Novel nicotinic acetylcholine receptor agonists containing carbonyl moiety as a hydrogen bond acceptor

A novel series of α4β2 nAChR agonists lacking common pyridine or its bioisosteric heterocycle have been disclosed. Essential pharmacophoric elements of the series are exocyclic carbonyl moiety as a hydrogen bond acceptor and secondary amino group within diaza- or azabicyclic scaffold. Computer modeling studies suggested that molecular shape of the ligand also contributes to promotion of agonism. Proof of concept for improving working memory performance in a novel object recognition task has been demonstrated on a representative of the series, 3-propionyl-3,7-diazabicyclo[3.3.0]octane (34).     

Coordination polymers derived from a bis-pyridyl-bis-amide ligand: Supramolecular structural diversities and anion binding properties

Six new coordination polymers namely [{Cu(μ-L1)(CH₃COO)₂}]_∝1a, [{Cu(μ-L1)₂(CH₃COO)₂]_∝1b, [{Cu(μ-L1)₂(H₂O)₂}(NO₃)₂]_∝2, [{Cu(μ-L1)₂(H₂O)₂}(ClO₄)₂]_∝3, [{Cu(μ-L1)(H₂O)₂(μ-SO₄)}·3H₂O]_∝4a and [{Cu(μ-L1)₂SO₄}·X]_∝4b (L1 = N,N′-bis-(3-pyridyl)terephthalamide) have been synthesized. Single crystal structures of five coordination polymers namely 1a, 2-4b and the free ligand L1 are discussed in the context of the effect of conformation dependent ligating topology of the ligands, hydrogen bonding backbone, counter anions on the resultant supramolecular structures observed in these coordination polymers. It was revealed from the single crystal X-ray structure analysis that conformation dependent ligating topology of the bis-amide ligand L1, counter anion’s ligating strength dependent metal: ligand ratio, hydrogen bonding ability of the ligand as well as counter anions are responsible for the formation of 1D zigzag, 1D looped chain, 2D corrugated sheet in 1a, 2-3, 4a−4b, respectively. By following in situ coordination polymer crystallization technique, anion binding and separation studies have also been performed; nitrate anion has been separated as neat coordination polymer crystals from a complex mixture of anions.     

Triaminoguanidine derivatives as supports to construct magnetic assemblies: Synthesis and characterization of trinuclear nickel(II) complexes

The synthesis of two nickel(II) complexes based on a central bridging triaminoguanidine scaffold and a capping ligand per metal ion is reported. When 2,2′-bipyridine (bipy) is utilized as co-ligand the complex [Ni₃L^Br(bipy)₃(H₂O)₃]NO₃ · 9H₂O · 1.5DMF (1) is obtained which crystallizes in the hexagonal space group P6₃/m. Complex 1 shows an interesting supramolecular structure pattern with alternating hydrophilic and hydrophobic layers characterized by extensive hydrogen-bonding and π-π-stacking, respectively. With 2,4,6-(2-pyridyl)-1,3,5-triazine (tptz) as capping ligand, complex [Ni₃L^Br(tptz)₃]ClO₄ · 7H₂O · 1.5DMF (2) is obtained. The magnetic susceptibility data can be fitted using an equilateral triangle model () with an isotropic coupling constant of J=-31.0±0.6 for 1 and for 2.     

The formation of hydrogen bond in the proximal heme pocket of HemAT-Bs upon ligand binding

HemAT-Bs is the heme-based O(2) sensor responsible for aerotaxis control in Bacillus subtilis. In this study, we measured the time-resolved resonance Raman spectra of full-length HemAT-Bs wild-type (WT) and Y133F in the deoxy form and the photoproduct after photolysis of CO-bound form. In WT, the nu(Fe-His) band for the 10 ps photoproduct was observed at higher frequency by about 2 cm(-1) compared with that of the deoxy form. This frequency difference is relaxed in hundreds of picoseconds. This time-dependent frequency shift would reflect the conformational change of the protein matrix. On the other hand, Y133F mutant did not show such a substantial nu(Fe-His) frequency shift after photolysis. Since a hydrogen bond to the proximal His induces an up-shift of the nu(Fe-His) frequency, these results indicate that Tyr133 forms a hydrogen bond to the proximal His residue upon the ligand binding. We discuss a functional role of this hydrogen bond formation for the signal transduction in HemAT-Bs.     

Synthesis and spectroscopic investigation of new nickel(II) complexes with the open chain asymmetric tetraamine 1,4,7,11-tetraazaundecane: Crystal structure of the square-planar complex

The synthesis of the X-ray structurally characterized square-planar [Ni(2,2,3-tet)](ClO₄)₂ (2) from the [Ni(2,2,3-tet)(NH₃)(H₂O)]Cl₂ · 1/2EtOH · H₂O (1), was based on their inter-conversion. The two sets of trans Ni-N bonds display similar to each other lengths (1.900 & 1.910 and 1.996 & 1.966 Å). The relaxation times (T_1,2) of water protons and NMR experiments indicate relatively slow octahedral-sq-planar equilibrium, while in the aqueous solutions of 1, the sq-planar species appear to display a structure analogous to 2 in solution. The square planar geometry, the hydrophilicity of the complex and the asymmetry of the ligand generate the conditions for catalytic site formation.     

Influence of the counter anion and solvent in the structure of copper derivatives with the 2,3-bis(2-pyridyl)pyrazine ligand

Several compounds have been isolated from the reaction between different copper bis(acetylacetonato) derivatives and the potentially bridging ligand 2,3-bis(2-pyridyl)pyrazine (bppz). A compound of formula [Cu(tfacac)₂(bppz)] (1) is obtained when the substituted trifluoromethylacetylacetonato is used. The use of different anions and the unsubstituted acetylacetonato give rise to new derivatives of general formula [{Cu(acac)}₂(μ-bppz)₂]X₂ (X⁻ = BF₄⁻, 2; PF₆⁻, 3; BPh₄⁻, 4). In these compounds the bppz ligand is acting as a bridge by chelating one copper atom and bonding monodentate a second copper atom. The presence of anions with different coordination abilities introduces variations in the copper environment and geometry. When the non-coordinating tetraphenylborate is used different compounds depending on the nature of the solvent are obtained. The dimer 4 was isolated from a methanol/chloroform mixture, while in the absence of chloroform the monomeric compound of formula [Cu(acac)(bppz)(ROH)](BPh₄)·ROH (ROH = MeOH, 5) was obtained. When ethanol was used instead of methanol the analogous derivative 6 (R = EtOH) was isolated. Both species show a mononuclear structure with the copper atom five-coordinated by the chelating acac and bppz ligands and one hydroxo group occupying the apical position. A similar environment for the copper appears in [Cu(tfacac)(bppz)(MeOH)](BPh₄), 7, which shows a dimeric structure through hydrogen bonds interactions. The magnetic susceptibility data of the dimeric compounds show very weak antiferromagnetic interactions between the copper atoms, an expected fact since the bridging bppz ligand is not planar but the monodentate pyridine is more or less perpendicular to the other two aromatic rings, precluding the spin exchange via the π ligand electrons.     

Successful prediction of the hydrogen bond network of the 3-oxo-12alpha-hydroxy-5beta-cholan-24-oic acid crystal from resolution of the crystal structure of deoxycholic acid and its three 3,12-dihydroxy epimers

Crystal structures of p-xylene-crystallized deoxycholic acid (3alpha,12alpha-dihydroxy-5beta-cholan-24-oic acid) and its three epimers (3beta,12alpha-; 3alpha,12beta-; and 3beta,12beta-) have been solved. Deoxycholic acid forms a crystalline (P21) complex with the solvent with a 2:1 stoichiometry whereas crystals of the three epimers do not form inclusion compounds. Crystals of the 3beta,12beta-epimer are hexagonal, whereas the 3alpha,12beta-and 3beta,12alpha-epimers crystallize in the P2(1)2(1)2(1) orthorhombic space group. The three hydrogen bond sites (two hydroxy groups, i. e. O3-H, and O12-H, and the carboxylic acid group of the side chain, O24bO24a-H) simultaneously act as hydrogen bond donors and acceptors. The hydrogen bond network in the crystals was analyzed and the following sequences have been observed: two chains (abcabc... or acbacb... ) and two rings (abc or acb), which constitute a complete set of all the possible sequences which can be drawn for an intermolecular hydrogen bond network formed by three hydrogen bond donor/acceptor sites forming crossing hydrogen bonds. The orientation of O3-H (alpha or beta) determines the sequence of the acceptor and the donor groups involved in the pattern: O24a --> O12 --> O3 --> O24b when it is alpha and O24a --> O3 --> O12--> O24B when it is beta. These observations were used to predict the hydrogen bond network of p-xylene-crystallized 3-oxo,12alpha-hydroxy-5beta-cholan-24-oic acid. This compound has two hydrogen bond donor and three potential hydrogen bond acceptor sites. According to the previous sequence set, this compound should crystallize in the monoclinic P21 system, should form a complex with the solvent, O24b should not participate in the hydrogen bond network, and the chain sequence O24a --> O12 --> O3 would be followed. All predictions were confirmed experimentally.     

2-Mercapto-1-t-butylimidazolyl as a bridging ligand: Synthesis and structural characterization of nickel and palladium paddlewheel complexes

Nickel and palladium paddlewheel complexes that feature 2-mercapto-1-t-butylimidazolyl (mim^But) bridging ligands, namely Ni₂[mim^But]₄ and Pd₂[mim^But]₄, have been synthesized and structurally characterized by X-ray diffraction. Since the mim^But ligand bridges in an asymmetric manner via a sulfur and nitrogen donor, paddlewheel compounds of the type M₂[mim^But]₄ may exist as isomers that are distinguished by the relative orientations of the ligands. In this regard, the (4,0)-Ni₂[mim^But]₄ and trans-(2,2)-Ni₂[mim^But]₄ isomers have been isolated for the nickel system, while the (4,0)-Pd₂[mim^But]₄ and (3,1)-Pd₂[mim^But]₄ isomers have been isolated for the palladium system.     

Studies on the structure and properties of nickel complexes in a set of amide-based 13-membered macrocyclic ligands

This work reports a systematic investigation to understand the structural, spectroscopic and redox properties of Ni(II) ion in a set of 13-membered amide-based macrocyclic ligands. Four macrocyclic ligands containing e⁻-donating/withdrawing substituents and their Ni(II) complexes have been synthesized and characterized. Structural analysis shows that the macrocyclic ligands create a square-planar environment and nicely accommodate the Ni(II) ion. Electrochemical results suggest that the complexes are capable of undergoing metal-centered oxidation. The electron-donating substituents on ligand lowers the redox potentials and better stabilizes the +3 oxidation state of metal. The electrochemically generated Ni^III species are shown to have rich spectroscopic features. For majority of complexes, the oxidized species are concluded to be Ni^III by their anisotropic EPR spectra typical for Ni^III ion in square-planar geometry. The absorption and EPR spectra for nickel complex bearing an -OMe group on the ligand; however, suggest a Ni(II) complex with a ligand-based radical.     

An unexpected cubane-like nickel(II) tetranuclear complex bridged by the anion of 2-hydroxymethylbenzimidazole: Crystal structure and magnetic properties

A novel tetranuclear cubane-like complex [Ni₄(hbzim)₄(N₃)₄(mal)₂(CH₃OH)(H₂O)] (Hhbzim = 2-hydroxymethylbenzimidazole, mal = 4-methoxyaniline) has been synthesized and characterized structurally as well as magnetically. The structure analyses reveal that this complex consists of a Ni₄O₄ cubane core and the different coordinate environments of the nickel(II) ions result in a cubane structure with differing Ni-Ni distances and Ni-O-Ni angles. The magnetic properties of this complex have been interpreted by employing one-J and two-J model. The results show that ferromagnetic interaction dominates in the complex.     

Hydrogen-bond assisted stabilization of the less favored conformation of a tridentate Schiff base ligand in dinuclear nickel(II) complex: An experimental and theoretical study

The Schiff base ligand, HL (2-[1-(3-methylamino-propylimino)-ethyl]-phenol), the 1:1 condensation product of 2-hydroxy acetophenone and N-methyl-1,3-diaminopropane, has been synthesized and characterized by X-ray crystallography as the perchlorate salt [H₂L]ClO₄ (1). The structure consists of discrete [H₂L]⁺ cations and perchlorate anions. Two dinuclear Ni^II complexes, [Ni₂L₂(NO₂)₂] (2), [Ni₂L₂(NO₃)₂] (3) have been synthesized using this ligand and characterized by single crystal X-ray analyses. Complexes 2 and 3 are centrosymmetric dimers in which the Ni^II ions are in distorted fac- and mer-octahedral environments, respectively, bridged by two μ₂-phenolate ions of deprotonated ligand, L. The plane of the phenyl rings and the Ni₂O₂ basal plane are nearly coplanar in 2 but almost perpendicular in 3. We have studied and explained this different behavior using high level DFT calculations (RI-BP86/def2-TZVP level of theory). The conformation observed in 3, which is energetically less favorable, is stabilized via intermolecular non-covalent interactions. Under the excitation of ultraviolet light, characteristic fluorescence of compound 1 was observed; by comparison fluorescence intensity decreases in case of compound 3 and completely quenched in compound 2.     

Coordination chemistry of the heterotopic 1,2-phenylenebis(thio)diacetic acid ligand: Rhodium(I), palladium(II) and nickel(II) complexes

Starting from the heterotopic multidentate ligand 1,2-phenylenebis(thio)diacetic acid (1), cis-rac-[PdCl₂{1,2-(HOOCCH₂S)₂C₆H₄-κ²S,S′}] (2), cis-rac-[Rh{1,2-(HOOCCH₂S)₂C₆H₄-κ²S,S′}(cod)]BF₄ (3) and cis-rac-[Ni{1,2-(OOCCH₂S)₂C₆H₄-κ⁴O,O′S,S′}{cis-(C₃H₄N₂)}₂] (4) were prepared and characterised by X-ray diffraction and conventional spectroscopic techniques. Compounds 1-4 show extensive hydrogen-bonded networks (XH?O, X = O, N) in the solid state.     

Different coordination modes of Hdipic and dipic ligands to nickel(II) ions in a same environment (dipic = 2,6-pyridinedicarboxylate, dipicolinate)

Two new nickel(II) complexes of the composition [Ni(cyclam)(Hdipic)₂] · 2H₂O (1) and [Ni(cyclam)(H₂O)₂][Ni(dipic)₂] · 2.5H₂O (2) (cyclam = 1,4,8,11-tetraazacyclotetradecane) have been prepared and structurally characterized by a combination of analytical, spectroscopic, thermogravimetric, and crystallographic methods. The structure of 1 shows that the central nickel(II) ion is coordinated axially by two monodentate Hdipic ligands. The discrete neutral complex 1 further extends its structure by hydrogen bonding interactions to form a one-dimensional supramolecule. The structure of 2 consists of two independent nickel(II) centers. Water molecules instead of dipic ligands prefer to coordinate to the Ni1 ion forming a divalent cation [Ni(cyclam)(H₂O)₂]²⁺. Two dipic ligands coordinate to the second Ni2 ion forming a divalent anion [Ni(dipic)₂]²⁻. The divalent cations and anions are charge-balanced, resulting in a molecular salt. The divalent cations and anions are interconnected by multiple types of hydrogen bonding interactions.     

One-dimensional nickel and cobalt phthalate coordination polymers incorporating the kinked dipodal organodiimine 4,4′-dipyridylamine: Hydrothermal synthesis, structural characterization and thermal properties

Hydrothermal synthesis has afforded a family of three structurally related metal phthalate (pht) 1-D coordination polymers incorporating the kinked dipodal organodiimine 4,4′-dipyridylamine (dpa), with a general formulation of [L₂M(dpa)₂M(H₂O)₄] · H₂O (L = pht, M = Co, 1, M = Ni, 2; L = 4-methylphthalate (4-mpht), M = Co, 3). Single crystal X-ray diffraction of 1 and 2 revealed the presence of one-dimensional (1-D) polymeric chains consisting of [M(H₂O)₄]²⁺ and [M(pht)₂]²⁻ subunits linked through dpa tethers. These chains in turn conjoin into pseudo 2-D layers and 3-D networks via extensive supramolecular hydrogen bonding pathways. An extremely similar structure is observed for 3 despite the presence of the bulkier methyl group substituent. 1-3 were further characterized via infrared spectroscopy and elemental and thermogravimetric analysis. 1-3 represent the first dicarboxylate coordination polymers incorporating dpa tethering ligands.     

Strong and weak hydrogen bonds in protein-ligand complexes of kinases: a comparative study

Strong and weak hydrogen bonds between protein and ligand are analyzed in a group of 233 X-ray crystal structures of the kinase family. These kinases are from both eukaryotic and prokaryotic organisms. The dataset comprises of 44 sub-families, out of which 35 are of human origin and the rest belong to other organisms. Interaction analysis was carried out in the active sites, defined here as a sphere of 10 A radius around the ligand. A majority of the interactions are observed between the main chain of the protein and the ligand atoms. As a donor, the ligand frequently interacts with amino acid residues like Leu, Glu and His. As an acceptor, the ligand interacts often with Gly, and Leu. Strong hydrogen bonds N-H...O, O-H...O, N-H...N and weak bonds C-H...O, C-H...N are common between the protein and ligand. The hydrogen bond donor capacity of Gly in N-H...O and C-H...O interactions is noteworthy. Similarly, the acceptor capacity of main chain Glu is ubiquitous in several kinase sub-families. Hydrogen bonds between protein and ligand form characteristic hydrogen bond patterns (supramolecular synthons). These synthon patterns are unique to each sub-family. The synthon locations are conserved across sub-families due to a higher percentage of conserved sequences in the active sites. The nature of active site water molecules was studied through a novel classification scheme, based on the extent of exposure of water molecules. Water which is least exposed usually participates in hydrogen bond formation with the ligand. These findings will help structural biologists, crystallographers and medicinal chemists to design better kinase inhibitors.     

The self-diffusion and hydrogen bond interaction in neat liquid alkanols: a molecular dynamic simulation study

Self-diffusion of methanol, ethanol, 1-propanol and 2-propanol has been studied by molecular dynamics simulation in the temperature range between the melting pressure curve and 478 K at pressures up to 300 MPa. The simulation results on self-diffusion of methanol, ethanol and 2-propanol (for 2-propanol, at high temperatures) agree well with experiment, which suggests that the simulation method is a powerful tool to obtain self-diffusion coefficients over wide range of temperature and pressure, under which it is rather difficult for experiments. The local structures of methanol, ethanol and 2-propanol are investigated by calculating the radial distribution functions, H-bond numbers, coordination numbers and the ratios of H-bond number divided by coordination number. The correlation between self-diffusion and structural properties, and the influence of temperature and pressure on them are discussed. The degree of forming H-bond space network in methanol, ethanol and water is higher than that in 2-propanol, and they are all higher than those in ammonia and methylamine. The simulation results demonstrate that the effect of hydrogen bonding on the translational dynamics in methanol and ethanol is more pronounced than that in 2-propanol.     

Unexpected reactivity resulting from modifications of the ligand periphery: Synthesis, structure, and spectroscopic properties of iron complexes of new tripodal N-heterocyclic carbene (NHC) ligands

The chelating ligand tris-[2-(3-aryl-imidazol-2-ylidene)ethyl]amine (TIMEN^R, R = aryl = 2,6-xylyl (xyl), mesityl (mes)) has provided access to reactive transition metal complexes. Here, two new tripodal N-heterocyclic carbene ligands of the TIMEN^R system (R = aryl = tolyl (tol), 3,5-xylyl (3,5xyl)), featuring sterically less demanding aryl substituents were synthesized. With these ligands, Fe(II) precursor complexes could be obtained, namely [(TIMEN^tol)Fe](BF₄)₂ (3) and [(TIMEN^3,5xyl)Fe(CH₃CN)](PF₆)₂ (7), which showed unexpected reactivity upon reduction. Treatment of the compounds with sodium amalgam yield the tris- and bis-metallated products, [(TIMEN^tol∗∗∗)Fe] (4) and [(TIMEN^3,5xyl∗∗)Fe] (8), respectively. While the Fe(III) complex 4 is relatively inert towards oxygen, the Fe(II) complex 8 is prone to oxidation. This oxidation of 8 can readily be observed in chlorinated solvents, producing the Fe(III) complex [(TIMEN^3,5xyl∗∗)Fe](PF₆) (9). All new ligand imidazolium precursors and metal complexes were characterized by single crystal X-ray structure determination.     

Generation of hydrogen peroxide,superoxide anion and the hydroxyl free radical from polyphenols and active benzene metabolites: Their possible role in mutagenesis

Benzene is strongly suspected of being an animal and human carcinogen, but the mechanisms by which it induces tumors of lymphoid and hematopoietic organs are unknown. Production of active oxygen species from benzene metabolites [hydroquinone (HQ), catechol and 1,2,4-benzenetriol (1,2,4-BT) and related polyphenols (resorcinol, pyrogallol and phloroglucinol) are investigated. Pyrogallol and 1,2,4-BT can produce H₂O₂, O ₂ ^– and^·OH simultaneously, and have powerful mutagenic potential. Resorcinol and phloroglucinol cannot produce all of the active oxygen species, and show no mutagenic effects. Catechol can produce H₂O₂, but cannot produce O ₂ ^– and^·OH, and has no mutagenic activity. These data strongly support the hypothesis that benzene metabolites can cause mutagenicity via the generation of oxygen radicals. Although HQ produces H₂O₂ only, and less than produced by pyrogallol and 1,2,4-BT, the mutagenicity of HQ is higher. The results indicate that HQ may act via another mechanism to cause mutagenicity. In the presence of trace metal ions, the reactivity of polyphenols is increased. The biological significance of these phenomena are investigated and discussed.     

A tridentate bis(pyrazolyl) ligand binds to Cu(II), without using the pyrazole group: a very unusual coordination mode of the ligand Hbdmpb, 1,3-bis(3,5-dimethylpyrazol-1-yl)-2-butanoic acid

A new pyrazole-based ligand, namely 1,3-bis(3,5-dimethylpyrazol-1-yl)-2-butanoic acid (Hbdmpb) was synthesised together with its copper complex Na[Cu(bdmpb)₂(OOCCH₃)H₂O] · 4H₂O. Both the free ligand and its Cu compound were fully characterised and their crystal structures were determined by X-ray analysis. The free-ligand molecular structure is uneventful. The Cu compound is highly unusual, as the pyrazole nitrogen atoms do not bind to the Cu ion. The copper(II) ion is coordinated by four nearly coplanar oxygen atoms from two dehydronated ligands bdmpb (CuO(1a) 1.942(4), CuO(1b) 1.933(4) Å), a monodentate acetate group (CuO(1) 1.927(3) Å) and a water molecule (CuO(1w) 1.937(4) Å). The nitrogen atoms of the pyrazole rings do not coordinate to the metal center, but instead are involved in strong intramolecular hydrogen bonds. The coordinated water molecule is strongly H-bonded to two pyrazole N atoms from two bdmpb ligands (N(12a) ? HO(1w) 2.762(7), N(12b) ? HO(1w) 2.774(7) Å). The other two pyrazole N atoms with a lone pair are hydrogen-bonded to water molecules in the lattice (N(22a) ? HO(2w) 2.763(7), N(22b) ? HO(6w) 2.892(7) Å). The sodium ion is six-coordinated by the oxygen atom O(2) of the acetato ligand and by five water molecules. The EPR spectrum recorded in the solid state shows a characteristic signal for an axial anisotropic S = 1/2 species. The spectrum recorded in methanol glass confirms the absence of the coordination of pyrazole nitrogen atoms to the copper centers.     

The use of the borocaptate anion as a ligand. Synthesis and X-ray crystal structure of pentaammine (1-thiolato-closo-undecahydrododecaborane)ruthenium(III) dihydrate

The complex [Ru(SB₁₂H₁₁)(NH₃)₅]·2H₂O has been prepared by the reaction of Cs₂B₁₂H₁₁SH with [RuCl(NH₃)₅]Cl₂ in aqueous solution. The complex represents the first reported example of the borocaptate anion acting as a ligand. The structure of the complex has been determined by single crystal X-ray diffraction analysis. The crystal parameters are monoclinic, space group P2₁/c, A = 8.056(1), B = 14.240(2), C = 15.172(2) Å, β=98.48° and Z = 4. The ruthenium atom has a distorted octahedral coordination. The distortion is probably due to the high (3⁻) charge and the large bulk of the borocaptate ligand. These features can also be observed in the spectroscopic properties of the complex.