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This review summarizes the recent advances concerning metal-organic frameworks (MOFs) modified with several biomolecules (e.g., amino acids, nucleobases, proteins, antibodies, aptamers, etc.) as ligands to prepare affinity-based sorbents for application in the sample preparation field. The preparation and incorporation strategies of these MOF-based affinity materials were described. Additionally, the different types of ligands that can be employed for the synthesis of these biocomposites and their application as sorbents for the selective extraction of molecules and clean-up of complex real samples is reported. The most important features of the developed biocomposites will be discussed throughout the text in different sections, and several examples will be also commented on in detail.

The interactions in model ionic YTX 3 ···Z (Y = NC, F, Cl, Br; X = F, Cl, Br, Z = F - , Cl - , Br - , Li + ) dyads containing the tetrel atoms, T = C, Si, Ge, were studied using ab initio computational methods, including an energy decomposition analysis, which found that the YTX 3 molecules were stabilized by both anions (via tetrel bonding) and cations (via polarization). For the tetrel-bonded dyads, both the electrostatic and polarization forces make comparable contributions to the binding in the C-containing dyads, whereas, electrostatic forces are by far the largest contributor to the binding in the Si- and Ge-containing analogues. Model metastable Li + ···NCTCl 3 ···F - (T = C, Si, Ge) triads were found to be lower in energy than the combined energy of the Li + + NCTCl 3 + F - fragments. The pair energies and cooperative energies for these highly polar triads were also computed and discussed.

Metal-ligand cooperation (MLC) plays an important role in bond activation processes, enabling many chemical and biological catalytic reactions. A recent new mode of activation of chemical bonds involves ligand aromatization-dearomatization processes in pyridine-based pincer complexes in which chemical bonds are broken reversibly across the metal centre and the pincer-ligand arm, leading to new bond-making and -breaking processes, and new catalysis. In this short review, such processes are briefly exemplified in the activation of C-H, H-H, O-H, N-H and B-H bonds, and mechanistic insight is provided. This new bond activation mode has led to the development of various catalytic reactions, mainly based on alcohols and amines, and to a stepwise approach to thermal H2 and light-induced O2 liberation from water., (© 2015 The Author(s) Published by the Royal Society. All rights reserved.)

Co(II) complexes and Co(H2O)6(2+) are used as catalysts in advanced oxidation processes. Therefore it was decided to study the kinetics of reaction of Co(H2O)6(2+) with H2O2. Surprisingly, the kinetic results point out that the process involves three consecutive reactions, each of them requiring an H2O2 molecule, i.e. three H2O2 molecules ligate to the central cobalt cation prior to the formation of radicals. DFT analysis suggests that the transient (H2O)3Co(II)(OOH)2(H2O2) decomposes via: (H2O)3Co(II)(OOH)2(H2O2) → (H2O)3Co(II)(OOH)(˙OOH)(OH) + ˙OH ΔG(0) = -5.975 kcal mol(-1), with no evidence for the formation of a Co(III) transient. It is proposed that analogous mechanisms are involved whenever the redox potential of the central cation is too high to enable the reaction: M(H2O)6(n+) + H2O2 → M((n+1)+)aq + ˙OH + OH(-).

The Hammett σ constant has for a long time been known to be one of most important linear free-energy related parameters that correlate with biological activity. It is a conventionally used electronic parameter in studies of enzymatic quantitative structure-activity relationships (QSAR). However, it is not necessarily obvious why σ represents variations in the free-energy change associated with the complex formation between a congeneric series of ligands with their target protein. So far, several powerful molecular calculations, such as the ab initio fragment molecular orbital (FMO) one, that are directly applicable to ligand-protein complexes have emerged. In this study, we comprehensively reevaluate experimentally derived parameter σ confirming it represents intermolecular interaction energy terms, by applying molecular orbital (MO) calculations to a simple ligand-protein complex model. The current results provide a rational and quantitative basis for bridging the gap between the traditional QSAR approach and 'the modern QSAR one', which involves the molecular calculations to evaluate the overall free-energy change for complex formation., (Copyright © 2011 Elsevier Ltd. All rights reserved.)

Water ordering near a charged membrane surface is important for many biological processes such as binding of ligands to a membrane or transport of ions across it. In this work, the mean-field Poisson-Boltzmann theory for point-like ions, describing an electrolyte solution in contact with a planar charged surface, is modified by including the orientational ordering of water. Water molecules are considered as Langevin dipoles, while the number density of water is assumed to be constant everywhere in the electrolyte solution. It is shown that the dielectric permittivity of an electrolyte close to a charged surface is decreased due to the increased orientational ordering of water dipoles. The dielectric permittivity close to the charged surface is additionally decreased due to the finite size of ions and dipoles.

The use of quantum dots (QDs) as donors in fluorescence resonance energy transfer (FRET) offer several advantages for the development of multiplexed solid-phase QD-FRET nucleic acid hybridization assays. Designs for multiplexing have been demonstrated, but important challenges remain in the optimization of these systems. In this work, we identify several strategies based on the design of interfacial chemistry for improving sensitivity, obtaining lower limits of detection (LOD) and enabling the regeneration and reuse of solid-phase QD-FRET hybridization assays. FRET-sensitized emission from acceptor dyes associated with hybridization events at immobilized QD donors provides the analytical signal in these assays. The minimization of active sensing area reduces background from QD donor PL and allows the resolution of smaller amounts of acceptor emission, thus lowering the LOD. The association of multiple acceptor dyes with each hybridization event can enhance FRET efficiency, thereby improving sensitivity. Many previous studies have used interfacial protein layers to generate selectivity; however, transient destabilization of these layers is shown to prevent efficient regeneration. To this end, we report a protein-free interfacial chemistry and demonstrate the specific detection of as little as 2 pmol of target, as well as an improved capacity for regeneration.

Nano-structures of two new Pb(II) two-dimensional coordination polymers, [Pb(micro-4-pyc)(micro-NCS)(micro-H(2)O)](n) (1) and [Pb(micro-4-pyc)(micro-N(3))(micro-H(2)O)](n) (2), 4-Hpyc=4-pyridinecarboxylic acid were synthesized by a sonochemical method. The new nano-structures were characterized by scanning electron microscopy, X-ray powder diffraction, IR spectroscopy and elemental analyses. Compounds 1 and 2 were structurally characterized by single crystal X-ray diffraction and consist of two-dimensional polymeric units. The thermal stability of compounds 1 and 2 were studied by thermal gravimetric and differential thermal analyses and compared. Pb(2)(SO(4))O and PbO nanoparticles were obtained by calcination of the nano-structures of compounds 1 and 2 at 600 degrees C, respectively.

Computer-based and theoretical approaches to chemical problems can provide atomistic understanding of complex processes at the molecular level. Examples ranging from rates of ligand-binding reactions in proteins to structural and energetic investigations of diastereomers relevant to organo-catalysis are discussed in the following. They highlight the range of application of theoretical and computational methods to current questions in chemical research.

The mechanism of ligand binding coupled to conformational changes in macromolecules has recently attracted considerable interest. The 2 limiting cases are the "induced fit" mechanism (binding first) or "conformational selection" (conformational change first). Described here are the criteria by which the sequence of events can be determined quantitatively. The relative importance of the 2 pathways is determined not by comparing rate constants (a common misconception) but instead by comparing the flux through each pathway. The simple rules for calculating flux in multistep mechanisms are described and then applied to 2 examples from the literature, neither of which has previously been analyzed using the concept of flux. The first example is the mechanism of conformational change in the binding of NADPH to dihydrofolate reductase. The second example is the mechanism of flavodoxin folding coupled to binding of its cofactor, flavin mononucleotide. In both cases, the mechanism switches from being dominated by the conformational selection pathway at low ligand concentration to induced fit at high ligand concentration. Over a wide range of conditions, a significant fraction of the flux occurs through both pathways. Such a mixed mechanism likely will be discovered for many cases of coupled conformational change and ligand binding when kinetic data are analyzed by using a flux-based approach.

The design of substituted lactols is described, which in their reaction with racemic alkyl aryl carbinols react preferentially with one of the enantiomers exhibiting selectivities up to 14:1.

We have explored in this work the stability and the reactivity of multiarm cyclam-grafted mesoporous silica samples in aqueous solution. A series of hybrid materials have been prepared by grafting silylated cyclam molecules bearing one, two, or four silyl groups onto both amorphous silica gel (K60) and ordered mesoporous silica (SBA15). Under these conditions, cyclam moieties are attached to the silica walls via one, two, or four arms. Various physicochemical techniques have been applied to characterize the functionalized solids (elemental analysis, 1H-29Si and 1H-13C CPMAS NMR, and N2 adsorption-desorption isotherms). The interest in two and four arms for improving the chemical stability in solution, by comparison with the system displaying only one arm, has been demonstrated by using a set of complementary experiments involving pH measurements and silicon determination with ICP-AES. Then, the investigation of their protonation and binding properties toward copper(II) has revealed a significant decrease in the reactivity of these hybrids as a consequence of multiarm tethering. A comparison of amorphous and ordered materials has permitted us to point out the influence of mesostructuration on the reactivity of these functionalized solids, especially from a kinetic point of view.

Chelated enolates are versatile nucleophiles for palladium-catalysed allylic alkylations. Even with complex allylic substrates the reaction proceed without significant isomerisation. This allows the stereoselective introduction of polyhydroxylated allylic sidechains into amino acids and peptides with retention of the olefin geometry.

The asymmetric transfer hydrogenation of imines was performed with the use of a polymer-immobilized chiral catalyst. The chiral catalyst, prepared from crosslinked polystyrene-immobilized chiral 1,2-diamine monosulfonamide, was effective in the asymmetric transfer hydrogenation of N-benzyl imines in CH(2)Cl(2) to give a chiral amine in high yield and good enantioselectivity. Furthermore, an amphiphilic polymeric catalyst prepared from crosslinked polystyrene containing sulfonated groups successfully catalyzed the asymmetric transfer hydrogenation of cyclic imines in water. Enantioenriched secondary amines with up to 94% ee were obtained by using a polymeric catalyst.

A rhodium(I) catalyst incorporating the Me-DuPhos ligand promotes enantioselective intermolecular hydroacylation between beta-S-aldehydes and 1,3-disubstituted allenes. The nonconjugated enone products are obtained in good yields and with high enantioselectivities.

While chiral materials are common, few are known that integrate molecular chirality, absolute helicity, and 3-D intrinsically chiral topological nets in one material. Such multihomochiral features may lead to enhanced chiral recognition processes that are important for enantioselective catalysis or separation. Reported here are a series of 3-D open-framework materials with unusual integration of various homochiral and homohelical features, even in the bulk sample.

A new class of oligopyridine ligands bearing disaccharides linked to the 4- and 4'-positions of a 2,2'-bipyridine or the 4'-position of a 2,2':6',2''-terpyridine metal-binding domain are described. Representative ligands with furanosylfuranose and pyranosylpyranose (cellobiose) substituents have been prepared.

This work describes the computation and accurate reproduction of subtle shifts in reduction potentials for two mutants of the iron-sulfur protein Pyrococcus furiosus ferredoxin. The computational models involved only first-sphere ligands and differed with respect to one ligand, either acetate (aspartate), thiolate (cysteine), or methoxide (serine). Standard procedures using vacuum optimization gave qualitatively wrong results and errors up to 0.07 V. Using electrostatically screened geometries and large basis sets for expanding the wave functions gave quantitatively correct results, with errors of only 0.03 V. Correspondingly, only this approach predicted a change in the coordination mode of aspartate (i.e., a carboxylate shift) accompanying the reduction of the wild-type cluster, confirming results from synthetic models and explaining why electrostatic screening is necessary. Hence, the carboxylate shift appears to occur in the proteins from which data were collected. The results represent the most accurate predictions of shifts in reduction potentials for modified proteins, the success in part being due to the similar nature of the three amino acid ligands involved. The predicted carboxylate shift is expected to tune aspartate's degree of electron donation to the cluster's two oxidation states, thus making the reversible redox reaction feasible.

Reaction of RhCl(1,5-cod)(THP), where THP = P(CH(2)OH)(3), with several PRR'2 phosphines (R = or not equal R') generates, concomitantly with R'H, the derivatives RhCl(PRR'(2))[P,P-R'(R)POCH(2)P(CH(2)OH)(2)] in two isomeric forms. The hydrogen of the hydrocarbon co-product derives from a THP hydroxyl group which becomes an 'alkoxy' group at the residual PRR' moiety, this resulting in the P,P-chelated R'(R)POCH(2)P(CH(2)OH)(2) ligand. One of the isomers of the PPh(3) system, cis-RhCl(PPh(3))[P,P-P(Ph)(2)OCH(2)P(CH(2)OH)(2)], was structurally characterized (cis refers to the disposition of the P atoms with Ph substituents).

The synthesis of 3-(2-methoxy-1,1-dimethylethyl)pyrazole, pz*H is described together with its reactions with the borohydrides MBH(4), where M = Li, Na, and K, under melt conditions. At 180 degrees C, this procedure leads to a mixture of products for M = Li, and at higher temperatures, a derivative LiTp'pz*H, 1, is isolated, wherein a B-H bond and a methyl group have been eliminated and a B-O bond has been formed. For M = Na, the reaction proceeds to give the tris-pyrazolylborate derivative NaTp*, 2, but at higher temperatures the tetra-pyrazolylborate complex NaB(pz*)(4), 3, is obtained. The reactions involving KBH4 and pz*H yield the dinuclear complex K(2)(Tp*)(2)pz*H, 4. The reaction between NaTp* and TlOAc in CH(2)Cl(2) at room temperature leads to the formation of TlTp*, 5, along with NaOAc. Thallium 5 reacts with methyllithium in diethylether to give LiTp*, 6, and thallium metal, and, similarly, 5 and KH react in tetrahydrofuran to give KTp*, 7 and Tl(0). 1-7 have been characterized by elemental analysis, NMR spectroscopy, and by single-crystal X-ray studies, the latter of which reveal the versatile modes of binding for this new ligand bearing hemilabile ether appendages.

The alpha-diimine iron complexes, (R',R'')[N,N]FeCl(2) ((R',R'')[N,N] = R'-N=CR' '-CR' '=N-R', where R' = tert-butyl (tBu), cyclohexyl (Cy) and R' ' = phenyl (Ph), para-fluorophenyl (F-Ph), para-bromophenyl (Br-Ph), para-methylphenyl (Me-Ph), or para-methoxyphenyl (MeO-Ph)), are found to polymerize styrene through a catalytic chain transfer (CCT) mechanism. Magnetic moment measurements indicate that Fe(III) complexes containing these ligands possess intermediate (S = 3/2) spin-state iron centers. In contrast, Fe(III) complexes bearing proton (R' ' = H) and para-dimethylaminophenyl (R' ' = NMe(2)-Ph) substituents are high-spin and are efficient atom transfer radical polymerization (ATRP) catalysts. Hammett plots show a linear correlation of the substituent constant, sigma, with polymerization rate and polymer molecular weight, respectively.

A tetracationic supramolecular helicate, [Fe2L3]4+ (L = C25H20N4), with a triple-helical architecture is found to induce the formation of a three-way junction (3WJ) of deoxyribonucleotides with the helicate located in the center of the junction. NMR spectroscopic studies of the interaction between the M enantiomer of the helicate and two different oligonucleotides, [5'-d(TATGGTACCATA)]2 and [5'-d(CGTACG)]2, show that, in each case, the 2-fold symmetry of the helicate is lifted, while the 3-fold symmetry around the helicate axis is retained. The 1:3 helicate/DNA stoichiometry estimated from 1D NMR spectra supports a molecular model of a three-way junction composed of three strands. Three separate double-helical arms of the three-way junction are chemically identical giving rise to one set of proton resonances. The NOE contacts between the helicate and DNA unambiguously show that the helicate is fitted into the center of the three-way junction experiencing a hydrophobic 3-fold symmetric environment. Close stacking interactions between the ligand phenyl groups and the nucleotide bases are demonstrated through unusually large downfield shifts (1-2 ppm) of the phenyl protons. The unprecedented 3WJ arrangement observed in solution has also been found to exist in the crystal structure of the helicate adduct of [d(CGTACG)2] (Angew. Chem., Int. Ed. 2006, 45, 1227).

Vibrational circular dichroism (VCD) spectra of a series of [M(III)(acac)3] (acac = acetylacetonato; M = Cr, Co, Ru, Rh, Ir, and Al) and [M(III)(acac)2(dbm)] (dbm = dibenzoylmethanato; M = Cr, Co, and Ru) have been investigated experimentally and/or theoretically in order to see the effect of the central metal ion on the vibrational dynamics of ligands. The optical antipodes give the mirror-imaged spectra in the region of 1700-1000 cm(-1). The remarkable effect of the central metal ion is observed experimentally on the VCD peaks due to C-O stretches (1500-1300 cm(-1)) for both [M(III)(acac)3] and [M(III)(acac)2(dbm)]. In the case of Delta-[M(III)(acac)3], for example, the order of frequency of two C-O stretches (E and A2 symmetries) is dependent on the kind of a central metal ion as follows: E (-) > A2 (+) for M = Co, Rh, and Ir, while A2 (+) > E (-) for M = Cr and Ru. In the case of Delta-[M(III)(acac)2(dbm)], the order of frequency of three C-O stretches (A, B, and B symmetries) is as follows: A (-) > B (+) > B (+) for Co(III), B (+) > A (-) > B (-) for Cr(III), and A (-) > B (+) > B (-) for Ru(III). These results imply that the energy levels of C-O stretches are delicately affected by the kind of central metal ion. Since such detailed information is not obtained from the IR spectra alone, the VCD spectrum can probe the effect of the central metal ion on interligand cooperative vibration modes.

The reaction in water of M(II) [M = Ni or Mn] with 1,10-phenanthroline (phen) and sodium pyrophosphate (Na4P2O7) in a 2:4:1 stoichiometry resulted in the crystallization of dinuclear complexes featuring the heretofore rare bridging pyrophosphate. Single-crystal X-ray diffraction studies revealed the complexes to be {[(phen)2Ni]2(micro-P2O7)} . 27H2O (1) and {[(phen)2Mn]2(micro-P2O7)} . 13H2O (2) where the asymmetric M(phen)2 units are bridged by bis-bidentate pyrophosphate, each metal ion exhibiting a distorted octahedral geometry. The bridging pyrophosphate places adjacent metal centers at 5.031 A in 1 and 4.700 A in 2, and its conformation also gives rise to an intramolecular pi-pi interaction between two adjacent phen ligands. Intermolecular pi-pi interactions between phen ligands from adjacent dinuclear complexes create an ornate 3D network in 1, whereas a 2D sheet results in 2. The hydrophilic nature of the pyrophosphate ligand leads to heavy hydration with the potential solvent-accessible area for 1 and 2 accounting for 45.7% and 26.4% of their unit cell volumes, respectively. Variable-temperature magnetic susceptibility measurements on polycrystalline samples of 1 and 2 revealed net weak intramolecular antiferromagnetic coupling between metal centers in both compounds with J = -3.77 cm(-1) in 1 and J = -0.88 cm(-1) in 2, the Hamiltonian being defined as H = -JSA.SB. The ability of the bis-bidentate pyrophosphate to mediate magnetic interactions between divalent first row transition metal ions is discussed bearing in mind the number and nature of the interacting magnetic orbitals.

Silver(I) and thallium(I) complexes of a diarylamido-based PNP pincer ligand have been prepared and characterized. The silver complex [(PNP)Ag]2 exists as a dimer both in solution and in the solid state and is stable under an ambient atmosphere. Thallium complex (PNP)Tl is, however, monomeric and acutely sensitive to moisture and air. Both reagents serve to transfer PNP into the coordination sphere of divalent nickel, palladium, and platinum. [(PNP)Ag]2 is able to effect PNP transfer in air, but the transfer to nickel(II) is less efficient than that with the thallium(I) analogue.

The syntheses, characterization, epsilon-caprolactone (CL) polymerization activity, and kinetics investigation of two zinc(II) bis(phenolato)amine complexes L2Zn2 are reported (L = methylamino-N,N-bis(2-methylene-4,6-di-tert-butylphenolato) and/or methylamino-N,N-bis(2-methylene-4-adamantyl-6-tert-butylphenolato)). X-ray crystallographic and 1H NMR studies, including NOESY and PGSE experiments, provided insight into the solid and solution state structures, respectively, as well as evidence for the catalytically active species responsible for the ring-opening polymerization of CL. Additionally, solution polymerizations and kinetic experiments involving (L1)2Zn2 in the presence of benzyl alcohol (BnOH) were performed to elucidate the influence of catalyst structure, solvent, and the concentration dependence of the catalytically active species, CL, and BnOH on the rate and control of poly-epsilon-caprolactone (PCL) formation. The structural, polymerization, and kinetic data support equilibria involving both mononuclear and dinuclear forms of (L1)2Zn2 as well as a monomer-activated route to PCL.

Co(III) complexes of N(3)O-donor tripodal ligands, 2,4-di(tert-butyl)-6-{[bis(2-pyridyl)methyl]aminomethyl}phenolate (tbuL), 2,4-di(tert-butyl)-6-{[bis(6-methyl-2-pyridyl)methyl]aminomethyl}phenolate (tbuL(Mepy)(2)), were prepared, and precursor Co(II) complexes, [Co(tbuL)Cl] (1) and [Co(tbuL(Mepy)(2))Cl] (2), and ternary Co(III) complexes, [Co(tbuL)(acac)]ClO(4) (3), [Co(tbuL)(tbu-cat)] (4), and [Co(tbuL(Mepy)(2))(tbu-SQ)]ClO(4) (5), where acac, tbu-cat, and tbu-SQ refer to pentane-2,4-dionate, 3,5-di(tert-butyl)catecholate, and 3,5-di(tert-butyl)semiquinonate, respectively, were structurally characterized by the X-ray diffraction method. Complexes 3 and 5 have a mononuclear structure with a fac-N(3)O(3) donor set, while 4 has a mer-N(3)O(3) structure. The cyclic voltammogram (CV) of complex 3 exhibited one reversible redox wave centered at 0.93 V (vs Ag/AgCl) in CH(3)CN. Complex 5 was converted to a phenoxyl radical species upon oxidation with Ce(IV), showing a characteristic pi-pi* transition band at 412 nm. The ESR spectrum at low temperature and the resonance Raman spectrum of 3 established that the radical species has a Co(III)-phenoxyl radical bond. On the other hand, the CVs showed two oxidation processes at E(1/2) = 0.01 and E(pa) = 0.92 V for 4 and E(1/2a) = 0.05 and E(1/2b) = 0.69 V for 5. The rest potential of 4 (-0.11 V) was lower than the E(1/2) value, whereas that of 5 (0.18 V) was higher, indicating that the first redox wave of 4 and 5 is assigned to the tbu-cat and the tbu-SQ redox process, respectively. One-electron oxidized 4 showed absorption, resonance Raman, and ESR spectra which are similar to those of 5, suggesting formation of a stable Co(III)-semiquinonate species, which has the same oxidation level of 5. The resonance Raman spectrum of two-electron oxidized 4 showed the nu(8a) bands of the semiquinonate and phenoxyl radical, which were absent in the spectrum of one-electron oxidized 5. Since both oxidized species were ESR inactive at 5 K, the former was concluded to be a biradical species containing semiquinonate and phenoxyl radicals coupled antiferromagnetically and the latter to a species with a coordinated quinone.

Three new bis(aryl)triazene ligands, Ar-NNNH-Ar' [Ar = o-C(6)H(4)-CO(2)Me, Ar' = p-C(6)H(4)-CH(3) (2); Ar = Ar' = o-C(6)H(4)-CO(2)Me (3); Ar = o-C(6)H(4)-SMe, Ar' = p-C(6)H(4)-CH(3)) (4)], have been synthesized. The reaction of 1-4 with PdCl(2)(NCCH(3))(2) in the presence of a base afforded a series of binuclear diamagnetic palladium complexes. In these reactions, ligands 1-3 afforded the palladium(I) complexes [Pd(I)(o-MeO(2)C-C(6)H(4)-NNN-o-C(6)H(4)-CO(2)Me)](2) (5, monoclinic, space group P21/c, a = 8.6070(10) Angstrom, b = 14.3220(10) Angstrom, c = 12.7310(10) Angstrom, beta = 100.2950(10) degrees, Z = 2), [Pd(I)(o-MeO-C(6)H(4)-NNN-o-C(6)H(4)-OMe)](2) (6, triclinic, space group P, a = 6.6288(5) Angstrom, b = 10.2631(10) Angstrom, c = 11.0246(11) Angstrom, alpha = 85.579(6) degrees, beta = 80.885(6) degrees, gamma = 74.607(6) degrees, Z = 1), and [Pd(I)(o-MeO(2)C-C(6)H(4)-NNN-p-C(6)H(4)-CH(3))](2) (7, tetragonal, space group I41/a, a = 20.866(3) Angstrom, b = 20.866(3) Angstrom, c = 13.156(2) Angstrom, Z = 8). In contrast, the reaction of ligand 4 with PdCl(2)(NCCH(3))(2) resulted in the formation of a palladium(II) dimer, [Pd(II)(o-MeS-C(6)H(4)-NNN-p-C(6)H(4)-CH(3))Cl](2) (8, orthorhombic, space group P2(1)2(1)2, a = 10.4058(5) Angstrom, b = 16.2488(8) Angstrom, c = 9.9500(5) Angstrom, Z = 2).

We report on the synthesis of alkynyl ruthenium colorimetric sensors whose receptors are constituted by thiazolidinedione, rhodanine, or barbituric heads as recognition centers for anions. As modifications in the charge density at these recognition centers affect the whole molecule, through the alkynyl ligand acting as a communicating wire, the effects of hydrogen-bonding interactions with the anions were observed with the naked eye and monitored by UV-vis absorption spectrometry. The selectivity of the sensors was improved through electronic modifications of the alkynyl ruthenium subunit: the higher the electron density at the receptor head, the higher the selectivity is. TD-DFT calculations rationalize the long-range electronic communication as a main characteristic of the alkynyl ruthenium species and as a key to improve the selectivity of alkynyl ruthenium-based sensors toward anions.

The purple triiron(II,III,III) complex, [Fe(3)Cl(2)(TMRASQ)(4)(HTMRA)(2)] x C(5)H(12) (1 x C(5)H(12)), where H(2)TMRA is a tetramethyl reductic acid, 4,4,5,5-tetramethyl-2,3-dihydroxy-2-cyclopenten-1-one, and HTMRASQ is the semiquinone form of this ligand, was prepared from (Et(4)N)(2)[Fe(2)OCl(6)] and H(2)TMRA and characterized by X-ray crystallography, Mössbauer spectroscopy, and redox titrations. The physical properties of the complex in solution are consistent with its mixed-valent character, as delineated by a solid-state structure analysis. Assignments of the iron and ligand oxidation states in the crystal were made on the basis of a valence bond sum analysis and the internal ligand geometry. As the first well-characterized iron complex of an ascorbic acid H(2)AA analogue, 1 provides insight into the possible coordination geometry of the family of complexes containing H(2)AA and its analogues. In the presence of air and H(2)TMRA, 1 is able to catalyze the oxidation of cyclohexane to cyclohexanol with remarkable selectivity, but the nature of the true catalyst remains unknown.

Ni(II) complexes of N,N'-di(pyrazin-2-yl)pyridine-2,6-diamine (H2dpzpda) with different anions were synthesized and their structures were determined by X-ray diffraction. Hydrogen bonds between the amino groups and anions assembled the mononuclear molecules into different architectures. The perchlorate complex had a 1-D chain structure, whereas switching the anion from perchlorate to nitrate resulted in a corresponding change of the supramolecular structure from 1-D to 3-D. When the nitrate complex packed with the co-crystallized water, a double chain structure was formed through hydrogen bonding. The magnetic studies revealed values of g = 2.14 and D = 3.11 cm(-1) for [Ni(H2dpzpda)2](ClO4)2 (1) and g = 2.18 and D = 2.19 cm(-1) for [Ni(H2dpzpda)2](NO3)2 (2), respectively.

The chelating behavior of the thiosemicarbazone derivatives of 2-hydroxy-8-R-tricyclo[7.3.1.0.(2,7)]tridecane-13-one (where R = H, CH3, C6H5) towards Co(II), Ni(II) and Cu(II) has been investigated by elemental analysis, molar conductivity measurements, UV-VIS, IR, ESR spectroscopy and thermal studies. It was deduced from the experiments performed that the ligands coordinate to metal ions in different ways--neutral bidentate or mononegative bidentate--depending on the nature of R. Also, if metal acetates are used instead of metal chlorides, the ligands coordinate in a mononegative bidentate fashion, regardless of the nature of R or the thiosemicarbazone type ligand. The antimicrobial activity of the ligands and of the complexes towards samples of Acinetobacter boumanii, Klebsiella pneumoniae, Escherichia coli, Staphylococcus aureus and Pseudomonas aeruginosa was determined.

The effective integration of detailed structural information with computational chemistry, medicinal chemistry, and informatics transforms the dream of virtual screening into reality. One of the most important technologies essential for virtual screening is an effective docking method to find molecules that efficaciously interact with their target molecules. Since an efficient docking method can be a powerful tool for virtual screening, many different approaches to solving docking problems have been proposed. Docking problems have not yet been solved and none of the currently available programs are perfect in predicting all possible scenarios. Despite the limits and imperfections of the methodology, currently available docking methods are very useful for drug discovery. The basic principles and limits of docking methods together with matters for attention in applying the methods are described in this paper.

Protein structure-based molecular design using the computational techniques of protein structure prediction, ligand docking, and virtual screening is an integral part of drug discovery for limiting the application of the structure-based approach to target proteins such as G-protein-coupled receptors (GPCRs). GPCRs play an important role in living organisms and are of major interest to the pharmaceutical industry. However, structural data on ligand-binding forms for GPCRs from experiments to elucidate structural templates for docking simulations are lacking due to the difficulties associated with crystallization and crystallography. Therefore structural prediction of GPCRs in the ligand-bound state using computational methods has been introduced, but the prediction of ligand conformation onto target GPCRs is still constructed manually by human experts. We developed a molecular modeling technique for the prediction of ligand-receptor binding using comparative ligand-binding analysis (CoLBA) that not only considers interaction energy but also the similarity of interaction profiles among ligands. The advantage of CoLBA is that it can facilitate intuitive and flexible screening based on docking results when protein structures with low resolution (or theoretical models) are targeted. We applied CoLBA to ligand-binding prediction in several GPCRs. The predicted ligand-binding models were evaluated in site-directed mutagenesis experiments in collaborative research, and the enrichment rate of activated ligands was compared with random compounds in virtual screening simulations. We propose that CoLBA can be applied in large-scale modeling of ligand-receptor complexes and virtual screening for GPCRs.

Reaction between [VO(acac)(2)] and the ONN donor Schiff base Hsal-ambmz (I) (Hsal-ambmz = Schiff base obtained by the condensation of salicylaldehyde and 2-aminomethylbenzimidazole) resulted in the formation of the complexes [V(IV)O(acac)(sal-ambmz)] (1), [V(V)O(2)(acac-ambmz)] (2) (Hacac-ambmz = Schiff base derived from acetylacetone and 2-aminomethylbenzimidazole), and the known complex [V(IV)O(sal-phen)] (3) (H(2)sal-phen = Schiff base derived from salicylaldehyde and o-phenylenediamine). Similarly, [V(IV)O(acac)(sal-aebmz)] (7) has been isolated from the reaction with Hsal-aebmz (II) (Hsal-aebmz derived from salicylaldehyde and 2-aminoethylbenzimidazole). Aerial oxidation of the methanolic solutions/suspensions of 1 and 7 yielded the dioxovanadium(V) complexes [V(V)O(2)(sal-ambmz)] (4) and [V(V)O(2)(sal-aebmz)] (8), respectively. Reaction of VOSO(4) with II gave [{V(IV)O(sal-aebmz)}(2)SO(4)] (9) and [V(IV)O(sal-aebmz)(2)] (10), along with 3 and 8. Under similar reaction conditions, I gave only [{V(IV)O(sal-ambmz)}(2)SO(4)] (5) and 3 as major products. Treatment of 1 and 7 with benzohydroxamic acid (Hbha) yielded the mixed-chelate complexes [V(V)O(bha)(sal-ambmz)] (6) and [V(V)O(bha)(sal-aebmz)] (11). The crystal and molecular structures of 2, 3.1/2DMF, 7.1/4H(2)O, 8, 9.2H(2)O, 10, and 11 have been determined, confirming the ONN binding mode of the ligands. In complex 10, one of the ligands is coordinated through the azomethine nitrogen and phenolate oxygen only, leaving the benzimidazole group free. In the dinuclear complex 9, bridging functions are the phenolate oxygens from both of the ligands and two oxygens of the sulfato group. The unstable oxoperoxovanadium(V) complex [V(V)O(O(2))(sal-aebmz)] (12) has been prepared by treatment of 7 with aqueous H(2)O(2). Acidification of methanolic solutions of 7 and 10 lead to (reversible) protonation of the bemzimidazole, while 8 was converted to an oxo-hydroxo species. Complexes 2, 4, and 8 catalyze the oxidation of methyl phenyl sulfide to methyl phenyl sulfoxide and methyl phenyl sulfone, a reaction mimicking the sulfideperoxidase activity of vanadate-dependent haloperoxidases. These complexes are also catalytically active in the oxidation of styrene to styrene oxide, benzaldehyde, benzoic acid, and 1-phenylethane-1,2-diol.

As part of an ongoing effort to deliberate synthesis of polynuclear heterometal complexes, we are exploring synthetic routes to high-nuclearity complexes using "metal oximates" as building blocks. Series of tetranuclear linear complex ions of the general types M(A)M(B)M(B)M(A), where M(A) is a trivalent or tetravalent metal ion and M(B) is a divalent metal ion, e.g., Mn(II), have been synthesized by using the dimetal(II) anionic cores, [(M(II)(B))(2)(dfmp)(3)](5)(-) as a bridging ligand for the terminal LM(A) fragments where H(3)dfmp is a dinucleating phenol-oxime ligand, 2,6-diformyl-4-methylphenol oxime, and L denotes a facially coordinating cyclic tridentate amine, 1,4,7-trimethyl-1,4,7-triazacyclononane. The following combinations are reported here, B(III)Mn(II)Mn(II)B(III) (1), Mn(III)Mn(II)Mn(II)Mn(III) (2), Mn(IV)Mn(II)Mn(II)Mn(IV) (3), Fe(III)Mn(II)Mn(II)Fe(III) (4), and Cr(III)Mn(II)Mn(II)Cr(III) (5). The compounds have been characterized spectroscopically and by magnetic susceptibility measurements in the temperature range 2.0-290 K at different field strengths. Complexes 1-4 have also been structurally characterized by single-crystal X-ray diffraction techniques at 100 K. The magnetic behaviors of the compounds indicate weak antiferromagnetic coupling between the manganese(II) centers in the central trisphenoxo-bridged dimanganese(II) core, whereas the coupling between the terminal M(A) and its neighboring Mn(II) center varies and is weak ferromagnetic or antiferromagnetic. The relative interaction intensity in such a series of complexes is discussed. Finally, a profound influence of the charge on the terminal metal ions on the strength of the exchange coupling in the central dimanganese(II) core has been observed and discussed in relation to the covalency of the metal-ligand bonding.

We report the synthesis, spectroscopy, and structural characterization of iron-alkyne and -alkene complexes of the type L(Me)Fe(ligand) [L(Me) = bulky beta-diketiminate, ligand = HCCPh, EtCCEt, CH2CHPh, EtCHCHEt, HCC(p-C6H4OCH3), HCC(p-C6H4CF3)]. The neutral ligand exchanges rapidly at room temperature, and the equilibrium constants have been measured or estimated. The binding affinity toward the low-coordinate Fe follows the trend HCCPh > EtCCEt > CH2CHPh > EtCHCHEt approximately PPh3 > benzene >> N2. This trend is consistent with a model in which pi back-bonding from the formally Fe(I) center is the dominant interaction in determining the relative binding affinities. In nitrogenase, alkynes are reduced while alkenes are unreactive, and this work suggests that the different binding affinities to low-coordinate Fe might explain the differential activity of the enzyme toward these two substrates.

The fluorescence of Tb(3+) is sensitized by complexation with dibutylphosphate (DBP) and tri-n-butylphosphate (TBP). The excitation maximum for the Tb(3+)-DBP complex occurs at 218.5 nm, while that for the Tb(3+)-TBP complex is observed at 228.0 nm. Both complexes yield Tb(3+) fluorescence at 548 nm. The difference in the excitation maxima for the two complexes has been used to advantage for the estimation of DBP in the presence of TBP. DBP is the main degradation product of TBP in the PUREX process and the method described in this work can thus serve as a useful analytical tool in monitoring the quality of the TBP in the process. This method has been shown to be applicable for the estimation of DBP when present to an extent of 0.1-10% of TBP, in TBP/dodecane solutions.

The syntheses, magnetochemistry and crystallography of [Fe(L1)2]I0.5[I3]1.5 (1), [Fe(L1)2][Co(C2B9H11)2]2 (2) and [Fe(L2)2][SbF6]2 (3) (L1 = 2,6-di(pyrazol-1-yl)pyridine; L2 = 2,6-di(3-methylpyrazol-1-yl)pyridine) are described. Compounds 1 and 3 are high-spin between 5-300 K. For 1, this reflects a novel variation of an angular Jahn-Teller distortion at the iron centre, which traps the molecule in its high-spin state. No such distortion is present in 3; rather, the high-spin nature of this compound may reflect ligand conformational strain caused by an intermolecular steric contact in the crystal lattice. Compound 2 exhibits a gradual high --> low spin transition upon cooling with T(1/2) = 318 +/- 3 K, that is only 50% complete. This reflects the presence of two distinct, equally populated iron environments in the solid. One of these unique iron centres adopts the same angular structural distortion shown by 1 and so is trapped in its high-spin state, while the other, which undergoes the spin-crossover, has a more regular coordination geometry. In contrast with 3, the solvated salts [Fe(L2)2][BF4]2 x 4 CH3CN and [Fe(L2)2][ClO4]2 x (CH3)2CO both undergo gradual thermal spin-transitions centred at 175 +/- 3 K.

The cobalt(III) complexes, [(NH3)5CoBr]2+ and [(NH3)5CoI]2+ are reduced by Ti(II) solutions containing Ti(IV), generating nearly linear (zero-order) profiles that become curved only during the last few percent of reaction. Other Co(III)-Ti(II) systems exhibit the usual exponential traces with rates proportional to [Co(III)]. Observed kinetics of the biphasic catalyzed Ti(II)-Co(III)Br and Ti(II)-Co(III)I reactions support the reaction sequence: [Ti(II)(H20)n]2+ + [Ti(IV)F5]- (k1)<==>(k -1) [Ti(II)(H2O)(n-1)]2+ + [(H2O)Ti(IV)F5]-, [Ti(II)(H2O)(n-1)]2+ + Co(III) (k2)--> Ti(III) + Co(II) with rates determined mainly by the slow Ti(IV)-Ti(II) ligand exchange (k1 = 9 x 10(-3) M(-1) s(-1) at 22 degrees C). Computer simulations of the catalyzed Ti(II)-Co(III) reaction in perchlorate-triflate media yield relative rates for reduction by the proposed active [Ti(II)(H2O)(n-1)]2+ intermediate; k(Br)/k(I) = 8.

Redox transmetallation/ligand exchange reactions of lanthanoid metals (Ln), Hg(C6F5)2 and HOAr(OMe) (Ar(OMe) = C6H2-2,6-Bu(t)-4-OMe), in thf (tetrahydrofuran) gave, for Ln = Yb, [Yb(OAr(OMe))2(thf)3], and for Ln = Sm, a mixture of [Sm(II)(OAr(OMe))2(thf)3] and mainly [Sm(III)(Ar(OMe))3(thf)] x thf. X-Ray structure determinations show the divalent complexes to have distorted square-pyramidal stereochemistry with transoid thf and OAr(OMe) ligands in the basal plane. Treatment of [Yb(OAr(OMe))2(thf)3] with diethyl ether or PhMe at room temperature gave [Yb(OAr(OMe))2] or [Yb(OAr(OMe))2] x 0.5 PhMe. For lanthanoids Ln = Nd, Er or Y, the reactions with Hg(C6F5)2 and HOAr(OMe) yielded complex product mixtures, from one of which the novel erbium aryloxide fluoride cage [Er3(OAr(OMe))4(mu2-F)3(mu3-F)2(thf)4] x thf x 0.5 C6H14 was isolated. The cage core consists of a triangle of Er atoms joined to two mu3-fluoride ligands and three further mu2-fluorides bridge adjacent Er atoms. One of the Er atoms is six-coordinate with additionally two OAr(OMe) ligands whilst the other two have one OAr(OMe) and two thf ligands and are seven coordinate. Substitution of Hg(C6F5)2 by Hg(CCPh)2 in the redox transmetallation/ligand exchange reactions gave the new derivatives [Ln(OAr(OMe))3(thf)] x thf (Ln = La, Pr, Nd, Sm, Gd, Ho) in good yields whilst Ln = Yb gave [Yb(OAr(OMe))2(thf)3]. Recrystallisation of [Sm(OAr(OMe))3(thf)] x thf from dme (1,2-dimethoxyethane) yielded [Sm(OAr(OMe))3(dme)]. Structural characterisation of [Ln(OAr(OMe))3(thf)] x thf (Ln = Nd, Ho) and [Sm(OAr(OMe))3(dme)] showed monomeric four-coordinate distorted tetrahedral and five-coordinate distorted square-pyramidal complexes respectively. For the smaller lanthanoids Ln = Y, Er or Lu, reactions with Hg(CCPh)2 and HOAr(OMe) gave the mixed aryloxide/alkynide complexes [Ln(OAr(OMe))2(CCPh)(thf)2]. Oxidation of the divalent ytterbium aryloxide [Yb(OAr(OMe))2(thf)3] by Hg(CCPh)2 in thf gave the analogous [Yb(OAr(OMe))2(CCPh)(thf)2]. The erbium alkynide [Er(OAr(OMe))2(CCPh)(thf)2] x 0.25 C6H14 has distorted square-pyramidal stereochemistry with transoid OAr(OMe) and thf ligands in the basal plane and a rare (for Ln) terminal alkynide ligand in the apical position. The reactive Lu-C bond in the [Lu(OAr(OMe))2(CCPh)(thf)2] complexes could be slowly cleaved by free HOAr(OMe) in hydrocarbon solvents, yielding Lu(OAr(OMe))3 species and fortuitous partial hydrolysis of [Er(Ar(OMe))2(CCPh)(thf)2] gave the dimeric [Er(OAr(OMe))2(mu-OH)2]2.

The complexes [(C-N-C)MX(n)(thf)(m)] with the 'pincer' 2,6-bis(imidazolylidene)pyridine, (C-N-C) = 2,6-bis(arylimidazol-2-ylidene)pyridine, aryl = 2,6-Pr(i)2C6H3, M = V, X = Cl, n = 2, m = 1 1a; M = Cr, X = Cl, n = 2, m = 0, 2a, X = Br, 2b; M = Mn, X = Br, n = 2, m = 0, 3; M = Nb, X = Cl, n = 3, m = 0, 4; and M = U, X = Cl, n = 4, m = 0, 5, were synthesised by (a) substitution of labile tmed (1a), thf (2a, 3, 5) or dme (4) by free (C-N-C) or by (b) reaction of the bisimidazolium salt (CH-N-CH)Br2 with {Cr[N(SiMe3)2]2(thf)2} followed by amine elimination (2b). Attempted alkylation of 1a, 2, 3a and 4 with Grignard or alkyl lithiums gave intractable mixtures, and in one case [reaction of 1a with (mesityl)MgBr] resulted in exchange of Cl by Br (1b). Oxidation of 1a or [(C-N-C)VCl3] with 4-methylmorpholine N-oxide afforded the trans-V(C-N-C)(=O)Cl2, 6, which by reaction with AgBF4 in MeCN gave trans-[V(C-N-C)(=O)(MeCN)2][BF4]2, 7. Reaction of 1a with p-tolyl azide gave trans-V(C-N-C)(=N-p-tolyl)Cl2 8. The complex trans-Ti(C-N-C)(=NBu(t))Cl2, 9, was prepared by substitution of the pyridine ligands in Ti(NBu(t))Cl2(py)3 by C-N-C.

A configuration of ligands around a phosphorus atom in P-chiral dinucleoside monophosphate analogues can be described using DP/LP stereochemical notation, which allows immediate correlation between the notation of configuration and the actual spatial arrangement of the phosphorus ligands. The area of applications of this new stereochemical nomenclature covers dinucleoside units bridged by virtually any type of tri-and tetra-coordinated phosphorus moieties, that is, phosphorothioates, phosphoramidates, phosphoramidites, boranephosphates, methanephosphonates, H-phosphonates, and many others.

The increasing amount of genomic and molecular information is the basis for understanding higher-order biological systems, such as the cell and the organism, and their interactions with the environment, as well as for medical, industrial and other practical applications. The KEGG resource (http://www.genome.jp/kegg/) provides a reference knowledge base for linking genomes to biological systems, categorized as building blocks in the genomic space (KEGG GENES) and the chemical space (KEGG LIGAND), and wiring diagrams of interaction networks and reaction networks (KEGG PATHWAY). A fourth component, KEGG BRITE, has been formally added to the KEGG suite of databases. This reflects our attempt to computerize functional interpretations as part of the pathway reconstruction process based on the hierarchically structured knowledge about the genomic, chemical and network spaces. In accordance with the new chemical genomics initiatives, the scope of KEGG LIGAND has been significantly expanded to cover both endogenous and exogenous molecules. Specifically, RPAIR contains curated chemical structure transformation patterns extracted from known enzymatic reactions, which would enable analysis of genome-environment interactions, such as the prediction of new reactions and new enzyme genes that would degrade new environmental compounds. Additionally, drug information is now stored separately and linked to new KEGG DRUG structure maps.