New organoantimony complexes with the isomers of chlorophenylacetic acid: Syntheses, characterizations and crystal structures of 1D polymeric chain, 2D network structure and 3D framework

A series of novel organoantimony(V) complexes have been synthesised by the reactions of the isomers of chlorophenylacetic acids with triphenylantimony(V) dichloride or tetraphenylantimony(V) bromide in 1:2 or 1:1 stoichiometries. All the complexes have been characterized by elemental analysis, IR and NMR (¹H, ¹³C) spectra analyses; furthermore, complexes 1, 2, 3 and 4 have been determined by X-ray single crystal diffraction. The structure of complexes show that the five-coordinated and six-coordinated antimony(V) atoms adopt distorted trigonal bipyramidal geometry and octahedral geometry. And the structural analyses show that complexes 1 and 3 have 2D network structures; complex 2 possesses a 1D polymeric chain structure and complex 4 has a 3D supramolecular framework.     

Crystallinity of plant epicuticular waxes: electron and X-ray diffraction studies

The crystal structure of the epicuticular waxes of 35 plant species has been examined by electron diffraction and X-ray powder diffraction. The waxes include the most common morphological wax types such as platelets, tubules, films and rodlets. Most of them were prepared with a special mechanical isolation method, which preserves the original crystal structure. Solvent-extracted recrystallized plant waxes were compared with mechanically isolated samples. The waxes were found to occur in three different crystal structures. Most of the waxes exhibited an orthorhombic structure which is the most common for aliphatic compounds. Tubules containing mainly secondary alcohols showed diffraction reflections of a triclinic phase; broad reflection peaks indicated a significant disorder. Ketones, in particular beta-diketone tubules, displayed the reflections of a hexagonal structure. Mixtures of different phases could be identified. For most of the waxes, the 'long spacing' diffraction reflections indicated a layer structure with the characteristics of the major component. Others showed no 'long spacing' reflections indicating a strong disorder of the molecular layers.     

Novel cyclopalladated and coordination palladium and platinum complexes derived from alpha-diphenyl ethanedione bis(thiosemicarbazones): structural studies and cytotoxic activity against human A2780 and A2780cisR carcinoma cell lines

The preparation of new palladium(II) and platinum(II) complexes derived from alpha-diphenyl ethanedione bis(thiosemicarbazone), 1, and alpha-diphenyl ethanedione bis(4-ethylthiosemicarbazone), 2, is described. The palladium complexes 3 and 4 and platinum complexes 5 and 6 have been characterized by elemental analyses, fast atom bombardment mass spectrometry (FAB(+)) and spectroscopic studies (IR, (1)HNMR). The crystal and molecular structures of the dimeric cyclopalladated compound 4 and the mononuclear platinum complex 6 have been determined by single crystal X-ray diffraction. The cytotoxic activity of the free ligands and palladium and platinum complexes against human A2780 and A2780cisR (acquired resistance to cisplatin) epithelial ovarian carcinoma cells lines is also reported. The IC(50) values for compounds 1, 5 and 6 were found to be higher than that of cisplatin but the maximum antiproliferative activity was similar. Furthermore, the compounds largely retain their activity in the A2780cisR cell line, having a much better resistance factor than cisplatin in the pair of cell lines tested.     

Structure and stability of columnar cyclomaltooctaose (gamma-cyclodextrin) hydrate

Rapid recrystallization of cyclomaltooctaose (gamma-cyclodextrin, gamma-CD) from aqueous solution resulted in formation of a columnar structure with only water as the guest molecule. Upon vacuum drying at 90 degrees C for 15 h, gamma-CD, which was initially in the columnar structure, became amorphous. Complementary water vapor sorption and wide-angle X-ray diffractometry experiments were performed on columnar gamma-CD in its vacuum dried and as-precipitated states to elucidate its stability in humid environments and the crystal structure present at varying sorption levels. These experiments show that both types of gamma-CD transform to the cage crystal structure upon exposure to water vapor at 40 degrees C and with an activity of 1.0. Sorption equilibrium is reached long before the crystal structure transformation is complete, indicating that a significant amount of molecular mobility exists in the various hydrated gamma-CD crystal structures.     

Complexes of Starchy Materials with Organic Compounds

The crystal structure of γ-cyclodextrin complexes with several organic compounds have been investigated by X-ray powder method. A two-dimensional tetragonal unit cell having a=b=27.2 Å and a two-dimensional hexagonal unit cell having a=b=32.7 Å, were reasonably proposed for hydrated and anhydrous γ-dextrin complexes, respectively. The change of the crystal structure caused by dehydration seemed to be resulted from the change of the packing arrangement of circular cylinders that are made by coaxial alignment of the dextrin molecules. Results obtained were tentatively applied to consider the 8₁-helical configuration of amylose.     

Synthesis, characterization, structure, molecular modeling studies and biological activity of sterically crowded Pt(II) complexes containing bis(imidazole) ligands

The syntheses, structures and biological evaluation of a series of cisplatin-like complexes containing bis(imidazole) derivatives - the so-called Joseph ligands - are described. Their cytotoxicity is discussed in terms of their polar surface area, rate of aquation, and lipophilicity. The X-ray crystal structure of the platinum diiodido derivative of dimethyl 2-(di(1H-imidazol-2-yl)methyl)malonate) is reported and compared to those of related systems. Molecular modeling studies are focused on the hydrogen bonding properties of such systems, and their relevance to antitumor activity.     

Nickel (II) complexes of naphthaquinone thiosemicarbazone and semicarbazone: synthesis, structure, spectroscopy, and biological activity

Ni(II) complexes of ortho-naphthaquinone thiosemicarbazone and semicarbazone were synthesized and spectroscopically characterized. The X-ray crystal structure of both the complexes describe a distorted octahedral coordination with two tridentate mono-deprotonated ligands. In vitro anticancer studies on MCF-7 human breast cancer cells reveal that the semicarbazone derivative along with its nickel complex is more active in the inhibition of cell proliferation than the thiosemicarbazone analogue.     

Exploiting powder X-ray diffraction for direct structure determination in structural biology: the P2X4 receptor trafficking motif YEQGL

We report the crystal structure of the 5-residue peptide acetyl-YEQGL-amide, determined directly from powder X-ray diffraction data recorded on a conventional laboratory X-ray powder diffractometer. The YEQGL motif has a known biological role, as a trafficking motif in the C-terminus of mammalian P2X4 receptors. Comparison of the crystal structure of acetyl-YEQGL-amide determined here and that of a complex formed with the μ2 subunit of the clathrin adaptor protein complex AP2 reported previously, reveals differences in conformational properties, although there are nevertheless similarities concerning aspects of the hydrogen-bonding arrangement and the hydrophobic environment of the leucine sidechain. Our results demonstrate the potential for exploiting modern powder X-ray diffraction methodology to achieve complete structure determination of materials of biological interest that do not crystallize as single crystals of suitable size and quality for single-crystal X-ray diffraction.     

X-ray diffraction analysis of internal wool lipids

Polarised optical microscopy (POM) and X-ray diffraction techniques were applied to intercellular lipids extracted from wool to study their structural arrangement in order to determine their role in the diffusion properties of wool fibre. Intercellular wool lipids (IWL) arranged as concentrated liposomes were shown to be a good intercellular lipid model, allowing their study by X-ray diffraction techniques. The results confirm that intercellular lipids of wool fibre are organised in a lamellar structure of 5.0–8.0 nm width, termed β-layer, which had been assumed to be lipids arranged as a bilayer. Structurally, internal wool lipids are distributed at least in two domains at low temperatures: an ordered phase made up of ceramides and free fatty acids (FFA) alone, arranged in crystal orthorhombic states separately, and a liquid crystal state when mixed together. At 40 °C there is a reversible phase transition produced by the melt of the crystal orthorhombic states, whereas the liquid crystal state remains until 65 °C.     

Crystal structure determination of the β-cyclodextrin-p-aminobenzoic acid inclusion complex from powder X-ray diffraction data

The 1:1 inclusion complex of β-cyclodextrin and p-aminobenzoic acid was prepared and characterized by TG-DTA. The crystal structure of the complex was solved directly from powder X-ray diffraction data using the direct space approach and refined using Rietveld refinement techniques. The complex crystallizes in monoclinic P2₁ space group, with unit cell parameters a = 20.7890 ?, b = 10.2084 ?, c = 15.1091 ?, β = 110.825°, V = 2997 ?³. The amino group is located at the wide side of the β-cyclodextrin cavity, forming hydrogen bonds with β-cyclodextrin, and the carboxyl group is located at the narrow side. The crystallographic data obtained from powder diffraction data were compared with the single crystallographic data, and the result shows that solving crystal structure of cyclodextrins inclusion complexes of such complexity is accessible to powder diffractionists to some extent.     

X-ray structural study of noncrystalline regenerated Bombyx mori silk fibroin

X-ray diffraction measurements of regenerated Bombyx mori silk fibroin were carried out to determine its structural characteristic from an analysis of differential radial distribution functions (DRDFs). The temperature dependence of X-ray diffraction patterns from noncrystalline and crystal structures of regenerated silk fibroin was investigated using a high temperature furnace. Time resolved X-ray diffraction profiles were also obtained to construct kinematical models of structural changes caused by the addition of water. DRDFs, calculated from the experimental data, were compared with the DRDFs simulated on the basis of the Monte Carlo method. In order to model the noncrystalline structures, structural units were assumed to be parts of the crystalline structure of silk and those with appropriate structural defects reported previously. From the comparison of experimental and simulated DRDFs, it was determined that noncrystalline regenerated silk consisted of locally ordered atomic sheets similar to the atomic arrangement in the silk I crystal (Type-I sheets), and the final state of the structural change was noncrystalline, consisting of small crystallites, the structure of which is similar to that of silk II (Type-II crystallites). Time resolved DRDFs were also qualitatively interpreted by both the ordering of Type-I sheets and structural changes from Type-I to Type-II. The formation of the small Type-II crystallites obtained in this study was consistent with the nucleation of silk II by birefringence measurements of silk glands and the spinneret of Bombyx mori silkworm reported previously. X-ray diffraction should be a useful technique to understand the structural characteristics of noncrystalline organic materials.     

The solution structure of the Sac7d/DNA complex: a small-angle X-ray scattering study.

Small-angle X-ray scattering has been used to study the structure of the multimeric complexes that form between double-stranded DNA and the archaeal chromatin protein Sac7d from Sulfolobus acidocaldarius. Scattering data from complexes of Sac7d with a defined 32-mer oligonucleotide, with poly[d(GC)], and with E. coli DNA indicate that the protein binds along the surface of an extended DNA structure. Molecular models of fully saturated Sac7d/DNA complexes were constructed using constraints from crystal structure and solution binding data. Conformational space was searched systematically by varying the parameters of the models within the constrained set to find the best fits between the X-ray scattering data and simulated scattering curves. The best fits were obtained for models composed of repeating segments of B-DNA with sharp kinks at contiguous protein binding sites. The results are consistent with extrapolation of the X-ray crystal structure of a 1:1 Sac7d/octanucleotide complex [Robinson, H., et al. (1998) Nature 392, 202-205] to polymeric DNA. The DNA conformation in our multimeric Sac7d/DNA model has the base pairs tilted by about 35 degrees and displaced 3 A from the helix axis. There is a large roll between two base pairs at the protein-induced kink site, resulting in an overall bending angle of about 70 degrees for Sac7d binding. Regularly repeating bends in the fully saturated complex result in a zigzag structure with negligible compaction of DNA. The Sac7d molecules in the model form a unique structure with two left-handed helical ribbons winding around the outside of the right-handed duplex DNA.     

Towards bioreductively activated prodrugs: Fe(III) complexes of hydroxamic acids and the MMP inhibitor marimastat

Fe(III)-salen (N,N-bis(salicylidene)-ethane-1,2-diimine) complexes of simple hydroxamic acids and the MMP (matrix metalloproteinase) inhibitor marimastat have been evaluated as hypoxia activated drug carriers. The aceto- (aha), propion- (pha), benzohydroxamato (bha), and marimastat complexes were prepared and characterised by single crystal X-ray diffraction and electrochemical analysis. The hydroxamato ligands form a bidentate chelate to Fe(III) with the remaining octahedral coordination sites occupied by the tetradentate salen ligand. Bonding of the hydroxamato ligands is in the typical motif of the majority of Fe(III) complexes in the literature. The reduction potentials of the complexes are of the order of -1300 mV (vs ferrocene/ferrocenium) and show partial reversibility in the re-oxidation waveforms of the cyclic voltammetry scans. This suggests that the Fe-salen carrier system would provide a suitably redox inert framework yet would release the ligands at hypoxic tumour sites upon reduction to the more labile Fe(II) oxidation state. Furthermore, biological testing of the marimastat complex established that these carriers are stable in non-reducing biological environments and would serve to deliver MMP inhibitors to tumour sites intact.     

Hydrogen-deuterium exchange strategy for delineation of contact sites in protein complexes

We use NMR spectra to determine protein-protein contact sites by observing differences in amide proton hydrogen-deuterium exchange in the complex compared to the free protein in solution. Aprotic organic solvents are used to preserve H/D labeling patterns that would be scrambled in water solutions. The binding site between the mammalian co-chaperone Aha1 with the middle domain of the chaperone Hsp90 obtained by our H/D exchange method corresponds well with that in the X-ray crystal structure of the homologous complex from yeast, even to the observation of a secondary binding site. This method can potentially provide data for complexes with unknown structure and for large or dynamic complexes inaccessible via NMR and X-ray methods.     

Productive and nonproductive binding to ribonuclease A: X-ray structure of two complexes with uridylyl(2',5')guanosine

Guanine-containing mono- and dinucleotides bind to the active site of ribonuclease A in a nonproductive mode (retro-binding) (Aguilar CF, Thomas PJ, Mills A, Moss DS, Palmer RA. 1992. J Mol Biol 224:265-267). Guanine binds to the highly specific pyrimidine site by forming hydrogen bonds with Thr45 and with the sulfate anion located in the P1 site. To investigate the influence of the anion present in the P1 site on retro-binding, we determined the structure of two new complexes of RNase A with uridylyl(2',5')guanosine obtained by soaking two different forms of pre-grown RNase A crystals. In one case, RNase A was crystallized without removing the sulfate anion strongly bound to the active site; in the other, the protein was first equilibrated with a basic solution to displace the anion from the P1 site. The X-ray structures of the complexes with and without sulfate in P1 were refined using diffraction data up to 1.8 A (R-factor 0.192) and 2.0 A (R-factor 0.178), respectively. The binding mode of the substrate analogue to the protein differs markedly in the two complexes. When the sulfate is located in P1, we observe retro-binding; whereas when the anion is removed from the active site, the uridine is productively bound at the B1 site. In the productive complex, the electron density is very well defined for the uridine moiety, whereas the downstream guanine is disordered. This finding indicates that the interactions of guanine in the B2 site are rather weak and that this site is essentially adenine preferring. In this crystal form, there are two molecules per asymmetric unit, and due to crystal packing, only the active site of one molecule is accessible to the ligand. Thus, in the same crystal we have a ligand-bound and a ligand-free RNase A molecule. The comparison of these two structures furnishes a detailed and reliable picture of the structural alterations induced by the binding of the substrate. These results provide structural information to support the hypotheses on the role of RNase A active site residues that have recently emerged from site-directed mutagenesis studies.     

Structure and stability of columnar cyclomaltohexaose (alpha-cyclodextrin) hydrate

Rapid recrystallization of cyclomaltohexaose (alpha-cyclodextrin, alpha-CD) from aqueous solution resulted in formation of the columnar crystal structure of alpha-CD containing only water as the guest molecule. Complementary water vapor sorption and wide-angle X-ray diffractometry (WAXD) experiments were performed on the alpha-CD columnar structure to elucidate the crystal structure present at varying sorption levels. Equilibrium isothermal water vapor sorption experiments at 40 degrees C revealed that the alpha-CD columnar structure is unstable above a water activity of approximately 0.67. This was confirmed by WAXD diffractograms collected over time, which further revealed that alpha-CD columnar structure undergoes a phase transformation to the cage structure after approximately 0.25 h at 40 degrees C and a water activity of 1.0.     

Activity of crystalline turkey egg white lysozyme.

Hexagonal crystals of turkey egg white lysozyme have been examined for activity in order to evaluate their potential for use in time-resolved X-ray crystallographic experiments. Substrates used in this study were hexa-N-acetylglucosamine (hexa-GlcNAc) and a modified analogue of hexa-GlcNAc where the terminal sugar ring was opened by reduction with tritiated sodium borohydride. This gave a labeled beta-N-acetylglucosaminitol unit at the sixth position of the sugar chain and allowed easy quantitation of enzymatic cleavage on TLC plates. Using these substrates, it has been shown that turkey egg white lysozyme is enzymatically active in the crystal. Enzyme dispersed in the buffer surrounding the crystal does not show detectable activity under conditions relevant to an X-ray experiment. Unmodified hexa-GlcNAc is hydrolyzed into di-, tri-, and tetrasaccharides in the crystal. This cleavage pattern is different from that obtained with hen egg white lysozyme in solution and likely causes of the differences are discussed. The reduced radiolabeled oligosaccharide has a unique cleavage pattern with trisaccharides as the products. The specific activity of the enzyme with the radiolabelled analogue was 9.8 (+/- 1.0) x 10(-7) mmol/min/mg protein at 22 degrees C in the crystal.     

Transition metal complexes of phenanthrenequinone thiosemicarbazone as potential anticancer agents: synthesis,structure, spectroscopy,electrochemistry and in vitro anticancer activity against human breast cancer cell-line,T47D

The thiosemicarbazone derivative of 9,10-phenanthrenequinone, 1, and its metal complexes were synthesized. The X-ray crystal structure for 1 confirms the presence of the E tautomeric arrangement in this compound. Its copper complex shows 1:1 stoichiometry while nickel and cobalt compounds show 1:2 stoichiometry. The X-ray crystal structure of the nickel complex indicates two tridentate ligands coordinating in the thiolato form yielding an octahedral geometry for the 'mer' isomer. The copper complex exhibits maximum antiproliferative activity against human breast cancer cell-line, T47D probably due to inhibition of steroid binding to the cognitive receptor or by preventing dimerization of the estrogen receptor.     

Vancomycin forms ligand-mediated supramolecular complexes

The emergence of resistance to vancomycin and related glycopeptide antibiotics is spurring efforts to develop new antimicrobial therapeutics. High-resolution structural information about antibiotic-ligand recognition should prove valuable in the rational design of improved drugs. We have determined the X-ray crystal structure of the complex of vancomycin with N-acetyl-d-Ala-d-Ala, a mimic of the natural muramyl peptide target, and refined this structure at a resolution of 1.3 Å to R and R_free values of 0.172 and 0.195, respectively. The crystal asymmetric unit contains three back-back vancomycin dimers; two of these dimers participate in ligand-mediated face-face interactions that produce an infinite chain of molecules running throughout the crystal. The third dimer packs against the side of a face-face interface in a tight “side-side” interaction that involves both polar contacts and burial of hydrophobic surface. The trimer of dimers found in the asymmetric unit is essentially identical to complexes seen in three other crystal structures of glycopeptide antibiotics complexed with peptide ligands. These four structures are derived from crystals belonging to different space groups, suggesting that the trimer of dimers may not be simply a crystal packing artifact and prompting us to ask if ligand-mediated oligomerization could be observed in solution. Using size-exclusion chromatography, dynamic light scattering, and small-angle X-ray scattering, we demonstrate that vancomycin forms discrete supramolecular complexes in the presence of tripeptide ligands. Size estimates for these complexes are consistent with assemblies containing four to six vancomycin monomers.     

Studies on Xylanase from Microorganisms

X-Ray diffraction analysis of the α-cyclodextrin complexes with a number of organic guest molecules were carried out. Several different kinds of the X-ray diffraction patterns were obtained. It was found that different guest molecules enclosed within the void of the dextrin cause large changes in the diffraction patterns of the complexes. However, most of the diffraction patterns could be reasonably interpreted in terms of the hexagonal unit cells with minor differences in the unit cell dimensions ranging a = b = 27.0 ~ 27.8 Å and c = 14.7 ~ 16.7 Å. The crystal structure of the complexes could be accounted for by a closest packing of channel cylinders that are made by coaxial alignments of the dextrin molecules and the cage structure in the crystal, in which the dextrin molecules align non-coaxially, may not be plausible.