Journal of Chemical Crystallography最新文献

The reaction between (Me₄N)₄[Nb₆Cl₁₂(CN)₆], [Mn(salen)Cl(H₂O)] (salen = N, N’-bis (salicylidene)ethylenedi-amine dianion), and trans-1,2-bis(4-pyridyl)-ethylene (bpe) led to the formation of {[Mn(salen)(H₂O)](bpe)[Mn(salen)]}₂[Nb₆Cl₁₂(CN)₆]⋅17H₂O (1). 1 features assemblies of 4.47 nm-long molecular nanorods in each of which two [Mn(salen)]⁺ connects via one bpe linker to form a dimeric unit and two dimeric units are trans-coordinated to one [Nb₆Cl₁₂(CN)₆]⁴⁻via cyanido. Its magnetic properties and thermal stability are also reported.

Graphic Abstract

Direct Assembly of {Nb₆} Cluster Units, [Mn(salen)]⁺, and Bpe Leads To Neutral Supramolecular Nanorods of 4.47 nm long

This work is devoted to the semisynthesis of 4-allyl-2-methoxyphenyl-4-nitrobenzenesulfonate 3 from naturally occurring eugenol. The structure of the titled compound is established using IR, (¹H and ¹³C) NMR, and mass spectrometry. Single crystal X-ray diffraction is used to corroborate the structure of the compound 3. Crystallographic study shows that compound 3 crystallizes in the monoclinic system with P2₁/n as the space group. DFT studies are carried out to calculate HOMO and LUMO energies. ADMET properties, Molecular docking and dynamic simulation studies are also performed towards the SARS-CoV-2 protein.

Graphical Abstract

This paper describes a combined crystallographic and computational studies of the 4-allyl-2-methoxyphenyl-4-nitrobenzenesulfonate synthesized from naturally occurring eugenol

The synthesis of 3-methyl-4-nitro-1,1-biphenyl (3-MNB) and its crystal structure elucidated using experimental and theoretical methods has been reported in this paper. It crystallizes in the orthorhombic crystal system (space group P2₁2₁2₁) with unit cell parameters: a = 7.2918(4) Å, b = 12.0928(6) Å and c = 12.6759(7) Å and Z = 4. The structure has been characterized by FT-IR, NMR (¹H and ¹³C) and X-ray diffraction methods. There exists two C—H⋯O intermolecular hydrogen bond and two π…π interactions. Density functional theory (DFT/B3LYP/6-311 + + G(d, p)) has been employed for the optimization of the structure and the same was compared with the X-ray structure. The HOMO-LUMO energy gap and molecular electrostatic potential maps have been computed. The energy gap of 4.06 eV indicates that the molecule is stable and less reactive. Besides this, the molecular electrostatic potential (MEP) help determine the reactive sites of the molecule. The Hirshfeld surface analysis and 2-D fingerprint plots help explore the nature and percentage contribution of intermolecular interactions. The highest contribution to the total Hirshfeld surface area is from H…H contacts (47.2%) while the contribution of O…H/H…O contacts is 26.4%. The strength and nature of interactions present in the molecule have been characterized by RDG-based NCI and QTAIM analysis. DOS analysis has been performed to investigate the contribution of various orbitals. The molecular docking analysis analysis was performed to determine the binding patterns of 3-MNB with 1CX2, revealing a binding energy of -7.3 Kcal/mol, suggesting its potential as a COX-2 inhibitor.

The structure of [Fe(CO)₃(η⁴-6-exo-(4-biphenylamino)cyclohepta-2,4-dien-1-one] [monoclinic, a = 20.368 (1), b = 6.2757(4), c = 29.5214(14), β = 101.024(5), space group C2/c] has been determined. There is a moderate hydrogen-bond between the amine proton and the oxygen atom of the ketone in another molecule. There is no significant π-stacking of the phenyl rings, but the nitrogen atom is fairly planar likely due to interaction with the π-system of the 4-biphenyl group and the hydrogen-bonding.

Graphical Abstract

Addition of two equivalents of 4-biphenylamine to [Fe(CO)₃(η⁵-cyclohepta-2,4-dien-5-yl-1-one)][BF₄] results in exo- attack at the coordinated ring forming the [Fe(CO)₃(η⁴-6-exo-(NH(4-biphenyl)))cyclohepta-2,4-dien-1-one], which was structurally characterized

Lithiated N-(2,6-diisopropylphenyl)-[6-(2,4,6-triisopropylphenyl)-pyridine-2-yl]-amine (ApH) undergoes a salt metathesis reaction with MnBr₂ in tetrahydrofuran (THF) at 50 °C in the presence of two equivalents of 4-tert-butylpyridine (^tBuPy) to yield only the second example of mononuclear manganese aminopyridinates, [Mn(Ap)₂(^tBuPy)]. The compound [C₅₉H₇₁MnN₅], crystallized in the monoclinic space group, P2₁/c with unit cell parameters: a = 11.9650(5) b = 17.9530(7) c = 24.3110(10) Å, β = 95.081(3)°, V = 5201.7(4) A³, Z = 4. Hirshfeld analyses show that H⋯H (89.1%) and H⋯C/C⋯H (10.9%) interactions are the two main contributors that lead to intermolecular stabilization in the solid-state structure.

The crystal structures of four 2-pyridineformamide thiosemicarbazone derivatives viz, (Z, Z’)-4-methyl-N’-(morpholine-4-carbonothioyl)picolinohydrazonamide (1), (Z, Z’)-4-methyl-N’-(thiomorpholine-4-carbonothioyl) picolinohydrazonamide (2), (Z, Z’)-6-methyl-N’-(thiomorpholine-4-carbonothioyl)picolinohydrazonamide (3) and (Z, Z’)-N’-(azepane-1-carbonothioyl)-4-methylpicolinohydrazonamide (4) has been determined by single crystal X-ray diffraction analysis. Combined quantum mechanical methods (ORCA) and computation of non-spherical scattering form factors (NoSpherA2) were used for the refinement with anisotropic hydrogen atoms. The results of using independent atom model (IAM) and Hirshfield atom refinement (HAR) method based R2SCAN/ def2-TZVP functional were compared. All compounds show an improvement in the model after HAR refinement compared to independent atom model (IAM). There is a significant decrease in the residual factors with the use of anisotropic hydrogen refinement. HAR refinement provides a clearer understanding of electron delocalization, lone pairs, and the accumulation and depletion of electron density. The information obtained came from standard resolution single crystal X-ray diffraction data, indicating that high-quality structural analysis can now be performed without the need for neutron or synchrotron facilities.

Graphical Abstract

Structural studies of four 2-pyridineformamide thiosemicarbazone derivatives using non-spherical atomic form factors

Reaction of N-benzyl-1-chloromethanesulfonamide with phenyl isothiocyanate formed N-benzyl-3-phenylimino-1,4,2-dithiazolidine 1,1-dioxide. Crystals of this compound occurred in the monoclinic system, space group P 2(1), a = 26.7099(16) Å, b = 13.2518(5) Å, c = 8.2769(4) Å, β = 97.099(5)^o, Z = 8, with four molecules in the asymmetric unit. The structure confirms a prior assignment that the C = S bond of the isothiocyanate was the reactive moiety. Using the same reaction conditions, 3,5-dimethylphenyl isocyanate was reacted N-benzyl-1-chloromethanesulfonamide to produce a product in 81% yield, which was determined to be 2-benzyl-4-(3’,5’-dimethylphenyl)-1,2,4-thiadiazolidin-3-one 1,1-dioxide. Crystals of this compound are monoclinic, space group P 2(1)/n, a = 5.2243(11) Å, b = 15.844(5) Å, c = 18.628(3) Å, β = 96.72(2)^o, and Z = 4. This product demonstrated that the C = N bond of the aryl isocyanate reacted to form the 1,2,4-thiadiazolidin-3-one 1,1-dioxide ring system.

Graphical Abstract

Heterocyclic rings formed from N-benzyl-1-chloromethanesulfonamide and phenyl isothiocyanate via the C = S bond (structure on the left) or 3,5-dimethylphenyl isocyanate via the C = N bond (structure on the right)

8-Nitrobenzo-1,3-thiazin-4-ones (BTZs) are a promising class of antitubercular agents with a novel mechanism of action, viz. suicide inhibition of decaprenylphosphoryl-β-D-ribose 2’-epimerase 1 (DprE1), an enzyme crucial for cell wall synthesis in the pathogen Mycobacterium tuberculosis. 8-Nitro-2-(piperidin-1-yl)-6-(trifluoromethyl)-4H-benzo-1,3-thiazin-4-one (1) is a chemically simplified analogue of the anti-tuberculosis phase 2 clinical drug candidate BTZ-043. Structural elucidation of 1 in the solid-state has been carried out by X-ray crystallography and two polymorphic forms of 1 have been revealed. 1-I crystallizes in the triclinic system (space group P-1, Z = 6) with one molecule exhibiting whole-molecule disorder with a preferred orientation. The crystal structure of 1-II belongs to the tetragonal system (space group P4₃, Z = 4) and exhibits positional disorder in several parts of the molecule.

Graphical Abstract

X-ray crystallography revealed a triclinic (space group P-1, Z = 6) and a tetragonal (space group P4₃, Z = 4) polymorph of the antimycobacterial agent 8-nitro-2-(piperidin-1-yl)-6-(trifluoromethyl)-4H-benzo-1,3-thiazin-4-one