f-Element/crown ether complexes. 16. Synthesis,crystallization and crystal structure of [Dy(OH2)8]Cl3·18-crown-6·4H2O

When crystals of [Dy(OH₂)₇(OHMe)] [DyCl(OH₂)₂(18- crown-6)]₂Cl₇·2H₂O [1] are allowed to warm from 5 °C to ambient temperature (22 °C) under the original solvent mixture (1:3 CH₃OH: CH₃CN), they redissolve and the title complex can be isolated by slow evaporation of the resulting solution. The crystal structure of this complex, [Dy(OH₂)₈]Cl₃·18-crown-₆·4H₂O, has been determined. It crystallizes in the monoclinic space group, P2₁/c, with a = 10.395(1), b = 18.684(1), c = 16.259- (3) Å, β= 102.56(1)°, and D_calc = 1.61 g cm⁻³ for Z = 4. A final conventional R value of 0.041 was obtained by least-squares refinement using 3453 independent observed [F_o⩾5σ(F_o)] reflections. The [Dy(OH₂)₈]³⁺ cations and crown ether molecules are hydrogen bonded in a polymeric chain with the crown molecules separating the cations and a total of seven DyOH₂···O(crown ether) hydrogen bonds. The chains are connected by a hydrogen bonding network consisting of the cations, chloride ions, and uncoordinated water molecules. The geometry of the cation is best described as a bicapped trigonal prism with distortions on the reaction pathway toward dodecahedral symmetry. The two capping atoms average 2.41(1) Å from Dy, the remaining DyO distances average 2.38(2) Å. The 18-crown-6 molecule has the D_3d conformation normally observed except for a distortion of one OCCO unit containing the oxygen atom accepting two hydrogen bonds.     

Conformations of septanosides. The crystal and molecular structure of 5-O-(chloroacetyl)-1,2:3,4-di-O-isopropylidene-α-D-glucoseptanose

The crystal structure of 5-O-(chloroacetyl)-1,2:3,4-di-O-isopropylidene-α-D-glucoseptanose, a seven-membered ring sugar, has been determined by using 1234 reflections measured on a diffractometer. The crystals belong to the orthorhombic space group P2₁2₁2₁, having cell dimensions a  27.750, b  10.714, and c  5.702 Å. The measured and calculated densities are 1.25 g.cm⁻³ and 1.32 g.cm⁻³, respectively; the latter value assumed four molecules in the unit cell. The structure was determined by a combination of the heavy-atom technique and the tangent method. Full-matrix least-squares refinement with anisotropic temperature factors for the nonhydrogen atoms and isotropic temperature factors for the hydrogen atoms lowered the conventional R value to 0.066. The seven-membered ring adopts a ^5.6C₂(D) twist-chair conformation. Both of the dioxolane rings have the envelope shape, the puckered atoms being C-2 and C-4 of the seven-membered ring. The molecular packing is dominated by Van der Waals forces. The conformations of three known 7-membered ring sugars are compared. It is found that the pseudorotation of the septanose ring and the dioxolane rings are correlated to the position of attachment of the latter rings to the central septanose ring.     

Infrared and raman study of matrix isolated M(SO2) molecules. The structure of the molecular ion SO2−

The IR and Raman spectra of Cs(SO₂), K(SO₂) and Na(SO₂) molecules were studied by ³²S/³⁴S and ¹⁶O/¹⁸O isotopic substitution technique. These molecules have a planar ring configuration of C_2v symmetry with the OSO angle equal to 109°±5° and the SO bond length of 0.149±0.001 nm. The alkali metal atom interacts symmetrically with the oxygen atoms of the SO₂⁻ group. The doubling observed for the vibrations of Cs(S¹⁶O¹⁸O) was attributed to a matrix effect.     

The crystal structure of a Thermus thermophilus tRNA(Gly) acceptor stem microhelix at 1.6 Å resolution

tRNAs are aminoacylated with the correct amino acid by the cognate aminoacyl-tRNA synthetase. The tRNA/synthetase systems can be divided into two classes: class I and class II. Within class I, the tRNA identity elements that enable the specificity consist of complex sequence and structure motifs, whereas in class II the identity elements are assured by few and simple determinants, which are mostly located in the tRNA acceptor stem. The tRNA(Gly)/glycyl-tRNA-synthetase (GlyRS) system is a special case regarding evolutionary aspects. There exist two different types of GlyRS, namely an archaebacterial/human type and an eubacterial type, reflecting the evolutionary divergence within this system. We previously reported the crystal structures of an Escherichia coli and of a human tRNA(Gly) acceptor stem microhelix. Here we present the crystal structure of a thermophilic tRNA(Gly) aminoacyl stem from Thermus thermophilus at 1.6? resolution and provide insight into the RNA geometry and hydration.     

The search for a coordinated dialkyl disulphide: The crystal and molecular structure of (μ-ethanedithiolato)bis(tricarbonyliron)(FeFe)

Despite considerable effort, no compounds containing an alkyl disulphide linked to a single metalion have been isolated. The complex [{fFe(SCH₂CH₂- S)₂}₂]²⁻ is a strong reducing agent. [Fe₃(CO)₁₂] with 1,2,5,6-tetrathiacyclooctane yields [(SCH₂CH₂S){Fe- (CO)₃}₂], the structure of which has been determined by X-ray analysis.     

The crystal and molecular structure of O-(β-D-xylopyranosyl)-L-serine and its copper (II) complex and some of their reactions

The interatomic distances and angles have been evaluated in xylosyl serine and its Cu(II) complex by X-ray crystal analysis. Physical data are provided for the acid and alkaline degradation of the former, together with evidence for the catalytic effect on Cu(II) on its alkaline elimination.     

f-Element/crown ether complexes. 1. Synthesis and structure of [Y(OH2)8]Cl3·(15-crown-5)

The crystal and molecular structure of [Y(OH₂)₈]Cl₃·(15-crown-5) has been determined by single- crystal X-ray diffraction. The complex crystallizes in the monoclinic space group P2₁/n with Z = 4. Lattice parameters are a = 9.202(2), b = 17.247(3), c = 15.208(3) Å, and β = 92.39(2)°. The structure was solved by Patterson and Fourier techniques and refined by least-squares to a final conventional R value of 0.081. The Y(III) ion is eight coordinate, bonded to the oxygen atoms of the eight water molecules. Three of the water molecules are hydrogen bonded to crown ether molecules. The three chloride ions participate in hydrogen bonds with the remaining five water molecules. The YO(water) distances range from 2.322(6) to 2.432(7) Å and average 2.37(4) Å. The average O(water)···Cl and O(water)···O(crown) hydrogen bonded separations are 3.08(4) and 2.76(7) Å, respectively.     

The molecular and crystal structures of 4-N-(2-acetamido-2-deoxy-β-d-glucopyranosyl)-l-asparagine trihydrate and 4-N-(β-d-glucopyranosyl)-l-asparagine monohydrate. The X-ray analysis of a carbohydrate–peptide linkage

X-ray analyses have shown that the glucopyranose rings of GlcNAc-Asn [4-N-(2-acetamido-2-deoxy-beta-d-glucopyranosyl)-l-asparagine] and Glc-Asn [4-N-(beta-d-glucopyranosyl)-l-asparagine] both have the C-1 chair conformation and also that the glucose-asparagine linkage of each molecule is present in the beta-anomeric configuration. The dimensions (the estimated standard deviations of the last digit are in parentheses) of the glycosidic bond in GlcNAc-Asn and Glc-Asn are, respectively, C((1))-N((1)) 0.1441(6)nm, 0.146(2)nm; angle O((5))-C((1))-N((1)) 106.8(3) degrees , 105.7(8) degrees ; angle C((2))-C((1))-N((1)) 111.1(4) degrees , 110.4(9) degrees ; angle C((1))-N((1))-C((9)) 121.4(4) degrees , 120.5(9) degrees . The glycosidic torsion angle C((9))-N((1))-C((1))-C((2)) is 141.0 degrees and 157.6 degrees in GlcNAc-Asn and Glc-Asn respectively. Hydrogen-bonding is extensive in these two crystal structures and does affect one torsion angle in particular. Two very different values of chi(1)(N-C(alpha)-C(beta)-C(gamma)) occur for the asparagine residue of the two different molecules; the values of chi(1), -69.0 degrees in GlcNAc-Asn and 61.9 degrees in Glc-Asn, correspond to two different staggered conformations about the C(alpha)-C(beta) bond as the NH(3) (+) group is adjusted to different hydrogen-bonding patterns. The two trans-peptide groups in GlcNAc-Asn show small distortions in planarity whereas that in Glc-Asn is more non-planar. The mean plane through the atoms of the amide group at C((2)) in GlcNAc-Asn is approximately perpendicular (69 degrees ) to the mean plane through the C((2)), C((3)), C((5)) and O((5)) atoms of the glucose ring and that at C((1)) is less perpendicular (65 degrees ). The mean plane through the atoms of the amide group in Glc-Asn makes an angle of only 55 degrees with the mean plane through these same four atoms of the glucose ring. The N((1))-H bond of the amide at C((1)) is trans to the C((1))-H bond in these two compounds; the N((2))-H bond of the amide at C((2)) is trans to the C((2))-H bond in GlcNAc-Asn. The values of the observed and final calculated structure amplitudes have been deposited as Supplementary Publication SUP 50035 (26 pages) at the British Library (Lending Division), (formerly the National Lending Library for Science and Technology), Boston Spa, Yorks. LS23 7BQ, U.K., from whom copies may be obtained on the terms given in Biochem. J. (1973) 131, 5.     

Rhodium(III) cis-dihydrido complexes with 3,6-bis(2′-pyridyl)pyridazine (dppn) and bidiazines. Crystal and molecular structure of [Rh(H)2(dppn)(PPh3)2]PF6· CH2Cl2

The acetone complex [Rh(H)₂(acetone)₂(PPh₃)₂]- PF₆ reacts with bidiazines and 3,6-bis(2′-pyridyl)- pyridazine (dppn) giving the air stable cis-dihydrido rhodium(III) [Rh(H)₂(L)(PPh₃)₂]PF₆ complexes. The structure of the dichloromethane solvate of [Rh(H)₂(dppn)(PPh₃)₂]PF₆ has been determined by X-ray crystal structure analysis. Crystals are monoclinic, space group P2₁/a, with a = 18.629(6), b = 15.339(5), c = 17.146(5) Å, β = 101.02(3)° and Z = 4. The structure has been solved from diffractometer data by Patterson and Fourier methods and refined by block-matrix least-squares to R = 0.076 for 6225 observed reflections. In the structure discrete [Rh(H)₂(dppn)(PPh₃)₂]⁺ cationic complexes, PF₆⁻ anions and dichloromethane solvent molecules are present. The Rh atom is octahedrally surrounded by two cis hydride ligands and by two cis nitrogen atoms from a dppn molecule acting as a bidentate chelating ligand through two neighbouring pyridyl and pyridazinyl nitrogen atoms. Two P atoms from PPh₃, ligands in trans apical positions complete to octahedral the coordination of Rh.     

Copper(II) complexes with 2,2′-biimidazole. Preparation and crystal structure determination of a complex of stoichiometry Cu1.5Cl3(H2bim)2 (H2bim=2,2′-biimidazole)

By reacting 2,2′-biimidazole and copper(II) chloride in aqueous HCl we obtained the complex CuCl₂(H₂bim) as the main product and a compound with stoichiometry Cu_1.5Cl₃(H₂bim)₂ as a byproduct. The structure of the latter compound has been determined by X-ray analysis: monoclinic, a= 794.0(3), b=3146.8(6), c=722.9(4) pm, β= 114.2(1)°, space group P21/c. The compound actually contains two species, namely [Cu(H₂bim)₂]Cl₂ and [CuCl₂(H₂bim)] in a 1:2 molar ratio.     

The three-dimensional structure of the antigen-binding fragment of a monoclonal antibody to human interleukin-2 in two crystal forms at 2.2 and 2.9 Å resolution

The three-dimensional structure of the antigen-binding fragment of a monoclonal antibody to human interleukin-2 was determined in two crystal forms by the X-ray method of molecular replacement at 2.2 and 2.9 Å resolutions. The spatial structure of the protein and the stereochemistry of its antigen-binding site were analyzed.     

Reactions of Nb2Cl6(SMe2)3 and Ta2Cl6(SMe2)3 with compounds containing NN single bonds

Ta₂Cl₆(SMe₂)₃ reacts with PhHNNHPh to afford Ta₂Cl₄(μ-Cl)₂(μ-PhN)(PhNH₂)₃ (1) a compound with a Ta^IVTa^IV single bond, with a length of 2.644(1) Å. The compound crystallizes in space group Pnma with unit cell dimensions a = 22.960(8), b = 16.875(4), c = 6.367(3) Å, V = 2467(1) ų, and Z = 4. The reaction of Nb₂Cl₆(SMe₂)₃ with PhHCNNCHPh, merely on mixing at room temperature produced Nb₂Cl₆(SMe₂) [PhHC(N)PhHCNHNCHPh]·C₇H₈ (2) as large red crystals in ca. 50% yield. The molecule consists of two Nb^IV atoms, one six-coordinate and the other seven-coordinate, united by three bridging atoms (Cl, Cl, N) and a NbNb bond of length 2.681(1) Å. The way in which the tridentate triazo ligand is generated is completely obscure. Crystallographic data for 2: space group P2₁/n with a = 11.393(3), b = 11.988(3), c = 27.233(7) Å, β = 100.75(2)°, V = 3654(3) Å, and Z = 4.     

Platinum(II) complexes of methyl-substituted xanthines: crystal structures of K[Pt(theobromine)Cl3]·H2O,trans-[ Pt(isocaffeine)2Cl2]·H2O and K(isocaffeinium)[PtCl4]·H2O

The preparations of Pt(theophylline)₂Cl₂, K[Pt- (theophylline)Cl₃], K[Pt(theobromine)Cl₃]·H₂O (1), trans-[Pt(isocaffeine)₂Cl₂]·H₂O (2), and K(isocaffeinium)[PtCl₄]·H₂O (3) are reported.Crystals of 1 are monoclinic P2₁/n with a=7.641- (2), b=11.873(3), c=15.868(4) Å, β=90.80(2)°, Z=4. The structure was refined on 1443 reflections to R=0.028. In the planar [Pt(theobromine)Cl₃]⁻ anion Pt-N(9)=2.016(6) Å, Pt-Cl=2.299(2), 2.289(2), and 2.303(2) Å. The imidazole ring is rotated away from the coordination plane by 79.8°. Symmetry related theobromine units pack parallel to each other with a mean inter-ring separation of 3.27 Å.Crystals of 2 are monoclinic P2₁/a with a=7.345- (2), b=20.021(5), c=8.031(2) Å, β=104.18(2)°, Z=2. The structure was refined on 1132 reflections to R=0.029. The Pt-N(7) distance is 2.003(3) Å and Pt-Cl=2.298(1) Å. The imidazole ring is rotated away from the PtCl₂N₂ plane by 76.8°. In this compound, the isocaffeine units do not stack, but form a staggered arrangement within the unit cell.Crystals of 3 are monoclinic P₁/c with a= 7.382- (1), b=14.014(4), c=15.757(4) », β=92.30(2)°, Z=4. The structure was refined on 2057 reflections to R=0.032. The isocaffeine is protonated at N(7). The Pt-Cl distances in the PtCl₄²⁻ anion range between 2.29–2.31 Å. The protonated isocaffeine cations and the PtCl₄²⁻ anions form a very nearly parallel infinitely stacked arrangement with minimum interlayer atomic separations of 3.37 and 3.44 Å.