Semiconductive 2D arrays of pancake-bonded oligomers of partially charged TCNQ radicals.

Multicentre two-electron (mc/2e or 'pancake bonding') bonding between 7,7,8,8-tetra-cyano-quinodi-methane (TCNQ) radical anions was studied on its 14 novel salts with planar organic cations. The formal charges of the TCNQδ- moieties are -1/2 and -2/3, and they form mc/2e bonded dimers, trimers and tetramers which are further stacked into extended arrays. Multicentre bonding within these oligomers is characterized by short interplanar separations of 2.9-3.2 Å; distances between the oligomers are larger, typically >3.3 Å. The stacks are laterally connected by C-H⋯N hydrogen bonding, forming 2D arrays. The nature of mc/2e bonding is characterized by structural, magnetic and electrical data. The compounds are found to be semiconductors, and high conductivity [10-2 (Ω cm)-1] correlates with short interplanar distances between pancake-bonded oligomers.

Charge density studies of multicentre two-electron bonding of an anion radical at non-ambient temperature and pressure.

The variation of charge density of two-electron multicentre bonding (pancake bonding) between semi-quinone radicals with pressure and temperature was studied on a salt of 5,6-di-chloro-2,3-di-cyano-semi-quinone radical anion (DDQ) with 4-cyano-N-methyl-pyridinium cation (4-CN) using the Transferable Aspheric Atom Model (TAAM) refinement. The pancake-bonded radical dimers are stacked by non-bonding π-interactions. With rising pressure, the covalent character of interactions between radicals increases, and above 2.55 GPa, the electron density indicates multicentric covalent interactions throughout the stack. The experimental charge densities were verified and corroborated by periodic DFT computations. The TAAM approach has been tested and validated for atomic resolution data measured at ambient pressure; this work shows this approach can also be applied to diffraction data obtained at pressures up to several gigapascals.

The substrate selectivity of the two homologous SGNH hydrolases from Streptomyces bacteria: Molecular dynamics and experimental study.

Two extracellular enzymes of the SGNH hydrolase superfamily reveal highly homologous 3D structures, but act on different substrates; one is a true phospholipase A1 from Streptomyces albidoflavus (SaPLA1, EC: 3.1.1.32, PDB code: 4HYQ), whereas the promiscuous enzyme from Streptomyces rimosus (SrLip, EC: 3.1.1.3, PDB code: 5MAL) exhibits lipase, phospholipase, esterase, thioesterase, and Tweenase activities. To get insight into binding modes of phospholipid and triglyceride substrates in both enzymes and understand their chain-length preferences, we opted for computational approach based on in silico prepared enzyme-substrate complexes. Docking procedure and molecular dynamics simulations at microsecond time scale were applied. The modelled complexes of SaPLA1 and SrLip enzymes revealed substrate accommodation: a) the acyl-chain attached to sn-1 position fits into the hydrophobic pocket, b) the acyl-chain attached to sn-2 position fits in the hydrophobic cleft, whereas c) the sn-3 bound acyl chain of the triglyceride or polar head of the glycerophospholipid fits into the binding groove. Moreover, our results pinpointed subtle amino acid differences in the hydrophobic pockets of these two enzymes which accommodate the acyl chain attached to sn-1 position of glycerol to be responsible for the chain length preference. Slight differences in the binding grooves of SaPLA1 and SrLip, which accommodate the acyl chain attached to sn-3 position are responsible for exclusive phospholipase and both phospholipase/lipase activities of these two enzymes, respectively. The results of modelling correlate with the experimentally obtained kinetic parameters given in the literature and are important for protein engineering that aims to obtain a variant of enzyme, which would preferably act on the substrate of interest.

Towards understanding π-stacking interactions between non-aromatic rings.

The first systematic study of π interactions between non-aromatic rings, based on the authors' own results from an experimental X-ray charge-density analysis assisted by quantum chemical calculations, is presented. The landmark (non-aromatic) examples include quinoid rings, planar radicals and metal-chelate rings. The results can be summarized as: (i) non-aromatic planar polyenic rings can be stacked, (ii) interactions are more pronounced between systems or rings with little or no π-electron delocalization (e.g. quinones) than those involving delocalized systems (e.g. aromatics), and (iii) the main component of the interaction is electrostatic/multipolar between closed-shell rings, whereas (iv) interactions between radicals involve a significant covalent contribution (multicentric bonding). Thus, stacking covers a wide range of interactions and energies, ranging from weak dispersion to unlocalized two-electron multicentric covalent bonding ('pancake bonding'), allowing a face-to-face stacking arrangement in some chemical species (quinone anions). The predominant interaction in a particular stacked system modulates the physical properties and defines a strategy for crystal engineering of functional materials.

Pancake Bonding in π-Stacked Trimers in a Salt of Tetrachloroquinone Anion.

The crystal structure of [4-damp])2 [Cl4 Q]3 (4-damp=4-dimethylamino-N-methylpyridinium, Cl4 Q=tetrachloroquinone) salt is built up from slipped columnar stacks of quinoid rings composed of closely bound trimers with the intra-trimer separation distance of 2.84 Šand total charge of -2 whereas the inter-trimer distance is 3.59 Å. The individual rings exhibit partial negative charges that are distributed unevenly among the three Cl4 Qs in the trimer. The strong interactions within a trimer (Cl4 Q)32- have a partially covalent character with two-electron/multicentered bonding, that is extended over three rings, plausibly termed as "pancake bonding". The electron pairing within this multicentre bond leads to the fact that the crystals are diamagnetic and act as insulators. The studies of the structure and nature of bonding are based on X-ray charge density analysis and density functional theory.

Catalytic Dyad in the SGNH Hydrolase Superfamily: In-depth Insight into Structural Parameters Tuning the Catalytic Process of Extracellular Lipase from Streptomyces rimosus.

SrLip is an extracellular enzyme from Streptomyces rimosus (Q93MW7) exhibiting lipase, phospholipase, esterase, thioesterase, and tweenase activities. The structure of SrLip is one of a very few lipases, among the 3D-structures of the SGNH superfamily of hydrolases, structurally characterized by synchrotron diffraction data at 1.75 Å resolution (PDB: 5MAL ). Its crystal structure was determined by molecular replacement using a homology model based on the crystal structure of phospholipase A1 from Streptomyces albidoflavus (PDB: 4HYQ ). The structure reveals the Rossmann-like 3-layer αßα sandwich fold typical of the SGNH superfamily stabilized by three disulfide bonds. The active site shows a catalytic dyad involving Ser10 and His216 with Ser10-OγH···NεHis216, His216-NδH···O═C-Ser214, and Gly54-NH···Oγ-Ser10 hydrogen bonds essential for the catalysis; the carbonyl oxygen of the Ser214 main chain acts as a hydrogen bond acceptor ensuring the orientation of the His216 imidazole ring suitable for a proton transfer. Molecular dynamics simulations of the apoenzyme and its complex with p-nitrophenyl caprylate were used to probe the positioning of the substrate ester group within the active site and its aliphatic chain within the binding site. Quantum-mechanical calculations at the DFT level revealed the precise molecular mechanism of the SrLip catalytic activity, demonstrating that the overall hydrolysis is a two-step process with acylation as the rate-limiting step associated with the activation free energy of ΔG⧧ENZ = 17.9 kcal mol-1, being in reasonable agreement with the experimental value of 14.5 kcal mol-1, thus providing strong support in favor of the proposed catalytic mechanism based on a dyad.

An axial chirality and disorder of positional isomers in a crystal of highly cytotoxic 3-acetyl-1,3-bis(2-chloro-4-nitrophenyl)-1E-triazene.

Biologically active 4-nitro-substituted 1,3-diaryltriazene, a chemical analogue of 1,3-bis(4'-amidinophenyl)-triazene-berenil®, belongs to the novel, chemically modified class of potent antitumor agents. Its structural characterization by X-ray analysis and 1H NMR spectroscopy is performed to determine molecular overall conformation in view of its possible interaction to DNA.

A novel type of coordination mode of chloranilic acid leading to the formation of polymeric coordination ribbon in the series of mixed-ligand copper(II) complexes with 1,10-phenanthroline.

A series of four novel mixed-ligand complexes of copper(II) with 3,6-dichloro-2,6-dihydroxy-1,4-benzoquinone (chloranilic acid) and 1,10-phenanthroline was prepared and characterised by X-ray structure analysis and IR spectroscopy. Three complexes exhibit square-pyramidal coordination, whereas one exhibits octahedral coordination. The ligand 1,10-phenanthroline acts in a bidentate chelating mode with N,N-metal binding. The chloranilate dianion coordinates to the Cu(II) atom in a terminal bidentate ortho-quinone-like mode, forming a mononuclear complex species. However, in one structure a novel type of coordination mode of chloranilate is observed. In addition to the bidentate mode, a monodentate bridging mode through a carboxy oxygen of a symmetry-related dianion leads to the formation of polymeric coordination ribbon. The crystal packing of penta-coordinated species, in addition to hydrogen bonding, involves less common stacking interactions of chelate rings with the π-systems of the ligands.

Spin-coupling in dimers of 2,3-dicyano-5,6-dichlorosemiquinone radical anions in the crystalline state.

A crystal engineering approach is used to stabilize a radical anion in the crystalline state and to modulate the separation distance within π-stacks of anion radicals. Alkali metal salts of 2,3-dicyano-5,6-dichlorosemiquinone (C8Cl2N2O2, DDQ∙- radical anions were prepared and their crystal structures determined: LiDDQ·2H2O·(CH3)2CO, RbDDQ·2H2O and CsDDQ·2H2O. In these structures, stacked dimers of radical anions are formed within π-stacked columns. Within the stacked dimers, interplanar separation distances are significantly shorter than the sum of the van der Waals radii for two C atoms; the shortest is 2.812 Šfor the Li salt and the longest is 2.925 Šfor the Cs salt. Diamagnetic character, observed by electron paramagnetic resonance spectroscopy, indicates spin-coupling of the unpaired electrons within the radical anion dimer. The electron-rich cyano substituents on DDQ∙- influence the electron redistribution within the ring skeleton. The crystalline compounds are also characterized by IR spectroscopy, complemented by quantum-chemical calculations based on both isolated and periodic models.

Nitranilic acid hexahydrate, a novel benchmark system of the Zundel cation in an intrinsically asymmetric environment: spectroscopic features and hydrogen bond dynamics characterised by experimental and theoretical methods.

Nitranilic acid (2,5-dihydroxy-3,6-dinitro-2,5-cyclohexadiene-1,4-dione) as a strong dibasic acid in acidic aqueous media creates the Zundel cation, H5O2(+). The structural unit in a crystal comprises (H5O2)2(+) (2,5-dihydroxy-3,6-dinitro-1,4-benzoquinonate)(2-) dihydrate where the Zundel cation reveals no symmetry, being an ideal case for studying proton dynamics and its stability. The Zundel cation and proton transfer dynamics are studied by variable-temperature X-ray diffraction, IR and solid-state NMR spectroscopy, and various quantum chemical methods, including periodic DFT calculations, ab initio molecular dynamics simulation, and quantization of nuclear motion along three fully coupled internal coordinates. The Zundel cation features a short H-bond with the O···O distance of 2.433(2) Å with an asymmetric placement of hydrogen. The proton potential is of a single well type and, due to the non-symmetric surroundings, of asymmetric shape. The formation of the Zundel cation is facilitated by the electronegative NO2 groups. The employed spectroscopic techniques supported by calculations confirm the presence of a short H-bond with a complex proton dynamics.

Stacking of metal chelating rings with π-systems in mononuclear complexes of copper(II) with 3,6-dichloro-2,5-dihydroxy-1,4-benzoquinone (chloranilic acid) and 2,2'-bipyridine ligands.

A series of four novel mononuclear complexes of copper(II) with chloranilic acid and 2,2'-bipyridine were prepared and structurally characterised by X-ray structure analysis and IR spectroscopy. The complexes exhibit square-planar, square-pyramidal and octahedral coordination. The chloranilate dianion coordinates the Cu(II) atom in a terminal bidentate o-quinone-like mode forming a mononuclear complex species. The crystal packing of the aqua complex and the complexes with crystal water molecules are defined by hydrogen bonds. However, significant contributions are from interactions involving five-membered chelate rings with both types of ligands and intermolecular π-systems (bipyridine and chloranilate rings). The crystal packing of the complex with square planar Cu(II) coordination is dominated by interactions of the chelate rings with π-delocalised bonds and intermolecular π-systems. The occurrence of dimorphism could be related to the different types of these interactions in the stacks. The crystal packing of the octahedral complexes of the mono- and dihydrate solvates reveal 3D-networks with pores occupied by non-coordinated bipyridine molecules.

Structural and functional characterisation of TesA - a novel lysophospholipase A from Pseudomonas aeruginosa.

TesA from Pseudomonas aeruginosa belongs to the GDSL hydrolase family of serine esterases and lipases that possess a broad substrate- and regiospecificity. It shows high sequence homology to TAP, a multifunctional enzyme from Escherichia coli exhibiting thioesterase, lysophospholipase A, protease and arylesterase activities. Recently, we demonstrated high arylesterase activity for TesA, but only minor thioesterase and no protease activity. Here, we present a comparative analysis of TesA and TAP at the structural, biochemical and physiological levels. The crystal structure of TesA was determined at 1.9 Å and structural differences were identified, providing a possible explanation for the differences in substrate specificities. The comparison of TesA with other GDSL-hydrolase structures revealed that the flexibility of active-site loops significantly affects their substrate specificity. This assumption was tested using a rational approach: we have engineered the putative coenzyme A thioester binding site of E. coli TAP into TesA of P. aeruginosa by introducing mutations D17S and L162R. This TesA variant showed increased thioesterase activity comparable to that of TAP. TesA is the first lysophospholipase A described for the opportunistic human pathogen P. aeruginosa. The enzyme is localized in the periplasm and may exert important functions in the homeostasis of phospholipids or detoxification of lysophospholipids.

Inhibition of extracellular lipase from Streptomyces rimosus with 3,4-dichloroisocoumarin.

Kinetic characterization of lipase inhibition was performed by activity measurement and mass spectrometry (MS), for the first time with serine-protease inhibitor 3,4-dichloroisocoumarin (DCI). Inhibition of Streptomyces rimosus extracellular lipase (SrLip), a member of the SGNH superfamily, by means of DCI follows the mechanism of two-step irreversible inhibition. The dissociation constant of the noncovalent E•I complex and first-order rate constant for inactivation were determined by incubation (Ki* = 26.6 ± 2.8 µM, k2 = 12.2 ± 0.6 min-1) or progress curve (Ki* = 6.5 ± 1.5 µM, k2 = 0.11 ± 0.01 min-1) method. Half-times of reactivation for lipase inhibited with 10-fold molar excess of DCI were determined by activity measurement (t1/2 = 11.3 ± 0.2 h), matrix-assisted laser desorption/ionization (MALDI, t1/2 = 13.5 ± 0.4 h), and electro-spray ionization (ESI, t1/2 = 12.2 ± 0.5 h) MS. The active SrLip concentration was determined by incubating the enzyme with near equimolar concentrations of DCI, followed by activity and MS measurement.

2-(4-Amino-phen-yl)-3,4,5,6-tetra-hydro-pyrimidin-1-ium chloride.

In the title compound, C(10)H(14)N(3) (+)·Cl(-), the tetra-hydro-pyridinium ring of the cation, which adopts a slightly distorted envelope conformation, is disordered over two orientations with an occupancy ratio of 0.653 (5):0.347 (5). The amidinium fragment of the major conformer is twisted relative to the benzene ring by 22.5 (6)° and the two C-N bond lengths of this fragment are similar [1.3228 (16) and 1.319 (2) Å]. In the crystal, the chloride anions are involved in three N-H⋯Cl hydrogen bonds, which link the components into a two-dimensional hydrogen-bonded network parallel to (010).

Face-to-face stacking of quinoid rings of alkali salts of bromanilic acid.

A series of alkali salts of hydrogen bromanilic acid trihydrates (K(+), Rb(+) and Cs(+), potassium, rubidium and caesium 2,5-dibromo-4-hydroxy-3,6-dioxocyclohexa-1,4-dien-1-olate trihydrate), bromanilic acid tetrahydrate (Na(+), disodium 2,5-dibromo-3,6-dioxocyclohexa-1,4-diene-1,4-diolate tetrahydrate) and bromanilic acid dihydrates (K(+), Rb(+) and Cs(+), dipotasium, dirubidium and dicaesium 2,5-dibromo-3,6-dioxocyclohexa-1,4-diene-1,4-diolate dihydrate) were prepared and studied by single-crystal X-ray diffraction. Their crystal packings are dominated by quinoid ring stacking. The monoanionic quinoid rings pack face-to-face without offset and with short centroid separations (3.25-3.30 Å), while the dianionic rings form offset stacks (1.4-1.8 Å) with a larger centroid separation (3.8-4.1 Å).

Bis[2-(4-amino-phen-yl)-4,5-dihydro-1H-imidazol-3-ium] dichloride monohydrate.

The asymmetric unit of the title compound, 2C(9)H(12)N(3) (+)·2Cl(-)·H(2)O, comprises two mol-ecules, two chloride anions and one mol-ecule of crystal water. In the imidazolinium ring, the protonation contributes to delocalization of the positive charge over the two C-N bonds. Both chloride anions are acceptors of four hydrogen bonds in a flattened tetra-hedron environment. The donors are NH(2) groups, the NH groups of the imidazolinium rings and the water mol-ecule. These hydrogen bonds and N-H⋯O(H(2)O) hydrogen bonds form a three-dimensional network.

Synthesis, photochemistry, and photophysics of butadiene derivatives: influence of the methyl group on the molecular structure and photoinduced behavior.

Novel butadiene derivatives display diverse photochemistry and photophysics. Excitation of 2-methyl-1-(o-vinylphenyl)-4-phenylbutadiene leads to the dihydronaphthalene derivative, whereas photolysis of the corresponding model o-methyl analogue results in the formation of the naphthalene-like derivative, deviating from the nonmethylated analogue of the prior starting compound and producing benzobi- and -tricyclic compounds. The effect of the methyl substituents is even more dramatic in the case of the dibutadienes. The parent unsubstituted compound undergoes photoinduced intramolecular cycloaddition giving benzobicyclo[3.2.1]octadiene, whereas the photochemical reaction of the corresponding dimethylated derivative shows only geometrical isomerization due to the steric effect of the substituents. Methyl groups on the butadiene backbones reduce the extent of conjugation, causing a blue-shift of the characteristic absorption band. The fluorescence efficiency is dramatically decreased, as a consequence of nonplanarity and reduced rigidity of the molecules due to the crowding by the methyl and phenyl groups together. Four molecules of very similar structures show dramatically different photoinduced behavior, revealing how changes of the nature and position of the substituents are valuable in understanding the photophysics and photochemistry of these types of compounds.

Palladium(II) complexes of quinolinylaminophosphonates: synthesis, structural characterization, antitumor and antimicrobial activity.

Three types of palladium(II) halide complexes of quinolinylaminophosphonates have been synthesized and studied. Diethyl and dibutyl [α-anilino-(quinolin-2-ylmethyl)]phosphonates (L1, L2) act as N,N-chelate ligands through the quinoline and aniline nitrogens giving complexes cis-[Pd(L1/L2)X(2)] (X═Cl, Br) (1-4). Their 3-substituted analogues [α-anilino-(quinolin-3-ylmethyl)]phosphonates (L3, L4) form dihalidopalladium complexes trans-[Pd(L3/L4)(2)X(2)] (5-8), with trans N-bonded ligand molecules only through the quinoline nitrogen. Dialkyl [α-(quinolin-3-ylamino)-N-benzyl]phosphonates (L5, L6) give tetrahalidodipalladium complexes [Pd(2)(L5/L6)(3)X(4)] (9-12), containing one bridging and two terminal ligand molecules. The bridging molecule is bonded to the both palladium atoms, one through the quinoline and the other through the aminoquinoline nitrogen, whereas terminal ligand molecules are coordinated each only to one palladium via the quinoline nitrogen. Each palladium ion is also bonded to two halide ions in a trans square-planar fashion. The new complexes were identified and characterized by elemental analyses and by IR, UV-visible, (1)H, (13)C and (31)P nuclear magnetic resonance and ESI-mass spectroscopic studies. The crystal structures of complexes 1-4 and 6 were determined by X-ray structure analysis. The antitumor activity of complexes in vitro was investigated on several human tumor cell lines and the highest activity with cell growth inhibitory effects in the low micromolar range was observed for dipalladium complexes 11 and 12 derived from dibutyl ester L6. The antimicrobial properties in vitro of ligands and their complexes were studied using a wide spectrum of bacterial and fungal strains. No specific activity was noted. Only ligands L3 and L4 and tetrahalidodipalladium complexes 9 and 11 show poor activities against some Gram positive bacteria.

A partial proton transfer in hydrogen bond O-H···O in crystals of anhydrous potassium and rubidium complex chloranilates.

Hydrogen bonding and proton transfer in the solid state are studied on the crystals of isostructural anhydrous potassium and rubidium complex chloranilates by variable-temperature single crystal X-ray diffraction, solid state (1)H NMR and IR spectroscopies, and periodic DFT calculations of equilibrium geometries, proton potentials, and NMR chemical shifts. Their crystal structures reveal neutral molecules of chloranilic acid and its dianions connected into a chain by O-H···O hydrogen bond. A strong hydrogen bond with a large-amplitude movement of the proton with NMR shift of 13-17 ppm and a broad continuum in IR spectra between 1000 and 500 cm(-1) were observed. Periodic DFT calculations suggest that proton transfer is energetically more favorable if it occurs within a single pair of chloranilate dianion and chloranilic acid molecule but not continuously along the chains of long periodicity. The calculated chemical shifts confirm the assumption that the weak resonance signals observed at lower magnetic fields pertain to the case when the proton migrates to the acceptor side of the hydrogen bond. The detected situation can be described by a partial proton transfer.

Photochemical and thermal intramolecular 1,3-dipolar cycloaddition reactions of new o-stilbene-methylene-3-sydnones and their synthesis.

New trans- and cis-o-stilbene-methylene-sydnones 3a,b were synthesized by transforming the trans- and cis-o-aminomethylstilbene derivative, obtained by reduction of corresponding o-cyano derivatives, into glycine ester derivatives (43 and 31% yield) followed by hydrolysis (90 and 96% yield), nitrosation and ring closure with acetic acid anhydride (30 and 40% yield). The products were submitted to photochemical and thermal intramolecular [3 + 2] cycloadditions to afford diverse heteropolycyclic compounds. Photochemical reactions afforded cis-3-(4-methylphenyl)-3a,8-dihydro-3H-pyrazolo[5,1-a]isoindole (11, 12.5% yield) and trans-3-(4-methylphenyl)-3a,8-dihydro-3H-pyrazolo[5,1-a]isoindole (12, 5% yield). Thermal reactions afforded 3-(4-methylphenyl)-3,3a,8,8a-tetrahydroindeno[2,1-c]pyrazole (14, 50% yield) and 11-(4-methylphenyl)-9,10-diazatricyclo[7.2.1.0(2,7)]dodeca-2,4,6,10-tetraene (15, 22% yield).