, BDE((CO)5Th+-CO)=0.700.05 eV. The theoretical data calculated in this article are 0.934 eV, 1.056 eV, 1.082 eV, 0.82 eV, 0.634 eV, 0.708 eV correspondingly which is in good agreement with the literature. For the first time it was shown that experimental values of bond-dissociation energies, obtained with mass-spectrometry, can be successfully utilized in the calculations of the geometrical properties of molecules. The carried out calculations for thorium hexacarbonyl cation Th(CO)6+ determine its structure as tetragonal bipyramid. The found bond length values r((CO)x-1 Th+-CO) are 2.414 A and 2.444 A for equatorial and axial bonds correspondingly.

Polymorphic structures of 3-phenyl-1H-1,3-benzo-diazol-2(3H)-one.

Abstract: The polymorphic structures (I and II) of 3-phenyl-1H-1,3-benzo-diazol-2(3H)-one, C13H10N2O, acquired from pentane diffusion into the solution in THF, are reported. The structures show negligible differences in bond distances and angles, but the C-N-C-C torsion angles between the backbone and the phenyl substituent, 123.02 (15)° for I and 137.18 (11)° for II, are different. Compound I features a stronger C=O⋯H-N hydrogen bond than that in II, while the structure of II exhibits a stronger π-π inter-action than in I, as confirmed by the shorter inter-centroid distance [3.3257 (8) Å in II in comparison to 3.6862 (7) Å in I]. Overall, the supra-molecular inter-actions of I and II are distinct, presumably originating from the variation in the dihedral angle.

Unexpectedly Large Structural Variations in Benzyl-Substituted Sila[1]ferrocenophanes.

Abstract: A set of four planar-chiral sila[1]ferrocenophanes equipped with a benzyl group in the α-position, either on one or both Cp rings, and substituted on the bridging silicon atom, either by methyl or phenyl groups, were prepared. While NMR, UV/Vis, and DSC measurements did not show anything uncommon, single crystal X-ray analyses revealed unexpectedly large variations of the dihedral angles between both Cp rings (α tilt angle). While DFT calculations predicted α between 19.6 and 20.8°, measured values were found between 16.6(2) and 21.45(14)°. However, experimentally determined conformers differ significantly from those calculated for the gas phase. For the sila[1]ferrocenophane with the largest mismatch between the experimental and predicted α angle, it was shown that the orientation of benzyl groups have a significant influence on the ring-tilted structure. Packing of molecules in the crystal lattice forces benzyl groups into unusual orientations, resulting in a significantly reduced α angle through steric repulsions.

Nlo activity and computational discussion of halogen-substituted chalcone derivatives

Abstract: The four halogen-substituted chalcones 1–4 have been synthesized and analyzed to FT-Infrared, UV-Visible, GC-MS spectrometer, and 1D NMR (1H and 13C) spectroscopy techniques. Computational calculations were carried out for geometrical optimization of structure regards bond length, bond angle, and torsional angle estimated. The molecular properties of donor-acceptor electron delocalization (NBO), Electron density, and bond critical point are carryover in (AIM), the polar site of molecules is determined by (MEP), HOMO-LUMO, and the dipole moment was calculated by GAUSSUION-09 Package. The polarizability and first-order hyperpolarizability calculations derived from non-linear optical (NLO) properties for the synthesized compounds (1-4). The disc diffusion method was used to investigate the microbial activity of antibacterial and antifungal activity.

Synthesis, DFT and antioxidant studies of 2-(alkylamino)-4-(naphth-2-yl) thiazole

Abstract: 2-(Alkylamino)-4-(naphth-2-yl)thiazoles have been synthesised from 2-bromoacetyl naphthalene and characterized by UV, IR, and 1H NMR. The geometry of the molecules is optimised using the Gaussian 09 software programme and the B3LYP/6-31G density functional theory (DFT) approach. The bond lengths, bond angles, and dihedral angles of 2- (alkyamino)-4-(naphth-2-yl)thiazoles have been studied. Vibrational bands to distinct structural groups and their relevance have been predicted using vibrational spectra analysis and shown to be reliable when compared to experimental data and with literature observations. Atomic charges have been estimated using the Mulliken population analysis. The charge transfer within the molecule is confirmed by the computed energy gap between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO). The molecular docking study has been carried out.

Molecular Geometry-aware Transformer for accurate 3D Atomic System modeling

Abstract: Molecular dynamic simulations are important in computational physics, chemistry, material, and biology. Machine learning-based methods have shown strong abilities in predicting molecular energy and properties and are much faster than DFT calculations. Molecular energy is at least related to atoms, bonds, bond angles, torsion angles, and nonbonding atom pairs. Previous Transformer models only use atoms as inputs which lack explicit modeling of the aforementioned factors. To alleviate this limitation, we propose Moleformer, a novel Transformer architecture that takes nodes (atoms) and edges (bonds and nonbonding atom pairs) as inputs and models the interactions among them using rotational and translational invariant geometry-aware spatial encoding. Proposed spatial encoding calculates relative position information including distances and angles among nodes and edges. We benchmark Moleformer on OC20 and QM9 datasets, and our model achieves state-of-the-art on the initial state to relaxed energy prediction of OC20 and is very competitive in QM9 on predicting quantum chemical properties compared to other Transformer and Graph Neural Network (GNN) methods which proves the effectiveness of the proposed geometry-aware spatial encoding in Moleformer.

Solid-state molecular structures of Se(IV) and Te(IV) dihalides X2Se(CH3)(C6F5) and the gas-phase structure of Se(CH3)(C6F5)

Abstract: Abstract In a systematic study the Se(IV) and Te(IV) dihalides F2E(CH3)(C6F5), Cl2E(CH3)(C6F5) and Br2E(CH3)(C6F5) (E = Se, Te) have been synthesized and their crystal and molecular structures been investigated by X-ray diffraction and computational methods. The solid-state structures of all compounds show significant correlations between the lengths of the E–C1 bond and the intermolecular E···X (X = F, Cl and Br) contacts, indicating the presence of σ-hole interactions. For comparison, the crystal and gas phase (electron diffraction) structures of Se(CH3)(C6F5) are presented as well. They show very similar structural parameters in both phases. The structures of the single molecules X2E(CH3)(C6F5) have been analyzed by quantum-chemical methods in terms of their surface potentials. They show significant similarities of their molecular electrostatic-potential topologies (V s,max). The magnitude of V s,max correlates with the aggregation pattern.

Deeper insights into the density functional theory of structural, optical, and photoelectrical properties using 5-[(4-oxo-4H-chromen-3-yl) methylidene]-4-oxo (thioxo)-6-thioxo-2-sulfido-1, 3, 2-diazaphosphinanes

Abstract: Abstract The structure–activity relationship studied by DFT calculations and contacted with practical antimicrobial results for compounds 1–4 is discussed in detail. In light of this compounds 1–4 have been studied by using DFT/B3LYB/6-311++G (d,p) at the level of theory, the geometrical parameters, bond lengths and bond angles have been discussed. The results of quantum mechanical calculations showed that the presence of phosphorus and sulfur atoms changed the planarity of the parent compound 1 by the range from − 11 to 125°. The electronic parameter and dipole moment of these compounds in the ground state theoretically is analyzed by computing HOMO and LUMO pictures. Using frontier molecular orbital analysis, various spectroscopic and quantum chemical parameters are evaluated. Besides, absorption energies, oscillator strength, and electronic transitions of 1,3,2-diazaphosphinines 1–4 molecules have been derived at TD-DFT/CAM-B3LYP/6-311++G (d,p) computations utilizing, then the CAM-B3LYP method is “the Coulomb-attenuating method bases” set studied the electronic absorption spectra theoretically in the gas phase (TD-DFT) with the polarized split-valence 6-311++G (d, p) basis sets, in addition, the corrected linear response polarizable continuum model and measured experimentally in methanol and cyclohexane indicate a good agreement with the observed spectra (practically) in UV–Vis spectra. The molecular electrostatic potential surfaces plots have been computed to understand reactivity points.

Sequential bond dissociation energies of (Th(CO)x)+,x = 1-6: Quantum computational studies alternative approach. The capabilities of mass-spectrometry in the determination of molecule geometry

Abstract: The calculation problem of bond-dissociation energy BDE((CO)x-1Th+-CO), x = 1-6 was solved using the fundamental law of nature determining the dependence of chemical bond dissociation energy on its length. The recommended experimental values from literature are as follows bond dissociation energies BDE(Th+-CO)= 0.940.06 eV, BDE((CO)Th+-CO)=1.050.09 eV, BDE((CO)2Th+-CO)=1.090.05 eV, BDE((CO)3Th+-CO)=0.820.07 eV, BDE((CO)4Th+-CO)=0.630.05 eV, BDE((CO)5Th+-CO)=0.700.05 eV. The theoretical data calculated in this article are 0.934 eV, 1.056 eV, 1.082 eV, 0.82 eV, 0.634 eV, 0.708 eV correspondingly which is in good agreement with the literature. For the first time it was shown that experimental values of bond-dissociation energies, obtained with mass-spectrometry, can be successfully utilized in the calculations of the geometrical properties of molecules. The carried out calculations for thorium hexacarbonyl cation Th(CO)6+ determine its structure as tetragonal bipyramid. The found bond length values r((CO)x-1 Th+-CO) are 2.414 A and 2.444 A for equatorial and axial bonds correspondingly.

Combined Quantum-Mechanics/Molecular-Mechanics, Molecular docking studies on Hemorrhoid drug

Abstract: The Bioactive compounds have actions in the body that may escalate in good health. They are being used in the studies of prevention of heart disease, cancer and even more. Isoprene plays an important role in atmospheric chemistry; source is largely from woody plants. The molecular geometry shows larger bond length, this may be due to high nuclear charge attraction. The relationship between molecular geometry and potential energy visualizes by using potential energy surface. The scaled frequencies, Infrad, Raman with their vibrational assessment along with potential energy distribution are carried out. From the low energy to extrapolated energy, the geometry connectivity using B3LYP/6-31G (d, p): UFF was found to be higher than the B3LYP/cc-pvqz: HF/3-21G (ONIOM). The sites of electrophile and nucleophile sites, the tittle of compound was calculated at the B3LYP/6-31G (d, p) optimized geometry. FMO and NLO study shows the chemical activity. Docking studies explains how small molecules bind to a macromolecular target.

Assessing conformations of small molecules with crystallographic databases

Abstract: In this work, libraries of crystallographically determined bond lengths, valence angles and torsion angles derived from the Cambridge Structural Database (CSD) are used to generate a score to validate an individual bond length, valence angle or torsion angle. A single score can also be derived for each ensemble of bond lengths, ensemble of valence angles and ensemble of torsion angles in the molecule. The data used to compute the score for the individual parts of the molecule are also used to compute a single value assessing the specific conformation relative to the geometric molecular data contained in the CSD. Such a single-number summary may be used, for example, to validate geometries of modelled molecules or molecular conformations in experimentally or computationally determined crystal structures. An example of how the score can be applied to an individual conformation is provided. Validation of the new score is performed by comparison with existing software for validating molecular geometries ( Mogul ) and a comparison with the CSD Conformer Generator scores is also carried out. Further application to the experimental standard deviation of C—C bonds of CSD entries is demonstrated, and the Platinum diverse data set is also studied.