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A series of 2-(haloalkyl)-3-azidomethyl and 6-azido chromones has been synthetized, characterized and studied by theoretical (DFT calculations) and spectroscopic methods (UV-Vis, NMR). The crystal structure of 3-azidomethyl-2-difluoromethyl chromone, determined by X-ray diffraction methods, shows a planar framework due to extended π-bond delocalization. Its molecular packing is stabilized by F···H, N···H and O···H hydrogen bonds, π···π stacking and C-O···π intermolecular interactions. Moreover, AIM, NCI and Hirshfeld analysis evidenced that azido moiety has a significant role in the stabilization of crystal packing through weak intermolecular interactions, where analysis of electronic density suggested closed-shell (CS) interatomic interactions.

Two eucalyptol derivatives, namely 1,3,3-trimethyl-2-oxabicycle[2.2.2]oct-5-yl acetate (4) and 1,3,3-trimethyl-2-oxabicycle[2.2.2]oct-5,8-yl acetate (6) have been synthesized and characterized. Their crystal structures have been solved by single-crystal X-ray diffraction methods indicating that the molecular conformation of both compounds is stabilized by intramolecular C–H⋯O bonds between the H-atoms of the methyl group from the eucalyptol moiety and the O-atom of the acetoxy group. In addition, we have performed a detailed investigation of the intermolecular interactions that stabilize the crystal packing of both structures by using Hirshfeld surface analysis and their associated two-dimensional fingerprint plots. The analysis reveals that the solid-state structure of compounds 4 and 6 is mainly stabilized by C–H⋯O hydrogen bonds and H⋯H bonding interactions. These interactions have also been described and studied energetically using DFT calculations. The nature and strength of these intermolecular contacts have been rationalized by using several computational tools including molecular electrostatic potential (MEP) surfaces, natural bond orbital analysis (NBO), Bader's theory of atoms in molecules (QTAIM) and non-covalent interaction plot (NCI plot) index methods. Furthermore, the intermolecular contacts observed in the crystal lattice of both compounds were experimentally studied through vibrational (IR and Raman) and 1H and 13C NMR spectra. The computational molecular docking analysis of the compounds has been carried out against five potential leishmanial drug targets and the main protease of SARS-CoV-2. [ABSTRACT FROM AUTHOR]

A new perfluoromethylated vinylogous amide, (Z)‐4,4,4‐trifluoro‐1‐(2‐hydroxyphenyl)‐3‐(2‐methoxyethylamino)‐2‐buten‐1‐one, is chosen as an example to investigate the bonding interactions in solid state. The Z, s‐cis form is the dominant conformation in both solution and solid state. Intramolecular hydrogen bonding determines this conformational preference in a nonpolar solvent (NMR spectra). Carbonyl and phenol groups are sensitive to the intra‐ and intermolecular contacts (vibrational spectra). The supramolecular assembly (X‐ray diffraction) is governed by NH⋯O and OH⋯O strong intermolecular hydrogen bonds giving rise to center‐symmetric R22(16) and R22(12) graph‐set motifs. The π‐stacking, F⋯H and F⋯F interactions are also discussed (Hirshfeld analysis). [ABSTRACT FROM AUTHOR]

The synthesis, X-ray structure characterization, Hirshfeld surface analysis and DFT calculations of two new antipyrine derivatives are reported herein. Particularly, 2-bromo-N-(2,3-dihydro-1,5-dimethyl-3-oxo-2-phenyl-1H-pyrazol-4-yl)benzamide (1) and 2-chloro-N-(2,3-dihydro-1,5-dimethyl-3-oxo-2-phenyl-1H-pyrazol-4-yl)benzamide (2) are synthesized in good yields and characterized spectroscopically. Both compounds are isostructural and crystallize in the monoclinic P21/c space group. The crystal packing of both compounds is mainly stabilized by a combination of N–H⋯O and C–H⋯O hydrogen bonds. In addition, C–H⋯π and lone pair⋯π contacts were observed. Their solid-state structures have been analyzed through Hirshfeld surface analysis, including the evaluation of the different energy frameworks, indicating that the molecular sheets are primarily formed by hydrogen bonds and the stabilization is dominated via the electrostatic energy contribution. These studies are complemented with DFT calculations (B3LYP-D3/def2-TZVP), and a combination of QTAIM/NCIplot analyses disclosing that the H-bonding interactions are energetically relevant (ranging from 0.9 to 6.1 kcal mol−1), however the total binding energies of the different assemblies are dominated by a combination of π-interactions (of the type C–H⋯π, π⋯π, and lone pair halogen⋯π) that are able to stabilize cooperatively the assemblies up to 12 kcal mol−1. [ABSTRACT FROM AUTHOR]

An N,N,O,O donor Schiff base blocking ligand [H2L = 6,6′-((1E,1′E)-(ethane-1,2-diylbis(azaneylylidene))bis(methaneylylidene))bis(3-(diethylamino)phenol), 1] has been used to synthesize mononuclear [CuL]·H2O (2) and [VO(L)] (3) complexes. The ligand and complexes have been characterized by elemental, spectral (FTIR and UV-vis) and thermogravimetric analysis. The molecular structures of 1 and 2 have been confirmed by single crystal X-ray diffraction studies. The crystal structure of the ligand (1) indicates that the molecule is sited on a crystallographic inversion centre and the planar conformation of the salicylideneimine moiety is favored by two intramolecular O–H⋯N1 hydrogen bonds forming S(6) ring motifs. The copper(II) center in complex 2 is coordinated in a square planar fashion. The presence of an extended π-system in the complex (two chelate rings and two phenyl rings) facilitates the formation of chelate ring (CR)⋯π non-covalent interactions. DFT calculations have been performed to explore the energetic features of unconventional CR⋯π and hydrogen bonding interactions that are observed and described in the solid state of 2. Moreover, we have studied how the energy of the CR⋯π interaction is influenced by the substituent of the phenyl ring. In addition, the cytotoxic effect of the compounds has been tested against MG-63 (human osteosarcoma), HT-29 (human colorectal) and MCF7 (breast) cancer cell lines using the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. [ABSTRACT FROM AUTHOR]

The crystal structure of pyridinium 6-methyl-1,2,3,-oxathiazine-4(3H)-one-2,2-dioxide [(C5NH6)(C4H4NO4S)], for short, pyH(ace), was determined by X-ray diffraction methods. It crystallizes as a twin in the monoclinic space group P21/c with a=6.9878(9), b=7.2211(7), c=21.740(2) Å, β=91.67(1)° and Z=4 molecules per unit cell. The structure was determined employing 1599 reflections with I>2σ(I) from one of the twin domains and refined employing 2092 reflections from both crystal domains to an agreement R1 factor of 0.0466. Besides electrostatic attractions, intermolecular pyH···O=C(ace) hydrogen bonds stabilize the acesulfamate anion and the pyridinium cation into planar discrete units parallel to the (100) crystal plane. The units form stacks of alternating ace− and pyH+ ions along the a axis that favors inter-ring π–π interactions. The Fourier transform-infrared (FT-IR) spectrum of the compound was recorded and is briefly discussed. Some comparisons with related pyridinium saccharinate salts are also made. [ABSTRACT FROM AUTHOR]

The structure of a new perfluoromethyl derivative, ( Z ) -4,4,4-trifluoro-1-(2-hydroxyphenyl)-3-(methylamino)-2-buten-1-one (1) , was investigated in both crystalline state and solution since the prototropy enable the existence of three tautomeric species in equilibrium. The preference in the configurational E/Z arrangement is strongly dependent on the intramolecular hydrogen bond interactions. The vibrational and electronic spectra of 1 were discussed and assigned by using DFT calculations. The crystal, solved by single-crystal X-ray diffraction, shows the prevalence of the tautomer aminoenone over the imino-enol and imino-ketone forms. Therefore, an almost planar molecular conformation is observed due to the formation of two intramolecular amino and phenolic hydrogen bonds to the same carbonyl oxygen acceptor atom that stabilize the Z configuration. The molecular packing is held by the O H⋯O(keto) and N H⋯O hydrogen bonds, F⋯F, C H⋯π and π-stacking interactions that contribute to the crystal stabilization. The intra and intermolecular contacts were also characterized by Natural Bond Orbital (NBO) analysis and Atoms in Molecules (AIM) approach. Hirshfeld surfaces and their associated fingerprint plots were generated for 1 and for a related structure, to visualize different intermolecular interactions and their relative contributions to the total surface. [ABSTRACT FROM AUTHOR]

Abstract: Pure N,N′-di(methoxycarbonylsulfenyl)urea, [CH3OC(O)SNH]2CO, is quantitatively prepared by the hydrolysis reaction of CH3OC(O)SNCO and characterized by 1H NMR, GC–MS and FTIR spectroscopy techniques. Structural and conformational properties are analyzed using a combined approach with data obtained from X-ray diffraction, vibrational spectra and theoretical calculation methods. The IR and Raman spectra for normal and deuterated species are reported. The crystal structure of [CH3OC(O)SNH]2CO was determined by X-ray diffraction methods. The substance crystallizes in the orthorhombic P21212 space group with a =9.524(2), b =12.003(1), c =4.481(1)Å, and Z =2 moieties in the unit cell. The molecule is sited on a twofold crystallographic axis (C 2) parallel to c and shows the anti–anti conformation (S–N single bonds antiperiplanar with respect to the opposite C–N single bonds in sulfenyl-ureasic group). Neighboring molecules are arranged in a chain motif that extends along the C 2-axis and is held by bifurcated NH⋯O⋯HN intermolecular bonds. A local planar symmetry is observed in the crystal for the central –SN(H)C(O)N(H)S– skeleton. Experimental and calculated data allow to trace this structural feature to the occurrence of N–H⋯On bonding interactions. Calculated vibrational and structural properties are in good agreement with the experimentally determined features. [Copyright &y& Elsevier]

• Seven haloalkyl chromones (-CF2H, -CCl2H, -CF2CF3) linked to bromine and bromomethyl substituents were characterized and studied. • The crystal structure of 3-dibromomethyl-2-difluoromethyl chromone was determined by X-ray diffraction methods. • The Hirshfeld Surface Analysis showed non-covalent interactions O⋯Br, π⋯π and F⋯H hydrogen bonds. • AIM and NCI analysis of weak interactions were perform in compound 5. A set of seven new chromones with 2-haloalkyl (-CF 2 H, -CCl 2 H, -CF 2 CF 3) and 3-bromo and bromomethyl substituents were synthesized. The novel compounds were studied by DFT calculations and characterized by vibrational spectroscopy (IR and Raman) in solid state, and NMR (1H, 13C and 19F) and UV–vis spectroscopy in solution. The crystal structure of 3-dibromomethyl-2-difluoromethyl chromone was determined by X-ray diffraction. Due to extended π-bond delocalization, the organic framework is planar and lies on a crystallographic m-mirror plane. The intermolecular non-covalent interactions of 3-dibromomethyl-2-difluoromethyl chromone, as π⋯π stacking arrangements, F⋯H hydrogen bonds and O⋯Br contacts were evaluated by Hirshfeld surfaces analysis. These intermolecular contacts, which affect the absorption bands location of the involved groups, were also detected in the vibrational spectra. [ABSTRACT FROM AUTHOR]