Hydrogen Bond Type Interactions Research Articles

Crystal structure, hydrogen bond patterns, Hirshfeld surface analysis, and topological studies (NCI) of 1,5,5-trimethyl-imidazolidine-2,4-dione; an organic compound with high symmetry crystallizing in the tetragonal space group I4/m

The title compound, 1,5,5-trimethyl-imidazolidine-2,4‑dione was characterized by FT-IR, 1H NMR, and 13C NMR spectroscopy techniques. The crystal structure was established by single-crystal X-ray diffraction. The powder X-ray powder diffraction analysis confirms the phase purity of the crystalline sample. The hydantoin with formula C6H10N2O2 crystallizes in the tetragonal space group I4/m (N°87), Z=8, and unit cell parameters a=15.554(2) Å, c=6.623(6) Å. This space group is very infrequent to find in purely organic molecules and is since, in the asymmetric unit, the hydantoin ring lies on a mirror plane m. The crystalline packing is stabilized by the formation of intermolecular interactions of the strong hydrogen bond type of the N–H···O between the neighboring hydantoin rings. In addition, the crystalline structure presents the formation of weaker unconventional hydrogen bonds of the C–H···O type. These hydrogen bonds give rise to the formation of 8, 24, and 36-membered ring-type supramolecular structures described by the graphs R22(8), R44(24), and R88(36), respectively, which govern the packing of the supramolecular structure of 1,5,5-trimethyl-imidazolidine-2,4‑dione.Hirshfeld surface analysis of the crystal structure shows that the most important contributions for the crystal packing are from H···H (58.3%) and H··O/O··H (34.0%) interactions, which indicate that van der Waals interactions are the dominant forces in the crystal packing. Energy framework calculations suggest that the contacts formed between molecules are slightly electrostatic.These intermolecular interactions were also investigated through topological analysis of the electron density (ρ) employing the NCI method. Experimental and theoretical results obtained for this new hydantoin compound suggest that N–H···O and C–H···O interactions play an important role in the stabilization of its supramolecular structure.

Study of the Molecular Architectures of 2-(4-Chlorophenyl)-5-(pyrrolidin-1-yl)-2H-1,2,3-triazole-4-carboxylic Acid Using Their Vibrational Spectra, Quantum Chemical Calculations and Molecular Docking with MMP-2 Receptor.

1,2,3-triazole skeleton is a valuable building block for the discovery of new promising anticancer agents. In the present work, the molecular structure of the synthesized anticancer drug 2-(4-chlorophenyl)-5-(pyrrolidin-1-yl)-2H-1,2,3-triazole-4-carboxylic acid (1b) and its anionic form (2b) was characterized by means of the B3LYP, M06-2X and MP2 quantum chemical methods, optimizing their monomer, cyclic dimer and stacking forms using the Gaussian16 program package. The molecular structure was found to be slightly out of plane. The good agreement between the IR and Raman bands experimentally observed in the solid state with those calculated theoretically confirms the synthesized structures. All of the bands were accurately assigned according to functional calculations (DFT) in the monomer and dimer forms, together with the polynomic scaling equation procedure (PSE). Therefore, the effect of the substituents on the triazole ring and the effect of the chlorine atom on the molecular structure and on the vibrational spectra were evaluated through comparison with its non-substituted form. Through molecular docking calculations, it was evaluated as to how molecule 1b interacts with few amino acids of the MMP-2 metalloproteinase receptor, using Sybyl-X 2.0 software. Thus, the relevance of triazole scaffolds in established hydrogen bond-type interactions was demonstrated.

A Computational Chemistry Approach to the Molecular Design of SiO2 Nanoparticles Coated with Stearic Acid and Sodium Stearate in Ethanol Solvent.

Preparation of hydrophobic SiO2 nanoparticles (NPs) coated with different surfactants is important due to their potential application in different fields of chemistry. In this work, a combined experimental and Molecular Dynamics (MD) simulation approach, is advanced to characterize the adsorption process, in ethanol as a solvent, of stearic acid and sodium stearate on SiO2 spherical NPs with different ionization degrees (0%, 10%, and 23.3%). The main objective is to gain molecular insight into the factors involved in the preparation of hydrophobic coated NPs, which involves the intervention of ion-dipole, electrostatic, and hydrogen bond-type interactions depending on the surfactants and the nature SiO2 NPs. Our results demonstrate that the SiO2 NPs have a good affinity for ethanol solvent medium., as confirmed through the analysis of the Radial Distribution Functions (RDFs)), which indicates that hydrogen bonds are formed at a distance of ∼0.192 nm between ethanol and SiO2 NPs. The presence of Na+ ions reduce the electrostatic repulsion between the -COO- and -SiO- groups in NPs with degrees of ionization of 10% and 23.3%, because it acts as a bridge and thus favors the adsorption between the silanol and carboxylic groups. The investigation of the Potentials of Mean Force (PMFs) suggests that the adsorption on these NPs, is a spontaneous process compared with the case with 0% ionization degree. The experimental coating of the NPs was studied using Atomic Force Microscopy (AFM), a technique that allows the indirect measure of the Work of Adhesion (Wadh), a key quantity to estimate the energy needed to separate the interfaces AFM tip-sample. The experimental values of Wadh for the pure SiO2 NPs and two modified SiO2 NPs correspond to 2.01 J/m2, 1.72 J/m2 and 1.43 J/m2, respectively. The main conclusion is that the interaction energies between surfactants and SiO2 NPs, estimated from MD simulations, and the Wadh obtained from AFM measurements are correlated, in the sense that the reduction in the Wadh, in a solvent-free environment, corresponds to an increment of the interaction energy in the presence of the solvent. This reduction in Wadh is also associated with the fact that the nature of the coating of the SiO2 NPs surfaces increases the NPs hydrophobicity. Our analysis provides a path for the computational design and the prediction of hydrophobicity of coated NPs, which is the main focus of our work.

Synthesis, crystal structure, and intrinsic reactivity descriptors of coordination complexes of [(cis-PdCl2·L-proline) L-proline] and [trans-PdCl2·(glycine-OMe)2

This work describes the synthesis and structural characterization of two palladium (II) complexes elucidated by infrared spectroscopy, dispersive energy analysis (EDS) with Scanning Electron Microscopy (SEM) and X-ray single-crystal diffraction analysis. The first chiral complex is derivatized from l-proline amino acid, obtaining [Cis-PdCl2·L-proline(L-proline)] (1), in which the structure does not have symmetry elements and crystallized in a triclinic crystal system on a non-centrosymmetric space group P1. The comparison with the structural complex of [trans-PdCl2·(glycine-OMe)2] (3) becomes necessary due to the anticancer activity of its analog, cis-platinum, and the catalytic activity caused by Pd as a metallic center. Complex 1 is therefore made up of a free proline molecule linked by a single hydrogen bond to a PdCl2 molecule forming a 5-member chelate ring of the COO···Pd···NH type with another proline molecule and displaying distorted angles and bond sizes to the square planar geometry of the palladium (Pd) center. Ring formation generates a new stereogenic center chemically correlated with the induction caused by the absolute configuration S of the initial amino acid. The crystal results strongly indicate the confirmed configuration by the Flack parameter and its crystal packing stabilization by an intermolecular H-bond network, highlighting as a secondary mimicking structure the β sheets formed by hydrogen bonding interaction of the N—H···Cl type responsible for the disorder moldered on pyrrolidine ring.Furthermore, the Pd(II) complex obtained by the glycine was [trans-PdCl2·(glycine-OMe)2] (3). Regarding its chemical structure, this complex is constituted by the union of two glycine methyl ester molecules binding to a Pd in a trans disposition concerning the almost perfect square plane, which also contains a C2 axis of rotation. Complex 3 crystallized in a monoclinic system and centrosymmetric space group P21/c, the packing is favored by four strong hydrogen bond type interactions presenting helices with 90° rotations between each layer.Owing to their great interest and relevance in Pd—N amino acid in catalytic and medicinal chemistry, the electronic and global reactivity properties of complexes 1 and 3 were further explored by computational methods in the framework of Density Functional Theory, finding 1 as the most reactive complex due to the narrower E-LUMO/E-HOMO energy gap, having this band gap in agreement with the lowest hardness value compared to those shown for 3, in which band gap and hardness are higher with a tendency to kinetic stability and controlled reactivity.

In silico docking based screening of constituents from Persian shallot as modulators of human glucokinase.

Small molecule glucokinase (GK) modulators not only decrease fasting and basal plasma sugar contents but also progress glucose tolerance. The hydro-ethanolic extract of the Persian shallot (Allium hirtifolium Boiss.) decreased blood glucose, improved plasma insulin and amplified GK action. The present study was proposed to screen phytoconstituents from Persian shallot as human GK activators using in silico docking studies. A total of 91 phytoconstituents reported in Persian shallot (A. hirtifolium Boiss.) were assessed in silico for the prediction of drug-like properties and molecular docking investigations were carried out with human GK using AutoDock vina with the aim of exploring the binding interactions between the phytoconstituents and GK enzyme followed by in silico prediction of toxicity. Almost all the phytoconstituents tested showed good pharmacokinetic parameters for oral bioavailability and drug-likeness. In the docking analysis, cinnamic acid, methyl 3,4,5-trimethoxy benzoate, quercetin, kaempferol, kaempferol 3-O-β-D-glucopyranosyl-(1- > 4)-glucopyranoside, 5-hydroxy-methyl furfural, ethyl N-(O-anisyl) formimidate, 2-pyridinethione and ascorbic acid showed appreciable hydrogen bond and hydrophobic type interactions with the allosteric site residues of the GK enzyme. These screened phytoconstituents may serve as promising hit molecules for further development of clinically beneficial and safe allosteric activators of the human GK enzyme.

Transition Metal Complexes of 2,6‐Dibenzhydryl Derived Bisphosphine: Synthesis, Structural Studies and Palladium Complex Promoted Suzuki‐Miyaura Reactions

AbstractTransition metal chemistry of [Ar*N(CH2PPh2)2] (1) derived from the sterically demanding backbone 2,6‐dibenzhydryl‐4‐methylphenyl core is described. The reactions of 1 with 30 % aq. H2O2 and S8 afforded bischalcogenides [Ar*N(CH2P(O)Ph2)2] (2) and [Ar*N(CH2P(S)Ph2)2] (3), respectively. Treatment of 1 with [M(COD)Cl2] (M=Pd, Pt) in 1 : 1 molar ratios produced chelate complexes cis‐[MCl2{Ar*N(CH2PPh2)2}‐κ2‐P,P] (4, M=Pd; 5, M=Pt), whereas similar reaction between 1 and [Pd(η3‐C3H5)Cl]2 afforded dinuclear complex [{Pd(η3‐C3H5)Cl}2{Ar*N(CH2PPh2)2}‐κ1‐P,P] (6). The reaction of 1 with [Ru(η5‐C5H5)Cl(PPh3)2] in 1 : 1 ratio yielded [{Ru(η5‐C5H5)Cl}{Ar*N(CH2PPh2)2}‐κ2‐P,P] (7). Treatment of 1 with [M(C5H11N)2(CO)4] (M=Mo, W) in 1 : 1 molar ratios afforded cis‐[M(CO)4{Ar*N(CH2PPh2)2}‐κ2‐P,P] (8, M=Mo; 9, M=W). The reaction of 1 with copper(I) halides in 1 : 1 molar ratios produced [Cu(μ2‐X)]2 dinuclear complexes [{Cu(μ2‐X)}2{Ar*N(CH2PPh2)2}2‐κ2‐P,P}] [10, X=Cl; 11, X=Br; and 12, X=I]. Most of these compounds show various C−H⋅⋅⋅π interactions. Bischalcogenides 2 and 3 showed intramolecular hydrogen bonding type interactions, C−H⋅⋅⋅O (2.554 Å) and C−H⋅⋅⋅S (2.825 Å) between the methylene hydrogens of –NCH2PPh2 groups with O or S atoms, which was also evinced by QTAIM and NCI analysis. Bisphosphine 1 was found to be very effective in palladium catalyzed Suzuki‐Miyaura couplings of aryl chlorides with aryl boronic acids.

Click Synthesis, Anticancer Activity, and Molecular Docking Investigation of some Functional 1,2,3-triazole Derivatives

1,2,3-triazole skeleton is a privileged building block for the discovery of new promising anticancer agents. In this report, new 1,4-disubstituted 1,2,3-triazoles with the bioisoster triazole moiety were straightforwardly prepared under copper-catalyzed azide-alkyne [3+2] cycloaddition reactions (CuAAC) regime using a variety of both functional organic azides and terminal alkynes. The resulting functional 1,4-disubstituted 1,2,3-triazole compounds were fully characterized and subsequently tested for their antiproliferative activity against four different cancer cell lines. The cytotoxicity tests carried out with these 1,2,3-triazole derivatives show average IC50 values ranging from 15 to 50 µM by comparison with the standard reference drug, namely doxorubicin. The phosphonate 1,2,3-triazole derivative was found to exhibit the best antiproliferative activity among the studied compounds against the HT-1080 cell lines. It was chosen to evaluate its mode of action in these cancer cell lines. The cell cycle study showed that the phosphonate derivative, compound 8, is the most active inhibitor of the cell cycle at the G0/G1 phase, inducing apoptosis independently of Caspase-3 and causing an increase in the mitochondrial membrane potential (ΔΨm) in the HT-1080 cell lines. Molecular docking studies of this phosphonate derivative into the MMP-2 and MMP-9 metalloproteinases receptors demonstrated the relevance of triazole scaffolds and the pendant phosphonate group in establishing -anion, -alkyl and hydrogen bonding type interactions with residual components in the active MMP pocket.

Infrared Spectroscopy in the Middle Frequency Range for Various Imidazolium Ionic Liquids-Common Spectroscopic Characteristics of Vibrational Modes with In-Plane +C(2)-H and +C(4,5)-H Bending Motions and Peak Splitting Behavior Due to Local Symmetry Breaking of Vibrational Modes of the Tetrafluoroborate Anion.

Various alkyl-methylimidazolium ionic liquids (ILs) were inspected using infrared spectroscopy in the middle frequency range. In the 1050–1200 cm–1 range, there is a skeletal vibrational mode accompanied with a large in-plane +C(2)–H bending motion and +C(4)–H and +C(5)–H motions, and in the 1500–1650 cm–1 range, there are two skeletal vibrational modes with in-plane +C(4,5)–H bending motions. Interestingly, in both ranges, we found that skeletal vibrational modes with a large in-plane +C(2)–H bending motion and in-plane +C(4,5)–H bending motions are insensitive to increases in the basicity of anions or the strengthening of hydrogen bond-type interactions, and the behaviors are completely different from those in the +C–H stretching vibrational modes in the 3000–3200 cm–1 range and the skeletal vibrational modes with large out-of-plane +C–H motions in the 700–950 cm–1 range. Furthermore, in alkyl-methylimidazolium tetrafluoroborate [Cnmim+][BF4–] ILs, we found that absorption due to the (threefold) degenerate vibrational mode of [BF4–] was observed as a broad absorption band with three splitting peaks in the 900–1150 cm–1 range as a result of local symmetry breaking due to the cation–anion interactions.

Na-cholate micelle mediated synthesis of polypyrrole nanoribbons for ethanol sensing

Abstract The low-level sensing of ethanol has gained enormous importance due to its application in human health monitoring, road safety, fermentation and food industries. In this investigation, we report the synthesis of ribbonlike nanostructures of polypyrrole (PPY), a conducting polymer, using sodium cholate micelles as a soft template. The PPY nanoribbons were found to exhibit good sensor response along with high degree of selectivity to ethanol vapour as opposed to several common volatile organic compounds (VOCs) showing its suitability as a selective sensing layer to detect ethanol from a mixture containing ethanol, methanol, 2-propanol, toluene, n-hexane, and humidity. The sensing mechanism and its selectivity to ethanol vapor were explained by considering a hydrogen bond type interaction of the OH groups of ethanol molecules with large number of N or NH groups of the PPY available on the surface due to its nanoribbon morphology. Investigation of the cytotoxicity of the PPY nanoribbons revealed good biocompatibility.

Docking-based inverse virtual screening strategy for identification of novel protein targets for triclosan

Triclosan (TCS) is chemically designated as 5-chloro-2-(2,4-dichlorophenoxy) phenol and is considered as endocrine-disrupting chemical (EDC). The various diseases found due to exposure of TCS, have been linked with modulation of the human enoyl-acyl carrier protein-reductase (hER). However, the new protein targets for TCS other than hER, which are responsible for various diseases, are still unknown. In the present study, a bioinformatics approach was used to identify new possible targets for TCS. A text mining study was initially performed to understand the association of TCS in various biochemical processes. Discovery studio software 4.1 was used to carry out inverse virtual screening for 226 numbers of pathway proteins by docking study using CHARMm based docking tool, and twenty proteins were screened. CDOCKER energy values lower than −12.65 kcal/mol was considered for the screening of selected proteins. Three new proteins; Receptor-interacting protein 1 (RIP1), Apoptosis signal-regulating kinase 1 (ASK1) and B-cell lymphoma 2 (Bcl-2) from Apoptosis Signaling Pathway revealed best CDOCKER energy with triclosan which was −26.88, −23.34 and −22.96 kcal/mol respectively. The interaction of TCS with RIP1 and ASK1 were mostly hydrophobic; however, hydrogen bond type interaction was found in TCS/Bcl2 complex. Therefore, docking-based inverse virtual screening study suggests that TCS has other targets rather than hER, which can modulate various biochemical processes. The docking protocol was validated through evaluation of root-mean-square deviation (RMSD), key interaction score system (KISS) and the relationship between the docking energy and toxicity data available in ToxCast database. Low RMSD value (0.55 ˚A) and high KISS score (0.66) along with higher correlation (R2 = 0.9798) between docking affinity and toxicity indicated that docking protocol can be used to optimize the binding energetics.

New diazo-containing phenolic oximes: structural characterization, computationalstudies, and solvent extraction of Cu(II), Ni(II), and Zn(II) ions

In the current study, four new phenolic oxime ligands (HL1ox-HL4ox) containing diazo groups (-N$=$N-) were synthesized and used for liquid-liquid extraction of heavy metal ions [Cu(II), Ni(II), and Zn(II)]. The new compounds were characterized by analytical and spectroscopic methods. Solid-state structures of HL1ox-HL3ox were determined by single-crystal X-ray diffraction studies. Hirshfeld surface analysis of the compounds was performed to determine the contribution of different intermolecular contacts to the stability of the structures. The HL1ox-HL4ox ligands showed higher extraction performance for Cu(II) ion than Ni(II) and Zn(II) ions. The effect of pH on extraction capacity was investigated and the oxime compounds showed high extraction capacity at low pH values. The effects of the substitute groups (at the meta position of the phenol ring) on the extraction were investigated. Within the oxime ligands, the HL3ox compound exhibited higher extraction capacity for Cu(II) ions. The better extraction value of HL3ox is attributed to the weak hydrogen bond type interactions, which result in more stable complexes.

Highly sensitive SERS quantification of organophosphorous chemical warfare agents: A major step towards the real time sensing in the gas phase

A surface-enhanced Raman scattering (SERS)-based sensor was developed for the label-free real-time gas phase detection of dimethyl methylphosphonate (DMMP); a surrogate molecule of the G-series nerve agents which are of particular concern due to its extreme toxicity, persistence and previous deployment. The SERS platform was designed using simple elements (Au nano-particles) coated with a citrate layer, and a self-assembly procedure that yields near- optimum distances among the nanoparticles. The citrate coating acts as an effective trap of the target molecules on the immediate vicinity of the Au nanoparticle surface under ambient conditions by reversible hydrogen bonding type interactions. For the first time, we have been able to detect sub-ppm concentrations of DMMP in gas phase (130 parts-per-billion), as might be found on potential emergency scenarios. The high sensitivity, simple preparation and reusability of the SERS platforms developed in this work open up the way for immediate detection of chemical warfare agents in realistic scenarios.

Charge Fluctuations in the Dimer-Mott Insulating State of (rac-DM-EDT-TTF)2PF6

Low-dimensional molecular conductors are known to display various insulating ground states that result from significant electronic correlations, depending on the degree of dimerization. Of particular interest are intermediate systems where the interplay between dimer-Mott and charge-ordered phases is observed. Here we report an optical study of (rac-DM-EDT-TTF)2PF6, a weakly dimerized organic conductor that is based on the chiral DM-EDT-TTF donor molecule. Variable-temperature infrared reflectance spectra clearly demonstrate a quasi-one-dimensional response together with a metal–insulator phase transition at 110 K. Both the broadening of the charge-sensitive vibrational ν2 mode observed in Raman spectra and the strong EMV-activated ν3 mode in the reflectance spectra polarized in the stack direction suggest the charge fluctuations to develop in the insulating state. Significant modification of the hydrogen-bonding type interaction between the conducting DM-EDT-TTF layer and the PF6 anions is detected below 110 K. We suggest that the low-temperature insulating state in (rac-DM-EDT-TTF)2PF6 should be regarded as a coexistence of the dimer-Mott state and fluctuating charge-order.

Intermolecular contacts in the crystal structures of specifically varied halogen and protonic group substituted azines

A series of azines featuring differently halogen and protic group substituted pyridine, pyrimidine and pyridazine compounds have been synthesized and studied in terms of their crystal structures in order to develop a better understanding of the links between structural conditions and molecular packing behavior. Complemented by the structure results of related compounds known from the literature, intermolecular contact relationships connected to the present substance types were found, having potential use in future crystal engineering of similar compounds. This primarily involves the formation of N⋯I contacts aside from specific halogen⋯halogen and hydrogen bond type interactions.

Encapsulation of curcumin in cyclodextrin-metal organic frameworks: Dissociation of loaded CD-MOFs enhances stability of curcumin

Curcumin has been successfully encapsulated in cyclodextrin-metal organic frameworks (CD-MOFs) without altering their crystallinity. The interaction between curcumin and CD-MOFs is strong through hydrogen bond type interaction between the OH group of cyclodextrin of CD-MOFs and the phenolic hydroxyl group of the curcumin. Interestingly, dissolving the curcumin loaded CD-MOFs crystals in water results in formation of a unique complex between curcumin, γCD and potassium cations. In fact, the initial interaction between curcumin and CD-MOF is crucial for the formation of the latter. This new complex formed in alkaline media at pH 11.5 has maximum absorbance at 520nm and emittance at 600nm. Most importantly, the stability of curcumin in this complex was enhanced by at least 3 orders of magnitude compared to free curcumin and curcumin:γ-CD at pH 11.5. These results suggest a promising benign system of CD-MOFs, which can be used to store and stabilize curcumin for food applications.

Laccase from Aspergillus niger: A novel tool to graft multifunctional materials of interests and their characterization.

In the present study, we propose a green route to prepare poly(3-hydroxybutyrate) [(P(3HB)] grafted ethyl cellulose (EC) based green composites with novel characteristics through laccase-assisted grafting. P(3HB) was used as a side chain whereas, EC as a backbone material under ambient processing conditions. A novel laccase obtained from Aspergillus niger through its heterologous expression in Saccharomyces cerevisiae was used as a green catalyst for grafting purposes without the use of additional initiator and/or cross-linking agents. Subsequently, the resulting P(3HB)-g-EC composites were characterized using a range of analytical and imagining techniques. Fourier transform infrared spectroscopy (FT-IR) spectra showed an increase in the hydrogen-bonding type interactions between the side chains of P(3HB) and backbone material of EC. Evidently, X-ray diffraction (XRD) analysis revealed a decrease in the crystallinity of the P(3HB)-g-EC composites as compared to the pristine individual polymers. A homogeneous P(3HB) distribution was also achieved in case of the graft composite prepared in the presence of 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) (ABTS) as a mediator along with laccase as compared to the composite prepared using pure laccase alone. A substantial improvement in the thermal and mechanical characteristics was observed for grafted composites up to the different extent as compared to the pristine counterparts. The hydrophobic/hydrophilic properties of the grafted composites were better than those of the pristine counterparts.

An azo-azomethine ligand and its copper(II) complex: Synthesis, X-ray crystal structure, spectral, thermal, electrochemical and photoluminescence properties

In this study, a new azo-azomethine ligand, 4-[(E)-phenyldiazenyl]-2-[(E)-{[4-(propan-2-yl)phenyl]imino}methyl]phenol (HL) and its Cu(II) complex, [CuL2] were synthesized and characterized by the analytical and spectroscopic methods such as elemental analyses, FT-IR, 1H, 13C NMR and mass spectra. Molecular structures of the ligand and its Cu(II) complex were determined by single crystal X-ray diffraction studies. In the structure of the ligand, there is an intramolecular phenol-imine hydrogen bond (O1⋯N1) with a distance of 2.580(3)Å. There are also intermolecular hydrogen bond type interactions CH⋯O and CH⋯NN stabilizing the structure. The crystal structure of the Cu(II) was solved in the triclinic space group P1¯. In the structure of the complex, the Cu(II) ion is four coordinate bonded to two phenolate oxygens and two imine nitrogens of two ligand molecules in an approximate square-planar geometry. The Cu–O bonds are in trans configuration. Thermogravimetric data revealed that the Cu(II) complex is thermally more stable than the azo-azomethine compound (HL). Upon coordination with Cu(II) ion, both excitation and emission intensities of the ligand shifted to lower values.

Synthesis, X-ray structure analysis and density functional study of an unusual anhydrous 5,6-dimethylbenzo-1,3-imidazolium(H3) chloride

The heteroaromatic base 5,6-dimethylbenzo-1,3-imidazole (DMBI) proved to be a Brönsted base in an anhydrous ethanol solution, which contained fac,trans-[Ru(CO)3Cl2]2 at 55°C in air when the DMBI:Ru molar ratio was 2:1. The reaction produced colorless anhydrous single crystals of {(HDMBI)+Cl−}, C9H11ClN2, which were collected and analyzed using X-ray diffraction (XRD) techniques. A network of N–H⋯Cl hydrogen bond type interactions linking the protonated hetero-aromatic base to the chloride anions (bridging bases) stabilizes the crystal and mimics the N–H⋯Cl− interactions that play important roles in CCl channel biological systems. The shortest N⋯Cl contact distance and corresponding N–H⋯Cl angle are 3.073(3)Å and 173(3)°, respectively. The packing is also assisted by weaker C–H⋯Cl− hydrogen bond-type interactions and an extensive network of π⋯π stacking interactions involving HDMBI+ cations. Density functional calculations at the B3LYP/6-31G∗∗ and /6-311++G∗∗ levels for models of fragments of the crystal structure allowed for the evaluation of geometric parameters, hydrogen bond-type interaction formation energies, and infrared parameters for {(HDMBI)+Cl−} and {(HDMBI)+⋯Cl−⋯(HDMBI)+}.

The Unusual Monomer Recognition of Guanine-Containing Mixed Sequence DNA by a Dithiophene Heterocyclic Diamidine

DB1255 is a symmetrical diamidinophenyl-dithiophene that exhibits cellular activity by binding to DNA and inhibiting binding of ERG, an ETS family transcription factor that is commonly overexpressed or translocated in leukemia and prostate cancer [Nhili, R., Peixoto, P., Depauw, S., Flajollet, S., Dezitter, X., Munde, M. M., Ismail, M. A., Kumar, A., Farahat, A. A., Stephens, C. E., Duterque-Coquillaud, M., Wilson, W. D., Boykin, D. W., and David-Cordonnier, M. H. (2013) Nucleic Acids Res. 41, 125–138]. Because transcription factor inhibition is complex but is an attractive area for anticancer and antiparasitic drug development, we have evaluated the DNA interactions of additional derivatives of DB1255 to gain an improved understanding of the biophysical chemistry of complex function and inhibition. DNase I footprinting, biosensor surface plasmon resonance, and circular dichroism experiments show that DB1255 has an unusual and strong monomer binding mode in minor groove sites that contain a single GC base pair flanked by AT base pairs, for example, 5′-ATGAT-3′. Closely related derivatives, such as compounds with the thiophene replaced with furan or selenophane, bind very weakly to GC-containing sequences and do not have biological activity. DB1255 is selective for the ATGAT site; however, a similar sequence, 5′-ATGAC-3′, binds DB1255 more weakly and does not produce a footprint. Molecular docking studies show that the two thiophene sulfur atoms form strong, bifurcated hydrogen bond-type interactions with the G-N-H sequence that extends into the minor groove while the amidines form hydrogen bonds to the flanking AT base pairs. The central dithiophene unit of DB1255 thus forms an excellent, but unexpected, single-GC base pair recognition module in a monomer minor groove complex.

Ruthenium complexes as nitric oxide donors and scavengers. Synthesis and crystal and molecular structure for mer,trans-[RuIICl3(NO+)(N-4-ethylisonicotinate)2], and mer,trans-[RuIIICl3(N-CH3CN)(N-4-ethylisonicotinate)2] as obtained via UV-photochemical activation of {RuII(NO+)}3+-core parent complex in acetonitrile solution

The synthesis of mer,trans-[RuIICl3(NO+)(EINT)2] (EINT=N-4-ethylisonicotinate), 1, was achieved by carefully working under ultrapure nitrogen atmosphere, by mixing RuIIICl3(NO)·H2O and EINT (1:2M ratio in anhydrous ethanol) under stirring and at reflux conditions. Single crystals of 1 suitable for X-ray diffraction XRD techniques were also obtained by slow evaporation of solvent under nitrogen from the mother alcoholic solution. The IR spectrum of the solid (KBr matrixes) showed the characteristic sharp and intense band (1866cm−1) relevant to the N–O stretching vibration for the nitrosyl ligand (RuIINO+ core). Then, on irradiating at 25°C a solution of 1 in ultrapure acetonitrile (contained in quartz cuvette) under an UV source (250 throughout 366nm) a color turning from pink to yellow occurred. After a prolonged irradiation (250nm for at least 6h) the cuvette (yellow solution) was stored in a dry nitrogen atmosphere and allowed to slowly concentrate via spontaneous solvent evaporation. The solution produced brown crystals as parallelepipeds, suitable for XRD data collection, that belong to the monoclinic system, C2/c space group, and the molecular structure (mer,trans-[RuIICl3(N-NCCH3)(EINT)2], 2) consists of complex molecules that are mostly paired via stacking interactions that involve the pyridine moiety and through (ethyl)CH3⋯Cl(Ru), (pyridine)CH⋯Cl(Ru) and (ethyl)CH3⋯O(C) hydrogen bond type interactions. The crystals of the parent nitrosyl complex belong to the orthorhombic Pccn space group and the complex molecule has three chlorido ligands in the equatorial positions and two EINT ligands in the axial positions. The nitrosyl ligand occupy two positions that are trans to each other and have half occupancy each.