W. B. T. Cruse

Ordered water structure in an A-DNA octamer at 1.7 A resolution.

The crystal structure of the deoxyoctamer d(G-G-Br U-A-BrU-A-C-C) was refined to a resolution of 1.7 A using combined diffractometer and synchrotron data. The analysis was carried out independently in two laboratories using different procedures. Although the final results are identical the comparison of the two approaches highlights potential problems in the refinement of oligonucleotides when only limited data are available. As part of the analysis the positions of 84 solvent molecules in the asymmetric unit were established. The DNA molecule is highly solvated, particularly the phosphate-sugar back-bone and the functional groups of the bases. The major groove contains, in the central BrU-A-BrU-A region, a ribbon of water molecules forming closed pentagons with shared edges. These water molecules are linked to the base O and N atoms and to the solvent chains connecting the O-1 phosphate oxygen atoms on each strand. The minor groove is also extensively hydrated with a continuous network in the central region and other networks at each end. The pattern of hydration is briefly compared with that observed in the structure of a B-dodecamer.

Crystalline A-DNA: the X-ray analysis of the fragment d(G-G-T-A-T-A-C-C)

An A-DNA type double helical conformation was observed in the single crystal X-ray structure of the octamer d(G-G-T-A-T-A-C-C), 1, and its 5-bromouracil-containing analogue, 2. The structure of the isomorphous crystals (space group P 61 was solved by a search technique based on packing criteria and R-factor calculations, with use of only low order data. At the present stage of refinement the R factors are 31% for 1 and 28% for 2 at a resolution of 2.25 Å (0.225 nm). The molecules interact through their minor grooves by hydrogen bonding and base to sugar van der Waals contacts. The stable A conformation observed in the crystal may have some structural relevance to promoter regions where the T-A-T-A sequence is frequently found.

Horner-Wittig reactions of β-aminoalkyl- and β-N-acylaminoalkyldiphenylphosphine oxides: synthesis of N-allyl amines and amides and 5-diphenylphosphinoyl-2-phenyl-5,6-dihydro-4H-1,3-oxazines

Lithium derivatives of β-diphenylphosphinoyl-alkyl amines and dilithium derivatives of the corresponding amides combine with aldehydes or ketones in the Horner-Wittig reaction. Separation of the diastereoisomeric intermediates leads to single positional and geometrical isomers of N-allyl amines and amides. Attempted rearrangement of the same intermediates in acid solution gives dihydro-oxazines or, in one case, a γ-N-acylaminoallyl diphenylphosphine oxide.

Evidence for homoquadricyclene, a possible carbon ylide

Abstract The endo-epimer of the formal homo-1,4 adduct of monochlorocarbene and norborna-2,5-diene on treatment with lithium 2,2,6,6-tetramethylpiperidide in THF in the presence of diphenylisobenzofurane (DPIBF) gave a single Diels-Alder adduct. The same cyclo-adduct was obtained by subjecting the homo-1,4 adduct of dibromocarbene and norborna-2,5-diene to lithiummethyl in THF. By single crystal X-ray analysis the adduct is shown to be the result of the normal Diels-Alder cyclo-addition of DPIBF to the least hindered side of tetracyclo[3.2.1.0. 2,7 0. 4,6 ]oct-2-ene, a novel anti-Bredt olefine, best considered as a carbon ylide.

The crystal structure of 4-nitrophenyl-α-D-glucopyranoside

The structure of the title compound has been determined and refined to R 0.032 [P2U a = 28.045(6), b = 6.767(2), c = 6.719(2) Â, β = 90.30(2)°, Ζ = 4], The two independent molecules differ mainly in relative ring orientation. Bond lengths at the acetal centre are not significantly different.

Trans-Adenosine 3′,5′-Cyclic N,N-Dimethylphosphoramidate Ether Solvate, a Cyclic Nucleotide with an Equatorial Dimethylamino Group on Phosphorus

Abstract trans-Adenosine 3′ 5′ -cyclic N,N-dimethylphosphoramidate ether solvate crystallizes as monoclinic prisms elongated about the b-axis. The dioxaphosphorinane ring adopts a flattened chair conformation with an almost planar dimethylamino substituent equatorial. The purine ring conformation is anti. The ribose ring exists in a 3T4 conformation.

Diastereoselectivity in the Horner-Wittig reaction: X-ray crystal structure of 2-(1RS,2SR)-diphenylphosphinoyl-1-phenylpropan-1-ol

Ethyldiphenylphosphine oxide reacts with butyl-lithium and benzaldehyde to give the title compound which eliminates diphenylphosphinate ion in base to give Z-1 -phenylpropene. The elimination is stereo-specific and syn. The (1RS,2RS) isomer, prepared by sodium borohydride reduction of the corresponding ketone, gives E-1 -phenylpropene.

The X-Ray Structure of the Ligand-Free Antibiotic Ristocetin-A Reveals the Role of the Monomer/Dimer Equilibrium in Its Binding Mode

Ristocetin-A belongs to the group of the glycoheptapeptide antibiotics. The sulfate salt of ristocetin-A was crystallized in the P21 monoclinic space group with a homodimer in the asymmetric unit. The two subunits are linked back-to-back like the other members of the family via four peptide bonds forming a twisted β-sheet and exposing the binding pockets to the exterior. The two tetrasaccharide parts of this ligand-free antibiotic are in the anti/anti orientations contrary to what was found in the mono- and diliganded ristocetin-A/-(D-Ala-D-Ala) complexes in which the two tetrasaccharides of the dimer are syn/anti. The ligand-free dimer shows however some conformational differences between the two subunits, particularly in the terminal arabinose leading to one extended and one bent conformation of the tetrasaccharide moiety. Comparison between this structure and the two available mono- and diliganded structures confirms that the anti/anti to syn/anti flipping of the tetrasaccharide is a key step in the binding to the D-Ala-D-Ala-containing target sequence and cannot proceed without displacement of the monomer/dimer equilibrium.

X-Ray crystal structures of bridged porphyrins

X-Ray crystal structures of an anthracene-bridged porphyrin and of a pyridine-bridged analogue show ‘off-set’ conformations with close van der Waals stacking of the bridging groups on the porphyrin macrocycles.