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  • Articles: DFG German National Licenses  (20,818)
  • 1995-1999  (19,897)
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  • crystal structure
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  • Articles: DFG German National Licenses  (20,818)
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  • 1995-1999  (19,897)
  • 1880-1889  (921)
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  • 1
    Electronic Resource
    Electronic Resource
    Springer
    Journal of chemical crystallography 28 (1998), S. 11-15 
    ISSN: 1572-8854
    Keywords: Mebendazole–propionic acid complex ; molecular complex ; crystal structure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Geosciences , Physics
    Notes: Abstract Recrystallization of the anthelmintic drug mebendazole from propionic acid yields a 1:1 molecular complex which crystallizes in the triclinic system space group $${P\bar 1}$$ , a = 5.928(2), b = 11.066(2), c = 14.337(6)Å, α = 94.89(3), β = 101.56(3), γ = 96.18(2)°, and Z = 2 complex units in the unit cell. An x-ray diffraction study revealed an R 2 2 (8) hydrogen bonding system in the complex, involving the unprotonated imidazole N and amide N–H function of the drug and the acid carboxylic group. Complex molecules form centrosymmetric dimers by intermolecular N–H···O hydrogen bonding involving the protonated imidazole N atom and the benzoyl O atom of the drug molecule.
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  • 2
    ISSN: 1572-8854
    Keywords: Cu(II) complex ; crystal structure ; EPR spectra
    Source: Springer Online Journal Archives 1860-2000
    Topics: Geosciences , Physics
    Notes: Abstract The title compound, Cu(glyglygly)Br·1·5H2O, crystallizes in the space group C2/c, with a = 21.468(7), b = 6.716(5), c = 16.166(6) Å, β = 98.39°, and Z = 8. The tripeptide is bonded to one Cu(II) ion through the nitrogen [Cu–N=1.97(1)Å] and oxygen [Cu–O=2.019(8)Å] atoms of the amino end glycine residue and to another Cu(II) through one oxygen atom [Cu–O=1.931(9)Å] of the terminal carboxyl group. This give rise to covalently bonded and infinite ···–Cu–tripeptide–Cu–··· chains. These chains are linked to one another by a network of H-bonds involving the water molecules and bromide ions. The Cu(II) ion is in a distorted tetragonal pyramidal coordination polyhedron. At the corner of the base of the pyramid are the terminal glycine nitrogen and oxygen atoms of one tripeptide, a carboxylic oxygen of another tripeptide and a bromide ion. The fivefold coordination is completed with a water molecule at the top of the pyramid [Cu–Ow=2.286(9)Å]. For all orientations of the applied magnetic field the single crystal EPR spectra display a single anisotropic exchange collapsed resonance without hyperfine structure. Its position was measured in three perpendicular planes and the crystal g-tensor evaluated from the data. This tensor is interpreted in terms of the contributing Cu(II) complexes in the unit cell to deduce the principal values g1 = 2.273, g2 = 2.050 and g3 = 2.131 for the molecular gyromagnetic tensor. We also discuss the magnitude of the exchange interaction between neighboring copper ions in the lattice on the basis of the features in the EPR spectra and the structural information.
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  • 3
    ISSN: 1572-8854
    Keywords: 2-Methylnaphthalene ; hexachlorocyclopentadiene ; crystal structure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Geosciences , Physics
    Notes: Abstract 2-Methylnaphthalene undergoes Diels-Alder addition and substitution with hexachlorocyclopentadiene to give two products, 1,2,3,4,5,6,7,8,13,13,14,14-dodecachloro-1,4,4a,4b,5,8,8a,12b-octahydro-10-methyl-1,4;5,8-dimethanotriphenylene 1 and 1,2,3,4,5,6,7,8,13,13,14,14-dodecachloro-1,4,4a,4b,5,8,8a,12b-octahydro-10-(1′,2′,3′,4′,5′-pentachlorocyclopentadienyl)methyl-1,4;5,8-dimethanotriphenylene 2. The molecular structure of 2 has been characterized by X-ray crystallography: C26H9Cl17, monoclinic, space group P21/c, with a = 15.316(3), b = 13.698(3), c = 16.116(3) Å, β = 96.113(3)°, and Z = 4.
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  • 4
    ISSN: 1572-8854
    Keywords: Halobismuthate(III) ; phenanthroline ; synthesis ; crystal structure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Geosciences , Physics
    Notes: Abstract The reaction between bismuthate oxide and phen (1,10-phenanthroline) in acid medium led to the isolation of the unusual [(PhenH)(PhenH2)][BiCl6]·2H2O derivative, which has been characterized by X-ray analysis and IR spectroscopy. The compound crystallizes in the triclinic space group $$[\text[P\bar 1]]$$ with a = 8.313(2), b = 9.349(2), c = 9.807(3) Å, α = 86.39(3), β = 110.27(3) and γ = 106.48(3)°. The crystal structure is made of [BiCl6]3− anions and [(PhenH)(PhenH2)]3+ cations. A network of hydrogen bond interactions involving the two clathrated water molecules, the phenanthroline moiety and the chlorines characterizes the entire structure.
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  • 5
    ISSN: 1572-8854
    Keywords: Lanthanum complex ; hexamethylenetetramine ; IR spectra ; thiocyanates ; coordination number nine ; tricapped trigonal prism ; crystal structure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Geosciences , Physics
    Notes: Abstract The title compound (LaC15H42N11O9S3) was prepared and characterized by means of X-ray, IR and Raman measurements. The crystals are orthorhombic: Pnma (No. 62), a = 21.117(2), b = 14.736(2), c = 10.082(1) Å, and Z = 4. The structure consists of polyhedra with a La(III) ion in the center of them and hexamethylene molecules, which link these polyhedra. Each La(III) ion coordinates seven molecules of water and two thiocyanate ions via nitrogen atoms. The IR and Raman spectra, which have been obtained and interpreted, are in good agreement with X-ray results.
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  • 6
    ISSN: 1572-8854
    Keywords: Cerium(IV) ; β-diketonate ; volatility ; crystal structure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Geosciences , Physics
    Notes: Abstract The cerium(IV) β-diketonate compounds [Ce(β-diket)4] [where β-diket = tmhd (2,2,6,6-tetramethylheptane-3,5-dionate) 1, pmhd (1-phenyl-5-methylhexane-1,3-dionate) 2] were prepared by reacting cerium(IV) ammonium nitrate [CAN; Ce(NH4)2(NO3)6] with the respective Na(β-diket) compound in ethanol, and structurally characterized by single crystal X-ray diffraction. Compound 1 crystallizes in the triclinic space group $$P \bar 1$$ with a = 12.472(4), b = 19.972(5), c = 21.436(3) Å, α = 97.05(7), β = 90.16(2), γ = 106.55(3)°, V = 5076(2) Å3, Z = 4, T = 150(2) K. Compound 2 crystallizes in the monoclinic space group P21/n. with a = 14.817(6), b = 17.123(6), c = 19.146(3) Å, β = 105.46(4)°, V = 4682(3) Å3, Z = 4, T = 150(2) K. Crystals of 1 contain two independent [Ce(tmhd)4] molecules, with four chelating tmhd ligands bonded to each metal in a distorted dodecahedral arrangement; the cerium atom in 2 is also bonded to four chelating pmhd ligands but in this case the coordination geometry is closer to square antiprism. Both complexes are air and moisture stable. Sublimation studies reveal that 1 sublimes almost quantitatively, while 2 is comparatively involatile.
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  • 7
    ISSN: 1572-8854
    Keywords: Nickel(II) complex ; crystal structure ; Schiff base
    Source: Springer Online Journal Archives 1860-2000
    Topics: Geosciences , Physics
    Notes: Abstract A nickel(II) complex of the pyridine-2-aldehyde Schiff base of S-methyldithiocarbazate (HNNS) has been synthesized and characterized by means of elemental analysis, IR and UV-vis spectra. The crystal structure of the complex has been determined by single-crystal X-ray diffraction. The complex crystallizes in the monoclinic, space P21/c, with a = 14.092(2), b = 16.886(2), c = 8.857(2)Å; β = 105.78(3) °, V = 2028.2(6) Å3, and Z = 4. The nickel atom is octahedrally coordinated by two uninegatively charged tridentate Schiff base in a mer-configuration via the pyridine nitrogen atom, azomethine nitrogen atom, and mecaptide sulfur atom.
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  • 8
    Electronic Resource
    Electronic Resource
    Springer
    Journal of chemical crystallography 28 (1998), S. 885-892 
    ISSN: 1572-8854
    Keywords: Benztropine mesylate ; crystal structure ; thermal analysis ; dehydration kinetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Geosciences , Physics
    Notes: Abstract The crystal structure of benztropine mesylate has been determined. It is orthorhombic, Pbca, with a = 12. 885(8)Å, b = 32.012(9)Å, and c = 10.027(3) Å. It exhibits similar packing to that seen in the previously reported crystal structure of benztropine mesylate monhydrate. X-ray powder diffraction patterns have been used to identify the anhydrous and monohydrate forms. The dehydration of the monohydrate follows a first-order reaction mechanism with activation energy of 92(8) kJ mol−1.
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  • 9
    Electronic Resource
    Electronic Resource
    Springer
    Journal of chemical crystallography 28 (1998), S. 521-527 
    ISSN: 1572-8854
    Keywords: Cadmium ; crown ether ; 15-crown-5 ; 18-crown-6 ; crystal structure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Geosciences , Physics
    Notes: Abstract Reaction of 15-crown-5 or 18-crown-6 in 3:1 (v/v) CH3CN:CH3OH with Cd(NO3)2·4H2O followed by slow evaporation produces [Cd(NO3)2(15-crown-5)] or [Cd(NO3)2(18-crown-6)]. Crystals of [Cd(NO3)2(15-crown-5)] are orthorhombic with space group Pbca and cell parameters a = 13.562(5), b = 15.941(9), and c = 15.011(7) Å at 295 K. [Cd(NO3)2(18-crown-6)] crystallizes in the monoclinic space group C2/c with a = 11.235(2), b = 11.196(5), c = 15.385(3) Å, and β = 99.89(2)° at 295 K. The metal center in [Cd(NO3)2(15-crown-5)] rests atop the macrocyclic donor array with two cis-bound nitrate anions and adopts a distorted tricapped trigonal prismatic geometry. [Cd(NO3)2(18-crown-6)] resides on an equatorial two-fold rotation axis with Cd2+ coordinated in the 18-crown-6 cavity and the nitrate anions oriented in twisted trans positions.
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  • 10
    Electronic Resource
    Electronic Resource
    Springer
    Journal of chemical crystallography 28 (1998), S. 577-579 
    ISSN: 1572-8854
    Keywords: (−)—Crinine ; Pancratium ; alkaloid ; Amaryllidaceae ; crystal structure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Geosciences , Physics
    Notes: Abstract (−)—Crinine, C16H17NO3, is an alkaloid extracted from the bulbs of Pancratium maritimum L. (Amaryllidaceae). The compound crystallizes in the space group P212121 with cell dimensions a = 6.040(1), b = 12.382(1), c = 17.861(2) Å, with Z = 4. The molecule has five rings and an OH group. The N-containing, five-membered ring and the D ring have envelope conformations. The A and B rings have distorted chair and half-chair conformations, respectively.
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  • 11
    Electronic Resource
    Electronic Resource
    Springer
    Journal of chemical crystallography 28 (1998), S. 217-220 
    ISSN: 1572-8854
    Keywords: Metal carbonyl complexes ; chelate complexes ; crystal structure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Geosciences , Physics
    Notes: Abstract The x-ray crystal structure of the complex η2-PDOW(CO)4 (five-membered ring, PDO = 2, 2, 4, 7, 7-pentamethyl-3,6-dithiaoctane) is reported. The complex crystallizes in the monoclinic crystal system, space group P21/c, [#14] with unit cell parameters a = 14.002(14) Å, b = 9.340(10) Å, c = 15.094(12) Å, β = 92.67(4)°, V = 1972(3) Å3; Z = 4. The arrangement of the ligands around the metal atom is distorted from octahedral geometry. Large C–O bond distances and short W–C bond distances of the carbonyl groups located at a trans position with respect to PDO is indicative of a trans influence. The W–S(1) and W–S(2) bond distances of 2.545(3) and 2.545(2) Å, respectively, are shorter than observed for closely related complexes.
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  • 12
    ISSN: 1572-8854
    Keywords: Triphenylsiloxy ; silanol ; borane ; crystal structure ; adduct
    Source: Springer Online Journal Archives 1860-2000
    Topics: Geosciences , Physics
    Notes: Abstract The title compound crystallizes in the triclinic space group $$P \bar 1$$ , with a = 14.458(6), b = 14.630(5), c = 14.721(8) Å, α = 79.75(2), β = 80.11(3), γ = 80.50(3)°, and Z = 2. The crystal structure consists of molecules of (Ph3SiO)3B and Ph3SiOH linked by an weak B···(silanol) acceptor-donor bond, additionally stabilized by OH(silanol)···O(siloxy) hydrogen bonds. The average B–O, Si–O distances and B–O–Si angle are 1.369, 1.649 Å and 137.2°, respectively.
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  • 13
    ISSN: 1572-8854
    Keywords: Steroid ; pregnadiene ; x-ray diffraction ; crystal structure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Geosciences , Physics
    Notes: Abstract The title compound is C29H34O4, tetragonal, P43, a = b = 10.310(1), c = 23.871(2)Å. The A, B, C, and D rings adopt envelope, half-chair, chair, and distorted chair conformations, respectively. The phenyl ring is planar. The methyl substituents at the A/B, C/D, and at C(17) are axial; and the –OCOCH3 group at C(17) and phenyl ring at C(16) are equatorial. The molecules in the crystal are held together by van der Waals forces and several C–H···O hydrogen bond interactions.
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  • 14
    Electronic Resource
    Electronic Resource
    Springer
    Journal of chemical crystallography 28 (1998), S. 539-543 
    ISSN: 1572-8854
    Keywords: Antimalarial ; crystal structure ; peroxy bridge
    Source: Springer Online Journal Archives 1860-2000
    Topics: Geosciences , Physics
    Notes: Abstract The crystal and molecular structure of the antimalarial compound Artemisinin (formerly known as Qinghaosu), C15H22O5 has been determined by direct methods. Crystals are orthorhombic colorless needles, space group P212121, Z = 4. D c = 1.299 g cm −3, with unit cell parameters a = 6.3543(9), b = 9.439(3), c= 24.066(4) Å. The molecule incorporates a fused ring system containing a six-membered ring C which includes an oxygen bridge and a peroxy-bridge. The ring C has a distorted boat conformation and the C - O - O - C torsion angle is 47.8(2)°. Rings A and D have symmetrical chair and distorted chair conformations, repectively. Ring junctions A/B, A/D, and C/D are cis, junction B/D is trans. All inter-molecular contacts are van der Waals. The absolute configuration of Artemisinin was determined from the refined value of the Flack x parameter. [The atomic coordinates given in a previous structure analysis, “Crystal Structure and Absolute Configuration of Qinghaosu,” Qinghaosu Research Group, Institute of Biophysics, Academica Sinica, Scientia Sinica, Vol. XXIII No. 3, 380 (1980), do not display the molecule in its absolute configuration.]
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  • 15
    ISSN: 1572-8862
    Keywords: Ruthenium ; thioether macrocycle ; crystal structure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: Abstract The reaction of a mixture of cis-3,7,11-trimethyl-1,5,9-trithiacyclododecane, cis-Me312S3, 1 and trans-3,7,11-trimethyl-l,5,9-trithiacyclododecane, trans-Me312S3, 2, with Ru6(CO)17(μ 6-C), 3, yielded three new cluster compounds Ru6(CO)13(μ-η3-cis-SCH2CHMe(CH2SCH2CHMe)2CH2)(μ 6-C) 4, and two isomers of Ru6(CO)13(μ-η3-cis-SCH2CHMe(CH2SCH2CHMe)2CH2)(μ 6-C) 5a and 5b. The molecular structures of 4 and 5b were established by single crystal X-ray diffraction analyses. In both complexes, the macrocycles have adopted tridentate coordination with one of the sulfur atoms in a bridging position. Two carbonyl ligands occupy bridging positions in each compound. Crystal Data for 4·Me2CO: space group=P21/n, a=11.295(1) Å, b=17.547(3) Å, c=20.318(3) Å, β=93.71(1)°, Z=4, 2900 reflections, R=0.025. Crystal Data for 5b·1.5 C6H6: space group=Pbca, a=31.8900(8) Å, b=23.4330(6) Å, c=21.6240(4) Å, Z=16, 12163 reflections, R=0.040.
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  • 16
    ISSN: 1572-8862
    Keywords: Mixed-metal cluster ; crystal structure ; magnetic properties
    Source: Springer Online Journal Archives 1860-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: Abstract The preparation, magnetic properties, and crystal structure of [(salen)Cu]4[(salen)Fe(H2O)2]2(ClO4)2 via hydrogen bonding are described [salen=N,N′-ethylenebis (salicylideneiminate)]. Crystals are triclinic, of space group $$\rm P\bar 1$$ , with cell constants a=12.853(3), b=13.921(3), c=14.251(3) Å, α=68.68(3)°, β=87.86(3)°, γ=86.82(3)°, and Z=1. The structure was solved and refined to R=0.064 and R′=0.068. The structure comprises the hexanuclear units which result from the linking of four mononuclear fragments [(salen)Cu] and two mononuclear fragment [(salen)Fe(H2O)]+, through Cu -O ⋯ H -O -Fe -O -H ⋯ O -Cu hydrogen bonds of coordinating H2O. In this complex, FeIII ions are in almost square-planar surroundings. The temperature dependences of the magnetic susceptibilities of the complex have been studied in the 4.2–300 K range, indicating the presence of an antiferromagnetic interactions between metal ions.
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  • 17
    ISSN: 1572-8862
    Keywords: Dynamic disorder ; crystal structure ; ruthenium cluster
    Source: Springer Online Journal Archives 1860-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: Abstract The disorder in the X-ray crystal structures of Ru3(CO)11(L), L=CN t Bu 1 and PMe3 3 has been re-examined. Crystallographic data for 1 at 100 K: C16H9NO11Ru3, space group P21/n, a=11.796(5), b=11.748(2), c=16.040(7) Å, β=109.81(3)°, Z=4, 6077 reflections, R=0.028. For 3 at 223 K: C14H9O11PRu3, space group P21/n, a=8.5971(15), b=12.391(7), c=40.345(8) Å, β=94.43(2)°, Z=8, 7966 reflections, R=0.031. The disorder present in 1 and 3 at room temperature disappears reversibly on cooling, showing that it is dynamic in origin. The ligator atoms of the isonitrile and phosphine ligands move by a maximum of ∼0.8 Å, indicating that the whole cluster does not rotate intact within the crystal lattice, but rather that the Ru3 triangle effectively oscillates within a relatively rigid ligand polyhedron. The crystal structure of Ru3(CO)9{P(OMe)3 3} 7, which crystallizes in triclinic (7-t) and monoclinic (7-m) modifications is also reported. Both modifications have two independent molecules in the asymmetric unit, and both modifications display dynamic disorder in the metal framework. Crystalllographic data for 7-t at 173 K: C18H27O18P3Ru3, space group P-1, a=11.8085(18), b=15.915(2), c=17.350(3) Å, α=99.929(14), β=101.811(14), γ=90.630(12)°, Z=4, 11242 reflections, R=0.048. For 7-m at 120 K: C18H27O18P3Ru3, space group P21/c, a=11.708(8), b=15.922(5), c=33.950(10) Å, β=99.29(4), Z=8, 10191 reflections, R=0.027.
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  • 18
    Electronic Resource
    Electronic Resource
    Springer
    Journal of applied electrochemistry 28 (1998), S. 559-563 
    ISSN: 1572-8838
    Keywords: electroless Ni–Co–B alloy ; dimethylamineborane ; complexing agent ; deposition rate ; crystal structure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology , Electrical Engineering, Measurement and Control Technology
    Notes: Abstract Fundamental aspects of electroless Ni–B, Co–B and Ni–Co–B alloys have been systematically examined. The composition, crystal structure and deposition rate of the alloys were determined as a function of the concentration of reducing agent (dimethylamineborane) and complexing agents (tartrate, citrate, malonate and succinic acid), bath pH and Ni2+/Co2+ ratio. Changes in the deposition rate and metallurgical features of the alloys induced by the change in plating parameters are discussed, based on electrochemical polarization data and the formation enthalpy of the nickel and cobalt borides.
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  • 19
    ISSN: 1572-8854
    Keywords: Copper ; 1,10-phenanthroline ; trifluoroacetate ; crystal structure ; magnetic exchange
    Source: Springer Online Journal Archives 1860-2000
    Topics: Geosciences , Physics
    Notes: Abstract The compound [Cu(phen)(O2CCF3)2]n (phen = 1,10-phenanthroline) has been synthesized and its crystal structure determined. It crystallizes in monoclinic space group C2/c, with a = 19.229(7), b = 11.281(5), c = 7.621(2) Å, β = 104.305(12)°, and Z = 4. The crystal structure is polymeric, being built from infinite zigzag chains of trifluoroacetate bridged copper(II), with the phenanthroline ligands being stacked between the chains. The variable-temperature (13–300 K) magnetic susceptibility and ESR data are reported and a weak ferromagnetic exchange interaction is observed with the exchange parameter estimated as J = 2.9 cm−1.
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  • 20
    Electronic Resource
    Electronic Resource
    Springer
    Journal of chemical crystallography 28 (1998), S. 839-841 
    ISSN: 1572-8854
    Keywords: π-allyl ; carbonyl ; nitrile ; chloro ; crystal structure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Geosciences , Physics
    Notes: Abstract The title compound crystallizes in the monoclinic spacegroup P21/m with a = 6.796(9), b = 12.145(14), c = 7.749(8)Å, β = 101.86(1)°, and Z = 2. The crystal structure consists of molecules of [MoCl(CO)2(NCMe)2(η3-C3H4Me-2)] with crystallographically imposed Cs symmetry and has a pseudo-octahedral geometry, with the π-allyl group trans- to the chloro group and the two cis-carbonyl and acetonitrile groups occupying the equatorial plane.
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  • 21
    ISSN: 1572-8854
    Keywords: 1,10-Phenanthroline ; bis-phenanthrolineprotium ; adduct ; crystal structure ; hydrogen bonding
    Source: Springer Online Journal Archives 1860-2000
    Topics: Geosciences , Physics
    Notes: Abstract Herzog's reported bis-1,10-phenanthrolineammonium perchlorate, [(phen)2(NH4)](ClO4) is in fact the known 2:1 adduct of l,10-phenanthroline (phen) with perchloric acid, [(phen)2H](CIO4). Its crystal structure, mode of formation, and properties are described. The compound crystallizes in the triclinic space group with $$P\bar 1$$ , a = 7.2510(8), b = 13.120(2), c = 22.083(12) Å, α = 77.4550(12), β = 84.45(2), γ = 82.204(14)°, V = 2026.7(6) Å3, Z = 4, and D c = 1.510 g cm−3. It contains cationic columns of alternating 1,10-phenanthroline and its conjugate acid.
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  • 22
    Electronic Resource
    Electronic Resource
    Springer
    Journal of chemical crystallography 28 (1998), S. 645-648 
    ISSN: 1572-8854
    Keywords: 2-Bromoleptoclinidinone ; marine alkaloid ; cytotoxic ; crystal structure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Geosciences , Physics
    Notes: Abstract 2-Bromoleptoclinidinone methanol solvate, C18H8BrN3O·CH4O, crystallizes in the orthorhombic space group Pbca with a = 15.7013(2), b = 7.3308(1), and c = 26.9326(1) Å. The molecule is essentially planar, with the largest deviations occurring at bromine (−0.21 Å), carbonyl oxygen O(l) (+0.19 Å) and in ring-A (C(9) −0.15 Å, C(10) −0.15 Å). Methanol occupies the 1,10-phenanthroline-like metal binding site of the title compound.
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  • 23
    Electronic Resource
    Electronic Resource
    Springer
    Journal of chemical crystallography 28 (1998), S. 925-929 
    ISSN: 1572-8854
    Keywords: Quinoline ; chloroquine ; antimalarial ; crystal structure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Geosciences , Physics
    Notes: Abstract The preparation of N12-(7-chloro-4-quinolinyl)-N 1,N 1-diethyl-1,12-diaminododecane, AQ-40, was accomplished by a five-step process in 80% overall yield from 12-aminododecanoic acid and 4,7-dichloroquinoline. AQ-40 crystallizes as a monohydrate from reagent grade chloroform/ diethyl ether mixtures in the triclinc space group P-1 with a = 8.667(2), b = 8.9425(10), c = 17.217(3) Å, α = 99.34(1), β = 99.89(2), γ = 91.56(1)°, V = 1295.0 Å3 and Z = 2. The l2-(N 1,N 1-diethylamino)dodecyl side chain is in the fully extended conformation and the water molecule forms hydrogen bonds to the two tertiary nitrogen atoms as well as with the secondary amino group. The nitrogen of the secondary amino group bound to the four-position of the quinoline moiety is virtually planar. This together with the rather short C–N distance of 1.347(3) Å to the quinoline moiety suggests involvement of the lone pair on this nitrogen with the π system of the ring.
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  • 24
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    Journal of chemical crystallography 28 (1998), S. 69-72 
    ISSN: 1572-8854
    Keywords: Co(III) complex ; crystal structure ; kinetics ; steric effects
    Source: Springer Online Journal Archives 1860-2000
    Topics: Geosciences , Physics
    Notes: Abstract The title compound crystallizes in the orthorhombic space group Pnma, with a = 7.9209(5), b = 9.818(1), c = 16.867(2) Å, and Z = 4. The structure was solved employing 1864 independent x-ray reflections with I〉2σ(I) by Patterson and difference Fourier techniques and refined by full-matrix least-squares to R = 0.036. The trans-[CO(NH3)4(NH2CH3)Cl](ClO4)2 molecule is on a crystallographic mirror plane. The cobalt ion is in an elongated octahedral coordination with four equatorial ammonia ligands [average Co–N distance equal to 1.966(2) Å], an axial methylamine [Co–N=1.965(3)Å], and an axial chlorine ion [Co–Cl=2.2771(9)Å]. Kinetic steric effects of the complex are interpreted in terms of structural results.
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  • 25
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    Journal of chemical crystallography 28 (1998), S. 209-212 
    ISSN: 1572-8854
    Keywords: Bismuth ; crystal structure ; inorganic polymer
    Source: Springer Online Journal Archives 1860-2000
    Topics: Geosciences , Physics
    Notes: Abstract The ethylenediammonium pentachlorobismuthate(III) dihydrate salt is monoclinic with the following unit cell dimensions: a = 10.902(8)Å, b = 7.926(6)Å, c = 15.199(6)Å, β = 96.40(1)°, space group P21/n with Z = 4. The structure shows a layer arrangement parallel to the $$\vec a$$ axis: planes of the [Bi2Cl10]4− bioctahedra alternate with planes of [NH3(CH2)2NH3]2+ dications. The [Bi2Cl10]4− bioctahedra are connected through O(W)–H··· Cl hydrogen bonds, so that infinite unidimensional chains of composition [Bi2Cl10(H2O)2] n 4n− are formed in the structure parallel to the $$\vec a$$ axis. These chains are themselves interconnected by means of the N–H···Cl bonds originating from the [NH3(CH2)2NH3]2+ entities, forming a three-dimensional network.
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  • 26
    ISSN: 1572-8854
    Keywords: Strontium ; triphenylsiloxy ; crystal structure ; ammonia
    Source: Springer Online Journal Archives 1860-2000
    Topics: Geosciences , Physics
    Notes: Abstract The title complex [Sr2(OSiPh3)4(NH3)5]·0.5C7H8 was prepared by the reaction of strontium metal granules with triphenylsilanol in an ammoniacal-toluene solution at −40°C. It crystallizes in monoclinic space group P21/n with a = 14.465(3), b = 20.715 (6), c = 25.199(6) Å, β = 95.98(2)°, and Z = 4. The complex has a dimeric structure with one terminal and three bridging triphenylsiloxy ligands, the remaining coordination sites being occupied by five ammonia molecules. The central Sr2O4N5 moiety adopts a distorted M2X9 face-sharing bioctahedral arrangement.
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  • 27
    ISSN: 1572-8854
    Keywords: Mixed rubidium–ammonium acid sulfate ; crystal structure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Geosciences , Physics
    Notes: Abstract The structure of Rb0.7(NH4)0.3HSO4 has been determined by X-ray analysis. The mixed compound crystallizes in the monoclinic space group P21/n with unit cell parameters a = 14.374(6) Å, b = 4.618(6) Å, c = 14.412(2) Å, β = 118.03(2)°, V = 844.4(4) Å3, and D cal = 1.536 g cm−3 for Z = 8. The mixed compound Rb0.7(NH4)0.3HSO4 is a chain-based structure. The Rb+ and NH4 + cations are intercalated between chains, formed of HSO4 - groups linked with OH⋯O hydrogen-bonding. Rb0.7(NH4)0.3HSO4 presents a new type of structural arrangement different from those of pure RbHSO4 and NH4HSO4.
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  • 28
    ISSN: 1572-8854
    Keywords: 2-[1,5-Dimethyl-4-hexenyl]-6-hydroxy-5-methyl-1,4-benzoquinone ; 2-[1,5-dimethyl-4-hexenyl]-6-amino-3-hydroxy-5-methyl-1,4-benzoquinone ; 2-[1,5-dimethyl-4-hexenyl]-3-amino-6-hydroxy-5-methyl-1,4-benzoquinone ; crystal structure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Geosciences , Physics
    Notes: Abstract The crystal structures of isoperezone (1), aminoperezone (2), and isoaminoperezone (3) have been determined by single-crystal X-ray diffraction. Compound (1) yields orange crystals, orthorhombic space group P212121 with unit cell dimensions a = 6.271(6), b = 30.373(7), c = 7.257(1) Å, and Z = 4; compound (2) yields purple crystals, orthorhombic space group P212121 with unit cell dimensions a = 6.498(3), b = 7.500(1) c = 29.200(6) Å, and Z = 4; compound (3) yields purple crystals, monoclinic space group P21 with unit cell dimensions a = 7.354(1), b = 7.511(1), c = 13.283(1) Å, β = 102,07(1)°, and Z = 2. The side chains in (1)–(3) are oriented out of the plane of the quinone ring at an angle of 124, 144, and 97°, respectively. The molecules in the crystal are held together by hydrogen-bonding networks and van der Waals interactions.
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  • 29
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    Journal of chemical crystallography 28 (1998), S. 639-643 
    ISSN: 1572-8854
    Keywords: Tungsten(II) ; diiodo ; carbonyl ; trimethylphosphite ; crystal structure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Geosciences , Physics
    Notes: Abstract [WI2(CO)3{P(OMe)3}2]crystallizes in the orthorhombic space group Pca21, with a = 26.924(5), b = 10.726(2), c = 14.136(3) Å, and Z = 8. There are two molecules in the asymmetric unit, the metal atoms in each case being seven-coordinate with a capped fac-(CO)3 octahedral geometry. The molecular dimensions in the two molecules are nearly identical. The W–P distance to the capping atom 2.397 Å (average) is significantly shorter than the other W–P distance, 2.525 Å (average).
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  • 30
    ISSN: 1572-8854
    Keywords: Pyrimidine ; carboxamide ; sulfonyl ; chiral ; crystal structure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Geosciences , Physics
    Notes: Abstract Three novel dihydropyrimidine compounds N8,6-di(4-nitrophenyl)-(3R)-ethyl-(7R)-methyl-5-oxo-2,3,6,7-tetrahydrooxazolo[3,2,c] pyrimidine-8-carboxamide (2), N8,6-di((4-methylphenyl)-sulfonyl)-(3R)-ethyl-5-oxo-(7R)-phenyl-2,3,6,7-tetrahydrooxazolo [3,2,c]pyrimidine-8-carboxamide (3) and N8,6-di ((4-methylphenyl)sulfonyl)-(3R)-ethyl-(7R)-methyl-5-oxo-2,3,6,7-tetrahydrooxazolo[3,2,c] pyrimidine-8-carboxamide (4) have been prepared (from 2-amino-1-butanol of 64.4% e.e.) and structurally characterized by X-ray crystallography. All three compounds contain stereogenic centers, but the crystal of (2) chosen was found to be racemic whilst those of (3) and (4) were found to be homochiral. Compound (2) crystallizes in the monoclinic space group P21/c, with a = 17.958(4), b = 12.431(2), c = 9.653(2) Å, β = 96.20(3)°, U = 2142.3(7) Å3, Z = 4, and D c = 1.449 g cm−3. Compounds (3) and (4) both crystallize in the monoclinic space group P21, with a = 9.349(2), b = 5.824(5), c = 26.513(8) Å, β = 99.43(2)°, U = 1424.1(13) Å3, Z = 2 and D c = 1.389 g cm−3 for (3), and a = 5.9526(9), b = 16.3521(10), c = 13.2263(11) Å, β = 92.81(12)°, U = 1285.9(2) Å3, Z = 2 and D c = 1.378 g cm−3 for (4).
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  • 31
    ISSN: 1572-8854
    Keywords: Heterotrimetallic sulfido cluster ; linear ; synthesis ; crystal structure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Geosciences , Physics
    Notes: Abstract The complex Cu(PPh3)3I reacts with [Et4N]2MoS4 and FeBr2 to give the heterotrimetallic complexes [Et4N][(Ph3P)2{CuS2MoS2Fe}Br2] (1). [Et4N][(Ph3P)2{CuS2MoS2Fe}Br2] (1) crystallizes in the triclinic space group P-1, a = 13.537(4), b = 15.316(4), c = 12.381(4) Å, α = 105.16(2), β = 93.27(3), γ = 101.18(2)°, and V = 2415.0(12) Å3 for Z = 2. The three metal atoms of the structure [Et4N][(Ph3P)2{CuS2MoS2Fe}Br2] (1) are nearly distributed along a line, where three metal atoms (Mo, Cu, Fe) are each in an approximate tetrahedral coordination, the lengths Mo-Fe and Mo-Cu distances are 2.772(2) and 2.798(2) Å, respectively.
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  • 32
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    Journal of chemical crystallography 28 (1998), S. 447-452 
    ISSN: 1572-8854
    Keywords: Bimetallic EDTA complex ; crystal structure ; antimony
    Source: Springer Online Journal Archives 1860-2000
    Topics: Geosciences , Physics
    Notes: Abstract The synthesis and crystal structure of a new EDTA complex, [CaSb2(EDTA)2(H2O)8]n, are reported. This compound crystallizes in the monoclinic space group P21/n, with a = 7.132(1) Å, b = 21.893(3) Å, c = 10.891(2) Å, β = 91.15(2)°. Sb(EDTA) entities are connected through carboxylate bridges to the calcium atoms resulting in layers parallel to the (101) plane. These layers are linked through a weak Sb···O bond (3.171 Å). Pyrolysis of this complex under sulfur vapor, between 400 and 800°C, leads to a mixture of the monometallic sulfides. Pyrolysis in air above 700°C allows the easy preparation of the mixed oxide CaSb2O6.
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  • 33
    ISSN: 1572-8854
    Keywords: 1-1′-Diphosphaferrocene conformation ; P···P secondary bonding ; bis-[W(CO)5](l,l′-diphosphaferrocene system) ; crystal structure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Geosciences , Physics
    Notes: Abstract The structures of (3,3′,4,4′-tetramethyl-1,1′-diphosphaferrocen-2-yl)carboxylic acid (1) and its bis-[W(CO)5] pentane solvate complex (2) have been determined by X-ray analysis. The compound 1 crystallizes in the monoclinic P21 /n space group with Z = 4; a = 7.8404(9), b = 14.9441(16), c = 11.7730(14) Å, β = 92.773(10)°, V = 1377.8(3) Å3, and Dcalc = 1.553 g cm−3. The compound 2 crystallizes in the triclinic $$P\bar 1$$ space group with two complex molecules and one pentane molecule in the unit cell. Cell parameters: a = 10.7070(2), b = 12.577(2), c = 13.239(3) Å, α = 84.00(2), β = 77.58(1), γ = 66.06(1)°, V = 1591.0(5) Å3, and Dcalc = 2.100 g cm−3 .The fully eclipsed conformation of the phospholyl rings with P···P secondary bonding of 3.353(1) Å is observed in 1 and a partially eclipsed conformation is found in 2. The 10 possible conformations of 1,1′-diphosphaferrocenes were described as the function of conformational parameter θ and observed geometry of the phospholyl rings.7 We suppose that the earlier conclusions concerning the destabilizing nature of 1,1′-diphosphaferrocene conformations with θ 〈 100° cannot be considered as general. The mode of W – P coordination, the structural changes of 1 by W(CO)5 coordination, the structural effect of phospholyl rings substitution by the –COOH group, and hydrogen bonds are analyzed.
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  • 34
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    Journal of chemical crystallography 28 (1998), S. 635-638 
    ISSN: 1572-8854
    Keywords: Cobalt(II) ; 2-aminobenzenethiol ; trimethylphosphite ; crystal structure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Geosciences , Physics
    Notes: Abstract A cobalt-thiolato-phosphite complex [Co(o-SC6H4NH2){P(OMe)3}3]PF6 has been prepared and characterized by X-ray crystallography. The complex crystallizes in the triclinic space group $$P\bar 1$$ with a = 10.590(4), b = 11.122(3), c = 13.577(5) Å, α = 101.85(1), β = 108.50(1), γ = 101.75(1)°, V = 1420.6(8) Å3, and Z = 2. The structure comprises discrete [Co(o-SC6H4NH2){P(OMe)3}3]+ cations and PF 6 − anions where the metal atom is coordinated in a highly distorted square-pyramidal environment by one chelate o-SC6H4NH 2 − (abt) and two P(OMe)3 ligands in the basal positions, and a third P(OMe)3 in the axial site with Co–N,, 1.847(5), Co–S, 2.166(2), Co–P, 2.157(2), 2.147(2), and 2.125(2) Å.
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  • 35
    ISSN: 1572-8862
    Keywords: Silver cluster ; crystal structure ; tetrameric cluster
    Source: Springer Online Journal Archives 1860-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: Abstract The sought-after member of the [(PDBP) n AgX] m (n, m=1,4; 2,2; 3,1; PDBP=5-Phenyldibenzophosphole, X=halides) series, the tetrameric [(PDBP)AgCl]4 cluster has been prepared and structurally characterized. The [P4Ag4Cl4] cluster core of [(PDBP)AgCl]4 bears striking similarity to that of [(Ph3P)AgCl]4.
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  • 36
    ISSN: 1572-9001
    Keywords: 1-Acetyl-indoline ; crystal structure ; electronic structure ; AM1 calculation ; CI calculation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract The crystal and molecular structures of the following molecules have been determined: 1-acetyl-indoline, 1-acetyl-5-nitro-indoline, l-acetyl-5-nitro-7-bromo-indoline, 1-acetyl-5-bromo-7-nitroindoline, and l-acetyl-5-bromo-7-nitro-indol. Molecular orbital calculations are performed for these compounds and two related species.
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  • 37
    ISSN: 1572-8951
    Keywords: hydrogen bond ; ferrocenyl carbonyl proanoic ; supermolecule ; crystal structure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract Selective recognition in the title compound, (C14H14FeO3)2 ċ (C10H8N2), between ferrocenyl carbonyl propanoic acid and 4,4'-bipyridine through strong O–-HċN intermolecular hydrogen bonds results in a novel supramolecular architecture. Its crystal structure has been solved by single-crystal X-ray diffraction methods while its characterization has been studied by IR and DSC.
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  • 38
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    Structural chemistry 9 (1998), S. 39-45 
    ISSN: 1572-9001
    Keywords: Enantioselective chromatographic technique ; chiral selector ; ergot alkaloid derivative ; crystal structure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract The structure of (+)1-(3-allylpropyl)-(5R,8S,10R)-N,N-diethyl-N′-[6-methylergolin-8-yl]urea, C22H33N4O (allyl-terguride), has been determined as part of a study on the chiral recognition mechanism of ergot alkaloids when they are used as the chiral stationary phase for the separation of racemic mixtures in liquid chromatographic methods. At the pH of the solution used for the crystallization, the molecules of allyl-terguride are protonated at N(6). All bond distances and angles are in the expected ranges. In the asymmetric unit one hydroxide ion is present. Hydrogen bonds join molecules of allyl-terguride in pairs along the b axis, connecting O(2) of the hydroxide ion to O(1) of one molecule and to N(2) and N(6) of another.
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  • 39
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    Journal of sol gel science and technology 13 (1998), S. 987-990 
    ISSN: 1573-4846
    Keywords: mullite ; MnO ; crystal structure ; electronic paramagnetic resonance (EPR) ; sol-gel chemistry
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract Gels were synthesized from solutions of tetraethylorthosilicate (TEOS) and aluminium nitrate (with and without manganese nitrate). The structural evolution of the gels as a function of manganese content and heat-treatment temperature was studied by visible spectrophotometry (VIS), electron paramagnetic resonance (EPR), X-ray diffraction (XRD) and scanning electron microscopy (SEM). The results show that the presence of manganese can induce mullitization at lower temperatures. However, the effect of manganese depends on its content and how it enters into the mullite structure.
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  • 40
    ISSN: 1573-4943
    Keywords: Artificial neural network ; crystal structure ; statistics ; tetanus toxin ; botulinum neurotoxin
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract Earlier studies used Rost and Sander's artificial neural network [(1993a), J. Mol. Biol. 232, 584–599] to predict the secondary structures [Lebeda and Olson (1994), Proteins 20, 293–300] and residue solvent accessibilities [Lebeda and Olson (1997), J. Protein Chem. 16, 607–618] of the clostridial neurotoxins. Because the X-ray crystal structure of the 50-kDa C-terminal half of the heavy chain of tetanus toxin was recently determined, this report evaluates the accuracy of these network-derived predictions. For this predominantly β-strand-containing fragment, predictions, on a per-residue basis, for both secondary structure and solvent accessibility were about 70% accurate. A more flexible and realistic analysis based on overlapping segments yielded accuracies of over 80% for the three-state secondary structure and for the two-state accessibility predictions. Because the accuracies of these predictions are comparable to those made by Rost and Sander using a dataset of 126 nonhomologous globular proteins, our predictions provide a quantitative foundation for gauging the results when building by homology the structures of related proteins.
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  • 41
    ISSN: 1573-5079
    Keywords: bacterial photosynthesis ; crystal structure ; electron transfer ; proton transfer
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Structural features that have important implications for the fundamental process of transmembrane proton transfer are examined in the recently published high resolution atomic structures of the reaction center (RC) from Rhodobacter sphaeroides in the dark adapted state (DQAQB) and the charged separated state (D+QAQB −); the latter is the active state for proton transfer to the semiquinone. The structures have been determined at 2.2 Å and 2.6 Å resolution, respectively, as reported by Stowell et al. (1997) [Science 276: 812–816]. Three possible proton transfer pathways (P1, P2, P3) consisting of water molecules and/or protonatable residues were identified which connect the QB binding region with the cytoplasmic exposed surface at Asp H224 & Asp M240 (P1), Tyr M3 (P2) and Asp M17 (P3). All three represent possible pathways for proton transfer into the RC. P1 contains an uninterrupted chain of water molecules. This path could, in addition, facilitate the exchange of quinone for quinol during the photocycle by allowing water to move into and out of the binding pocket. Located near these pathways is a cluster of electrostatically interacting acid residues (Asp-L213, Glu-H173, Asp-M17, Asp H124, Asp-L210 and Asp H170) each being within 4.5 Å of a neighboring carboxylic acid or a bridging water molecule. This cluster could serve as an internal ‘proton reservoir’ facilitating fast protonation of QB − that could occur at a rate greater than that attainable by proton uptake from solution.
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  • 42
    ISSN: 1573-6881
    Keywords: Terminal oxidase ; redox coupling ; electrochemical gradient ; electron transport ; energy transduction ; proton translocation ; crystal structure ; site-directed mutagenesis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology , Physics
    Notes: Abstract One of the challenging features of energy-transducing terminal oxidases, like the aa 3 cytochrome c oxidase of Paracoccus denitrificans, is the translocation of protons across the cytoplasmic membrane, which is coupled to the transfer of electrons to oxygen. As a prerequisite for a more advanced examination of the enzymatic properties, several amino acid residues, selected on the basis of recent three-dimensional structure determinations, were exchanged in subunit I of the Paracoccus enzyme by site-directed mutagenesis. The properties of the mutated oxidases were analyzed by different methods to elucidate whether they are involved in the coupled and coordinated transfer of protons via two different pathways either to the site of oxygen reduction or through the enzyme from the cytoplasm to the periplasmic side.
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  • 43
    ISSN: 1572-9605
    Keywords: GdBa2Cu3O7−δ ; Ca substitution ; Mo substitution ; Hf substitution ; crystal structure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Electrical Engineering, Measurement and Control Technology , Physics
    Notes: Abstract The structural and superconducting properties of (Gd1−x−y Ca y M x )Ba2Cu3O z with M = Mo, Hf are investigated using X-ray diffraction, electrical resistivity, and oxygen content measurements. The effect of increasing the Mo concentration in (Gd1−x Mo x )Ba2Cu3O z changes the structure from orthorhombic to tetragonal accompanied by a large increase in resistivity and a fast decrease in T c at the rate of 1.9 K per at.% of Mo, unlike that of Hf substitution in (Gd1−x Hf x )Ba2Cu3O z , which maintains the orthorhombic structure and decreases T c very slowly at the rate of 0.6 K per atm.% of Hf with nearly no change in resistivity. The suppression of T c by M = Mo, Hf can be counterbalanced by hole doping by Ca which increases T c with increasing Ca content showing maximum compensation for Mo. A comparative study of M = Mo, Hf doped samples in (Gd1−x−y Ca y M x )Ba2Cu3O z indicates that the valence of the dopant M = Mo4+,6+, Hf4+ and its ionic radius play an important role in controlling the structural and superconducting properties of the systems.
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  • 44
    ISSN: 0006-3525
    Keywords: folding type-specific secondary structure propensities ; amino acids ; α-helical proteins ; β sheet proteins ; α/β proteins ; α+β proteins ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Folding type-specific secondary structure propensities of 20 naturally occurring amino acids have been derived from α-helical, β-sheet, α/β, and α+β proteins of known structures. These data show that each residue type of amino acids has intrinsic propensities in different regions of secondary structures for different folding types of proteins. Each of the folding types shows markedly different rank ordering, indicating folding type-specific effects on the secondary structure propensities of amino acids. Rigorous statistical tests have been made to validate the folding type-specific effects. It should be noted that α and β proteins have relatively small α-helices and β-strands forming propensities respectively compared with those of α+β and α/β proteins. This may suggest that, with more complex architectures than α and β proteins, α+β and α/β proteins require larger propensities to distinguish from interacting α-helices and β-strands. Our finding of folding type-specific secondary structure propensities suggests that sequence space accessible to each folding type may have differing features. Differing sequence space features might be constrained by topological requirement for each of the folding types. Almost all strong β-sheet forming residues are hydrophobic in character regardless of folding types, thus suggesting the hydrophobicities of side chains as a key determinant of β-sheet structures. In contrast, conformational entropy of side chains is a major determinant of the helical propensities of amino acids, although other interactions such as hydrophobicities and charged interactions cannot be neglected. These results will be helpful to protein design, class-based secondary structure prediction, and protein folding. © 1998 John Wiley & Sons, Inc. Biopoly 45: 35-49, 1998
    Additional Material: 6 Ill.
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  • 45
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    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 45 (1998), S. 69-83 
    ISSN: 0006-3525
    Keywords: DNA branched junctions ; branch migration ; superhelical torque ; control of DNA structure ; endonuclease VII ; nanomechanical device ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: DNA branched junctions are analogues of Holliday junction recombination intermediates. Partially mobile junctions contain a limited amount of homology flanking the branch point. A partially mobile DNA branched junction has been incorporated into a synthetic double-stranded circular DNA molecule. The junction is flanked by four homologous nucleotide pairs, so that there are five possible locations for the branch point. Two opposite arms of the branched junction are joined to form the circular molecule, which contains 262 nucleotides to the base of the junction. This molecule represents a system whereby torque applied to the circular molecule can have an impact on the junction, by relocating its branch point. Ligation of the molecule produces two topoisomers; about 87% of the product is a relaxed molecule, and the rest is a molecule with one positive supercoil. The position of the branch point is assayed by cleaving the molecule with endonuclease VII. We find that the major site of the branch point in the relaxed topoisomer is at the maximally extruded position in the relaxed molecule. Upon the addition of ethidium, the major site of the branch point migrates to the minimally extruded position. © 1998 John Wiley & Sons, Inc. Biopoly 45: 69-83, 1998
    Additional Material: 9 Ill.
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  • 46
    ISSN: 0006-3525
    Keywords: conformation ; aggregation ; κ-carrageenan ; flow field-flow fractionation ; multiangle light scattering ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The relatively novel combination of flow field-flow fractionation (FFF) and multiangle light scattering (MALS) was employed to study a nondegraded κ-carrageenan in different 0.1M salt solutions. The applicability of the technique was tested, and the effects of salt type and salt composition on the molar mass and radius of gyration were studied. A conformational ordering was induced at room temperature by switching the solvent from 0.1M NaCl (coil form) to 0.1M NaI (helix form). An approximate doubling of the average molar mass and an increase in radius of gyration was then observed, in agreement with results obtained previously using size exclusion chromatography-MALS. This increase in size was attributed to conformational ordering and to the formation of double helices. Severe aggregation was observed above 40% CsI in the 0.1M mixed salt solution of CsI and NaI. This was ascribed to the association of helices into large aggregates. For these large associates, having molar masses of several millions, a reversal of the elution order in flow FFF was detected. © 1998 John Wiley & Sons, Inc. Biopoly 45: 85-96 1998
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  • 47
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    Biopolymers 45 (1998), S. 119-133 
    ISSN: 0006-3525
    Keywords: conformations of D-alanyl-D-alanine ; β-lactam ; structural overlay ; AMBER force field ; AM1 ; ab initio ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In this article a conformational analysis of the D-alanyl-D-alanine dipeptide, both charged and neutral, has been carried out. The preferred conformations were determined by means of ab initio and semiempirical quantum, together with empirical force field calculations. The AMBER* force field and the 6-31 + G** and 6-31G** ab initio levels give rise to a coincident minimum energy structure, which, on the other hand, differs from that determined by AM1, 3-21 + G, and 3-21G. The solvent effect on the different charged and neutral conformations have been considered through the AMSOL semiempirical method. A quantification regarding the structural similarities between the different dipeptide conformations and the ampicillin has been performed. The results show that the best overlay is attained by the minimum structure energy obtained by using the 6-31 + G** methodology, which presents a planar amidic nitrogen. © 1998 John Wiley & Sons, Inc. Biopoly 45: 119-133, 1998
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  • 48
    ISSN: 0006-3525
    Keywords: chemical oxidation ; cellulose ; conformational transition ; capillary viscosity ; microcalorimetry ; calcium ions ; gels ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The conformational behavior of different molecular weight fractions of a synthetic C6-oxidized derivative of cellulose were investigated by means of capillary viscometry, CD, and microcalorimetric measurements. Experiments were carried out in the presence of either monovalent or divalent counterions.The experimental data indicated that C6-oxidized cellulose can assume an ordered extended conformation at low ionic strength, induced by the intrachain repulsions of negative charges. This conformation was suggested to be very similar to the fully extended structure of cellulose. In addition to this, upon increasing the ionic strength, a conformational transition of the order-to-disorder type occurred. In fact, the screening of the electrostatic repulsions introduced a number of conformational kinks into the cellulosic backbone, which enabled the polymer to assume a more coiled conformation hence producing less viscous aqueous solutions. © 1998 John Wiley & Sons, Inc. Biopoly 45: 157-163, 1998
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  • 49
    ISSN: 0006-3525
    Keywords: conformational stability ; biological polyelectrolytes ; enthalpy ; entropy ; conformational transitions ; carrageenan ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A new method is proposed for the determination of the enthalpy and entropy changes of nonionic origin upon conformational transition of linear biopolyelectrolytes in solution. For all transition midpoints, defined by given temperature and ionic strength, the total free energy change of the system is zero, which means that the nonionic contribution to the free energy change is equal in value and opposite in sign to the polyelectrolytic one. The counterion condensation theory of linear polyelectrolytes provides for the appropriate analytical expression to be used in such calculations. Linear plots of the proper functions of the calculated free energy changes vs the proper functions of temperature allows for the determination of the enthalpic and entropic terms of the nonionic free energy change of transition.The method has been applied to the extensive available data of the ion-induced conformational change of κ-carrageenan, a linear sulfated galactan extracted from seaweeds. The method has proved very successful, with the results showing a remarkable convergency of the enthalpy values for different monovalent counterions. On the other hand, the above approach has made it possible to explain the known effect of counterion specificity on the transition by a small difference in the nonionic entropic contributions. © 1998 John Wiley & Sons, Inc. Biopoly 45: 203-216, 1998
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  • 50
    ISSN: 0006-3525
    Keywords: uv resonance Raman spectroscopy ; Raman cross section ; hypochromism ; DNA ; deoxynucleoside ; protein ; aromatic amino acid ; virus assembly ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Ultraviolet resonance Raman (UVRR) spectra of H2O and D2O solutions of the nucleoside (dA, dG, dC, dT) and aromatic amino acid (Phe, Trp, Tyr) constituents of DNA viruses have been obtained with laser excitation wavelengths of 257, 244, 238, and 229 nm. Using the 981 cm-1 marker of Na2SO4 as an internal standard, Raman frequencies and scattering cross sections were evaluated for all prominent UVRR bands at each excitation wavelength. The results show that UVRR cross sections of both the nucleosides and amino acids are strongly dependent on excitation wavelength and constitute sensitive and selective probes of the residues. The results provide a library of UVRR marker bands for structural analysis of DNA viruses and other nucleoprotein assemblies. © 1998 John Wiley & Sons, Inc. Biopoly 45: 247-256, 1998
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  • 51
    ISSN: 0006-3525
    Keywords: hemoglobin ; hexagonal bilayer ; Lumbricus ; electron microscopy ; three-dimensional reconstruction ; small-angle x-ray scattering ; three-dimensional models ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The quaternary structure of Lumbricus terrestris hemoglobin was investigated by small-angle x-ray scattering (SAXS). Based on the SAXS data from several independent experiments, a three-dimensional (3D) consensus model was established to simulate the solution structure of this complex protein at low resolution (about 3 nm) and to yield the particle dimensions. The model is built up from a large number of small spheres of different weights, a result of the two-step procedure used to calculate the SAXS model. It accounts for the arrangement of 12 subunits in a hexagonal bilayer structure and for an additional central unit of cylinder-like shape. This model provides an excellent fit of the experimental scattering curve of the protein up to h = 1 nm-1 and a nearly perfect fit of the experimental distance distribution function p(r) in the whole range. Scattering curves and p(r) functions were also calculated for low-resolution models based on 3D reconstructions obtained by cryoelectron microscopy (EM). The calculated functions of these models also provide a very good fit of the experimental scattering curve (even at h 〉 1 nm-1) and p(r) function, if hydration is taken into account and the original model coordinates are slightly rescaled. The comparison of models reveals that both the SAXS-based and the EM-based model lead to a similar simulation of the protein structure and to similar particle dimensions. The essential differences between the models concern the hexagonal bilayer arrangement (eclipsed in the SAXS model, one layer slightly rotated in the EM model), and the mass distribution, mainly on the surface and in the central part of the protein complex. © John Wiley & Sons, Inc. Biopoly 45: 289-298, 1998
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  • 52
    ISSN: 0006-3525
    Keywords: conformational changes ; vicinal glycosylation ; branched α-l-Rhap(1-2)[β-d-Galp(1-3)]-β-d-Glc1-OMe trisaccharide ; parent disaccharides ; hydrogen bond ; isotope effect ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Conformations of the α-l-Rhap(1-2)-β-d-Glc1-OMe and β-d-Galp(1-3)-β-d-Glc1-OMe disaccharides and the branched title trisaccharide were examined in DMSO-d6 solution by 1H-nmr. The distance mapping procedure was based on rotating frame nuclear Overhauser effect (NOE) constraints involving C- and O-linked protons, and hydrogen-bond constraints manifested by the splitting of the OH nmr signals for partially deuteriated samples. An “isotopomer-selected NOE” method for the unequivocal identification of mutually hydrogen-bonded hydroxyl groups was suggested. The length of hydrogen bonds thus detected is considered the only one motionally nonaveraged nmr-derived constraint. Molecular mechanics and molecular dynamics methods were used to model the conformational properties of the studied oligosaccharides. Complex conformational search, relying on a regular Φ,Ψ-grid based scanning of the conformational space of the selected glycosidic linkage, combined with simultaneous modeling of different allowed orientations of the pendant groups and the third, neighboring sugar residue, has been carried out. Energy minimizations were performed for each member of the Φ,Ψ grid generated set of conformations. Conformational clustering has been done to group the minimized conformations into families with similar values of glycosidic torsion angles. Several stable syn and anti conformations were found for the 1→2 and 1→3 bonds in the studied disaccharides. Vicinal glycosylation affected strongly the occupancy of conformational states in both branches of the title trisaccharide. The preferred conformational family of the trisaccharide (with average Φ,Ψ values of 38°, 17° for the 1→2 and 48°, 1° for the 1→3 bond, respectively) was shown by nmr to be stabilized by intramolecular hydrogen bonding between the nonbonded Rha and Gal residues. © 1998 John Wiley & Sons, Inc. Biopoly 46: 417-432, 1998
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  • 53
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    Biopolymers 46 (1998), S. 489-492 
    ISSN: 0006-3525
    Keywords: refractive index increment ; proteins ; solvent ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The refractive index increment of a protein solution is a property not only of the protein, but also of the solvent. This is demonstrated theoretically and confirmed experimentally using analytical interferometry. © 1998 John Wiley & Sons, Inc. Biopoly 46: 489-492, 1998
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  • 54
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    Biopolymers 47 (1998), S. 1-1 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: No abstract.
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  • 55
    ISSN: 0006-3525
    Keywords: hepatitis A ; synthetic peptides ; CD ; liposomes ; computational study ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The present study was undertaken to examine the structural features that may be important to explain the immunogenicity of the (110-121) peptide sequence (FWRGDLVFDFQV) of VP3 capsid protein of hepatitis A virus. A conformational analysis of the preferred conformations by CD and molecular mechanics was carried out. Present results suggest that the interaction with liposomes as biomembrane model induces and stabilizes the amphipathic β-structure of the peptide.To study the contribution of amino acid replacements at the RGD tripeptide as well as the influence of the peptide chain length on peptide conformation, solid-phase peptide synthesis of several peptide analogs was carried out and the peptide conformation was studied using CD spectroscopy. The results show that the RGD sequence is necessary to induce the β-structure in the presence of liposomes. © 1998 John Wiley & Sons, Inc. Biopoly 45: 479-492, 1998
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  • 56
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    Biopolymers 46 (1998), S. 31-37 
    ISSN: 0006-3525
    Keywords: DNA liquid crystals ; DNA fragments ; screened Coulomb interactions ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The critical volume fractions pertaining to the formation of DNA liquid crystals were obtained from polarization microscopy, 31P-nmr, and phase separation experiments. The DNA length (approximately one to two times the persistence length 50 nm), ionic strength, and counterion variety dependencies are reported. The cholesteric-isotropic transition is interpreted in terms of the coexistence equations, which are derived from the solution free energy including orientational entropy and excluded volume effects. With the wormlike chain as reference system, the electrostatic contribution to the free energy is evaluated as a thermodynamic perturbation in the second virial approximation with a Debye-Hückel potential of mean force. The hard core contribution has been evaluated with scaled particle theory and/or a simple generalization of the Carnahan-Starling equation of state for hard spheres. For sufficiently high ionic strengths, the agreement is almost quantitative. At lower amounts of added salt deviations are observed, which are tentatively attributed to counterion screening effects. The contour length dependence agrees with a DNA persistence length 50 nm. © 1998 John Wiley & Sons, Inc. Biopoly 46: 31-37, 1998
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  • 57
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    Biopolymers 46 (1998), S. 245-252 
    ISSN: 0006-3525
    Keywords: gelatin ; gelation ; atomic force microscopy ; interfacial rheology ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Gelation of gelatin under various conditions has been followed by atomic force microscopy (AFM) with the objective of understanding more fully the structure formed during the gelation process. AFM images were obtained of the structures formed from both the bulk sol and in surface films during the onset of gelation. While gelation occurred in the bulk sol, the extent of helix formation was monitored by measurements of optical rotation, and the molecular aggregation was imaged by AFM. Interfacial gelatin films formed at the air-water interface were also studied. Measurements of surface tension and surface rheology were made periodically and Langmuir-Blodgett films were drawn from the interface to allow AFM imaging of the structure of the interfacial layer as a function of time. Structural studies reveal that at low levels of helical content the gelatin molecules assemble into aggregates containing short segments of dimensions comparable to those expected for gelatin triple helices. With time larger fibrous structures appear whose dimensions suggest that they are bundles of triple helices. As gelation proceeds, the number density of fibers increases at the expense of the smaller aggregates, eventually assembling into a fibrous network. The gel structure appears to be sensitive to the thermal history, and this is particularly important in determining the structure and properties of the interfacial films. © 1998 John Wiley & Sons, Inc. Biopoly 46: 245-252, 1998
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  • 58
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    Biopolymers 48 (1998), S. 65-81 
    ISSN: 0006-3525
    Keywords: nucleotide analogue interference mapping ; phosphorothioate ; group I intron ; interference suppression ; RNA ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In this review I will outline several chemogenetic approaches used to determine the chemical basis of large ribozyme function and structure. The term chemogenetics was first used to describe site-specific functional group modification experiments in the analysis of DNA-protein interactions. Within the past few years equivalent experiments have been performed on large catalytic RNAs using both single-site substitution and interference mapping techniques with nucleotide analogues. While functional group mutagenesis is an important aspect of a chemogenetic approach, chemical correlates to genetic revertants and suppressors must also be realized for the genetic analogy to be intellectually valid and experimentally useful. Several examples of functional group revertants and suppressors have now been obtained within the Tetrahymena group I ribozyme. These experiments define an ensemble of tertiary hydrogen bonds that have made it possible to construct a detailed model of the ribozyme catalytic core. The model includes a functionally important monovalent metal ion binding site, a wobble-wobble receptor motif for helix-helix packing interactions, and a minor groove triple helix. © 1998 John Wiley & Sons, Inc. Biopoly 48: 65-81, 1998
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  • 59
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    Biopolymers 48 (1998), S. 83-96 
    ISSN: 0006-3525
    Keywords: nucleic acid ; disulfide cross-link ; structure ; dynamics ; stability ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In this review I discuss straightforward and general methods to modify nucleic acid structure with disulfide cross-links. A motivating factor in developing this chemistry was the notion that disulfide bonds would be excellent tools to probe the structure, dynamics, thermodynamics, folding, and function of DNA and RNA, much in the way that cystine cross-links have been used to study proteins. The chemistry described has been used to synthesize disulfide cross-linked hairpins and duplexes, higher order structures like triplexes, nonground-state conformations, and tRNAs. Since the cross-links form quantitatively by mild air oxidation and do not perturb either secondary or tertiary structure, this modification should prove quite useful for the study of nucleic acids. © 1998 John Wiley & Sons, Inc. Biopoly 48: 83-96, 1998
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  • 60
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    Biopolymers 48 (1998), S. 113-135 
    ISSN: 0006-3525
    Keywords: divalent cations ; magnesium ; RNA ; ion binding ; RNA folding ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Divalent cations, like magnesium, are crucial for the structural integrity and biological activity of RNA. In this article, we present a picture of how magnesium stabilizes a particular folded form of RNA. The overall stabilization of RNA by Mg2+ is given by the free energy of transferring RNA from a reference univalent salt solution to a mixed salt solution. This term has favorable energetic contributions from two distinct modes of binding: diffuse binding and site binding. In diffuse binding, fully hydrated Mg ions interact with the RNA via nonspecific long-range electrostatic interactions. In site binding, dehydrated Mg2+ interacts with anionic ligands specifically arranged by the RNA fold to act as coordinating ligands for the metal ion. Each of these modes has a strong coulombic contribution to binding; however, site binding is also characterized by substantial changes in ion solvation and other nonelectrostatic contributions. We will show how these energetic differences can be exploited to experimentally distinguish between these two classes of ions using analyses of binding polynomials. We survey a number of specific systems in which Mg2+-RNA interactions have been studied. In well-characterized systems such as certain tRNAs and some rRNA fragments these studies show that site-bound ions can play an important role in RNA stability. However, the crucial role of diffusely bound ions is also evident. We emphasize that diffuse binding can only be described rigorously by a model that accounts for long-range electrostatic forces. To fully understand the role of magnesium ions in RNA stability, theoretical models describing electrostatic forces in systems with complicated structures must be developed. © 1999 John Wiley & Sons, Inc. Biopoly 48: 113-135, 1998
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  • 61
    ISSN: 0006-3525
    Keywords: 1H-nmr ; molecular modeling ; peptaibol ; peptide-lipid interaction ; sodium dodecyl sulfate micelles ; trichorzianin TA VII ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Trichorzianin TA VII, Ac0 U1 A2 A3 U4 J5 Q6 U7 U8 U9 S10 L11 U12 P13 V14 U15 I16 Q17 Q18 Fol19, is a nonadecapeptide member of the peptaibol antibiotics biosynthesized by Trichoderma soil fungi, which is characterized by a high proportion of the α,α-dialkylated amino acids, α-aminoisobutyric acid (Aib, U) and isovaline (Iva, J), an acetylated N-terminus and a C-terminal phenylalaninol (Pheol, Fol). The main interest in such peptides stems from their ability to interact with phospholipid bilayers and form voltage-dependent transmembrane channels in planar lipid bilayers. In order to provide insights into the lipid-peptide interaction promoting the voltage gating, the conformational study of TA VII in the presence of perdeuterated sodium dodecyl sulfate (SDS-d25) micelles has been carried out. 1H sequential assignments have been performed with the use of two-dimensional homo- and -heteronuclear nmr techniques including double quantum filtered correlated spectroscopy, homonuclear Hartmann-Hahn, nuclear Overhauser effect spectroscopy, 1H-13C heteronuclear single quantum correlation, and heteronuclear multiple bond correlation. Conformational parameters, such as 3JNHCαH coupling constants, temperature coefficients of amide protons (Δδ/ΔTNH) and quantitative nuclear Overhauser enhancement data, lead to detailed structural information. Ninety-eight three-dimensional structures consistent with the nmr data were generated from 231 interproton distances and six Φ dihedral angle restraints, using restrained molecular dynamics and energy minimization calculations. The average rms deviation between the 98 refined structures and the energy-minimized average structure is 0.59 Å for the backbone atoms. The structure of trichorzianin TA VII associated with SDS micelles, as determined by these methods, is characterized by two right-handed helical segments involving residues 1-8 and 11-19, linked by a β-turn that leads to an angle about 90°-100° between the two helix axes; residues 18 and 19 at the end of the C-terminal helix exhibit multiple conformations. © 1998 John Wiley & Sons, Inc. Biopoly 46: 75-88, 1998
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  • 62
    ISSN: 0006-3525
    Keywords: 9-hydroxyellipticine ; DNA ; CD ; linear dichroism ; resonance light scattering ; intercalation ; drug-drug interactions ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The binding of 9-hydroxyellipticine to calf thymus DNA, poly[d(A-T)]2, and poly-[d(G-C)]2 has been studied in detail by means of CD, linear dichroism, resonance light scattering, and molecular dynamics. The transition moment polarizations of 9-hydroxyelliptiycine were determined in polyvinyl alcohol stretched film. Spectroscopic solution studies of the DNA/drug complex are combined with theoretical CD calculations using the final 50 ps of a series of molecular dynamics simulations as input. The spectroscopic data shows 9-hydroxyellipticine to adopt two main binding modes, one intercalative and the other a stacked binding mode involving the formation of drug oligomers in the DNA major groove. Analysis of the intercalated binding mode in poly[d(A-T)]2 suggests the 9-hydroxyellipticine hydroxyl group lies in the minor groove and hydrogen bonds to water with the pyridine ring protruding into the major groove. The stacked binding mode was examined using resonance light scattering and it was concluded that the drug was forming small oligomer stacks rather than extended aggregates. Reduced linear dichroism measurements suggested a binding geometry that precluded a minor groove binding mode where the plane of the drug makes a 45° angle with the plane of the bases. Thus it was concluded that the drug stacks in the major groove. No obvious differences in the mode of binding of 9-hydroxyellipticine were observed between different DNA sequences; however, the stacked binding mode appeared to be more favorable for calf thymus DNA and poly[d(G-C)]2 than for poly[d(A-T)]2, an observation that could be explained by the slightly greater steric hindrance of the poly[d(A-T)]2 major groove. A strong concentration dependence was observed for the two binding modes where intercalation is favored at very low drug load, with stacking interactions becoming more prominent as the drug concentration is increased. Even at DNA : drug mixing ratios of 70:1 the stacked binding mode was still important for GC-rich DNAs. © 1998 John Wiley & Sons, Inc. Biopoly 46: 127-143, 1998
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  • 63
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    Biopolymers 46 (1998), S. 169-179 
    ISSN: 0006-3525
    Keywords: macromolecular carriers ; drug targeting and delivery ; branched chain synthetic polypeptides ; membrane-synthetic polypeptide interaction ; lipid monolayers/bilayers ; polymer therapeutics ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The surface properties at the air/water interface and the interaction of branched chain polymeric polypeptides with a general formula poly[Lys-(DL-Alam-X1)], where X = Π (AK), Ser (SAK), or Glu (EAK), with phospholipids were investigated. Polylysine derivatives with polycationic (SAK, AK) or amphoteric (EAK) were capable to spread and form stable monomolecular layers. The stability of monolayers at the air/water interface was dependent on the side-chain terminal amino acid residue of polymers and can be described by SAK 〈 AK 〈 EAK order. The area per amino acid residue values calculated from compression isotherms were in the same range as compared to those of linear poly-α-amino acids and proteins. Moreover, these polymers interact with phospholipid monomolecular layers composed of dipalmitoyl phosphatidyl choline (DPPC) or DPPC/PG (PG: phosphatidyl glycerol; 95/5, mol/mol). Data obtained from compression isotherms of phospholipids spread on aqueous polymer solutions at different initial surface pressure indicated that insertion into lipid monolayers for SAK or AK is more pronounced than for EAK. The interaction between branched polypeptides and phospholipid membranes was further investigated using lipid bilayers with DPPC/PG and fluorescent probes located either at the polar surface [1-(4-trimethylammonium-phenyl)-6-phenyl-1,3,5-hexatriene (TMA-DPH) sodium anilino naphthalene sulfonate (ANS)] or within the hydrophobic core (DPH) of the liposome. Changes in fluorescence intensity and in polarization were observed when TMA-DPH or ANS, but not DPH were used. Comparative data also indicate that all three polymers interact only with the outer surface of the bilayer, but even the most marked penetration of polycationic polypeptide (SAK) did not result in alteration of the ordered state of the alkyl chains in the bilayer. Taken together, data obtained from mono- or bilayer experiments suggest that the interaction between branched polymers and phospholipids are highly dependent on the charge properties (Ser vs Glu) and on the identity (Ser vs Ala) of side-chain terminating amino acids. The binding of polymers to the model membranes could be mainly driven by electrostatic forces, but the significant role of hydrophilic properties in case of SAK cannot be excluded. © 1998 John Wiley & Sons, Inc. Biopoly 46: 169-179, 1998
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  • 64
    ISSN: 0006-3525
    Keywords: Cα,α-dialkylated glycines ; molecular dynamics ; geometry and conformation ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The relationship between the local backbone conformation and bond angles at Cα of symmetrically substituted Cα,α-dialkylated glycines (Cα,α-dimethylglycine or α-aminoisobutyric acid, Aib; Cα,α-diethylglycine, Deg; Cα,α-di-n-propylglycine, Dpg) has been investigated by molecular dynamics (MD) simulation adopting flat bottom harmonic potentials, instead of the usual harmonic restraints, for the Cα bond angles. The MD simulations show that the Cα bond angles are related to the local backbone conformation, irrespectively of the side-chain length of Aib, Deg, and Dpg residues. Moreover, the N-Cα-C′ (τ) angle is the most sensitive conformational parameter and, in the folded form, is always larger and more flexible than in the extended one. © 1998 John Wiley & Sons, Inc. Biopoly 46: 239-244, 1998
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  • 65
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    Biopolymers 46 (1998), S. 319-327 
    ISSN: 0006-3525
    Keywords: methionine ligation ; parathyroid hormones ; biomimetic ligation ; S-methylation ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In biological systems, both proteolysis and aminolysis of amide bonds produce activated intermediates through acyl transfer reactions either inter- or intramolecularly. Protein splicing is an illustrative example that proceeds through a series of catalyzed acyl transfer reactions and culminates at an O- or S-acyl intermediate. This intermediate leads to an uncatalyzed acyl migration to form an amide bond in the spliced product. A ligation method mimicking the uncatalyzed final steps in protein splicing has been developed utilizing the acyl transfer amide-bond feature for the blockwise coupling of unprotected, free peptide segments at methionine (Met). The latent thiol moiety of Met can be exploited using homocysteine at the α-amino terminal position of a free peptide for transthioesterification with another free peptide containing an α-thioester to give an S-acyl intermediate. A subsequent, proximity-driven S- to N-acyl migration of this acyl intermediate spontaneously rearranges to form a homocysteinyl amide bond. S-methylation with excess p-nitrobenezensulfonate yields Met at the ligation site. The methionine ligation is selective and orthogonal, and is usually completed within 4 h when performed at slightly basic pH and under strongly reductive conditions. No side reactions due to acylation were observed with any other α-amines of both peptide segments as seen in the synthesis of parathyroid hormone peptides. Furthermore, cyclic peptide can also be obtained through the same strategy by placing both homocysteine at the amino terminus and the thioester at the carboxyl terminus in an unprotected peptide precursor. These biomimetic ligation strategies hold promise for engineering novel peptides and proteins. © 1998 John Wiley & Sons, Inc. Biopoly 46: 319-327, 1998
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  • 66
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    Biopolymers 46 (1998), S. 359-373 
    ISSN: 0006-3525
    Keywords: boundary element method ; DNA electrophoresis ; electrophoretic mobility of DNA ; free solution electrophoretic mobility of DNA ; ion relaxation, DNA electrophoresis ; modeling electrophoresis of polyions ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Boundary element methods are used to model the free solution electrophoretic mobility of short DNA fragments. The Stern surfaces of the DNA fragments are modeled as plated cylinders that reproduce translational and rotational diffusion constants. The solvent-accessible and ion-accessible surfaces are taken to be coincident with the Stern surface. The mobilities are computed by solving simultaneously the coupled Navier-Stokes, Poisson, and ion-transport equations. The equilibrium electrostatics are treated at the level of the full Poisson-Boltzmann equation and ion relaxation is included. For polyions as highly charged as short DNA fragments, ion relaxation is substantial. At .11 M KCl, the simulated mobilities of a 20 base pair DNA fragment are in excellent agreement with experiment. At .04 M Tris acetate, pH = 8.0, the simulated mobilities are about 10-15% higher than experimental values and this discrepancy is attributed to the relatively large size of the Tris counterion. The length dependence of the mobility at .11 M KCl is also investigated. Earlier mobility studies on lysozyme are reexamined in view of the present findings. In addition to electrophoretic mobilities, the effective polyion charge measured in steady state electrophoresis and its relationship to the preferential interaction parameter γgG is briefly considered. © 1998 John Wiley & Sons, Inc. Biopoly 46: 359-373, 1998
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  • 67
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    Biopolymers 45 (1998), S. 341-346 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: No abstract.
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  • 68
    ISSN: 0006-3525
    Keywords: diffusional encounter ; Brownian dynamics ; average Boltzmann factor ; acetylcholinesterase ; Poisson-Boltzmann ; electrostatics ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The utility of the average Boltzmann factor around the active site of an enzyme as the predictor of the electrostatic enhancement of the substrate binding rate is tested on a set of data on wild-type acetylcholinesterase and 18 charge mutants recently obtained by Brownian dynamics simulations. A good correlation between the average Boltzmann factors and the substrate binding rate constants is found. The effects of single charge mutations on both the Boltzmann factor and the substrate binding rate constant are modest, i.e., 〈5 fold increase or decrease. This is consistent with the experimental results of Shafferman et al. but does not support their suggestion that the overall rate of the catalytic reaction is not limited by the diffusional encounter of acetylcholinesterase and its substrate. © 1998 John Wiley & Sons, Inc. Biopoly 45: 355-360, 1998
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  • 69
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    Biopolymers 45 (1998), S. 469-478 
    ISSN: 0006-3525
    Keywords: molecular dynamics ; hydrated proteins ; crystal structures ; density distributions ; globular proteins ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Using molecular dynamics simulations of fully hydrated proteins and analysis of crystal structures contained in the Protein Data Bank, we develop a transferable set of perpendicular radial distribution functions for water molecules around globular proteins. These universal functions may be used to reconstruct the unique three-dimensional solvent density distribution around every individual protein with a modest error. We discuss potential applications of this solvent treatment in protein x-ray crystallographic refinements and in theoretical modeling. We also present a fast, grid-based algorithm for construction of the perpendicular solvent density distributions. © 1998 John Wiley & Sons, Inc. Biopoly 45: 469-478, 1998
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  • 70
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    Biopolymers 47 (1998), S. 23-29 
    ISSN: 0006-3525
    Keywords: independently folded polypeptide motifs ; miniproteins ; natural target domains ; BBA motif ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In this paper we present a redesign strategy for the development of uniquely folded polypeptide motifs of less than 40 residues. These mini proteins are based on natural target domains, including the zinc finger domains (BBA motif) Nomenclature corresponds to the defined elements of secondary structure, beginning at the N-terminus of the peptide. Roman lettering refers to a specific motif while Greek characters correspond to the elements of secondary structure within that motif. and the disulfide-rich snake and scorpion toxins (BBB motif). These motifs are designed to act as the molecular framework for the construction of novel functional polypeptides. We will explore the structural determinants of the folded BBA motif, inspired by the zinc finger peptides, in relation to the redesign process. © 1998 John Wiley & Sons, Inc. Biopoly 47: 23-29, 1998
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  • 71
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    Biopolymers 47 (1998), S. 75-81 
    ISSN: 0006-3525
    Keywords: ion channel ; synthetic peptide ; de novo design ; template-assembled synthetic proteins ; supramolecular assembly ; membrane protein ; planer lipid bilayers ; amphiphilic peptide ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: To create ion channel function by synthetic peptides is a challenge in the de novo design of artificial membrane proteins. Amphiphilic α-helical motifs of ∼ 20 amino acid residues to span lipid bilayers are most often used for the creation of peptide ion channels. Template molecules to tether helical peptides have been employed to obtain more organized pore structures. Approaches to form molecular assembly of peptides in the membranes by hydrogen bonding have been also investigated. We have developed approaches to assemble helices with individual amino acid sequences to construct artificial helical proteins. Using one of these approaches, four helices corresponding to the voltage sensor segments (S4 in repeat I-IV) of the sodium channel were assembled on a peptide template to give a protein having ion channel activity with rectification. © 1998 John Wiley & Sons, Inc. Biopoly 47: 75-81, 1998
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  • 72
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    Biopolymers 47 (1998), S. 127-142 
    ISSN: 0006-3525
    Keywords: collagen mimetics ; triple helix ; peptoid ; template ; biophysics ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Collagen peptidomimetics have been synthesized as an alternative to natural collagen. The incorporation of unnatural residues such as peptoids in the collagen sequences can demonstrate potent and specific biological activity and enhance the biostability against enzymatic degradation. Furthermore, the use of achiral peptoids simplifies synthetic strategies by reducing racemization problems. The peptoid residue N-isobutylglycine (Nleu) has been successfully incorporated into a series of collagen mimetics composed of Gly-Pro-Nleu, Gly-Nleu-Pro, and Gly-Nleu-Nleu. The discovery of template-assembled collagen mimetics and metal binding ability has laid the foundation for new opportunities in the design of novel collagen mimetic complexes. This review summarizes the synthesis and integrated biophysical analyses of the structures of these collagen mimetics. Solid phase segment condensation techniques have been utilized for the synthesis of the single chain and template-assembled analogues. The characterization of the collagen-like structures has been established by temperature-dependent optical rotation measurements, CD, NMR spectroscopy, and molecular modelling simulations. © 1998 John Wiley & Sons, Inc. Biopoly 47: 127-142, 1998
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  • 73
    ISSN: 0006-3525
    Keywords: non-natural amino acid ; peptide ; squarylium dye ; thin film ; poly(3-methylthiophene) ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We designed a polypeptide that behaves as a photodevice by using a non-natural amino acid with replacement of an α-hydrogen by a squarylium dye and succeeded in syntheses of the non-natural amino acid derivative containing a squarylium and its peptide with trialanine Ala-Ala-Ala. Strong dye-dye interactions were confirmed by absorption and CD spectra for the peptide in 2,2,2-trifluoroethanol solution and in water suspension. The non-natural amino acid derivative could be deposited onto a PMeT/Au electrode by the micelle disruption method. © 1998 John Wiley & Sons, Inc. Biopoly 47: 179-183, 1998
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  • 74
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    Biopolymers 47 (1998), S. 263-263 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: No abstract.
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  • 75
    ISSN: 0006-3525
    Keywords: electrostatically driven Monte Carlo method ; cluster analysis ; global energy minimum ; perturbed conformations ; conformational space ; lowest energy conformations ; polypeptide chain ; melittin, membrane-bound portion ; Empirical Conformational Energy Program for Peptides 3 ; annealing methods ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The electrostatically driven Monte Carlo (EDMC) method has been greatly improved by adding a series of new features, including a procedure for cluster analysis of the accepted conformations. This information is used to guide the search for the global energy minimum. Alternative procedures for generating perturbed conformations to sample the conformational space were also included. These procedures enhance the efficiency of the method by generating a larger number of low-energy conformations.The improved EDMC method has been used to explore the conformational space of a 20-residue polypeptide chain whose sequence corresponds to the membrane-bound portion of melittin. The ECEPP/3 (Empirical Conformational Energy Program for Peptides) algorithm was used to describe the conformational energy of the chain. After an exhaustive search involving 14 independent runs, the lowest energy conformation (LEC) (-91.0 kcal/mol) of the entire study was encountered in four of the runs, while conformations higher in energy by no more than 1.8 kcal/mol were found in the remaining runs with the exception of one of them (run 8). The LEC is identical to the conformation found recently by J. Lee, H.A. Scheraga, and S. Rackovsky [(1998) “Conformational Analysis of the 20-Residue Membrane-Bound Portion of Melittin by Conformational Space Annealing,” Biopolymers, Vol. 46, pp. 103-115] as the lowest energy conformation obtained in their study using the conformational space annealing method. These results suggest that this conformation corresponds to the global energy minimum of the ECEPP/3 potential function for this specific sequence; it also appears to be the conformation of lowest free energy. © 1998 John Wiley & Sons, Inc. Biopoly 46: 117-126, 1998
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  • 76
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    Biopolymers 46 (1998), S. 195-200 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: No abstract.
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  • 77
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    Biopolymers 46 (1998), S. 201-214 
    ISSN: 0006-3525
    Keywords: band broadening ; dispersion ; DNA ; gels ; electrophoresis ; fluorescence recovery ; photobleaching ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We determined quantitatively the band broadening effect during gel electrophoresis by measuring the longitudinal dispersion coefficient Dx, with a fluorescence recovery after photobleaching setup, coupled to an electrophoretic cell. We carried out measurements as a function of the electric field, the average pore size, and the molecular length of DNA fragments. Our results are in good agreement with the predictions of the biased reptation model with fluctuations described by T. A. Duke et al. [(1992) Physics Review Letters, vol. 69, pp. 3260-3263]. This agreement is observed on single-stranded DNA [persistence length ≅ 4 nm; B. Tinland et al. (1997) Macromolecules, vol. 30, pp. 5763-5765] in polyacrylamide gels and on double-stranded DNA (persistence length ≅ 50 nm) in agarose gels, two systems where the ratio between the average pore size and the Kuhn length is larger than 1. © 1998 John Wiley & Sons, Inc. Biopoly 46: 201-214, 1998
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  • 78
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    Biopolymers 46 (1998), S. 403-415 
    ISSN: 0006-3525
    Keywords: molecular dynamics ; DNA curvature ; DNA flexibility ; TATA box functionality ; TATA box binding protein (TBP) ; TBP recognition ; TBP binding ; TBP transcriptional activation ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Four 1.5 ns molecular dynamics (MD) simulations were performed on the d(GCTATAAAAGGG) · d(CCCTTTTATAGC) double helix dodecamer bearing the Adenovirus major late promoter TATA element and three iso-composition mutants for which physical and biochemical data are available from the same laboratory. Three of these DNA sequences experimentally induce tight binding with the TATA box binding protein (TBP) and induce high transcription rates; the other DNA sequence induces much lower TBP binding and transcription. The x-ray crystal structures have previously shown that the duplex DNA in DNA-TBP complexes are highly bent. We performed and analyzed MD simulations for these four DNAs, whose experimental structures are not available, in order to address the issue of whether inherent DNA structure and flexibility play a role in establishing these observed preferences. A comparison of the experimental and simulated results demonstrated that DNA duplex sequence-dependent curvature and flexibility play a significant role in TBP recognition, binding, and transcriptional activation. © 1998 John Wiley & Sons, Inc. Biopoly 46: 403-415, 1998
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  • 79
    ISSN: 0006-3525
    Keywords: vibrational CD ; solution conformation ; alanine oligopeptides ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The solution conformation of a number of small, linear alanine oligomers was investigated via ir (or vibrational) CD (VCD). We find that these oligopeptides assume distinct solution conformations that depend primarily on chain lengths, and to a lesser degree on temperature, ionic strength, and pH. As expected, the longer chain oligomers exhibit more distinct VCD features and, presumably, more stable solution structures. At the level of the hexamer, however, aggregation of the peptide occurs. The fast time scale of VCD allows solution structures to be detected that may not be observable using slower techniques such as various forms of nmr spectroscopy. The VCD results reported here confirm that it is generally possible to obtain conformational information for small, linear homo- and heterooligopeptides via VCD spectroscopy. In this respect, the sensitivity of VCD is similar to that of electronic CD. Furthermore, the temperature dependence of the VCD results indicate that at elevated temperatures, the increasing number of conformational states results in a loss of discernible conformers, and consequently, a broadening and weakening of the VCD features. © 1998 John Wiley & Sons, Inc. Biopoly 46: 455-463, 1998
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  • 80
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    Biopolymers 47 (1998), S. 5-22 
    ISSN: 0006-3525
    Keywords: hemoproteins ; model systems ; miniaturized proteins ; mimochromes ; helix structures ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The present paper highlights and reviews current research in the field of hemoprotein models. Hemoproteins have been extensively studied in order to understand structure-function relationships, and to design new molecules with desired functions. A wide number of synthetic analogues have been developed, using quite different approaches. They differ in molecular structures, ranging from simple meso-substituted tetraaryl-metalloporphyrins and peptide-porphyrin conjugates.In this paper we summarize the state of the art on peptide based hemoprotein models. We also report here the approach used by us to develop a new class of molecules, named mimochromes. They can be regarded as miniaturized hemoproteins, because mimochromes are low molecular weight compounds with some structural and functional properties common to those of the parent high molecular weight protein. The basic structure of mimochromes is a deuteroporphyrin ring covalently linked to two helical peptide chains. Two molecules of this series have been fully characterized. All the information derived from their structural analysis has been applied to the design of new analogues with additional functions. © 1998 John Wiley & Sons, Inc. Biopoly 47: 5-22, 1998
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  • 81
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    Biopolymers 46 (1998), S. 503-516 
    ISSN: 0006-3525
    Keywords: discrete charge model of DNA ; dielectric cylinder in water ; effective dielectric constant ; salt effects ; Debye shielding factor ; potential variations in DNA surface ; Boltzmann averaged bending angles ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We have studied electrostatic properties of DNA with a discrete charge model consisting of a cylindrical dielectric core with a radius of 8 Å and a dielectric constant Di = 4, surrounded by two helical strings of phosphate point charges at 10 Å from the axis, immersed in an aqueous medium with dielectric constant Dw = 78.54. Eliminating the dielectric core makes potentials in the phosphate surface less negative by about 0.5 kT/e. Salt effects are evaluated for the model without a dielectric core, using the shielded Coulomb potential. Smearing the phosphate charges increases their potential by about 2.5 kT/e, due mostly to the self-potential of the smeared charge. Potentials in the center of the minor and major grooves vary less than 0.02 kT/e along their helical path. The potential in the center of the minor groove is from 1.0 to 1.7 kT/e, more negative than in the center of the major groove, depending on dielectric core and salt concentration. So multivalent cations and also larger cationic ligands, such as some antibiotics, are likely to adsorb in the minor groove, in agreement with earlier computations by A. and B. Pullman. Dielectric effects on the surface potential and the local potential variations are found to be relatively small. Bending of DNA is studied by placing a multivalent cation, MZ+, in the center of the minor or major groove, curving DNA around it for a certain length, and calculating the free energy difference between the bent and the straight configuration. Boltzmann averaged bending angles, 〈β〉, are found to be maximal in 0.03M monovalent salt, for a length of about 50 or 25 Å of curved DNA when an MZ+ ion is adsorbed in the minor or the major groove, respectively. When the dielectric constant of water is used throughout the calculation, we find maximal bends of 〈β〉 = 11° for M2+ and 〈β〉 = 16° for M3+ in the minor groove, 〈β〉 = 13° for M3+ in the major groove. The absence of bends in DNA adsorbed to mica in the presence of Mg salts supports the role of Mg2+ in “ion bridging” between DNA and mica. The treatment of the effective dielectric constant between two points outside a dielectric cylinder in water is appended. © 1998 John Wiley & Sons, Inc. Biopoly 46: 503-516, 1998
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  • 82
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    Biopolymers 47 (1998), S. 63-73 
    ISSN: 0006-3525
    Keywords: protein de novo design ; novel macromolecules ; topological templates ; Template Assembled Synthetic Proteins (TASP) ; biosensors ; protein folding ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The ultimate goal in protein de novo design is the creation of novel macromolecules with tailor-made receptor, sensory, and catalytic functions. Despite considerable progress in understanding basic rules of secondary structure formation and protein stability, the well-known protein folding problem is still far from being solved and, in general, only a limited number of designed proteins are folded uniquely. In this article the state-of-the-art in protein design is demonstrated on some selected examples, indicating that the construction of protein-like macromolecules mimicking some essential features of natural proteins seems to be within reach. Thus, protein design and mimicry has become an interdisciplinary challenge with most intriguing perspectives. © 1998 John Wiley & Sons, Inc. Biopoly 47: 63-73, 1998
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  • 83
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    Biopolymers 47 (1998), S. 451-463 
    ISSN: 0006-3525
    Keywords: bacteria ; antibiotics ; linear amphipathic α-helical antimicrobial peptides ; peptide-lipid interactions ; membrane permeation ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The increasing resistance of bacteria to conventional antibiotics resulted in a strong effort to develop antimicrobial compounds with new mechanisms of action. Antimicrobial peptides seem to be a promising solution to this problem. Many studies aimed at understanding their mode of action were described in the past few years. The most studied group includes the linear, mostly α-helical peptides. Although the exact mechanism by which they kill bacteria is not clearly understood, it has been shown that peptide-lipid interactions leading to membrane permeation play a role in their activity. Membrane permeation by amphipathic α-helical peptides can proceed via either one of the two mechanisms: (a) transmembrane pore formation via a “barrel-stave” mechanism; and (b) membrane destruction/solubilization via a “carpet-like” mechanism. The purpose of this review is to summarize recent studies aimed at understanding the mode of action of linear α-helical antimicrobial peptides. This review, which is focused on magainins, cecropins, and dermaseptins as representatives of the amphipathic α-helical antimicrobial peptides, supports the carpet-like rather the barrel-stave mechanism. That these peptides vary with regard to their length, amino acid composition, and net positive charge, but act via a common mechanism, may imply that other linear antimicrobial peptides that share the same properties also share the same mechanism. © 1999 John Wiley & Sons, Inc. Biopoly 47: 451-463, 1998
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  • 84
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    Biopolymers 48 (1998), S. 39-55 
    ISSN: 0006-3525
    Keywords: modified nucleotides ; site-specific probes ; RNA structure ; RNA function ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Modified nucleotides can be incorporated site specifically into RNA by the use of total chemical synthesis as well as by use of a variety of recombinant RNA techniques. The range of nucleotide analogues includes modifications to base, sugar, and phosphate for structure-function analysis and for cross-linking studies as well as to answer specific mechanistic questions in RNA catalysis. We describe how RNA containing site-specific modifications are prepared, concentrating in particular on routes involving chemically synthesized oligoribonucleotides, and give examples of their application in studies of the hammerhead and hairpin ribozymes. © 1998 John Wiley & Sons, Inc. Biopoly 48: 39-55, 1998
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  • 85
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    Biopolymers 48 (1998), S. 29-37 
    ISSN: 0006-3525
    Keywords: amide synthase ; catalytic antibodies ; Diels-Alderase ; ideal catalyst platform ; in vitro selection ; Lewis acid ; modified uridines ; modified RNA ; ribozymes ; SELEX ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In this manuscript the catalytic ability of RNA is examined and compared to other biopolymers. Despite having considerably fewer catalytically enabling properties when compared to proteins, the power of in vitro selection has allowed for RNA and DNA catalysts to be isolated. RNA catalysis has been expanded by incorporating modified bases to enrich the structural and functional diversity of RNA. Successful examples of new RNA chemistry using base modifications include carbon-carbon bond forming reactions and creation of highly specific active sites that are capable of recognizing small organic molecules without the need for nucleic acid templating or intercalation. In fact, the scope of functional modifications available for use in the RNA platform may eventually surpass those that are found in proteins and there are already hints that well chosen modifications allow nucleic acid catalysts to take advantage of mechanisms not available to selected protein catalysts for similar reactions. The chemical versatility of RNA is just emerging and future research directions will likely entail more creative methods for functional modification that will lead to new catalysts. © 1998 John Wiley & Sons, Inc. Biopoly 48: 29-37, 1998
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  • 86
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    Biopolymers 48 (1998), S. 137-153 
    ISSN: 0006-3525
    Keywords: RNA ; pseudoknot ; Turnip Yellow Mosaic Virus ; Mouse Mammary Tumor Virus ; Beet Western Yellows Virus ; Simian Retrovirus type-1 ; Hepatitis Delta Virus ; translational frameshifting ; ribozyme ; nmr ; x-ray diffraction ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Recently, several high-resolution structures of RNA pseudoknots have become available. Here we review the progress in this area. The majority of the structures obtained belong to the classical or H-type pseudoknot family. The most complicated pseudoknot structure elucidated so far is the Hepatitis Delta Virus ribozyme, which forms a nested double pseudoknot. In particular, the structure-function relationships of the H-type pseudoknots involved in translational frameshifting have received much attention. All molecules considered show interesting new structural motifs. © 1999 John Wiley & Sons, Inc. Biopoly 48: 137-153, 1998
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  • 87
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    Helvetica Chimica Acta 81 (1998), S. 236-250 
    ISSN: 0018-019X
    Keywords: Chemistry ; Organic Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: To get informations on both the structure and dynamics of hydrogen chelates 1 of heteroaromatic systems, a great variety of quinazoline-2-acetonitrile chelates were synthesized (see 2-4). Similarly to the situation of the corresponding H-chelates in the pyrimidine-2-acetonitrile series, the investigation of these new derivatives 2-4 by NMR spectroscopic methods (DNMR, COSY, NOESY, ROESY, EXSY, HMQC, HMBC) confirms the presence of an equilibrium of the two possible H-chelate structures (two ‘rotamers’ I and II, i.e., (E)/(Z) isomers; see Scheme). The corresponding equilibria I ⇌ II were determined by complete 1H-NMR signal assignment at low temperatures (after freezing the rotational processes). In addition, the tautomer equilibria A ⇌ B (relative energies of the two minima of the nonsymmetrical double-well potential) for both ‘rotamers’ are ascertained by H,H and C,H couplings. The results are an important basis for the interpretation of both the UV/VIS absorptions and the dependence of fluorescence and fluorescence quantum yields on temperature.
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  • 88
    ISSN: 0018-019X
    Keywords: Chemistry ; Organic Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Stereoselective reactions of phthalimido-substituted radicals derived from (±)-threonine with different radical traps are reported (Scheme 3, Table 1). A strong influence of the nature of the radical trap on the stereoselectivity was noticed. Small nucleophilic radical traps gave preferentially the syn products. The observed selectivities are explained with the A1,3 strain model and depend on steric and electronic effects (Fig. 2). Reactions with electrophilic radical traps such as diphenyl diselenide gave the anti diastereoisomers with moderate stereocontrol, presumably due to stereoelectronic effects. The same stereochemical outcome, i.e., preferential formation of the anti products, was observed for the reactions of the related N-phthaloyliminium ion (Scheme 5, Table 2). The stereochemistry of the ionic reaction is rationalized by a Felkin-Anh model (Fig. 3).
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  • 89
    ISSN: 0018-019X
    Keywords: Chemistry ; Organic Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The cyclopalladation of 1,1′-azonaphthalene (= di(naphthalen-1-yl)diazene; 2) with bis(hexafluoroacetyl-acetonato)palladium(II) (3; [Pd(hfa)2]) yields the ortho-palladated complex (1,1,1,5,5,5-hexafluoropentane-2,4-dionato-κ2O,O′)[1-(naphthalen-1-ylazo-κN2)naphthalen-2-yl-κC2]palladium(II) (4) as well as the peri-palladated complex (1,1,1,5,5,5-hexafluoropentane-2,4-dionato-κ2O,O′)[8-(naphthalen-1-ylazo-κN2)naphthalen-1-yl-κC1]-palladium(II) (5); their structures were corroborated by X-ray analyses. The formation of the novel peri-metallated product 5 containing a six-membered palladacycle strongly depends upon the reaction conditions.
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  • 90
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    New York, NY : Wiley-Blackwell
    Helvetica Chimica Acta 81 (1998), S. 342-352 
    ISSN: 0018-019X
    Keywords: Chemistry ; Organic Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The photoisomerization behavior of three mono[(E)-3-(4-hydroxyphenyl)prop-2-enoyl]spermidines, 1, 2, and 3, and three bis[(E)-3-(4-hydroxyphenyl)prop-2-enoyl]spermidines, 4, 5, and 6, are investigated. The synthetic product (E)-1 could be almost quantitatively (〉 96%) converted into its isomer (Z)-1 under UV light irradiation. In the cases of (E)-2 and (E)-3, a mixture of (E)/(Z) ca. 1:2 was obtained, when the same conditions were applied. The comparison of their UV spectra provides the possible explanation for these different behaviors. Furthermore, it was noticed that the (Z) → (E) isomerization of the C=C bond took place during the purification by reverse-phase high-performance liquid chromatography (RP-HPLC), and the (E)/(Z)-mixture is thus inseparable. The same feature could be observed during the isolation of the (Z,Z)-N,N′-bis[3-(4-hydroxyphenyl)prop-2-enoyl]-spermidines, (Z,Z)-4, (Z,Z)-5, and (Z,Z)-6. Nevertheless, the fractions of (Z,Z)-5 and (Z,Z)-6 were in almost pure state collected, and their 1-NMR spectra are presented.
    Additional Material: 5 Ill.
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  • 91
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    New York, NY : Wiley-Blackwell
    Helvetica Chimica Acta 81 (1998), S. 153-162 
    ISSN: 0018-019X
    Keywords: Chemistry ; Organic Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The synthesis, absolute configuration, and olfactive evaluation of (-)-(E)-α-trans-bergamotenone (= (-)-(1′S,6′R,E)-5-(2′,6′-dimethylbicyclo[3.1.1]hept-2′-en-6′-yl)pent-3-en-2-one; (-)-1), as well as its homologue (-)-19 are reperted. The previously arbitrarily attributed absolute configuration of 1 and of (-)-α-trans-bergamotene (= (-)-(1 S,6R)-2,6-dimethyl-6-(4-methylpent-3-enyl)bicyclo[3.1. 1]hept-2-ene; (-)-2), together with those of the structurally related aldehydes (-)-3a,b and alcohols (-)-4a,b, have been rigorously assigned.
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  • 92
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    New York, NY : Wiley-Blackwell
    Helvetica Chimica Acta 81 (1998), S. 182-186 
    ISSN: 0018-019X
    Keywords: Chemistry ; Organic Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: (-)-(R)-4,4,4,4′,4′,4′-Hexafluorovaline hydrochloride ((R)-5) of 98% ee is prepared from β,β-bis(trifluoromethyl)acrylic acid (= benzyl 4,4,4-trifluoro-3-(trifluoromethyl)but-2-enoate; 1) in 4 steps with an overall yield of 9.6%. Key step is the separation of the TsOH salts of the diastereoisomers obtained by anti-Michael addition of (+)-(R)-1-phenylethylamine (2) to 1 (→ (R,R)-3). In contrast to the published (S)-chirality, the X-ray structure analysis of (R,S)-6 reveals, that (R)-chirality has to be assigned to the levorotatory (-)-4,4,4,4′,4′,4′-hexafluorovaline hydrochloride.
    Additional Material: 2 Ill.
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  • 93
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    New York, NY : Wiley-Blackwell
    Helvetica Chimica Acta 81 (1998), S. 207-218 
    ISSN: 0018-019X
    Keywords: Chemistry ; Organic Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The synthesis and characterization of tripodal dodecadentate ligands with salicylamide and bipyridine binding sites for iron(II) and iron(III) are presented.
    Additional Material: 1 Ill.
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  • 94
    ISSN: 0018-019X
    Keywords: Chemistry ; Organic Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The reaction of CuO'Bu with CO2, and iPr2NH in the presence of PPh3, gives the dialkylcarbamato complex [Cu(O2CNiPr2)(PPh3)2] (1). The CO2/R2NH system (R = Me, Et) in an appropriate organic medium reacts with Ag2O giving the corresponding N,N-dialkylcarbamato complexes of analytical formula [Ag(C2CNR2)] (R = Me, 2; R = Et, 3). The methyl derivative 2 was characterized by X-ray diffraction methods. Crystal data of 2: for [Ag2(O2CNMe2)2], C6H12Ag2N2O4, mol. wt. 391.9; monoclinic, space group P21/c, a = 12.08(1), b = 3.797(2), c = 11.316(7) Å, β = 113.37(6)°, V = 476.3 Å3, Z = 2, Dc = 2.732 g cm-3; μ(MoKα) = 40.64 cm-1, F(000) = 376.0; R = 0.059, Rw = 0.067; g.o.f. 1.27. The structure consists of dinuclear [(Ag2OCNMe2)2] units with slightly distorted linearly two-coordinated Ag-atoms containing bridging carbamato groups to form a substantially planar eight-membered ring with an intra-annular Ag—Ag distance of 2.837(2) Å; the dinuclear units are further joined by Ag—O bonds to form an infinite array. Compound 3, which is presumably dinuclear, as suggested by cryoscopic measurements in benzene, undergoes a structural fission with PPh3, giving the mononuclear triphenylphosphine derivative [Ag(O2CNEt2)(PPh3)2] (4). The amine-catalyzed conversion of Ag2O into Ag2CO3, in the presence of the iPr2NH/CO2 system, is also reported. Cl-Exchange from [AuCl(PPh3)] with [Ag(O2CNEt2)] (3) gives the first N,N-dialkylcarbamato complex of gold, namely [Au(O2CNEt2)(PPh3)] (5), which crystallizes in the monoclinic system: C23H25AuNO2P · 0.5 C7H16, mol. wt. 625.5, space group P21/c; a = 13.212(5), b = 12.25(1), c = 16.795(6) Å, β = 109.09(2)°, V = 2568(2) Å3, Z = 4, Dc, = 1.618 g cm-3; μ(AgKα) = 31.40 cm-1, F(000) = 1236.0; R = 0.058; Rw = 0.064; g.o.f. 2.121. The compound contains two-coordinated Au-atom, namely to the P-atom and to the O-atom of the monodentate carbamato group, the P—Au—O bond angle being 174.7(3)°. The reaction with MeI showed these compounds to react predominantly at the carbamato O-atom giving the corresponding urethanes R2NCO2Me. Evidence was gathered for the transient coordination of CO to Ag in 3.
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  • 95
    ISSN: 0018-019X
    Keywords: Chemistry ; Organic Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The reactions of α-diazo ketones 1a,b with 9H-fluorene-9-thione (2f) in THF at room temperature yielded the symmetrical 1,3-dithiolanes 7a,b, whereas 1b and 2,2,4,4-tetramethylcyclobutane-1,3-dithione (2d) in THF at 60° led to a mixture of two stereoisomeric 1,3-oxathiole derivatives cis- and trans-9a (Scheme 2). With 2-diazo-1,2-diphenylethanone (1c), thio ketones 2a-d as well as 1,3-thiazole-5(4H)-thione 2g reacted to give 1,3-oxathiole derivatives exclusively (Schemes 3 and 4). As the reactions with 1c were more sluggish than those with 1a,b, they were catalyzed either by the addition of LiClO4 or by Rh2(OAc)4. In the case of 2d in THF/LiClO4 at room temperature, a mixture of the monoadduct 4d and the stereoisomeric bis-adducts cis- and trans-9b was formed. Monoadduct 4d could be transformed to cis- and trans-9b by treatment with 1c in the presence of Rh2(OAc)4 (Scheme 4). Xanthione (2e) and 1c in THF at room temperature reacted only when catalyzed with Rh2(OAc)4, and, in contrast to the previous reactions, the benzoyl-substituted thiirane derivative 5a was the sole product (Scheme 4). Both types of reaction were observed with α-diazo amides 1d,e (Schemes 5-7). It is worth mentioning that formation of 1,3-oxathiole or thiirane is not only dependent on the type of the carbonyl compound 2 but also on the α-diazo amide. In the case of 1d and thioxocyclobutanone 2c in THF at room temperature, the primary cycloadduct 12 was the main product. Heating the mixture to 60°, 1,3-oxathiole 10d as well as the spirocyclic thiirane-carboxamide 11b were formed. Thiirane-carboxamides 11d-g were desulfurized with (Me2N)3P in THF at 60°, yielding the corresponding acrylamide derivatives (Scheme 7). All reactions are rationalized by a mechanism via initial formation of acyl-substituted thiocarbonyl ylides which undergo either a 1,5-dipolar electrocyclization to give 1,3-oxathiole derivatives or a 1,3-dipolar electrocyclization to yield thiiranes. Only in the case of the most reactive 9H-fluorene-9-thione (2f) is the thiocarbonyl ylide trapped by a second molecule of 2f to give 1,3-dithiolane derivatives by a 1,3-dipolar cycloaddition.
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  • 96
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    New York, NY : Wiley-Blackwell
    Helvetica Chimica Acta 81 (1998) 
    ISSN: 0018-019X
    Keywords: Chemistry ; Organic Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 97
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    Helvetica Chimica Acta 81 (1998), S. 491-506 
    ISSN: 0018-019X
    Keywords: Chemistry ; Organic Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The synthesis of a series of chiral enantiomerically pure C2-symmetric binucleating ligands is reported. Ligands of type 1-4, which consist of a phenolic or heterocyclic unit bridging two chiral dihydrooxazole rings. are readily accessible from chiral amino alcohols. Ligands 5a and 5b are composed of a cyclic urea or thiourea unit, respectively, and two 3,4-dihydro-2H-pyrrole rings containing a stereogenic center next to the N-atom. Compounds of this type are readily assembled from ethane-1,2-diamine and an imidothioic ester derived from pyroglutamic acid. These new ligands, which can coordinate two metals in close proximity to each other, are of interest regarding possible applications in asymmetric catalysis.
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  • 98
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    New York, NY : Wiley-Blackwell
    Helvetica Chimica Acta 81 (1998), S. 548-557 
    ISSN: 0018-019X
    Keywords: Chemistry ; Organic Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Stability constants have been measured for a series of ligands based on a 2,2′-(pyridine-2,6-diyl)bis[1H-benzimidazole] unit which forms dinuclear double-stranded helical complexes with copper(I). Variation of different structural parameters confirms the importance of the coordinate bond, the stacking interactions, and the weakly bridging pyridine units observed by X-ray crystallography. The stabilities of the complexes depend strongly on the solvent, and in MeCN, which is a good solvent for copper(I), the complexes are less stable and assemble in a stepwise manner. The interconversion of the enantiomers may be followed by 1H-NMR and takes place on a millisecond time scale around room temperature. The trends in lability are similar to those found for the stability of the complexes.
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  • 99
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    New York, NY : Wiley-Blackwell
    Helvetica Chimica Acta 81 (1998), S. 570-583 
    ISSN: 0018-019X
    Keywords: Chemistry ; Organic Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Oligodeoxyribonucleotides containing 7-deaza-2′-deoxy-8-methylguanosine (m8c7Gd; 2b) were prepared. For this purpose, the phosphonate 3a and the phosphoramidite 3b were synthesized and employed in solidphase oligodeoxyribonucleotide synthesis. The structures and the thermodynamic data of duplex formation of oligodeoxyribonucleotides containing 2b were investigated by temperature-dependent CD and UV spectra and compared with those containing 7-deaza-2′-deoxy-7-methylguanosine (m7c7Gd) or 7-deaza-2′-deoxy-guanosine (c7Gd; 2a). In general, compound 2b reduces the duplex stability. In case of the sequence d(m8c7G-C)4 (18), the B → Z transition was facilitated by the incorporation of 2b. Moreover, a single 7-deaza-8-methylguanine residue present in an oligodeoxyribonucleotide tract of guanine residues destabilizes the dG quadruplex significantly. This destabilization is more pronounced than in the case of 7-deazaguanine or 7-deaza-7-methyl-guanine.
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  • 100
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    New York, NY : Wiley-Blackwell
    Helvetica Chimica Acta 81 (1998), S. 770-780 
    ISSN: 0018-019X
    Keywords: Chemistry ; Organic Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Absolute rate constants and their Arrhenius parameters are obtained for the addition of a cyclic malonyl radical derived from Meldrum's acid to 20 mono- or 1,1-disubstituted alkenes in (±)-propylene oxide and for the addition of the open-chain di(tert-butyl)malonyl radical to six mono- or 1,1-disubstituted alkenes in 1,1,2-trichloro-1,2,2-trifluoroethane by time-resolved electron spin resonance spectroscopy. At room temperature, the radicals add at the unsubstituted C-atoms with rate constants ranging from 1.1. 105 M-1S-1 (acrolein) to 2.4. 106 M-1S-1 (1,1-diphenylethene). The frequency factors are in the narrow ranges of log (A/M-1S-1) = 8.7 ± 0.1 for the cyclic and log (A/M-1S-1) = 8.2 ± 0.2 for the open-chain malonyl species, whereas the activation energies vary from 12.9 kJ/mol (1,1-diphenylethene) to 21.7 kJ/mol (acrylonitrile). They correlate with the alkene ionization potentials and, more weakly, with the reaction enthalpy. No correlation was found between the activation energies and the alkene electron affinities. Hence, the results confirm and quantify the electrophilic nature of malonyl radicals in addition reactions.
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