Structure of 2-(2-(anthracen-9-ylmethylene)hydrazinyl)-4-(3-methyl-3-phenylcyclobutyl)thiazole by combined X-Ray crystallographic and molecular modelling studies

A single crystal of 2-(2-(anthracen-9-ylmethylene)hydrazinyl)-4-(3-methyl-3-phenylcyclobutyl)thiazole (C₂₉H₂₅N₃S) containing anthracene, thiazole and cyclobutane rings has been synthesised. The synthesised crystal structure was characterised using IR, ¹H-NMR and ¹³C-NMR spectroscopic and X-Ray analysis techniques. In the crystal, neighbouring molecules formed chains along [110] by interconnecting with N–H···N hydrogen bonding and π–π interactions. The geometrical parameters of the title compound were optimised by Gaussian 09 software in the gas phase and Quantum-Espresso software under Periodic Boundary Conditions (PBC) in the solid phase. Theoretically, IR, NMR spectra, Mulliken, NPA and AIM atomic charges, Hirshfeld surface and frontier molecular orbitals (FMOs) of the title compound were examined. Using the Hirshfeld surface and two-dimensional (2D) fingerprint graphics, the presence of intermolecular interactions in the crystal packing were analysed. The energies of these interactions and their distribution on the crystal structure were shown graphically. In general, it was seen that theoretical calculations were consistent with X-Ray results.     

New thiourea and urea derivatives containing trifluoromethyl- and bis-triflouromethyl-4H-chromen-3-yl substituents

Two new thiourea (1) and urea (2) derivatives, substituted with 2-trifluoromethyl-4H-chromen-3-yl moieties at defined positions, were obtained by convenient synthetic methodologies. The pure compounds were studied in solid state by vibrational spectroscopy (FT-IR and Raman) and in solution by NMR and UV–Vis spectroscopy. The crystal structure of the urea derivative (compound 2) was also determined by X-ray diffraction. The crystal packing is governed by N–H···O intramolecular interactions of moderate strength in a self-assembled dimer of the terminal amide fragment (C(=O)–NH₂). Hirshfeld surface and 2D-fingerprint plots were also performed to characterise the role in the packing stabilisation of all contacts, including weak C–H···F hydrogen bonds and π–π stacking interactions. For both compounds, the tentative assignment of vibrational and electronic spectra was assisted by theoretical calculations. Besides, to evaluate the influence on the pharmacokinetic and pharmacodynamic properties of molecules with –CF₃ groups, the anti-microbial activity of the title compounds was tested against the standard strains of various Gram-positive and Gram-negative organisms with noteworthy antimicrobial effect over Staphylococcus aureus, Klebsiella pneumoniae and Salmonella typhi.     

Weak and strong hydrogen bonds conducting the supramolecular framework of 1-butyl-3-(1-naphthoyl)thiourea: crystal structure,vibrational studies,DFT methods,Pixel energies and Hirshfeld surface analysis

A detailed structural and spectroscopic study of a new thiourea derivative 1-butyl-3-(1-naphthoyl)thiourea (1) is presented with the assistance of theoretical calculations. The X-ray diffraction structure analysis reveals a planar carbonylthiourea group, favoured by intra-molecular NH···O bond. The compound is arranged in the lattice as NH···O and NH···S bonded polymeric ribbons, that extend along the crystal b-axis. Molecular pairs involving N–H···S hydrogen bonds are a dominant contribution to packing stabilisation coming from coulombic component. Hirshfeld surfaces and two-dimensional-fingerprint plots show different intermolecular contacts and its relative contributions to total surface in each compound. The AIM approach shows the nature and strength of the strong and weak intramolecular interactions and the solvent effect, while NBO analysis reveals that the sulphur atom is responsible for the higher hyperconjugative stabilising energy.     

Tris(dimethylamino)-cyclopropenium radical dication

Tris(dimethylamino)-cyclopropenium cation (I^⊕) undergoes a facile oxidation to the radical dication (I^2⊕). The E.S.R. spectrum of I^2⊕, which covers a range of almost 200 gauss, has been analysed in terms of the coupling constants a _N =7·51 (three ¹⁴N nuclei) and a _H ^CH₃ =8·16 gauss (eighteen protons). The line-width can be expressed as

where M _I(N) is the magnetic quantum number for the set of three equivalent ¹⁴N nuclei. A simple molecular orbital model of the trisamino-cyclopropenium system satisfactorily accounts for some physico-chemical properties of I^⊕. The E.S.R. results for I^2⊕ are compared with those for the iso-π-electronic hexamethyl[3]radialene radical anion (II^?).     

Ligand exchange reactions between copper(II)- and nickel(II)-chelates of different sulphur- and selenium-containing ligands

A single-crystal E.S.R. and multi-nuclear ENDOR study of the mixed ligand complex tetra-n-butylammonium(maleonitriledithiolato)(monoethyldithiophosphato)cuprate(II), diamagnetically diluted by the corresponding Ni(II) complex, and the crystal structure of the host complex are reported. n-Bu₄N[Ni(mnt)(HEtdtp)].0·7 acetone is triclinic, space group P1, Z = 2 with a = 9·029(2), b = 13·432(4), c = 17·246(5) Å, α = 108·9(1), β = 90·2(1) and γ = 109·4(1)°. The spin-hamiltonian parameters are calculated from the results of an extended Hückel molecular orbital calculation. The experimental g-tensor and the copper and the four sulphur hyperfine coupling tensors are reporduced well. The almost isotropic and unexpectedly large coupling of the phosphorous atom is negative, which can be understood qualitatively from a spin polarization mechanism.

The hyperfine coupling tensors of eight protons, three of the acetone molecule, four of the tetra-n-butylammonium cation and one intramolecular one, could be determined. The E.S.R. linewidths are unusually small for Cu complexes. Unresolved proton hyperfine interactions are found to give the largest contribution.     

A cobalt (II) complex with 6-methylpicolinate: Synthesis,characterization, second- and third-order nonlinear optical properties,and DFT calculations

A cobalt(II) complex of 6-methylpicolinic acid, [Co(6-Mepic)₂(H₂O)₂]·2H₂O, was prepared and fully determined by single crystal X-ray crystal structure analysis as well as FT-IR, FT-Raman. UV–vis spectra were recorded within different solvents, to illustrate electronic transitions and molecular charge transfer within complex 1. The coordination sphere of complex 1 is a distorted octahedron according to single crystal X-ray results. Moreover, DFT (density functional theory) calculations with HSEH1PBE/6-311 G(d,p) level were carried out to back up the experimental results, and form base for future work in advanced level. Hyperconjugative interactions, intramolecular charge transfer (ICT), molecular stability and bond strength were researched by the using natural bond orbital (NBO) analysis. X-ray and NBO analysis results demonsrate that O−H···O hydrogen bonds between the water molecules and carboxylate oxygen atoms form a 2D supramolecular network, and also adjacent 2D networks connected by C−H···π and π···π interactions to form a 3D supramolecular network. Additionally, the second− and third−order nonlinear optical parameters of complex 1 were computed at DFT/HSEH1PBE/6-311 G(d,p) level. The refractive index (n) was calculated by using the Lorentz−Lorenz equation in order to investigate polarization behavior of complex 1 in different solvent polarities. The first−order static hyperpolarizability (β) value is found to be lower than pNA value because of the inversion symmetry around Co (II). But the second−order static hyperpolarizability (γ) value is 2.45 times greater than pNA value (15×10⁻³⁰ esu). According to these results, Co(II) complex can be considered as a candidate to NLO material. Lastly molecular electrostatic potential (MEP), frontier molecular orbital energies and related molecular parameters for complex 1 were evaluated.     

Electron density characteristics and charge transfer effect of hydrogen bond O–H···Pt(II): atoms in molecules study and natural bond orbital analysis

In this report, we extended the works of Rizzato et al. [Angew. Chem. Int. Ed. 49, 7440 (2010)] on the nature of O–H···Pt hydrogen bond in trans-[PtCl₂(NH₃)(N–glycine)]·H₂O(1·H₂O) complex, by computational study of O–H···Pt interaction in [NBu₄][Pt(C₆F₅)₃(8-hydroxyquinaldine)], with emphasis on charge transfer effect in this interaction of platinum(II) and hydrogen atom. According to the crystallographic geometry reported by José María Casas et al., [NBu₄][Pt(C₆F₅)₃(8-hydroxyquinaldine)] possesses one O–H···Pt hydrogen bridging interaction, similar to the case in trans-[PtCl₂(NH₃)(N–glycine)]·H₂O(1·H₂O) complex. On the basis of topological criteria of electron density, we characterised this O–H···Pt interaction. Charge transferred between platinum(II) and σ^*_O–H orbital in this complex was calculated by using NBO method. The stabilised energy associated to charge transfer was estimated using a direct proportionality, that is 2–3 eV per electron transferred. Charge transfer effects in O–H···Pt hydrogen bonds were studied for these two complexes. Our results indicate that the interaction of O–H···Pt is closed–shell in nature with significant charge transfer, and that charge transfer effect is not negligible in the interaction of O–H···Pt. The second conclusion is different from the result of Rizzato et al.     

Crystal structure of ethyl (2Z)-2-(3-methoxy-4-acetyloxy benzylidene)-7-methyl-3-oxo-5-phenyl-2,3-dihydro-5H-[1,3]thiazolo[3,2-a]pyrimidine-6-carboxylate

The title compound, C₂₆H₂₄N₂O₆S, (I), crystallizes in the monoclinic space group, P2₁/c, with cell parameters a = 16.248(1), b = 7.927(1), c = 19.371(4) ?, β = 105.295(2)°, Z = 4. The central pyrimidine ring in the compound (I) is significantly puckered, assuming a screw-boat conformation. The C11–C16 benzene ring stands vertical while thiazole and C18–C23 benzene rings are coplanar to the mean plane of pyrimidine ring having dihedral angles of 87.48(12), 3.63(11) and 0.94(12)°, respectively. In the absence of potential hydrogen bonding interaction, the crystal packing is influenced by intramolecular C-H…S interaction and intermolecular C-H…π interactions.     

On difference of properties between organic fluorine hydrogen bond C–H···F–C and conventional hydrogen bond

The existence of C–H···F–C hydrogen bonds in the complexes of trifluoromethane and cyclic molecule (oxirane, cyclobutanone, dioxane, and pyridine) has been experimentally proven by Caminati and co-workers. This study presents a theoretical investigation on these C–H···F–C hydrogen bonds at B97D/6-311++G^** and MP2/6-311++G^** levels, in terms of C–H vibrational frequency shifts, atoms in molecules characteristics, and the bonding feature of C–H···F–C hydrogen bonds. It is found that in three important aspects, there are significant differences in properties between C–H···F–C and conventional hydrogen bonds. The C–H···F–C hydrogen bonds show a blueshift in the C–H vibrational frequencies, instead of the X–H normal redshift in X–H···Y conventional hydrogen bonds. The natural bond orbital (NBO) analyses show that σ and p types of lone pair orbitals of the F atom to an antibonding σ^*_H–C orbital form a dual C–H···F–C hydrogen bond. Such a dual hydrogen bonding leads to the proton acceptor directionality of the C–H···F–C hydrogen bond softer. Our studies also show that the Laplacian of the electron density (▽²ρ_BCP) is not always a good criterion for hydrogen bonds. Therefore, we should not recommend the use of the Laplacian of the electron density as a criterion for C–H···F–C hydrogen bonds.     

Theoretical evaluation to improve the performance of composite wax powder: cooperativity effects involving the strong Na+···π/σ and weak hydrogen-bonding interactions in the complex of graphene oxide with Na+ and CH4

ABSTRACT

To provide a reasonable design scheme to improve the performance of composite wax powder, the ternary complex Na⁺···graphene oxide (GO)···CH₄ was selected as a model system to evaluate the cooperativity effect between the Na⁺···σ/π and H-bonding interactions in the composite wax powder doped with GO at the M06-2X/6-311++G(2d,p) and MP2/6-311++G(2d,p) levels. The cooperativities in GO···(CH₄)_n (n?=?1～10) and thermodynamic cooperativity effects in Na⁺···GO···CH₄ were also investigated. Although the changes of the absolute values of H-bonding interactions were slight, from those of relative values, the influence of the Na⁺···π or Na⁺···O interaction on the C–H···π, O–H···C or C–H···O interaction was notable upon the formation of ternary systems. The anti-cooperativity effect was found in the cyclic structure, while the cooperativity effect appeared in the linear conformation. The Na⁺···σ/π and H-bonding interactions as well as cooperativities in Na⁺···GO···CH₄ were stronger than those in Na⁺···coronene···CH₄. The formation of Na⁺···GO···CH₄ is a thermodynamic cooperativity process driven by the enthalpy change. Therefore, it could be inferred that, when graphite powder or carbon black was replaced by GO, the compatibilities could be strengthened among various components, and thus the performance of casting moulds could be improved. Atoms-in-molecules (AIM) and reduced density gradient (RDG) analyses confirmed the cooperativity effect and revealed the nature of the improved performance of composite wax powder with GO. The GO···(CH₄)_n (n?=?1～3) are positively cooperative, while the negative cooperativity is shown when n?=?4～10.     

Crystal structure,Hirshfeld surface analysis,vibrational properties,and electrical and dielectric studies of the bis (4-benzylpyridinium) tetrachlorocuprate (II)

The present paper undertakes the study of (C₁₂H₁₂N)₂CuCl₄, which is a new hybrid compound. It is synthesized and characterized by single-crystal X-ray diffraction, Hirshfeld surface analysis, and FT-IR, FT-Raman, and impedance spectroscopies. It is crystallized in the monoclinic system with C2/c space group. Its crystal structure was determined and refined down to an R value of 0.05 and a wR value of 0.14. The structure can be described by the alternation of two different, cationic–anionic layers parallel to (110) plan. This complex is assembled into 3D supramolecular architecture by hydrogen bonds (N–H…Cl, C–H…Cl) and π–π interactions. Hirshfeld surface analyses and fingerprint plots are used for decoding intermolecular interactions in the crystal network and contribution of component units for the construction of the 3D architecture. The presence of different functional groups and the nature of their vibrations were identified by FT-IR and FT-Raman spectroscopies. The material is characterized by impedance spectroscopy technique measured in 209–500 MHz frequency and 296–390 K temperature ranges. In addition, the Cole–Cole (Z? versus Z?) plots were well fitted to an equivalent circuit built up by a parallel combination of resistance (R) and constant phase elements (CPEs). The close values of activation energies obtained from the analysis of equivalent circuit data confirm that the transport is through ion hopping mechanism in the bis (4-benzylpyridinium) tetrachlorocuprate.     

The influence of halogen-bonding cooperativity on the hydrogen and lithium bonds: an ab initio study

ABSTRACT

Ab initio calculations are carried out to study linear NCH···(NCX)_1–5 and NCLi?…?(NCX)_1–5 clusters (X?=?F, Cl, Br). The aim is to study the influence of halogen-bonding cooperativity on the strength and bonding properties of hydrogen or lithium bond. Particular attention is given to parameters such as binding distances, interaction energies and cooperative energies in these systems. According to our results, the halogen-bonding cooperativity between the NCX molecules has an enhancing effect on the strength of hydrogen and lithium bonds, with an increase of 0.33–0.93 and 0.19–0.43?kcal/mol in NCH···(NCX)_n and NCLi···(NCX)_n, respectively. The enhancing effect of halogen bond on the hydrogen and lithium bond is dependent on the nature of halogen atom, and increases as X?=?F?相似文献   

Analysis of the interactions in FCCF:(H2O) and FCCF:(H2O)2 complexes through the study of their indirect spin–spin coupling constants

A theoretical study of FCCF:(H₂O)_n complexes, with n?=?1 and 2, has been carried out by means of ab initio computational methods. Three kinds of interactions are observed in the complexes: H···π and H···F hydrogen bonds and O···FC tetrel bonds. The indirect spin–spin coupling constants have been calculated at the CCSD/aug-cc-pVTZ-J computational level. Special attention has been paid to the dependence of the different intramolecular coupling constants in FCCF on the distance between the coupled nuclei and the presence or absence of water molecules. The exceptional sensitivity shown by these coupling constants to the presence of water molecules is quite notorious and can provide information on the bonding structure of the molecule.     

ESR studies of Cl2- (VK) centre trapped in irradiated Ca(ClO3)2 . 2H2O single crystals

A Cl₂- centre has been trapped in X or γ-irradiated Ca(ClO₃)₂. 2H₂O single crystals at 298 K, when the irradiated crystals were illuminated with ultra-violet light (360 nm). This centre is formed at the expense of ClO₂ centres in this crystal. This Cl₂ ^- centre is trapped at two magnetically inequivalent sites in the crystal lattice and these sites become equivalent when the static magnetic field is parallel or perpendicular to the b axis. At many orientations this centre reveals ‘super-hyperfine’ interaction with a proton (I = 1/2) of the water of crystallization. The magnetic parameters are close to those observed in alkali chlorides and the E.S.R. spectrum has been fitted to an orthorhombic spin hamiltonian. The principal g values are g_xx = 2·035, g_yy = 2·033 and g_zz = 2·000 and those of the A values are A_xx = 15·0, A_yy = 31·0 and A_zz = 109·0 G. The shfs parameters are A _‖' = 5·0 A _⊥' = 1·0 G. The V_K centre trapped in this lattice is exceptionally stable at room temperature.     

Theoretical investigation of the backbone···π and π···π stacking interactions in substituted-benzene||3-methyl-2′-deoxyadenosine: a perspective to the DNA repair

The π-stacking effects of substituted benzenes on the N-glycosidic bond strength of 3-methyl-2'-deoxyadenosine (3-MDA) were studied by quantum mechanical calculations. Although all substituents enhance the stacking interactions, enhancement is higher for the electron-donating (ED) substituents. When the overall binding energy is separated into the π···π (ΔE_π···π) and backbone···π (ΔE_bb···π) contributions, the ED and electron-withdrawing (EW) substituents increase those contributions, respectively. Both the ED and EW substituents decrease the distance between the centres of stacked rings, while the EW ones increase the N-glycosidic bond length. The electron charge density calculated at the C--N bond critical point (ρ_C–N) is in linear correlation with the backbone···π interaction, not with the π···π interaction. This study also shows that the charge transfer from X-Ben to 3-MDA is in linear correlation with the ΔE_π···π and the change in the charge on the sugar ring is in better accordance with the backbone···π interaction. The N7 proton affinity (PA_N7), with a key role in the depurination process, is highly affected by the π···π interactions. Thus, both interactions must be considered because of the balance between the backbone···π and π···π contributions in these biomolecular systems.     

Evolution of excess electron binding motifs under both internal‐push (from exo C–F bonds) and external‐push (from endo C–F bonds) electron effects in endohedral metallofullerenes with endo C–F bonds

How does the endo C–F bond influence the excess electron binding motif? For lithium‐doped endohedral perfluorofullerenes with endo C–F bonds, under both internal‐push (from exo C–F bonds) and external‐push (from endo C–F bonds) electron effects, the singly occupied molecular orbital electron cloud of the sphere‐like Li···F₈@C₆₀F₅₂ (D₂) is partially dispersed within the σ_p–s antibonding orbital of endo C–F bonds and the space between C^δ+–F_endo^δ– double electric layers, which makes Li···F₈@C₆₀F₅₂ have partial excess electron (electride characteristics) and partial lithium salt characteristics, while in the tube‐like Li···F₂@C₆₀F₅₈ (C_s), as the Li is changing from approaching F to keeping away from F and to approaching another one, the singly occupied molecular orbital electron cloud is mainly dispersed from within the p orbital of the short endo C–F bond to within the middle of the two F atoms and again to within the p orbital of the short endo C–F bond, which indicates an evolution from lithium salt characteristic to excess electron characteristic, and again to lithium salt characteristic. Copyright © 2012 John Wiley & Sons, Ltd.     

A new molecular C60 complex with bis(methylenedithio)tetrathiafulvalene (BMDT-TTF): Synthesis, crystal structure, and properties

A new molecular C₆₀ complex of the composition (BMDT-TTF) · C₆₀ · 2CS₂ (I) with the bis(methylenedithio)tetrathiafulvalene (BMDT-TTF) organic donor is synthesized. The molecular and crystal structures of this complex are determined by x-ray diffraction. The (BMDT-TTF) · C₆₀ · 2CS₂ (I) compound crystallizes in a monoclinic crystal system. The main crystal data are as follows: a=13.550(5) Å, b=9.964(7) Å, c=17.125(8) Å, β=99.52(4)°, V=2280(2) ų, M=1229.45, and space group P2₁/m. Crystals of I have a layered structure: layers consisting of C₆₀ molecules alternate with layers composed of BMDT-TTF and CS₂ molecules. It is found that, in complex I, the donor and C₆₀ molecules are linked through the shortest contacts, which leads to a change in the molecular geometry of BMDT-TTF. The donor molecules in a crystal layer are characterized by the shortest S...S contacts. The IR data indicate the electroneutrality of the fullerene molecule. The electrical conductivity of (BMDT-TTF) · C₆₀ · 2CS₂ single crystals is measured using the four-point probe method at room temperature: σ_RT=2×10^?5 Ω^?1 cm^?1.     

Recognition of aromatic amino acids and proteins with p‐sulfonatocalix[4]arene – A luminescence and theoretical approach

The host–guest interaction of p‐sulfonatocalix[4]arene (p‐SC4) with aromatic amino acids (AAs) and two proteins has been studied using UV–Vis absorption, fluorescence, and theoretical methods. Spectral studies supported by binding constant and calculated binding energy (BE) values show that p‐SC4 binds more strongly with tyrosine compared with other AAs. The application of Bader's theory of atoms in molecule shows the involvement of various types of noncovalent interactions in the formation of the host–guest complexes. Both tyrosine and histidine have strong electrostatic interaction with the sulfonato group and other two AAs have dominant π?π interaction with the aromatic rings of calixarene. In addition, the role of C?H···O, C?H···π and lone pair···π (lp···π) interactions in the stabilization of p‐SC4‐AA complexes has also been realized from the atoms in molecule analysis. The electron density at the bond critical points varies with the calculated BEs and trend in BEs is in good agreement with the experimental binding constant values. The work has been extended to the binding of p‐SC4 with proteins, bovine serum albumin and ovalbumin. Ovalbumin exhibits stronger binding with p‐SC4 than bovine serum albumin. Copyright © 2012 John Wiley & Sons, Ltd.     

Ultrasonic-assisted synthesis and structural characterization of two new nano-structured Hg(II) coordination polymers

Two new Hg(II) coordination polymers containing N,N′-Bis-pyridin-3-ylmethylene-naphtalene-1,5-diamine ligand were synthesized by conventional and sonochemical methods, characterized by spectroscopic techniques (FT-IR and elemental analysis), and their X-ray crystallographic structures were determined. The crystal packing and supramolecular features of these coordination polymers were studied using geometrical analysis and Hirshfeld surface analysis. The crystal structure analysis revealed that H⋯H contacts, C–H⋯π and C–H⋯X (X = Cl for 1 and X = Br for 2) hydrogen bonding interactions are strong enough to govern the supramolecular architecture. The BFDH analysis helps us to compare the predicted morphology to that obtained under ultrasonication. This study may provide further insight into discovering the role of weak intermolecular interactions in the context of nano-supramolecular assembly.