Competition between covalent and noncovalent bond cleavages in dissociation of phosphopeptide-amine complexes

Interactions between quaternary amino or guanidino groups with anions are ubiquitous in nature and have been extensively studied phenomenologically. However, little is known about the binding energies in non-covalent complexes containing these functional groups. Here, we present a first study focused on quantifying such interactions using complexes of phosphorylated A(3)pXA(3)-NH(2) (X = S, T, Y) peptides with decamethonium (DCM) or diaguanidinodecane (DGD) ligands as model systems. Time- and collision energy-resolved surface-induced dissociation (SID) of the singly charged complexes was examined using a specially configured Fourier transform ion cyclotron resonance mass spectrometer (FTICR-MS). Dissociation thresholds and activation energies were obtained from RRKM modeling of the experimental data that has been described and carefully characterized in our previous studies. For systems examined in this study, covalent bond cleavages resulting in phosphate abstraction by the cationic ligand are characterized by low dissociation thresholds and relatively tight transition states. In contrast, high dissociation barriers and large positive activation entropies were obtained for cleavages of non-covalent bonds. Dissociation parameters obtained from the modeling of the experimental data are in excellent agreement with the results of density functional theory (DFT) calculations. Comparison between the experimental data and theoretical calculations indicate that phosphate abstraction by the ligand is rather localized and mainly affected by the identity of the phosphorylated side chain. The hydrogen bonding in the peptide and ligand properties play a minor role in determining the energetics and dynamics of the phosphate abstraction channel.     

Syntheses and luminescence of four supramolecular coordination complexes with flexible ligand

Four d ¹⁰-based complexes with chemical formulae {[Zn(L¹)₂(H₂O)₂(4,4′-Bipy)₂] (I), {[Zn₂(L¹)₄(Mi)] · 4H₂O} (II), {[Zn(L¹)₂(Phen)] · H₂O} (III) {[Cd(L¹)₂(Phen)] · 2H₂O} (IV) (HL¹ = p-hydroxy phenylacetic acid, 4,4′-Bipy = 4,4′-bipyridine, Phen = 1,10-phenanthroline, Mi = 1,4-bis(imidazol-1-yl)butane) have been synthesized and structurally characterized by single crystal X-ray diffraction (CIF files CCDC nos. 1047119 (I), 1047120 (II), 1047121 (III), 1047122 (IV)). The significant effect of assistant ligands and metal ions on assembly of I?IV has been demonstrated, which leads to the formation of distinct crystalline products. Complexes I?IV show various coordination motifs with different existing forms and coordination modes of the organic ligands. Furthermore, extend supramolecular networks are connected by secondary interactions such as hydrogen-bonding and aromatic stacking. The thermal stability and luminescent properties of the compounds were discussed in detail.     

Solvent effects in ligand substitutions of square planar complexes

Data on solvent effects in ligand substitution in square planar complexes are reviewed. In view of the fact that solvent effects for reactions of the planar complexes are quite different from those observed for saturated carbon substrates, it is felt that previous explanations for protic-dipolar aprotic solvent effects may have to be reconsidered.     

Synthesis and characterisation of main-chain hydrogen-bonded supramolecular liquid crystalline complexes formed by azo-containing compounds

A series of azopyridine-containing hydrogen bonding acceptors (4a-c) with flexible spacers of oligo(methylene) were synthesised. Hydrogen-bonded polymeric complexes 4/5 and trimeric complexes 4/6₂ , where 5 and 6 are aromatic dicarboxylic acids and monocarboxylic acids, respectively, were prepared and their liquid crystallinity was examined using differential scanning calorimetry and polarising optical microscopy. The study showed that most of the complexes displayed reversible thermotropic nematic phase. The isotropic to nematic phase transition temperatures of polymeric complexes 4/5 and trimeric complexes 4/6₂ in general decreased with the increase in length of spacers and terminal groups in the corresponding proton acceptors 4 and the proton donors 5 and 6, respectively. Hydrogen bonding interactions in complexes 4/5 and 4/6₂ were studied by X-ray photoelectron spectroscopy and Fourier transform infrared spectroscopy.     

Self-assembly of hydrogen-bonded supramolecular structures of two copper(II) 2-bromobenzoate complexes with 4-pyridylmethanol and nicotinamide

The structures of [Cu(2-Brbz)₂(4PM)₂(H₂O)] (1) and [Cu(2-Brbz)₂(NIA)2] · 2H₂O 2 [where 2-Brbz is the 2-bromobenzoate anion, 4-PM is the 4-pyridylmethanol and NIA is nicotinamide] have been determined by X-ray and characterized by EPR spectroscopy. The Cu²⁺ cation in 1 is coordinated by a pair of oxygens from monodentate 2-bromobenzoate anions by a pair of pyridine nitrogens from monodentate 4-pyridylmethanol ligands and finally by a water forming a tetragonal-pyramidal coordination polyhedron. The Cu²⁺ cation in 2 is coordinated by two pairs of oxygens from the asymmetric bidentate 2-bromobenzoate anions and by a pair of pyridine nitrogen atoms from the monodentate nicotinamide in trans positions, forming an extremely elongated bipyramid. The molecules of both complexes are linked by O–H ··· O, C–H ··· O and for 2 by N–H ··· O hydrogen bonds, which create three-dimensional hydrogen-bonding networks. EPR spectra of 1 and 2 are in agreement with X-ray data. Nicotinamide as well as 4-pyridylmethanol are suitable ligands for construction of hydrogen bonding coordination polymers.     

Ruthenium complexes of substituted hydrazine: new solution- and solid-state binding modes

The methylhydrazine complex [Ru(NH(2)NHMe)(PyP)(2)]Cl(BPh(4)) (PyP=1-[2-(diphenylphosphino)ethyl]pyrazole) was synthesised by addition of methylhydrazine to the bimetallic complex [Ru(mu-Cl)(PyP)(2)](2)(BPh(4))(2). The methylhydrazine ligand of the ruthenium complex has two different binding modes: side-on (eta(2)-) when the complex is in the solid state and end-on (eta(1)-) when the complex is in solution. The solid-state structure of [Ru(PyP)(2)(NH(2)NHMe)]Cl(BPh(4)) was determined by X-ray crystallography. 2D NMR spectroscopic experiments with (15)N at natural abundance confirmed that in solution the methylhydrazine is bound to the metal centre by only the -NH(2) group and the ruthenium complex retains an octahedral conformation. Hydrazine complexes [RuCl(PyP)(2)(eta(1)-NH(2)NRR')]OSO(2)CF(3) (in which R=H, R'=Ph, R=R'=Me and NRR'=NC(5)H(10)) were formed in situ by the addition of phenylhydrazine, 1,1-dimethylhydrazine and N-aminopiperidine, respectively, to a solution of the bimetallic complex [Ru(mu-Cl)(PyP)(2)](2)(OSO(2)CF(3))(2) in dichloromethane. These substituted hydrazine complexes of ruthenium were shown to exist in an equilibrium mixture with the bimetallic starting material.     

Molecular structures and supramolecular association of chlorodiorganotin(IV) complexes with bis- and tris-dithiocarbamate ligand

Two series of di and trinuclear chlorodiorganotin(IV) complexes derived from bis- and tris-dithiocarbamate ligands have been prepared and structurally characterized. The dinuclear complexes 1-2 of the composition {(R₂SnCl)₂(bis-dtc)} (1, R = Me; 2, R = ⁿBu) have been obtained from R₂SnCl₂ (R = Me, ⁿBu) and the triethylammonium salt of N,N′-dibenzyl-1,2-ethylene-bis(dithiocarbamate). The trinuclear complexes 3-9 with the general formula {(R₂SnCl)₃(tris-dtc)} 3, R = Me, tris-dtc = tris-dtc-Me; 4, R = Me, tris-dtc = tris-dtc-ⁱPr; 5, R = Me, tris-dtc = tris-dtc-Bn; 6, R = ⁿBu, tris-dtc = tris-dtc-Me; 7, R = ⁿBu, tris-dtc = tris-dtc- ⁱPr; 8, R = ⁿBu, tris-dtc = tris-dtc-Bn; 9, R = ^tBu, tris-dtc = tris-dtc-Me) were prepared from R₂SnCl₂ (R = Me, ⁿBu, ^tBu) and the potassium dithiocarbamate salts of (tris[2-(methylamino)ethyl]amine) (tris-dtc-Me), (tris[2-(isopropylamino)ethyl]amine) (=tris-dtc-ⁱPr) and (tris[2-(benzylamino)ethyl]amine) (=tris-dtc-Bn). Compounds 1-9 have been analyzed as far as possible by elemental analysis, FAB⁺ mass spectrometry, IR and NMR (¹H, ¹³C, ¹¹⁹Sn) spectroscopy, and single-crystal X-ray diffraction analysis. The solid state and solution studies showed that the dtc ligands are coordinated to the tin atoms in the anisobidentate manner. In all cases the metal centers are five-coordinate. The coordination geometry is intermediate between square-pyramidal and trigonal-bipyramidal coordination polyhedra with τ-values in the range of 0.32-0.53. For the members of each series characterized in the solid state by X-ray diffraction analysis, different molecular conformations were found. The crystal structures show the presence of C-H?Cl, C-H?S, C-H?π, S?Cl, S?S, Cl?Sn and S?Sn contacts.     

A tetranuclear heterobimetallic square formed from the cooperative ligand binding properties of square planar and tetrahedral metal centers

Reaction of Rh(I) and Zn(II) metal centers with a ligand containing salicylaldiminato and thioether-phosphine moieties resulted in the formation of a tetranuclear heterobimetallic molecular square. The directionality required to form these structures is imparted by both the tetrahedral and square planar metal centers acting in concert with one another.     

A new carboxylic chelate ligand and its supramolecular complexes formed with sodium ions and alcohol molecules

The new hydrazone ligand 1, featuring a 2-carboxy group at the aromatic ring and a trifluoromethyl structural modification in the pentane-2,4-dione moiety, has been synthesised via the Japp–Klingemann route. The compound is shown to form binuclear multicomponent chelate complexes (2 and 3) composed of two sodium ions, two charge equalising carboxylates of the hydrazone molecule, two more carboxylic hydrazones and two alcohol solvent molecules, with the latter being either EtOH or n-BuOH. X-ray crystal structures of the free hydrazone ligand as well as of the complexes have been studied. They demonstrate for the free ligand a ribbon-type aggregation of carboxylic dimers, while the isomorphous complexes possess a remarkable binuclear structure with the two sodium ions in a distorted octahedral coordination geometry of six oxygen atoms coming, at the equatorial and apical sites, from the hydrazone carbonyl groups and the hydroxyl of the solvent molecules, respectively. The hydrogen bonds owing to the alcohol molecules give rise to the stack formation of the supramolecular cluster. Weak intermolecular contacts involving the fluorine atoms also contribute to the crystalline packing in the case of both the free ligand and the complexes.     

Understanding noncovalent interactions: ligand binding energy and catalytic efficiency from ligand-induced reductions in motion within receptors and enzymes

Noncovalent interactions are sometimes treated as additive and this enables useful average binding energies for common interactions in aqueous solution to be derived. However, the additive approach is often not applicable, since noncovalent interactions are often either mutually reinforcing (positively cooperative) or mutually weakening (negatively cooperative). Ligand binding energy is derived (positively cooperative binding) when a ligand reduces motion within a receptor. Similarly, transition-state binding energy is derived in enzyme-catalyzed reactions when the substrate transition state reduces the motions within an enzyme. Ligands and substrates can in this way improve their affinities for these proteins. The further organization occurs with a benefit in bonding (enthalpy) and a limitation in dynamics (cost in entropy), but does not demand the making of new noncovalent interactions, simply the strengthening of existing ones. Negative cooperativity induces converse effects: less efficient packing, a cost in enthalpy, and a benefit in entropy.     

Synthesis and characterization of square planar nickel(II)-arylthiolate complexes with the biphenyl-2,2'-dithiolate ligand

Two new NiIIS4 complexes with the biphenyl-2,2'-dithiolate ligand (L) are reported. The dinuclear complex 1, [Ni2L3]2-, was formed in the reaction of 2-3 equiv of Na2L and [NiCl4]2- and the mononuclear complex [NiL2]2- (2) by using 4-10 equiv of Na2L. Complexes 1 and 2 have been crystallographically characterized. (Et4N)2[1].0.5S2Ph2, CH3CN: C60H71N3Ni2S7, triclinic, P1, a = 13.806(2) A, b = 14.267(2) A, c = 16.873(2) A, alpha = 69.263(10) degrees, beta = 69.267(8) degrees, gamma = 83.117(10) degrees, Z = 2, R1 = 0.0752 (wR2 = 0.2011). (Et4N)(Na.CH3CN)[2]: C34H39N2NaNiS4, triclinic, P1, a = 9.9570(10) A, b = 13.2670(10) A, c = 13.9560(10) A, alpha = 108.489(7) degrees, beta = 90.396(6) degrees, gamma = 103.570(4) degrees, Z = 2, R1 = 0.0390 (wR2 = 0.0995). Both complexes are square planar about the nickel ion in the solid state as well as in solution. Most Ni(II)-thiolate complexes are square planar except the tetrahedral mononuclear complexes with monodentate arylthiolate ligands that cannot force a square planar geometry. The ligand (L) has some flexibility to change its bite angle via the phenyl-phenyl bond and should not force a planar geometry on its complexes either. Therefore, it is interesting that 2 has adopted a square planar structure. Complex 2 readily converts to 1 in solution when not in the presence of excess L in a process that is presumably similar to that known for other mononuclear, bidentate ligated Ni(II) complexes. Both complexes, at least in the solid state, appear to have an inclination to bind another metal ion on one face of the complex (Ni2+ in 1, Na+ in 2). We hope to take advantage of this in future work to synthesize relevant model complexes for the active sites of the nickel-iron hydrogenases after suitable modifications are made to L.     

Chemical and constitutional influences in the self-assembly of functional supramolecular hydrogen-bonded nanoscopic fibres

A new series of secondary amides bearing long alkyl chains with pi-electron-donor cores has been synthesized and characterised, and their self-assembly upon casting at surfaces has been studied. The different supramolecular assemblies of the materials have been visualized by using atomic force microscopy (AFM) and transmission electron microscopy (TEM). It is possible to obtain well-defined fibres of these aromatic core molecules as a result of the hydrogen bonds between the amide groups. Indeed, by altering the alkyl-chain lengths, constitutions, concentrations and solvent, it is possible to form different rodlike aggregates on graphite. Aggregate sizes with a lower limit of 6-8 nm width have been reached for different amide derivatives, while others show larger aggregates with rodlike morphologies which are several micrometers in length. For one compound that forms nanofibres, doping was performed by using a chemical oxidant, and the resulting layer on graphite was shown to exhibit metallic-like spectroscopy curves when probed with current-sensing AFM. This technique also revealed current maps of the surface of the molecular material. Fibre formation not only takes place on the graphite surface: nanometre scale rods have been imaged by using TEM on a grid after evaporation of solutions of the compounds in chloroform. Molecular modelling proves the importance of the hydrogen bonds in the generation of the fibres, and indicates that the constitution of the molecules is vital for the formation of the desired columnar stacks, results that are consistent with the images obtained by microscopic techniques. The results show the power of noncovalent bonds in self-assembly processes that can lead to electrically conducting nanoscale supramolecular wires.     

Influence of metal and ligand types on stacking interactions of phenyl rings with square-planar transition metal complexes

In order to find out whether metal type influences the stacking interactions of phenyl rings in square-planar complexes, geometrical parameters for Cu, Ni, Pd and Pt complexes, with and without chelate rings, were analyzed and compared. By searching the Cambridge Structural Database, 220 structures with Cu complexes, 211 with Ni complexes, 285 with Pd complexes, and 220 with Pt complexes were found. The results show that the chelate ring has a tendency to make the stacking interaction with the phenyl ring independent of metal type in the chelate ring. However, there are some differences among metals for complexes without a chelate ring. There are a number of structures containing Pd and Pt complexes, without chelate rings, that have short carbon-metal distances and parallel orientations of the phenyl ring with respect to the coordination plane. It was found that some of these complexes have a common fragment, CN, as a part of the ligands. This indicates that the CN supports stacking interactions of square planar complexes with the phenyl ring.      

A theoretical prediction of stability in hydrogen-bonded complexes formed between oxirane and oxetane rings with HX (X=F and Cl)

The optimised geometries of heterocyclic hydrogen-bonded complexes, C2H4O...HX and C3H6O...HX, where X=F or Cl, were determined at DFT/B3LYP/6-311++G(d,p) computational level. Structural, electronic and vibrational properties of these complexes are used in order to compare the strained ring, which confer the great reactivity of these heterocyclic rings with monoprotic acids, forming a primary hydrogen bond. A secondary hydrogen bond between the hydrogen atoms of the CH2 groups and the halide species also takes place, thus causing a nonlinearity (characterized by the theta angle), in the primary hydrogen bond.     

Computation of covalent and noncovalent structural parameters at low computational cost: Efficiency of the DH-SVPD method

DH-SVPD is a tailored atomic basis set originally developed to enhance the domain of applicability of double-hybrid density functionals to large molecular systems in weak interactions. In combination with any density functional belonging to this approximation, it provides an accurate estimate of noncovalent interaction energies at the cost of a double-ζ basis set, without adding a posteriori an empirical dispersion correction. Here, we show that the accuracy/cost ratio observed previously for energy properties can be safely extended to the modeling of structural parameters of small- and medium-sized organic molecules. In particular, we demonstrate that, in combination with the nonempirical PBE-QIDH double hybrid, DH-SVPD is competitive with very large quadruple-ζ basis sets when modeling both covalent and noncovalent structural parameters.     

Strong stacking between FH--N hydrogen-bonded foldamers and fullerenes: formation of supramolecular nano networks

The stacking interactions between FH--N hydrogen-bonded foldamers 1-3, bis-foldamer 4, and tris-foldamer 5 and C(60) and C(70) are described. Compound 4 contains two folded units, which are connected by an isophthalamide linker, whereas 5 has a C(3)-symmetrical discotic structure, in which three folded units are connected by a benzene-1,3,5-tricarboxamide unit. UV/Vis, fluorescence, and NMR experiments have revealed that the foldamers or folded units strongly stack with fullerenes in chloroform. The (apparent) association constants of the respective complexes have been determined by a fluorescence titration method. The strong association is tentatively attributed to intermolecular cooperative fluorophenylpi and solvophobic interactions. A similar but weaker interaction has also been observed between an MeOH--N hydrogen-bonded foldamer and fullerenes. AFM studies have revealed that the surfaces of 3 and 4 show fibrous networks, while the surface of 5 shows particles. In sharp contrast, mixtures of 3 and 4 with C(60) have been shown to generate thinner separated fibrils, whereas a mixture of 5 and C(60) produces honeycomb-like nano networks, for which a columnar cooperative stacking pattern is proposed. The results demonstrate the usefulness of FH--N hydrogen-bonded folded structures in the construction of nanoscaled materials.     

The 3,5-dimethyl-4-nitropyrazole ligand in the construction of supramolecular networks of silver(I) complexes

Three new ionic silver complexes based on the 3,5-dimethyl-4-nitropyrazole ligand (Hpz^NO₂) and 1:2 or 1:3 (Ag:Hpz^NO₂) stoichiometries, [Ag(Hpz^NO₂)₂][BF₄], [Ag(Hpz^NO₂)₃][SbF₆] and [Ag(Hpz^NO₂)₃][PO₂F₂]·Hpz^NO₂ have been prepared and structurally characterised. The linear or trigonal metallic coordination environment, the NO₂ groups on the pyrazole ligand as well as the presence of counteranions of the type as , or (the latter one evolving to ) were strategically selected to produce molecular assemblies established on the basis of hydrogen-bonds (N-H?X) and π?π or coordinative interactions involving the NO₂ group. The complex [Ag(Hpz^NO₂)₂][BF₄] exhibited polymeric N-H?F hydrogen-bonded chains which were assembled in a 3D network by weaker coordinative Ag?O(NO₂) and π(NO₂)?π(NO₂) interactions. In the complex [Ag(Hpz^NO₂)₃][SbF₆], consistent with the three-coordinated molecular environment, the interactions were extended to give rise an open 3D cationic sub-network in which the counteranions were encapsulated. By contrast, in the related complex [Ag(Hpz^NO₂)₃][PO₂F₂]·Hpz^NO₂ the presence of a fourth non-coordinated pyrazole Hpz^NO₂ avoided the formation of a 3D network giving rise to a double-chained 1D structure.     

Solution-state and solid-state structural characterization of complexes of a new macrocyclic ligand containing the 1,5-diazacyclooctane subunit

The synthesis and characterization of a new constrained tetraazamacrocyclic ligand, 1,4,8,11-tetraazabicyclo[9.3.3]heptadecane (1,11-C(3)-cyclam), is reported. Because of its basicity, this ligand (pK(a) of the protonated form >13.5) requires aprotic solvents for its metalation reactions. Two complexes of this ligand, [Ni(1,11-C(3)-cyclam](OTf)(2) and [Co(1,11-C(3)-cyclam)(NCS)(2)](OTf), have been characterized by single-crystal X-ray crystallography. For the Ni(II) complex, the 1,5-diazacyclooctane (daco) subunit of the ligand is in the chair-boat conformation, whereas that same subunit in the Co(III) complex is in the chair-chair conformation. For the Ni(II) complex, C(12) and H(12a) block one of the coordination sites. The (1)H and (13)C NMR spectra of the Ni(II) complex in D(2)O have very sharp resonances, indicative of low-spin Ni(II). The resonance for H(12a) appears at 4.5 ppm, suggesting an interaction with Ni(II). In acetonitrile, the (1)H and (13)C spectra are broadened, indicative of a low-spin/high-spin equilibrium due to axial coordination by acetonitrile. C(12) experiences the greatest degree of broadening in the (13)C NMR spectrum. Variable-temperature NMR spectroscopy from -70 to +80 degrees C shows no significant change as a function of temperature. The electronic spectrum of the Ni(II) complex (lambda(max) = 449.9 nm) is consistent with steric and electronic factors for this complex.     

Self-assembly hydrogen-bonded supramolecular arrays from copper(II) halogenobenzoates with nicotinamide: Structure and EPR spectra

Nicotinamide was employed as a supramolecular reagent in the synthesis of six new copper(II) bromo-, iodo-, fluoro- and dibromobenzoate complexes. Structures of [Cu(2-Brbz)₂(nia)₂(H₂O)₂] (I), [Cu(2-Ibz)₂(nia)₂(H₂O)2] (II), [Cu(2-Fbz)₂(nia)₂(H₂O)₂] (III), [Cu(4-Brbz)₂(nia)₂(H₂O)₂] (IV), [Cu(3,5-Br₂bz)2(nia)₂(H₂O)2] (V), [Cu(F-Fbz)₂(nia)₂(H₂O)] · H₂O (VI) (nia = nicotinamide, 2-Brbz = 2-bromobenzoate, 4-Brbz = 4-bromobenzoate, 3,5-Br₂bz = 3,5-dibromobenzoate, 2-Ibz = 2-iodobenzoate, 2-Fbz = 2-fluorobenzoate, 4-Fbz = 4-fluorobenzoate) were determined using X-ray analysis. Compound [Cu(2-Brbz)₂(nia)₂] · 2H₂O (VII) was prepared by a new method and also characterized by X-ray powder diffraction and EPR spectroscopy. Compounds I–V are monomeric complexes with a square-bipyramidal coordination sphere around the Cu²⁺ ion. Complex VI is monomeric with coordination environment around the Cu²⁺ ion of a tetragonal-pyramid. Complexes I and VII present examples of coordination isomerism. Molecules of all compounds are connected by N—H?O and O—H?O hydrogen bonds from the NH₂ groups of nicotinamide and water molecules which create supramolecular hydrogen-bonding-coordination chains and networks.