Buddenbrockia is a Cnidarian worm

A major evolutionary divide occurs in the animal kingdom between the so-called radially symmetric animals, which includes the cnidarians, and the bilaterally symmetric animals, which includes all worm phyla. Buddenbrockia plumatellae is an active, muscular, parasitic worm that belongs to the phylum Myxozoa, a group of morphologically simplified microscopic endoparasites that has proved difficult to place phylogenetically. Phylogenetic analyses of multiple protein-coding genes demonstrate that Buddenbrockia is a cnidarian. This active muscular worm increases the known diversity in cnidarian body plans and demonstrates that a muscular, wormlike form can evolve in the absence of overt bilateral symmetry.

The structure of echovirus type 12 bound to a two-domain fragment of its cellular attachment protein decay-accelerating factor (CD 55)

Echovirus type 12 (EV12), an enterovirus of the Picornaviridae family, uses the complement regulator, decay-accelerating factor (DAF, CD55) as a cellular receptor. We have calculated a three-dimensional reconstruction of EV12 bound to a fragment of DAF, consisting of short consensus repeat domains 3 and 4, from cryo-negative stain electron microscopy data (EMD #1057). This shows that, as for an earlier reconstruction of the related echovirus type 7 bound to DAF, attachment is not within the viral canyon but occurs close to the two-fold symmetry axes. Despite this general similarity, our reconstruction reveals a receptor interaction that is quite different from that observed for EV7. Fitting of the crystallographic co-ordinates for DAF34 and EV11 into the reconstruction shows a close agreement between the crystal structure of the receptor fragment and the density for the virus-bound receptor, allowing unambiguous positioning of the receptor with respect to the virion (PDB #1UPN). Our finding that the mode of virus-receptor interaction in EV12 is distinct from that seen for EV7 raises interesting questions regarding the evolution and biological significance of the DAF-binding phenotype in these viruses.

Molecular structures of trimethylchlorogermane, (CH3)(3)GeCl, and trimethylbromogermane, (CH3)(3)GeBr, obtained by gas-phase electron diffraction and theoretical calculations

The structures of trimethylchlorogermane ((CH3)(3)GeCl) and trimethylbromogermane ((CH3)(3)GeBr) have been determined by gas-phase electron diffraction (GED), augmented by the results from ab initio calculations employing second-order Moller-Plesset (MP2) level of theory and the 6-311+G(d) basis set. All the electrons were included in the correlation calculation. The results from the ab initio calculations indicated that these molecules have C-3v symmetry, and models with this symmetry were used in the electron diffraction analysis. The results for the principal distances (r(g)) and angles (angle(alpha)) from the combined GED/ab initio study of trimethylchlorogermane (with estimated 2sigma uncertainties) are: r(Ge-C) = 1.950(4) Angstrom, r(Ge-Cl) = 2.173(4) Angstrom, r(C-H) = 1.090(9) Angstrom, angleCGeC = 112.7(7)degrees, angleCGeCl = 106.0(8)degrees, angleGeCH = 107.8(12)degrees. The results for the principal distances (r(g)) and angles (angle(alpha)) from the combined GED/ab initio study of trimethylbromogermane (with estimated 2sigma uncertainties) are: r(Ge-C) = 1.952(7) Angstrom, r(Ge-Br) = 2.325(4) Angstrom, r(C-H) = 1. 140(28) Angstrom, angleCGeC = 114.2(11)degrees, angleCGeBr = 104.2(13)degrees, angleGeCH 106.9(43)degrees. Local C-3v symmetry and staggered conformation were assumed for the methyl groups.

The photodimerisation of the alpha- and beta-forms of trans-cinnamic acid: a study of single crystals by vibrational microspectroscopy

Infrared and Raman microspectroscopy have been used to follow the photodimerisation reactions of single crystals, the alpha- and beta-forms of trans-cinnamic acid. This approach allows the starting materials and products -alpha-truxillic acid that has C-i symmetry and beta-truxinic acid, which has C-s symmetry-to be identified. It also allows the topotactic nature of the reaction to be confirmed. Attempts to produce the poorly-defined unreactive gamma-form of trans-cinnamic acid resulted only in a mixture of the alpha- and beta-forms. The findings suggest a wide role for these spectroscopic methods in monitoring solid-state organic reactions. (C) 2002 Elsevier Science B.V. All rights reserved.

Synthesis and crystal structure of the thiophene-3-acetonitrile complex fac-[Mo(CO)(3){NCCH2(C4H3S-3)}(3)]

Reaction of fac-[ Mo( CO)(3)( NCMe)(3)] with three equivalents of NCCH2(C4H3S- 3) in acetonitrile gives the tris(thiophene- 3- acetonitrile) complex, fac-[Mo(CO)(3){NCCH2(C4H3S-3)}(3)] (1) in 7% yield. Complex 1 crystallizes out in the orthorhombic space group Pnma with a = 12.714( 17), b = 16.41( 2), c = 11.304(16) Angstrom, Z = 4. The structure has crystallographic m symmetry and the metal is in an almost perfect octahedral environment, with a facial arrangement of carbonyl and thiophene- 3- acetonitrile groups. The thiophene rings are disordered.

Dinuclear complexes of M-II thiocyanate (M = Ni and Cu) containing a tridentate Schiff-base ligand: synthesis, structural diversity and magnetic properties

A dinuclear Ni-II complex, [Ni-2(L)(2)(H2O)(NCS)(2)]center dot 3H(2)O (1) in which the metal atoms are bridged by one water molecule and two mu(2)-phenolate ions, and a thiocyanato-bridged dimeric Cull complex, [Cu(L)NCS](2) (2) [L = tridentate Schiff-base ligand, N-(3-aminopropyl)salicylaldimine, derived from 1:1 condensation of salicylaldehyde and 1,3-diaminopropane], have been synthesized and characterized by IR and UV/Vis spectroscopy, cyclic voltammetry and single-crystal X-ray diffraction studies. The structure of 1 consists of dinuclear units with crystallographic C-2 symmetry in which each Ni-II atom is in a distorted octahedral environment. The Ni-O distance and the Ni-O-Ni angle, through the bridged water molecule, are 2.240(11) angstrom and 82.5(5)degrees, respectively. The structure of 2 consists of dinuclear units bridged asymmetrically by di-mu(1,3)-NCS ions; each Cull ion is in a square-pyramidal environment with tau = 0.25. Variable-temperature magnetic susceptibility studies indicate the presence of dominant ferromagnetic exchange coupling in complex 1 with J = 3.1 cm(-1), whereas complex 2 exhibits weak antiferromagnetic coupling between the Cu-II centers with J = -1.7 cm(-1). ((c) Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005)

Cascade dicopper architectures of a dibenzodioxatetraazamacrocycle

The dibenzodioxatetraazamacrocycle [26]pbz(2)N(4)O(2) was characterised by single crystal X-ray diffraction and the protonation constants of this compound and the stability constants of its copper(II) and lead(II) complexes were determined by potentiometry in water at 298.2 K in 0.10 mol dm(-3) in KNO3. Mono- and dinuclear complexes were found for both metal ions, the dinuclear complexes being the main species in the 5-7.5 pH range for copper(II) and 7.5-8.5 for lead(II). As expected the values of the stability constants for the copper(II) complexes are lower than those for related macrocycles containing only nitrogen atoms. The presence of mono- and dinuclear copper complexes was also confirmed by electrospray ionization mass spectrometry. These results suggest that the symmetric macrocyclic cavity of [26]pbZ(2)N(4)O(2) has enough space for the coordination of two metal ions. Additionally, NMR spectroscopy showed that the dinuclear complex of lead(II) has high symmetry. The equilibrium constants of the dinuclear copper(II) complexes and dicarboxylate anions (oxalate, malonate and succinate) were also determined in 0.10 mol dm-3 aqueous KNO3 solution. Only species containing one anion, Cu(2)H(h)LA((2+h)), were found, strongly suggesting that the anion bridges the two copper(II) ions. The binding constants of the cascade species formed by [Cu-2[26]pbZ(2)N(4)O(2)(H2O)(4+) with dicarboxylate anions decrease with the increase in length of the alkyl chain of the anion, a fact which was attributed to a higher conformational energy necessary for the rearrangement of the macrocycle to accommodate the larger anions bridging the two copper(II) centres. The variation of the magnetic susceptibility with temperature Of [Cu-2(H-2[26]pbz(2)N(4)O(2))(oxa)(3)]-4H(2)O and [Cu-2([26]pbz(2)N(4)O(2))(suc)Cl-2] were measured and the two complexes showed different behaviour. (c) 2007 Elsevier Ltd. All rights reserved.

Dicopper(II) trihydroxide cyanoureate dihydrate

The title compound, poly[[mu-cyanoureato-tri-mu-hydroxidodicopper(II)] dihydrate], {[Cu-2(C2H2N3O)(OH)(3)]center dot 2H(2)O}(n), is a new layered copper(II) hydroxide salt (LHS) with cyanoureate ions and water molecules in the interlayer space. The three distinct copper(II) ions have distorted octahedral geometry: one Cu (symmetry (1) over bar) is coordinated to six hydroxide groups (4OH + 2OH), whilst the other two Cu atoms (symmetries (1) over bar and 1) are coordinated to four hydroxides and two N atoms from nitrile groups of the cyanoureate ions (4OH + 2N). The structure is held together by hydrogen-bonding interactions between the terminal-NH2 groups and the central cyanamide N atoms of organic anions associated with neighbouring layers.

Potassium nickel(II) gallium phosphate hydrate, K[NiGa2(PO4)(3)(H2O)(2)]

The title compound, potassium nickel(II) digallium tris-( phosphate) dihydrate, K[NiGa2(PO4)(3)(H2O)(2)], was synthesized hydrothermally. The structure is constructed from distorted trans-NiO4(H2O)2 octahedra linked through vertices and edges to GaO5 trigonal bipyramids and PO4 tetrahedra, forming a three-dimensional framework of formula [NiGa2(PO4)(3)(H2O)(2)](-). The K, Ni and one P atom lie on special positions (Wyckoff position 4e, site symmetry 2). There are two sets of channels within the framework, one running parallel to the [10 (1) over bar] direction and the other parallel to [001]. These intersect, forming a three-dimensional pore network in which the water molecules coordinated to the Ni atoms and the K+ ions required to charge balance the framework reside. The K+ ions lie in a highly distorted environment surrounded by ten O atoms, six of which are closer than 3.1 angstrom. The coordinated water molecules are within hydrogen-bonding distance to O atoms of bridging Ga-O-P groups.

Crystal and molecular structure of the thioether-analogue of PEEK from X-ray powder data and diffraction-modelling

Analysis of X-ray powder data for the melt-crystallisable aromatic poly(thioether thioether ketone) [-S-Ar-S-Ar-CO-Ar](n), ('PTTK', Ar= 1,4-phenylene), reveals that it adopts a crystal structure very different from that established for its ether-analogue PEEK. Molecular modelling and diffraction-simulation studies of PTTK show that the structure of this polymer is analogous to that of melt-crystallised poly(thioetherketone) [-SAr-CO-Ar](n) in which the carbonyl linkages in symmetry-related chains are aligned anti-parallel to one another. and that these bridging units are crystallographically interchangeable. The final model for the crystal structure of PTTK is thus disordered, in the monoclinic space group 121a (two chains per unit cell), with cell dimensions a = 7.83, b = 6.06, c = 10.35 angstrom, beta = 93.47 degrees. (c) 2005 Elsevier Ltd. All rights reserved.

Enantiospecific assembly of a homochiral, hexanuclear palladium complex

The linking of orthopalladated ferrocenylene units by parabanato(2-) ligands results in enantiospecific assembly of a hexanuclear complex in which (i) the steric bulk of the ferrocenylene moiety, (ii) the folded configuration dictated by the imidato(2-) bridging ligand, and (iii) the strong preference for a trans arrangement of the carbonyl oxygen and ferrocenyl carbon atoms, combine to ensure that only ferrocenylene-palladium units with the same chirality can be located at adjacent positions in the assembled complex. The resulting tris-parabanato(2-)-bridged, hexapalladium complex is thus homochiral (R,R,R,R,R,R or S,S,S,S,S,S), as demonstrated by H-1 NMR spectroscopy and by X-ray analysis of a racemic crystal which shows the complex to possess a tapering, twisted, trigonal-prismatic skeleton of palladium atoms with threefold crystallographic symmetry. ((C) Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2009)

The chemistry of intrinsically chiral surfaces

Intrinsically chiral metal and mineral surfaces show enantioselective behaviour without modifiers. Examples are artificial high-Miller-index surfaces of metal single crystals with cubic bulk lattice symmetry, which have no mirror planes and are therefore chiral, or surfaces of naturally occurring crystallites of some common minerals, such as alpha-quartz or calcite. Recent findings with regards to the surface geometry, reactivity and thermal stability of intrinsically chiral surfaces are discussed. A number of enantioselective effects have been reported in connection with the adsorption of small chiral molecules (e.g. alanine, cysteine) on intrinsically chiral surfaces under well-defined conditions. From a combination of experimental surface science techniques and theoretical ab initio model calculations it emerges that these effects are due to a combination of attractive and repulsive adsorbate-substrate and inter-adsorbate interactions.

X-ray crystallographic study of DNA duplex cross-linking: simultaneous binding to two d(CGTACG)(2) molecules by a bis(9-aminoacridine-4-carboxamide) derivative

Acridine-4-carboxamides form a class of known DNA mono-intercalating agents that exhibit cytotoxic activity against tumour cell lines due to their ability to inhibit topoisomerases. Previous studies of bis-acridine derivatives have yielded equivocal results regarding the minimum length of linker necessary between the two acridine chromophores to allow bis-intercalation of duplex DNA. We report here the 1.7 angstrom resolution X-ray crystal structure of a six-carbon-linked bis(acridine-4-carboxamide) ligand bound to d(CGTACG)(2) molecules by non-covalent duplex cross-linking. The asymmetric unit consists of one DNA duplex containing an intercalated acridine-4-carboxamide chromophore at each of the two CG steps. The other half of each ligand is bound to another DNA molecule in a symmetry-related manner, with the alkyl linker threading through the minor grooves. The two crystallographically independent ligand molecules adopt distinct side chain interactions, forming hydrogen bonds to either O6 or N7 on the major groove face of guanine, in contrast to the semi-disordered state of mono-intercalators bound to the same DNA molecule. The complex described here provides the first structural evidence for the non-covalent cross-linking of DNA by a small molecule ligand and suggests a possible explanation for the inconsistent behaviour of six-carbon linked bis-acridines in previous assays of DNA bis-intercalation.

Vibrations in the B-4 rhombic structure

A double minimum six-dimensional Potential energy surface (PES) is determined in symmetry coordinates for the most stable rhombic (D-2h) B-4 isomer in its (1)A(g) electronic ground state by fitting to energies calculated ab initio. The PES exhibits a barrier to the D-4h square structure of 255 cm(-1). The vibrational levels (J=0) are calculated variationally using an approach which involves the Watson kinetic energy operator expressed in normal coordinates. The pattern of about 65 vibrational levels up to 1600 cm-1 for all stable isotopomers is analyzed. Analogous to the inversion in ammonia-like molecules, the rhombus rearrangements lead to splittings of the vibrational levels. In B-4 it is the B-1g (D-4h mode which distorts the square molecule to its planar rhombic form. The anharmonic fundamental vibrational transitions of B-11(4) are calculated to be (splittings in parentheses): G(O) = 2352(22) cm(-1), v(1)(A(1g)) - 1136(24) cm(-1,) v(2)(B-1g)=209(144) cm(-1) v(3)(B-2g)=1198(19)cm(-1), v(4)(B-2u) = 271(24) cm(-1), and v(5) (E-u) = 1030( 166) cm(-1) (D-4h notation). Their variations in all stable isotoporners were investigated. Due to the presence of strong anharmonic resonances between the B-1g in-plane distortion and the B-2u, out-of-plane bending modes. the hiaher overtones and combination levels are difficult to assign unequivocally. (C) 2005 American Institute of Physics.

Chalcogenide-halides of niobium (V). 1. Gas-phase structures of NbOBr3, NbSBr3, and NbSCl3. 2. Matrix infrared spectra and vibrational force fields of NbOBr3, NbSBr3, NbSCl3, and NbOCl3

The molecular structures of NbOBr3, NbSCl3, and NbSBr3 have been determined by gas-phase electron diffraction (GED) at nozzle-tip temperatures of 250 degreesC, taking into account the possible presence of NbOCl3 as a contaminant in the NbSCl3 sample and NbOBr3 in the NbSBr3 sample. The experimental data are consistent with trigonal-pyramidal molecules having C-3v symmetry. Infrared spectra of molecules trapped in argon or nitrogen matrices were recorded and exhibit the characteristic fundamental stretching modes for C-3v species. Well resolved isotopic fine structure (Cl-35 and Cl-37) was observed for NbSCl3, and for NbOCl3 which occurred as an impurity in the NbSCl3 spectra. Quantum mechanical calculations of the structures and vibrational frequencies of the four YNbX3 molecules (Y = O, S; X = Cl, Br) were carried out at several levels of theory, most importantly B3LYP DFT with either the Stuttgart RSC ECP or Hay-Wadt (n + 1) ECP VDZ basis set for Nb and the 6-311 G* basis set for the nonmetal atoms. Theoretical values for the bond lengths are 0.01-0.04 Angstrom longer than the experimental ones of type r(a), in accord with general experience, but the bond angles with theoretical minus experimental differences of only 1.0-1.5degrees are notably accurate. Symmetrized force fields were also calculated. The experimental bond lengths (r(g)/Angstrom) and angles (angle(alpha)/deg) with estimated 2sigma uncertainties from GED are as follows. NbOBr3: r(Nb=O) = 1.694(7), r(Nb-Br) = 2.429(2), angle(O=Nb-Br) = 107.3(5), angle(Br-Nb-Br) = 111.5(5). NbSBr3: r(Nb=S) = 2.134(10), r(Nb-Br) = 2.408(4), angle(S=Nb-Br) = 106.6(7), angle(Br-Nb-Br) = 112.2(6). NbSCl3: Nb=S) = 2.120(10), r(Nb-Cl) = 2.271(6), angle(S=Nb-Cl) = 107.8(12), angle(Cl-Nb-Cl) = 111.1(11).