Weak CH Research Articles

Uranyl Complexes as Scaffolding or Spacers for Cucurbit[6]uril Molecules in Homo‐ and Heterometallic Species, Including a Uranyl–Lanthanide Complex

The reaction of uranyl nitrate with cucurbit[6]uril (CB6) and carboxylic or sulfonic ligands under hydrothermal conditions and in the presence of additional metal cations (KI or CeIII) or cosolvents provided four complexes, which were crystallographically characterized. The compound [(UO2)2K2(CB6)(adc)2(NO3)2(H2O)2]·5H2O (1), where H2adc is 1,3‐adamantanedicarboxylic acid, crystallizes in the form of a central K2(CB6)2+ column surrounded by two one‐dimensional (1D) polymeric UO2(adc)(NO3)– chains attached to the column by nitrate bridges, with a perfect match of the repeat lengths in the two subunits. The longer 1,3‐adamantanediacetic acid (H2adac) gives the complex [(UO2)2(adac)2(HCOOH)2]·CB6·6H2O (2), in which the 1D uranyl‐containing polymer and columns of CB6 molecules form a layered arrangement held by weak CH···O hydrogen bonds. The complex formed with the dipotassium salt of methanedisulfonic acid (K2mds), [(UO2)2K2(CB6)(mds)2(OH)2(H2O)8]·4H2O (3), is a 1D polymer, in which K2(CB6)2+ units are connected to one another by doubly hydroxide‐bridged uranyl dimers in which the disulfonates are terminal, chelating ligands; connection between the two subunits is solely through potassium oxo‐bonding to uranyl. The complex [(UO2)2Ce2(CB6)(C2O4)3(NO3)4(H2O)6]·2H2O (4) is a 1D polymer containing bridging oxalate ligands formed in situ, in which CB6 is coordinated to the lanthanide cations only; one nitrate ligand and one water ligand, hydrogen‐bonded to each other, are included in the CB6 cavity, with the possible occurrence of interactions between nitrate oxygen atoms and ureido carbon atoms.

Synthesis, crystal structure, catalytic and anti-Trypanosoma cruzi activity of a new chromium(III) complex containing bis(3,5-dimethylpyrazol-1-yl)methane

The reaction of CrCl36H2O with the ligand bis(3,5-dimethylpyrazol-1-yl)methane (L) yielded the cationic complex [(Cr(L)(H2O)2Cl2]+, which crystallized as the chloride trihydrate [(Cr(L)(H2O)2Cl2]Cl·3H2O. The chromium complex was characterized by elemental analysis, electrical conductivity, Infrared and Ultraviolet/Visible spectroscopy. The crystal structure determination using single-crystal X-ray diffraction showed a chromium center in a distorted octahedral coordination sphere. In the crystal, the packing was directed by OH⋯(O,Cl) hydrogen bonds and weak CH⋯O interactions to build a monoclinic P21/c supramolecular structure. The complex showed excellent properties as an initiator for the ring opening polymerization of є-caprolactone (CL) under solvent-free conditions. The obtained polymer showed high crystallinity (89.9%) and a decomposition temperature above 475 °C. In addition, the new complex was evaluated against epimastigotes from Trypanosoma cruzi (T. cruzi) strains. The results indicated that this complex has a high activity against this parasite with a minimum inhibitory concentration 50 (MIC50) of 1.08 μg/mL. Interestingly, this compound showed little effect on erythrocytes, indicating that it is not cytotoxic. These results provide interesting contributions to the design of metal complexes by using simple and accessible ligands with activity against T. cruzi and with potential applications in the polymerization of CL.

New di-μ-oxidovanadium(V) complexes with NNO donor Schiff bases: Synthesis, crystal structures and electrochemical studies

The reaction between vanadyl sulfate and an NNO donor Schiff base (HL1 or HL2) in methanol resulted in the formation of two new binuclear vanadium(V) complexes, viz., [(L1)VO(μ-O)2VO(L1)]0.5H2O (1) and [(L2)VO(μ-O)2VO(L2)] (2) (L1=N′-[(E)-phenyl(pyridin-2-yl)methylidene]benzohydrazide and L2=N′-[(E)-phenyl(pyridin-2-yl)methylidene]furan-2-carbohydrazide). During the reaction, atmospheric oxygen spontaneously acted as an oxidizing agent and yielded new (VIV→VV) vanadium(V) complexes. The electronic spectra of 1 and 2 shown the vanadium(V) centre is in a distorted octahedral environment in each case. The complexes were characterized by routine physico-chemical methods. The single crystal X-ray structures of 1 and 2 also revealed a distorted octahedral coordination around each of the vanadium(V) centres, confirming the NNO binding mode of the ligands L1 and L2. In these binuclear complexes, the bridging functions are the μ-oxido bonds. The occurrence of weak CH⋯π interactions in 1 and π⋯π stacking interactions in 2 contribute extra stabilization in their solid state. The complexes catalyzed the dismutation of superoxide in an alkaline nitroblue tetrazolium chloride assay and the IC50 values were estimated.

A combined molecular dynamics simulation, atoms in molecule analysis and IR study on the biologically important bulk fluorinated ethanols to understand the role of weak interactions in their cluster formation and hydrogen bond network

The unique physicochemical nature of the fluorocarbon group makes fluorinated alcohols an interesting class of molecules which have diverse applications from the field of biology to chemical industries. In this paper, we have performed molecular dynamics (MD) simulation, atoms in molecule analysis (AIM) as well as IR study on the two biologically important fluorinated alcohols, trifluoroethanol (TFE) and hexafluoroisopropanol (HFIP) as well as compared them with ethanol (ETH) in order to understand the cluster formation as well as hydrogen bond network in their respective bulk media. The cluster size calculation shows that HFIP prefer to form smaller clusters than TFE and ETH. We have found the evidence of weak fluorous (F⋯F) interaction in TFE and HFIP by the radial distribution function (rdf) calculations and the extent of interaction is more significant in the case of HFIP which has also been confirmed by the AIM analysis. Significant amount of weak CH⋯F as well as CH⋯O interactions have been found to contribute in the cluster formation of the bulk HFIP, whereas, only CH⋯F interaction was evident in the case of bulk TFE. The rdf data shows that OH⋯O and OH⋯F hydrogen bonds are the main contributors in the hydrogen bond network of TFE and HFIP. However, the number as well as the strength of OH⋯O hydrogen bond is significantly less for HFIP compared to TFE and the strength of OH⋯F hydrogen bond is more for HFIP. Due to the presence of less as well as weak OH⋯O hydrogen bond in HFIP, its average hydrogen bond strength is less as compared to TFE and ETH which is also reflected by the experimental IR data of HFIP which is significantly blue shifted as compared to TFE. The MD simulation, AIM analysis and IR data clearly indicate that the organic fluorine plays significant role in the cluster formation and hydrogen bond network of TFE and HFIP through the formation of weak OH⋯F hydrogen bond along with the fluorous interaction.

Synthesis, characterization, Hirshfeld surfaces and DFT computation of novel benzyl N-(1,3-benzothiazol-2-yl)-N-benzylcarbamate

The compound benzyl N-(1,3-benzothiazol-2-yl)-N-benzylcarbamate was synthesized from 2-aminobenzothiazole and characterized by FT-IR, NMR, UV–Vis, X-ray diffraction and quantum chemical calculations. The compound crystallizes in the monoclinic, space group P21, with unit cell parameters of a = 11.5904(18) Å, b = 5.5213(7) Å, c = 15.251(2) Å, β = 112.217(16)°, V = 903.5(2) Å3 and Z = 2. The weak intermolecular CH⋯O and CH⋯π hydrogen bonds stabilized the crystal structure. Hydrogen bonding patterns were investigated in proposed compound on the behalf of X-ray analysis and its assignment with recognized terminological notations. The optimized geometrical parameters, harmonic vibrational frequencies, electrostatic potential surface and Milliken charges were calculated using hybrid Density Functional Theory (DFT/B3LYP) method with 6-31 + G(d,p) basis set. 1H and 13C NMR chemical shifts were also calculated at the same level of theory. The TD-DFT calculations have been performed to explore the electronic absorption spectra. Our computed data are in good agreement with the experimental values.

The Born-Oppenheimer molecular simulations of infrared spectra of crystalline poly-(R)-3-hydroxybutyrate with analysis of weak C[sbnd]H⋯O[dbnd]C hydrogen bonds

In this letter we present results of study of weak CH⋯OC hydrogen bonds of crystalline poly-(R)-3-hydroxybutyrate (PHB) by using Born-Oppenheimer molecular dynamics. The polymeric structure and IR spectra of PHB result from the presence of the weak hydrogen bonds. We applied the post-molecular dynamics analysis to consider a CO motion as indirectly involved in the hydrogen bonds. Quantization of the nuclear motion of the oxygens was done to perform detailed analysis of the strength and properties of the CO bands involved in the weak hydrogen bonds. We have also shown the dynamic character of the weak hydrogen bond interactions.

Piperidin-1-ylamidomethyltellurium derivatives: Synthesis and solid state structures

Oxidative insertion of low valent tellurium, Te(0) and Te(II), into the CBr bond of α-bromoacetylpiperidine proceeds readily under mild conditions and provides a direct synthetic route to stable, crystalline piperidin-1-ylamidomethyltellurium(IV) dibromides, (C5H10NCOCH2)2TeBr2, 1b and (C5H10NCOCH2)ArTeBr2 (Ar=2,4,6-Me3C6H2, 2b; 1-C10H7, 3b; 4-MeC6H4, 4b). While the bisulfite reduction of 1b affords a yellow coloured telluroether, (C5H10NCOCH2)2Te, 1 as an oil, that of the unsymmetrical diorganotellurium dibromides, (C5H10NCOCH2)ArTeBr2 leads to the isolation of the respective diarylditellurides, ArTeTeAr. The symmetrical telluroether, 1 adds dihalogens oxidatively to give piperidin-1-ylamidomethyltellurium(IV) dihalides, (C5H10NCOCH2)2TeX2 (X=Cl, 1a; Br, 1b and I, 1c;). All the new piperidin-1-ylamidomethyltellurium derivatives have been characterized by elemental and 1H, 13C, 125Te NMR spectral analyses. Single-crystal X-ray diffraction data for 1b and 1c indicated a butterfly molecular shape for the two halo analogues in which the six-member heterocyclic rings in the organic ligands retain the chair conformation of the independent piperidine molecule. The piperidin-1-yl appended organic ligand invariably results in the amido O atom being involved in an intramolecular Te O secondary bonding interaction and acts as a small-bite (C, O) chelating agent, at least in the solid state. Steric congestion around the six-coordinate Te(IV) atom and the partial positive charge on N owing to the resonating character of the NCO amido group prevents these atoms from participating in the intermolecular associative forces. Instead, the weak CH⋯O and CH⋯Br interactions take centre-stage in the solid state self-assembly.

A new Z′=(2+0.5+0.5) amidophosphoester structure: Hirshfeld surface analysis of symmetry-independent molecules

Abstract Tetraethyl 1,3-phenylenebis(phosphoramidate) was synthesized and characterized by 1H, 13C, 31P NMR, IR and mass spectroscopies. The asymmetric unit is composed of two half-molecules, each residing on a two-fold axis, and two complete molecules, thus leading to a Z′=(2+0.5+0.5)=3 structure. The most plausible explanation for the occurrence of multiple independent molecules is a frustration between relatively strong hydrogen bond interactions and weaker CH···π interactions. In each of the molecules, the P atoms are in a similar distorted tetrahedral environment. The N atoms bonded to P atoms have mainly sp2 character tending towards a planar environment. In the crystal structure, the phosphoryl O atoms are involved in classical N–H···O=P and weaker C–H···O=P hydrogen bonds as (N–H)(C–H) ···O=P, acting as a double hydrogen-bond acceptor. These hydrogen bonds along with other C–H···O hydrogen bonds and C–H···π interactions create a 3D crystalline network. Hirshfeld surfaces and two-dimensional (2D) fingerprint plots are calculated for analyzing intermolecular interactions in each of the independent molecules of the title compound. For all four independent molecules, the contribution of H···H contacts to the total interactions is decisive, being larger than 60% for each molecule. The O···H/H···O contacts are the characteristic intermolecular contacts in the corresponding molecules. Furthermore, the C···H/H···C, including the C–H···π interactions, and N···H/H···N contacts cover other intermolecular contacts in the crystal lattice.

(3+2) Cycloaddition of N-methylazomethine ylide obtained from sarcosine and formaldehyde to CH- and NH-acidic enones and enamides

Conjugated unsaturated carbonyl compounds with weak CH or NH acidity were used in a three-component reaction with sarcosine and formaldehyde, forming (3+2) cycloaddition products in 32–73% yields. The conversion was estimated from NMR data and strongly depended on the acidity of dipolarophile and the steric accessibility of its double bond.

A Hirshfeld surface analysis, crystal structure and infrared characterization of a new organic cyclohexaphosphate, (C8H12N)4(Li)2(P6O18)(H2O)6

Single crystals of a new organic cyclohexaphosphate (C8H12N)4(Li)2(P6O18)(H2O)6 prepared by an acid/base reaction between cyclohexaphosphoric acid H6P6O18 and 2,6-dimethylaniline, have been successfully grown by slow evaporation technique at room temperature. This compound was characterized using X-ray diffraction (XRD) and FT-IR spectroscopy. The results show that the title compound was phased with a triclinic structure and P-1 space group. The crystal structure was solved by using 5203 independent reflections with a final R value of 0.031. The P6O18 ring is centrosymmetrical. Its main geometrical features are those commonly observed in others cyclohexaphosphates. The atomic arrangement of this compound can be described by an organization in a three-dimensional framework, built up from alternated organic and inorganic species. Adjacent P6O18 rings are linked via corner-sharing by LiO4 tetrahedra, generating anionic [Li2(P6O18)(H2O)]4- layers parallel to (110). Charge balance is achieved by the protonated amine which is trapped in the interlayer space and interacts with the organic framework through strong and medium hydrogen bonding. An extensive network of NH⋯O and OH⋯O hydrogen-bonding interactions link the components into a three-dimensional network and additional stabilization is provided by weak CH⋯O hydrogen bonds. Intermolecular interactions were investigated by Hirshfeld surfaces. The vibrational absorption bands were identified by infrared spectroscopy. The stretching modes of P6O18 ring and band assignments are described.

π–hole interactions at work: crystal engineering with nitro-derivatives

In this manuscript, we report the design, synthesis and X-ray characterization of nitrodiene derivatives that present crucial π–hole interactions involving the nitro group as a π–hole donor. The solid state structures of 1,4-dinitro-1,3-butadiene (1), its co-crystal 1·Diox, and homologous 1,4-dinitro-1,3-pentadiene (2) and 2,4-dinitro-2,4-hexadiene (3) feature competition of lone pair–π–hole interactions with common weak CH⋯O bonding and gradually increased role of the NO2⋯NO2 interactions. Regular evolution of the supramolecular patterns (1 to 3) results in generation of an unprecedented 3D non-covalent framework in 3 that is controlled exclusively by short π–hole contacts (O⋯N = 2.9615(18), 3.1304(18) A). These findings complement the results of high level ab initio calculations (MP2/def2-TZVP) and unite theory and experiment, thus supporting the functional relevance of this novel π–hole interaction.

Pinning-down molecules in their self-assemblies with multiple weak hydrogen bonds of C[sbnd]H⋯F and C[sbnd]H⋯N

Two-dimensional self-assemblies of four partially fluorinated molecules, 1,4-bis(2,6-difluoropyridin-4-yl)benzene, 4,4′-bis(2,6-difluoropyridin-4-yl)-1,1′-biphenyl, 4,4′-bis(2,6-difluoropyridin-4-yl)-1,1′:4′,1″-terphenyl and 4,4′-bis(2,6-difluoropyridin-3-yl)-1,1′-biphenyl, involving weak intermolecular CH⋯F and CH⋯N hydrogen bonds were systematically investigated on Au(111) with low-temperature scanning tunneling microscopy. The inter-molecular connecting modes and binding sites were closely related to the backbones of the building blocks, i.e., the molecule length determines its binding sites with neighboring molecules in the assemblies while the attaching positions of the N and F atoms dictate its approaching and docking angles. The experimental results demonstrate that multiple weak hydrogen bonds such as CH⋯F and CH⋯N can be efficiently applied to tune the molecular orientations and the self-assembly structures accordingly.

Structural variability, Hirshfeld surface analysis and properties of three Zn(II) coordination polymers based on flexible bis(thiabendazole) and aromatic dicarboxylate co-ligands

Three zinc(II) coordination polymers (CPs), {[Zn(L)0.5(tbta)]·0.5 L·2.5H2O}n (1), {[Zn(L)0.5(mip)]·H2O}n (2) and {[Zn(L)0.5(npht)(H2O)]·0.5H2O}n (3) (L = 1,4-bis(thiabendazole)butane, H2tbta = tetrabromoterephthalic acid, H2mip = 5-methylisophthalic acid, H2npht = 3-nitrophthalic acid) have been hydrothermally synthesized and structurally characterized. Single-crystal X-ray diffraction analyses reveal that CP 1 shows a 2D honeycomb-like (6, 3) network. CP 2 displays a hybrid helical chain, and further assembled into a 2D supramolecular layer via weak CH⋯O hydrogen bonding interactions, whereas CP 3 is a right-handed helical chain and finally extended into a 3D supramolecular structure by classical OH⋯O hydrogen bonds and π–π stacking interactions. Further, the Hirshfeld surfaces, fingerprint plots, fluorescence properties and catalytic performances of three CPs for the degradation of methyl orange dye in a Fenton-like process have been investigated.

Polymorphs of 4-isopropylbenzylidine thiophene-2-carbohydrazide: Crystal growth and density functional theory computations

The structural features of conformational isomerism in 4-isopropylbenzylidine thiophene-2-carbohydrazide (ITC) polymorphs have been investigated to conquer distinguishable strong NH⋯O and weak CH⋯S hydrogen bond interactions. The single crystals were grown at constant temperature and have characterized by density functional theory computations using B3LYP method by 3-21G basis set. The conformational isomers of ITC were compared and spectroscopically characterized by FT-IR and Raman spectroscopy. The bulk phases were studied by the powder X-ray diffraction patterns. External morphology of ITC was discussed using scanning electron microscopic and transmission electron microscopic studies. Comparisons between various types of intermolecular interactions in the two polymorphic forms have been quantified via Fingerprint and Hirshfeld surface analysis. DFT computations were used to illustrate molecular electrostatic potential, HOMO-LUMO, mulliken atomic charges and electron density of states.

Synthesis, characterization and intermolecular interactions in crystals of two p-tert-butylthiacalix[4]arene diisocyanide and diamine derivatives

The synthesis, the spectral characterization and the crystal structure of 25,27-bis(2-isocyanoethoxy)-5,11,17,23-tetra-tert-butyl-26,28-dihydroxythiacalix[4]arene and of the reaction intermediate 25,27-bis(2-aminoethoxy)-5,11,17,23-tetra-tert-butyl-26,28-dihydroxythiacalix[4]arene are here described. The target diisonitrile compound crystallizes in the triclinic system with space group P-1 while the diamine intermediate is trigonal with space group R-3. In both structures, the thiacalix[4]arene units adopt a broadly similar pinched cone conformation, where two aromatic rings bearing an ethereal group are almost parallel while two phenolic rings lie near-vertically. In the supramolecular structure of both molecules, various intermolecular interactions involving CH⋯O, CH⋯C, CH⋯π and weak CH⋯S interactions were found. Moreover, the Hirshfeld surface analysis of the target compound was made to further confirm the crystal packing driving forces.

Photoelectron spectroscopy of nitromethane anion clusters

Nitromethane anion and nitromethane dimer, trimer, and hydrated cluster anions were studied by photoelectron spectroscopy. Vertical detachment energies, estimated electron affinities, and solvation energies were obtained from the photoelectron spectra. Cluster structures were investigated using theoretical calculations. Predicted detachment energies agreed with experiment. Calculations show water binds to nitromethane anion through two hydrogen bonds. The dimer has a non-linear structure with a single ionic CH⋯O hydrogen bond. The trimer has two different solvent interactions, but both involve the weak CH⋯O hydrogen bond.

Supramolecular architecture of third-order nonlinear optical ammonium picrate: Crystal growth and DFT approach

Single crystals of ammonium picrate (AP), having potential applications in optical devices, were grown from a mixed solvent system methanol-acetone (2:1, v/v) by the slow evaporation technique at constant temperature. The structure is elucidated by single crystal X-ray diffraction analysis. The molecule is associated with accommodating weak CH⋯O, NH⋯O, CH⋯N, π…π and H⋯H stacking interactions, very much responsible for the formation and strengthening of supramolecular assembly. Inter- and intramolecular hydrogen bonding interactions show supramolecular architecture in the crystal packing. Two different types of architecture, i.e., a column like packing and cluster network type of infrastructure are observed. Fingerprint analysis was used to locate and analyze the quantity of the molecular interactions. Third-order non-linear optical properties of the grown crystal were derived by employing a single beam Z-scan technique at a wavelength of 532nm with He-Ne Laser system. Theoretical calculations were performed using density functional theory (DFT) method to derive the optimized geometry, dipole moment, polarizability, HOMO-LUMO energies at different levels, excited state energy and oscillator strength. Estimated large first—order molecular hyperpolarizality of >9.81 times of urea, suggests a charge transfer atmosphere facilitating micro level nonlinearity. Idea about the size, shape, charge density distribution and site of chemical reactivity of the molecule has been obtained by mapping electron density with electrostatic potential.

Crystal structure and theoretical studies of derivative of imidazo-1,2,4-triazine

In this study, we present the result of X-ray structure analysis of methyl [8-(3-chlorophenyl)-4-oxo-2,3,4,6,7,8-heksahydroimidazo[2,1-c][1,2,4]triazin-3-yl]acetate (1). The molecule conformation is flat, with a chlorophenyl substituent and the ester moiety lying in the plain of the heterobicyclic scaffold. Its conformation is stabilized by an intramolecular NH…O hydrogen bond. Within the crystalline structure of 1, molecules associate with one another by weak CH…O, CH…Cl and CH…π bonds. The molecular and crystal structure of 1 was compared with the previously described structurally similar compound possessing the same bicyclic rigid core and similar chemical nature of the functional ester moiety. Very interesting differences in molecules geometry and association were observed. Non-covalent bonds within the crystals are additionally visualized by determination of Hirshfeld surfaces.Moreover, the quantum chemical calculation for 1 in the gas phase were carried out. The DFT calculation methods was used to optimize of molecule geometry and obtain molecular energy profiles with respect to selected torsion angles. The quantum chemical conformational analysis that was carried out for compound 1 in the gas phase suggests that in the solid state the molecules adopt the minimum energy conformation.

Raman Spectroscopic Evidence of the Selective Extraction of Metallic SWNTs By Polymethyl(1-undecylic acidyl)Silane

Water soluble polymethyl(1-undecylic acidyl)silane was synthesized by the hydrosilylation of 10-undecylenic acid with polymethylsilane catalyzed by 2,20-azobisisbutyronitrile. The arc-discharged SWNTs were ultrasonically dispersed in an aqueous solution of polymethyl(1-undecylic acidyl)silane and then subjected to ultracentrifugation. Raman spectroscopic characterization confirmed that the supernatant is enriched in the metallic SWNTs, especially those with chiral indexes of (14,2), (15,0), (13,1), (12,3) and (19,1) metallic SWNTs. In this work, the SWNTs of larger diameters and smaller chiral angles than those reported previously were selectively extracted. Moreover, FT-IR spectroscopy and Raman scattering evidence the charge transfer between polymethyl(1-undecylic acidyl)silane and SWNTs. It is assumed that polymethyl(1-undecylic acidyl) silane could wrap chiral-index-selectively onto SWNTs through a fairly weak CH–p interaction, and that the stiffness and length of main chains and side chains as well as the charge state of the polymethylsilane derivative play vital roles in the selective extraction of metallic SWNTs.

Hydrogen bonded and stacked geometries of the temozolomide dimer.

Dispersion-corrected density functional theory (DFT) and MP2 quantum chemical methods are used to examine homodimers of temozolomide (TMZ). Of the 12 dimer configurations found to be minima, the antarafacial stacked dimer is the most favored, it is lower in energy than coplanar dimers which are stabilized by H-bonds. The comparison between B3LYP and B3LYP-D binding energies points to dispersion as a primary factor in stabilizing the stacked geometries. CO(π) → CO(π*) charge transfers between amide groups in the global minimum are identified by NBO, as well as a pair of weak CH∙∙N H-bonds. AIM analysis of the electron density provides an alternative description which includes N∙∙O, N∙∙N, and C∙∙C noncovalent bonds.