Basic Structural Motif Research Articles

Structure and properties of a heterocomplex compound based on lead(II) hexafluoroacetyl acetonate and copper(II) trifluoroacetyl acetonate Cu(tfa)2·Pb(hfa)2

The crystals of a heterobimetallic complex based on lead(II) hexafluoroacetyl acetonate and copper(II) trifluoroacetyl acetonate were investigated by X-ray diffraction. Crystal data for Cu(tfa)2·Pb(hfa)2: a = 9.3991(4) A, b = 11.7816(5) A, c = 13.9736(5) A, α = 88.311(2)°, β = 89.972(1)°, γ = 76.326(1)°, space group P-1, Z = 2, d calc = 2.190 g/cm3. The basic structural motif for the complexes is coordination polymer in the form of chains of alternating complex molecules. The Cu(tfa)2 molecules have a trans configuration. The results of a DTA-TG analysis of the compound are given.

Coordination structures of the silver ion: infrared photodissociation spectroscopy of Ag+(NH3)n (n = 3–8)

Infrared (IR) spectra are measured for Ag(+)(NH(3))(n) with n = 3-8 in the NH-stretch region using photodissociation spectroscopy. The spectra of n = 3 and 4 exhibit absorption features only near the frequencies of the isolated NH(3), indicating that every NH(3) molecule is coordinated individually to Ag(+). For n >or= 5, the occupation of the second shell is evidenced by lower-frequency features characteristic of hydrogen bonding between NH(3) molecules. Density functional theory and MP2 calculations are carried out in support of the experiments. A detailed comparison of the experimental and theoretical IR spectra reveals the preference for a tetrahedral coordination in the n = 5 and 6 ions. Likewise, most of the features observed in the spectra of n = 7 and 8 can be assigned to isomers containing a tetrahedrally coordinated inner shell as the basic structural motif. These results signify that the ammonia-solvated Ag(+) ion has a propensity toward a coordination number of four and the resulting tetrahedral Ag(+)(NH(3))(4) complex forms the central core of further solvation process.

The structure of tetrahedral network glass forming systems at intermediate and extendedlength scales

The atomic scale structure of network glass forming systems with theAX2 stoichiometry is considered and particular attention is paid to the systemsGeSe2,ZnCl2 and GeO2 for which the partial-pair correlation functions have been measured by using the method ofisotopic substitution in neutron diffraction. The basic structural motif in all of these systems is theA(X1/2)4 tetrahedron, although homopolar bonds are also a significant feature in the case of liquid and glassyGeSe2. The structural motifs link to form a network in which ordering occurs on two differentlength scales at distances greater than the nearest-neighbour. One of these length scales isassociated with an intermediate range and manifests itself by the appearance of a so-calledfirst sharp diffraction peak in the measured diffraction patterns at a scattering vectorkFSDP where and rAX is the nearest-neighbour distance for unlike chemical species. The other is associated withan extended range, which has a periodicity given by , where kPP denotes the scattering vector of the principal peak and . The nature and interplay between the ordering on the intermediate and extended lengthscales is characterized and discussed.

The Structure of Ferrihydrite, a Nanocrystalline Material.

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Influence of Copper Salts, Solvents, and Ligands on the Structures of Precatalytic Phosphoramidite Copper Complexes for Conjugate Addition Reactions

For copper-catalyzed enantioselective conjugate addition reactions of organozinc reagents, the available knowledge about the mechanism and the structures involved is still insufficient to understand in detail the strong influences of solvent, salt, and ligand size, or to enable a rational control of this reaction. Screening with three phosphoramidite ligands and four copper(I) salts using NMR spectroscopy has revealed a binuclear copper complex with mixed trigonal/tetrahedral stereochemistry as the basic structural motif of the ground state of precatalysts with highly stereoselective ligands. Ligands with smaller amine moieties allow higher coordination numbers and higher aggregation levels, leading to reduced ee values. Since the ESI mass spectra of several precatalytic copper halide complexes show a striking correlation with the structures observed in solution, ESI-MS may be used as a fast tool to determine the maximum number of phosphoramidite ligands attached to copper.

The Structure of Ferrihydrite, a Nanocrystalline Material

Despite the ubiquity of ferrihydrite in natural sediments and its importance as an industrial sorbent, the nanocrystallinity of this iron oxyhydroxide has hampered accurate structure determination by traditional methods that rely on long-range order. We uncovered the atomic arrangement by real-space modeling of the pair distribution function (PDF) derived from direct Fourier transformation of the total x-ray scattering. The PDF for ferrihydrite synthesized with the use of different routes is consistent with a single phase (hexagonal space group P6(3)mc; a = approximately 5.95 angstroms, c = approximately 9.06 angstroms). In its ideal form, this structure contains 20% tetrahedrally and 80% octahedrally coordinated iron and has a basic structural motif closely related to the Baker-Figgis delta-Keggin cluster. Real-space fitting indicates structural relaxation with decreasing particle size and also suggests that second-order effects such as internal strain, stacking faults, and particle shape contribute to the PDFs.

Monothiol glutaredoxins: a common domain for multiple functions

Monothiol glutaredoxins with the CGFS sequence at the active site are widespread among prokaryotes and eukaryotes. Two subclasses exist, those with a single glutaredoxin domain and those with a thioredoxin-like region followed by one or more glutaredoxin domains. Studies in Saccharomyces cerevisiae have demonstrated the role of the Grx5 protein in the biogenesis of iron-sulfur clusters. Grx5 homologues in other eukaryotes could carry out similar functions. Two S. cerevisiae monothiol glutaredoxins with the thioredoxin-like extension, Grx3 and Grx4, are modulators of the transcriptional activator Aft1, which regulates iron uptake in yeast. The human PICOT protein is a Grx3/Grx4 homologue with the same hybrid primary structure that regulates protein kinase C activity and may participate in physiological processes such as control of cardiac function. Therefore, monothiol glutaredoxins share a common basic structural motif and biochemical mechanism of action, while participating in a diversity of cellular functions as protein redox regulators.

Structural disorder of the atom cluster in a highly-ordered decagonal quasicrystal of Al72Ni20Co8

Spherical-aberration-corrected high-resolution transmission electron microscopy observation has been carried out for a highly ordered decagonal quasicrystal of water-quenched Al72Ni20Co8. Atom clusters with a 2 nm diameter, which are considered to be basic structural motifs of the present alloy, show triangular shaped atomic arrangements in the central part, as observed previously by high-angle annular dark-field scanning transmission electron microscopy. The triangular arrangement is not identical for all the atom clusters but varies from cluster to cluster, although the orientational order of the triangles agrees well with the quasiperiodic order. The present results indicate that decagonal Al72Ni20Co8 with a highly perfect quasiperiodic order contains a relatively large amount of structural disorder inside the atom cluster, which may be caused by a local relaxation to form the highly-ordered quasiperiodic arrangement of the atom-cluster.

Cover Picture: A New Basic Motif in Cyanometallate Coordination Polymers: Structure and Magnetic Behavior of M(μ‐OH2)2[Au(CN)2]2 (M=Cu, Ni) (Chem. Eur. J. 26/2006)

Watery bridges play the key role in a new basic structural motif exhibited by M(μ‐OH2)2[Au(CN)2]2 (M=Cu, Ni) materials. This motif is unique for cyanometallate‐based polymers and rare in aqueous coordination chemistry: a 1D chain propagated by double aqua‐bridges. These metal–water chains, shown here cascading down a rock‐studded waterfall, aggregate through hydrogen bonds to form stacked ribbons in 3D. The magnetic properties of both compounds were studied by using short‐lived subatomic muons as highly sensitive local probes in zero‐magnetic field, as shown here. D. B. Leznoff, J. E. Sonier et al. describe these CuII and NiII cyanoaurate coordination polymers on page 6748 ff.

A New Basic Motif in Cyanometallate Coordination Polymers: Structure and Magnetic Behavior of M(μ‐OH2)2[Au(CN)2]2(M=Cu, Ni)

The structures of two cyanoaurate-based coordination polymers, M(mu-OH(2))(2)[Au(CN)(2)](2) (M=Cu, Ni), were determined by using a combination of powder and single-crystal X-ray diffraction techniques. The basic structural motif for both polymers contains rarely observed M(mu-OH(2))(2)M double aqua-bridges, which generate an infinite chain; two trans [Au(CN)(2)](-) units also dangle from each metal center. The chains form ribbons that interact three dimensionally through CNH hydrogen bonding. The magnetic properties of both compounds and of the dehydrated analogue Cu[Au(CN)(2)](2) were investigated by direct current (dc) and alternating current (ac) magnetometry; muon spin-relaxation data was also obtained to probe their magnetic properties in zero-field. In M(mu-OH(2))(2)[Au(CN)(2)](2), ferromagnetic chains of M(mu-OH(2))(2)M are present below 20 K. Interchain magnetic interactions mediated through hydrogen bonding, involving water and cyanoaurate units, yield a long-range magnetically ordered system in Cu(mu-OH(2))(2)[Au(CN)(2)](2) below 0.20 K, as indicated by precession in the muon spin polarization decay. Ni(mu-OH(2))(2)[Au(CN)(2)](2) undergoes a transition to a spin-glass state in zero-field at 3.6 K, as indicated by a combination of muon spin-relaxation and ac-susceptibility data. This transition is probably due to competing interactions that lead to spin frustration. A phase transition to a paramagnetic state is possible for Ni(mu-OH(2))(2)[Au(CN)(2)](2) upon application of an external field; the critical field was determined to be 700 Oe at 1.8 K. The dehydrated compound Cu[Au(CN)(2)](2) shows weak antiferromagnetic interactions at low temperatures.

Infrared spectroscopy of Li(NH3)n clusters for n=4–7

Infrared spectra of Li(NH3)(n) clusters as a function of size are reported for the first time. Spectra have been recorded in the N-H stretching region for n=4-->7 using a mass-selective photodissociation technique. For the n=4 cluster, three distinct IR absorption bands are seen over a relatively narrow region, whereas the larger clusters yield additional features at higher frequencies. Ab initio calculations have been carried out in support of these experiments for the specific cases of n=4 and 5 for various isomers of these clusters. The bands observed in the spectrum for Li(NH3)(4) can all be attributed to N-H stretching vibrations from solvent molecules in the first solvation shell. The appearance of higher frequency N-H stretching bands for n > or =5 is assigned to the presence of ammonia molecules located in a second solvent shell. These data provide strong support for previous suggestions, based on gas phase photoionization measurements, that the first solvation shell for Li(NH3)(n) is complete at n=4. They are also consistent with neutron diffraction studies of concentrated lithium/liquid ammonia solutions, where Li(NH3)(4) is found to be the basic structural motif.

Stereodynamics of Chlorine Atom Reactions with Organic Molecules

A series of recent experimental and computational studies has explored how the dynamics of hydrogen abstraction from organic molecules are affected by the presence of functional groups in the molecule and by basic structural motifs such as strained ring systems. Comparisons drawn between reactions of Cl atoms with alkanes such as ethane, Cl + CH3CH3--> HCl + CH3CH2, which serve as benchmark systems, and with functionalized molecules such as alcohols, amines, and alkyl halides, Cl + CH3X --> HCl + CH2X (X = OH, NH2, halogen, etc.) expose a wealth of mechanistic detail. Although the scattering dynamics, as revealed from measured angular distributions of the velocities of the HCl with quantum-state resolution, show many similarities, much-enhanced rotational excitation of the HCl products is observed from reactions of the functionalized molecules. The degree of rotational excitation of the HCl correlates with the dipole moment of the CH2X radical and is thus attributed, at least in part, to post-transition-state dipole-dipole interactions between the separating, polar reaction products. This interpretation is supported by direct dynamics trajectories computed on-the-fly, and the HCl rotation is thus argued to serve as an in situ probe of the angular anisotropy of the reaction potential energy surface in the post-transition-state region. Comparisons between the dynamics of reactions of dimethyl ether and the three- and four-membered-ring compounds oxirane (c-C2H4O) and oxetane (c-C3H6O) raise questions about the role of reorientation of the reaction products on a time scale commensurate with their separation. The shapes and structures of polyatomic molecules are thus demonstrated to have important consequences for the stereodynamics of these direct abstraction reactions.

Oligomerization of Cyclohexylisonitrile by tBuELi2 (E = P, As)

The reaction of tBuAsLi2 with cHexNC in THF at 20 °C leads to a trimerization of the isonitrile. Crystallization from cyclohexane/diglyme gave the salt [Li4{tBuAs(CNcHex)3}2(diglyme)2] (1). In contrast to that, six molecules of cHexNC were consumed in a similar reaction with tBuPLi2 in THF at 20 °C. Recrystallization from DME gave the salt [Li2{tBuP(CNcHex)5(CH)}(DME)2] (2). By treatment of the reaction mixture containing 2 with wet THF, the octanuclear Li+ complex [Li8(O)(cHexNC(H)NHexc)6]·THF (3) was obtained. The existence of 3 is a strong hint at the intermediate NcHex, which had reacted with the isonitrile to give the carbodiimide cHexNCNcHex. Reduction of the carbodiimide with excess tBuPLi2 is probably responsible for the formation of the anion [cHexNC(H)NcHex]- in 3. 1−3 have been characterized by NMR and IR spectroscopy as well as by X-ray analyses. According to this, 1 can be described as a vicinal dilithiated amine in which one negative charge is delocalized over a allylic C3 sequence connected to imine functions and the other negative charge is more or less localized at a nitrogen atom. This arrangement forms dimers in the solid state with a 10-membered LiNC ring. The basic structural motif in 2 is the four-membered EC4 ring already observed in 1 with two additional units of cHexNC and one CH unit, which form a five-membered N2C3 ring. In 1 and 2 the isonitrile molecules are connected to each other by head-to-head linking. 3 consists of an O-centered Li8-cube, the faces which are capped by six anions [cHexNC(H)NcHex]-.

New Model for Crystalline Polyglutamine Assemblies and Their Connection with Amyloid Fibrils

Based on the interpretation of X-ray diffraction data reported for crystals of the poly-L-glutamine-rich 19-peptide D(2)Q(15)K(2), Perutz et al. (Proc. Natl. Acad. Sci. USA 2002, 99, 5591-5595) proposed that hollow, water-filled nanotubes are the basic structural motif of amyloid fibers. We are able to offer an alternative interpretation for the same X-ray diffraction data. Our proposed structure consists of beta-sheets, limited in size in the chain direction that stack at an intersheet distance of 0.83 nm to form cross-beta crystallites. The beta-sheets are composed of individual D(2)Q(15)K(2) molecules hydrogen bonding together in the a direction. The relatively linear interchain amide hydrogen bonds in this growth direction occur at two sites: (i) between neighboring backbone amides and (ii) between adjacent (glutamine) side chain amides decorating both surfaces of the beta sheet. The polyQ sub-lattice unit cell is orthorhombic with parameters a =0.950 nm, b = 1.660 nm, and c = 0.695 nm; contains two beta-sheet segments; and has a calculated density of 1.54 g cm(-3). A key ingredient in the proposed structure is the locking of the Q side chains by hydrogen bonding, which allow high-density packing. In addition, there is evidence suggesting that the D(2)Q(15)K(2) molecules adopt a once-folded hairpin conformation.

Design, synthesis and characterization of monomolecular interfacial layers

We have designed a series of monomolecular films comprised of four basic structural motifs. We have used these films for a variety of purposes, ranging from support structures for chromophore arrays to the creation of selective and biomimetic interfaces. We will discuss the several different types of interfacial binding chemistry that are used in the construction of these interfacial films, for both monomeric and polymeric layer structures. Following a discussion of the construction of the adlayers, we describe several uses of these assemblies, in areas ranging from adsorption to optical signal processing, and the formation of biomimetic interfacial structures.

Phosphorylation of Conserved Casein Kinase Sites Regulates cAMP-response Element-binding Protein DNA Binding in Drosophila

The Drosophila homolog of cAMP-response element-binding protein (CREB), dCREB2, exists with serine 231, equivalent to mammalian serine 133, in a predominantly phosphorylated state. Thus, unlike the mammalian protein, the primary regulation of dCREB2 may occur at a different step from serine 231 phosphorylation. Although bacterially expressed dCREB2 bound cAMP-response element sites, protein from Drosophila extracts was unable to do so unless treated with phosphatase. Phosphorylation of recombinant protein by casein kinase (CK) I or II, but not calcium-calmodulin kinase II or protein kinase A, inhibited DNA binding. Up to four conserved CK sites likely to be phosphorylated in vivo were responsible for this effect, and these sites were phosphorylated by a kinase present in Drosophila cell extracts that biochemically resembles CKII. We propose that the relative importance of different signaling pathways in regulating CREB activity may differ between Drosophila and mammals. In Drosophila, the dephosphorylation of CK sites appears to be the major regulatory step, while phosphorylation of serine 231 is necessary but secondary.

Motor-protein "roundabouts": microtubules moving on kinesin-coated tracks through engineered networks.

Nanotechnology promises to enhance the functionality and sensitivity of miniaturized analytical systems. For example, nanoscale transport systems, which are driven by molecular motors, permit the controlled movement of select cargo along predetermined paths. Such shuttle systems may enhance the detection efficiency of an analytical system or facilitate the controlled assembly of sophisticated nanostructures if transport can be coordinated through complex track networks. This study determines the feasibility of complex track networks using kinesin motor proteins to actively transport microtubule shuttles along micropatterned surfaces. In particular, we describe the performance of three basic structural motifs: (1) crossing junctions, (2) directional sorters, and (3) concentrators. We also designed track networks that successfully sort and collect microtubule shuttles, pointing the way towards lab-on-a-chip devices powered by active transport instead of pressure-driven or electroosmotic flow.

Synthesis and Structural Study of Two New Heparin‐Like Hexasaccharides.

Two new heparin-like hexasaccharides, 5 and 6, have been synthesised using a convergent block strategy and their solution conformations have been determined by NMR spectroscopy and molecular modelling. Both hexasaccharides contain the basic structural motif of the regular region of heparin but with negative charge distributions which have been designed to get insight into the mechanism of fibroblast growth factors (FGFs) activation.

Molecular evolution of CXC chemokines: extant CXC chemokines originate from the CNS

The mammalian CXC chemokine system comprises 16 ligands and six receptors, and its actions stretch well beyond the immune system. Recent elucidation of the pufferfish genome, a representative of an evolutionary ancient vertebrate class, has enabled analysis of the mammalian CXC chemokine system in a phylogenetic context. Comparison of the phylogenies of vertebrate CXC chemokines revealed that fish and mammals have found different solutions to similar problems, grafted on the same basic structural motif. Phylogenetic analyses showed that the large, highly redundant CXC chemokine family is a very recent phenomenon that is exclusive to higher vertebrates. Moreover, its ancestral role is found within the central nervous system and not within the immune system.

Non-pungent capsaicinoids from sweet pepper synthesis and evaluation of the chemopreventive and anticancer potential.

Capsiate, the non-pungent ester isoster of capsaicin, and its dihydroderivative are the major capsaicinoids of sweet peppers. The remarkable difference between the sensory properties of capsaicin vs capsiate is solely due to the way the vanillyl and the acyl moieties of this basic structural motif are linked, via an amide bond in capsaicin-type compounds and via an ester bond in capsiate-type compounds. Since capsaicin induces apoptosis in tumoral cells by a vanilloid receptor type 1(VR1)-independent pathway, we examined the effects of capsiates derived from sweet peppers in the ROS generation and induction of apoptosis in tumoral cells and if these are mediated independently from VR1. We have developed an expeditious synthesis of capsiates based on the esterification of vanillol with the Mitsunobu protocol. Capsiate-induction of apoptosis, generation of reactive oxygen species and disruption of the mitochondria transmembrane potential in tumoral cell lines were measured by flow cytometry. Chemopreventive activity was studied in a two-stage mouse skin carcinogenesis assay. Capsiates induce apoptosis that was preceded by an increase in the production of reactive oxygen species and by a subsequent loss of mitochondria transmembrane potential (DeltaPsi(m)). These properties were retained in simplified synthetic analogues of natural capsiates, one of which (nor-dihydrocapsiate) showed powerful chemopreventive activity. These results suggest that capsiates and related synthetic analogues target a variety of pathways involved in cancer development and inflammation, and have considerable potential for dietary health benefits as well as for pharmaceutical development.