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1.
The crystal structure of a synthetic analog of valinomycin, cyclo[-(D -Ile-Lac-Ile-D -Hyi)3-] (C60H102N6O18), has been determined by x-ray diffraction procedures. The crystals are orthorhombic, space group P212121, with cell parameters a = 11.516, b = 15.705, c = 39.310 Å, and Z = 4. The atomic coordinates for the C, N, O atoms were refined in the anisotropic thermal motion approximation and for the H atoms in the isotropic approximation. Values of standard (R) and weighted (Rw) reliability factors after refinement are 0.073 and 0.056, respectively. The structure is completely asymmetric. The cyclic molecular backbone is stabilized by six intramolecular hydrogen bonds N? H…?O?C, five bonds being of the 4→1 type and one being of the 5→1 type. The side chains are located on the molecular periphery. The conformational state of isoleucinomycin in the crystal is intermediate between the corresponding crystalline states of valinomycin and meso-valinomycin. The observed conformation suggests that complexation could proceed via entry of the ion at the face possessing the L -Lac residues, the less crowded face.  相似文献   

2.
The structure of the complex [Pt(trans-1,2-di- aminocyclohexane) (acetate)2]·H2O has been determined by X-ray diffraction. This racemic compound is orthorhombic, space group Aba2, a = 20.813(9), b = 7.926(5), c = 17.296(8) Å, Z = 8. The structure was refined on 1214 nonzero Cu Kα reflections to R = 0.028. The square planar environment of Pt includes the amino groups of the diamine in cis positions and oxygens from two monodentate acetates. The PtN and PtO distances average 2.00(3) and 2.02(3) Å, respectively. The bite of the diamine ligand imposes a NPtN angle of 85(1)°, whereas the small OPtO angle of 85(1)° probably results from packing effects. The average plane through the puckered cyclohexyl ring makes an angle of 19° with the PtN2O2 plane. The molecules are stacked by pairs along the b axis. The two molecules of each pair are 180° apart about the stacking axis, and form altogether four NH···O hydrogen bonds.  相似文献   

3.
Studies on the interactions between L ‐O‐ phosphoserine, as one of the simplest fragments of membrane components, and the Cinchona alkaloid cinchonine, in the crystalline state were performed. Cinchoninium L ‐O‐phosposerine salt dihydrate (PhSerCin) crystallizes in a monoclinic crystal system, space group P21, with unit cell parameters: a = 8.45400(10) Å, b = 7.17100(10) Å, c = 20.7760(4) Å, α = 90°, β = 98.7830(10)°, γ = 90°, Z = 2. The asymmetric unit consists of the cinchoninium cation linked by hydrogen bonds to a phosphoserine anion and two water molecules. Intermolecular hydrogen bonds connecting phosphoserine anions via water molecules form chains extended along the b axis. Two such chains symmetrically related by twofold screw axis create a “channel.” On both sides of this channel cinchonine cations are attached by hydrogen bonds in which the atoms N1, O12, and water molecules participate. This arrangement mimics the system of bilayer biological membrane. Chirality 2010. © 2009 Wiley‐Liss, Inc.  相似文献   

4.
The compound VOCl2·2(3-Etpy)·H2O (Etpy = ethylpyridine) was prepared by slow hydrolysis of the toluene suspension obtained from the reaction of VCl4 with 3-ethylpyridine The crystal was found to be monoclinic C2/c, Z = 4, ϱ(calc.) = 1.426 × 103 kg m−3, a = 13.281(5), b = 13.989(7), c = 9.277(8) Å, V = 1723(2) Å3 β = 90.53(5)°.Final full matrix least-square refinement with anisotropic thermal parameters for all non-hydrogen atoms gave R = 0.039, Rw = 0.042, Rg = 0.053. The vanadium atom is hexacoordinate with the pyridine ligands in mutually trans positions in the plane containing the Cl atoms. The O vanadyl atom is in an axial position trans to the coordinated H2O molecule, and the OVO line is a binary axis for the molecule.  相似文献   

5.
In the course of investigation of 8-alkylamino substituted adenosines, the title compounds were synthesized as potential partial agonists for adenosine receptors. The structure determination of these compounds was carried out with the X-ray crystallography study. Crystals of 8-(2-hydroxyethylamino)adenosine are monoclinic, space group P 21; a = 7.0422(2), b = 11.2635(3), c = 8.9215(2) Å, β = 92.261(1)°, V = 707.10(3) Å3, Z = 2; R-factor is 0.0339. The nucleoside is characterized by the anti conformation; the ribose ring has the C(2′)-endo conformation and gauchegauche form across C(4′)–C(5′) bond. The molecular structure is stabilized by intramolecular hydrogen bond of N–H·O type. Crystals of 8-(pyrrolidin-1-yl)adenosine are monoclinic, space group C 2; a = 19.271(1), b = 7.3572(4), c = 11.0465(7) Å, β = 103.254(2)°, V = 1524.4(2) Å3, Z = 4; R-factor is 0.0498. In this compound, there is syn conformation of the nucleoside; the ribose has the C(2′)-endo conformation and gauchegauche form across C(4′)–C(5′) bond. The molecular structure is stabilized by intramolecular hydrogen bond of O–H·N type. For both compounds, the branching net of intermolecular hydrogen bonds occur in the crystal structures.  相似文献   

6.
The preparation and molecular and crystal structure of the complex [(ethylenediamine)bis(7,9,-dimethylhypoxanthine)platinum(II)] hexafluorophosphate, [Pt(C2H8N2)(C7H8N4O)2] (PF6)2, are reported. The complex crystallizes in the monoclinic system, space group C2/c, with a = 12.334(2)Å, b = 10.256(2)Å, c = 22.339(3)Å, β = 101.31(1)°, V = 2771.0Å3, Z = 4, Dmeasd = 2.087(3) g cm?3, Dcalc = 2.094 g cm?3. Intensities for 3992 symmetry-averaged reflections were collected in the θ-2o scan mode on an automated diffractometer employing graphite-monochromatized MoKα radiation. The structure was solved by standard heavy-atom Patterson and Fourier methods. Full matrix least-squares refinement led to a final R value of 0.051. Both the ethylenediamine chelate and the PF6? anion are disordered. The primary coordination sphere about the Pt(II) center is approximately square planar with the bidentate ethylenediamine ligand and the N(1) atoms [Pt(II) ? N(1) = 2.020(5)Å] of two 7,9-dimethylhypoxanthine bases (related by a crystallographic twofold axis of symmetry) occupying the four coordination sites. The exocyclic O(6) carbonyl oxygen atoms of the two 7,9-dimethylhypoxanthine ligands participate in intracomplex hydrogen bonding with the amino groups of the ethylenediamine chelate [N(ethylenediamine) ? O(6) = 2.89( )Å]. The observed Pt ? O(6) intramolecular distances of 3.074(6)Å are similar to those found in other Pt(II) N(1)-bound 6-oxopurine complexes and in several Pt(II) N(3)-bound cytosine systems.  相似文献   

7.
[N,N′-bis(2′-pyridinecarboxamido)-1,3-propane] - nickel(II) monohydrate, C15H16N4O3Ni is monoclinic, space group P21/c, with a = 7.174(4), b = 18.590(3), c = 11.641(5) Å, β = 110.69(2)°, Z = 4. The structure was refined to R = 0.030 for 1826 diffractometer data using full-matrix least-squares methods. The N4-ligand coordinates to the nickel atom in an irregular square plane [average Ni-Namide 1.864(4), Ni-Npyridine 1.912(3) Å and Namide-Ni-Namide 96.0(1), Npyridine-Ni-Npyridine 98.7(1)°] with a tetrahedral twist of 15.9° at the nickel atom. The two picolinamide units are related by an approximate two-fold axis and the enforced strain in the molecule results in significant non-planar distortions in the amide chelate rings and the pyridyl rings. The plane of the chelate molecule lies approximately perpendicular to [100] and the lattice water molecule hydrogen bonds amide oxygen atoms to form chains parallel to [101]  相似文献   

8.
The three-dimensional structure was determined by x-ray crystallography for d(T[p](CE)T), a uv photoproduct of the cyanoethyl (CE) derivative of d(TpT), having the cis-syn cyclobutane (CB) geometry and the S-configuration at the chiral phosphorus atom. The crystals of C23H30N5O12P · 2H2O belong to the orthorhombic space group P212121 (Z = 4), with cell dimensions a = 11.596 Å, b = 14.834 Å, and c = 15.946 Å, containing two water molecules per asymmetric unit. The CB ring is puckered with a dihedral angle of 151°. The two pyrimidine bases are rotated by –29° from the position of direct overlap of their corresponding atoms. This represents a major distortion of DNA, since in DNA adjacent thymines are rotated by +36°. The pyrimidine rings are puckered with Cremer–Pople parameters for T[p] and in parentheses [p]T: Q: 0.24 Å (0.31 Å); θ: 123° (120°); ?: 141° (86°). These represent half-chairs designated as 6H1 (T[p]) and 6H5 ([p]T). The CB and pyrimidine ring conformations are interrelated, and we postulate that they execute a coupled interconversion in solution. The T[p] segment has the syn glycosyl conformation, a 2T3 sugar pucker, and gauche? conformation at C4′-C5′; the [p]T segment is anti, 3T4, trans. The C5′-O5′ torsion of the [p]T unit is –124.5°, and the C3′-O3′ torsion of the T[p] unit is –152.9°. Bond angles and bond lengths involving the phosphorus atom are similar to those of other phosphotriesters. The P-O3′ and P-05′ torsion angles are –138.1° and 58.6°, respectively. Several intermolecular (but no intramolecular) hydrogen bonds are found in the crystal.  相似文献   

9.
An apolar synthetic octapeptide, Boc-(Ala-Aib)4-OMe, was crystallized in the triclinic space group P1 with cell dimensions a = 11.558 Å, b = 11.643 Å, c = 9.650 Å, α = 120.220°, β = 107.000°, γ = 90.430°, V = 1055.889 Å3, Z = 1, C34H60O11N8·H2O. The calculated crystal density was 1.217 g/cm3 and the absorption coefficient ? was 6.1. All the intrahelical hydrogen bonds are of the 310 type, but the torsion angles, ? and ψ, of Ala(5) and Ala(7) deviate from the standard values. The distortion of the 310-helix at the C-terminal half is due to accommodation of the bulky Boc group of an adjacent peptide in the nacking. A water molecule is held between the N-terminal of one peptide and the C-terminal of the other. The oxygen atom of water forms hydrogen bonds with N (1) -H and N (2) -H, which are not involved in the intrahelical hydrogen bonds. The hydrogen atoms of water also formed hydrogen bonds with carbonyl oxygens of the adjacent peptide molecule. On the other hand, 1H-nmr analysis revealed that the octapeptide took an α-helical structure in a CD3CN solution. The longer peptides, Boc-(Ala-Aib)6-OMe and Boc-(Ala-Aib)8-OMe, were also shown to take an α-helical structure in a CD3CN solution. An α-helical conformation of the hexadecapeptide in the solid state was suggested by x-ray analysis of the crystalline structure. Thus, the critical length for transition from the 310- to α-helix of Boc-(Ala-Aib)n-OMe is 8. © 1993 John Wiley & Sons, Inc.  相似文献   

10.
A conformational study of poly-L -serine has shown that it can exist in the left-handed α-helical form. A study of a pair of peptide units with the serine sidegroup attached to the α carbon atom linking the two units showed that O? H ?O hydrogen bonds between the OH group of the side chain and a carbonyl oxygen of the first peptide group in the backbone can occur in two regions of ?, namely, ? = 15°–30° for χ1 = 300° and for ? = 225°-230° for ? = 60°. The latter is close to a possible left-handed helix of poly-L -serine, stabilized by N? H ?O hydrogen bonds. From a study of contact criteria, the best conformation for this helix is found to be ? = 227°, Ψ = 238°, χ1 = 65° which has n = 3.65, h = 1.51 A. The N? H ?O hydrogen bond has a length of 2.90 A. (6°) and the O? H ?O hydrogen bond is of length 2.60 A. (0°). There are no other bad short contacts in the structure. The cylindrical coordinates of the atoms, as well as a perspective view of the structure arc given in this paper.  相似文献   

11.
Neodymium complex compound with glycine: Nd2(Gly)6·(ClO46·9H2O was synthesized and obtained in the form of monocrystals. Absorption spectra recorded in the region of 8000–35 000 cm-1 were measured along the crystallographic axes. Intensities of the f-f transitions were analysed on the basis of the Judd theory. The X-ray crystal structure determination of the complex is reported. Crystals are triclinic, space group PI, with a = 11.554(4) Å, b = 14.108(1) Å, c = 15.660(3) Å, α = 97.14(1)°, β = 102.82(2)°, γ = 105.28(1)°, V = 2355.25 Å3 Z = 2, M.W. = 1495.4, Dc = 2.129)(3) g cm-3, Dm = 2.103(1) g cm-3. The structure was solved by Patterson's method and successive Fourier syntheses giving the locations of all nonhydrogen atoms. The final R factor was 0.062 and Rw = 0.073 for 12869 reflections with |Fo| > 5σ|(Fo)|. The asymmetric unit consists of a dimeric formula unit. The coordination polyhedron of Nd atoms comprises seven oxygen atoms from glycine and two from water molecules. The neodymium-glycine bonding mode is compared with that of the calcium-glycine complex.  相似文献   

12.
Abstract

1,10-Phenanthroline-platinum (II) ethylenediamine (PEPt) forms a 1:2 crystalline complex with 5′-phosphorylthymidylyl (3′-5′) deoxyadenosine (d-pTpA). Crystals are monoclinic, P21, with a - 10.204 Å, b =24.743 Å, c = 21.064 Å, β = 94.6°. The structure has been determined by Patterson and Fourier methods, and refined by least squares to a residual of 0.128 on 2,367 observed reflections.

PEPt molecules form sandwich-like stacks with adenine-thymine hydrogen-bonded pairs along the a axis. Intercalation in the classic sense is not observed in this structure. Instead, d-pTpA molecules form an open chain structure in which adenine-thymine residues hydrogen- bond together with the reversed Hoogsteen type base-pairing configuration. Deoxyadenosine residues exist in the syn conformation and are C3′ endo and C1′ exo. Thymidine residues are in the high anti conformation with C2′ endo puckers. The structure is heavily hydrated, forming a channel-like water network along the a axis. Other features of the structure are described.  相似文献   

13.
A molecular fragment comprising the first two domains of the human vascular cell adhesion molecule-l (VCAM-l) has been crystallized by the vapor diffusion method. Two crystal forms have been examined by X-ray analysis: One crystal form belongs to the space group C2 with two molecules in the asymmetric unit and cell parameters: a = 122.1 Å, b = 48.9 Å, c = 73.4 Å, and β = 117.4°. The other crystal form belongs to the space group P21 with one molecule in the asymmetric unit and cell parameters: a = 40.4 Å, b = 45.7 Å, c = 54.7 Å, and β = 100.5°. Diffraction data up to 1.9 Å resolution have been collected for the C2 crystal form. © 1994 Wiley-Liss, Inc.  相似文献   

14.
The folding of randomly coiled poly(L -glutamic acid) to the helical state has been studied in N-methylacetamide by titration methods. Since this solvent would be expected to form amide-peptide group hydrogen bonds with the unfolded form of the polymer, to a first approximation no helix stabilization could come from intrapolymer hydrogen bonds. The titration data, collected from 30 to 70°C yield the following values per residue for the thermodynamic parameters governing the coil-helix reaction for the uncharged polymer: ΔG30°C°, ?1. 9 ± 0.1 kcal; Δ H°, 0 ± 0.1 kcal; ΔS30°C°, 6.3 ± 0.6 eu. In N-methyl acetamide, the helix is an order of magnitude more stable than in water, and this stabilization appears to be entirely the result of the entropy gained by solvent molecules which are released from the polymer upon folding.  相似文献   

15.
Five-coordinate technetium(V) complexes of the form TcO(L)Cl where L is one of the two tridentate Schiff base ligands N-(2-oxidophenyl)salicylideneiminate or N-(2-mercaptophenyl)salicylideneiminate have been synthesized and characterized. These neutral complexes precipitate from methanol upon reaction of the Schiff base ligand with TcOCl4?. A single crystal X-ray structure determination shows that the chloro [[N-(2-oxidophenyl)salicylideneiminato](2?)-N,O,O′]oxotechnetium(V) complex, [TcO(C13H9NO2)Cl], formula weight 362, has a distorted square pyramidal coordination geometry with the oxo ligand in the axial position. The steric requirements of the oxo group cause the Tc atom to be displayed 0.67 Å out of the mean equatorial plane of the other four donor atoms. This complex crystallizes in the monoclinic space group P21/a with a = 13.423(6) Å, b = 12.570(5) Å, c = 7.769(3) Å, β = 106.53(5)°, V = 1256.7(9) Å3, and Z = 4. The structure has been refined to R = 0.047 for 1775 observed reflections.  相似文献   

16.
The crystal structures of the cadmium(II) and lead(II) complexes of phenoxyacetic acid (PAH) have been determined by single crystal X-ray diffraction techniques. The cadmium complex, [Cd(PA)2(H2O)2] (1), space group C2, with Z = 2 in a cell of dimensions, a = 11.801(2), b = 5.484(1), c = 13.431(3) Å, β = 100.87(2)°, possesses a distorted trapezoidal bipyramidal coordination around the metal atom, involving two water oxygens [2.210(5) Å] and four carboxyl oxygens from two symmetrical bidentate phenoxyacetate ligands [2.363(4), 2.365(4) Å] with Cd lying on the crystallographic two- fold axis. The lead complex, [Pb2(PA)4(H2O)]n(2) is triclinic, space group P1, Z = 2, with a cell of dimensions, a = 10.135(4), b = 10.675(3), c = 19.285(9) Å, α = 114.66(3), β = 91.94(3) and γ = 114.99(3)°. (2) is a two-dimensional polymer with a repeating dimer sub-unit. The first lead [Pb(1)] has an irregular MO8 coordination [2.34?2.96(2) Å: mean, 2.63(2) Å] involving the water molecule, two oxygens from an asymmetric bidentate carboxylate group, two from a bidentate chelate [O(ether), O(carboxylate)] group and three from bridging oxygens, one of which also provides a polymer link to another symmetry generated lead. The second lead [Pb(2)] is irregular seven-coordinate [PbO, 2.48?2.73(2) Å: mean, 2.61(2) Å] with three bonds from the bridging groups, two from an unsymmetrical bidentate carboxylate (O, O′) group and one from a second carboxyl group which also bridges two Pb(2) centres in the polymer.  相似文献   

17.
Abstract

This paper describes two complexes containing ethidium and the dinucleoside monophosphate, cytidylyl(3′-5′)guanosine (CpG). Both crystals are monoclinic, space group P21, with unit cell dimensions as follows: modification 1: a = 13.64 Å, b = 32.16 Å, c - 14.93 Å, β = 114.8° and modification 2: a = 13.79 Å, b = 31.94 Å, c = 15.66 Å, β = 117.5°. Each structure has been solved to atomic resolution and refined by Fourier and least squares methods; the first has been refined to a residual of 0.187 on 1,903 reflections, while the second has been refined to a residual of 0.187 on 1,001 reflections. The asymmetric unit in both structures contains two ethidium molecules and two CpG molecules; the first structure has 30 water molecules (a total of 158 non-hydrogen atoms), while the second structure has 19 water molecules (a total of 147 non-hydrogen atoms). Both structures demonstrate intercalation of ethidium between base-paired CpG dimers. In addition, ethidium molecules stack on either side of the intercalated duplex, being related by a unit cell translation along the a axis.

The basic feature of the sugar-phosphate chains accompanying ethidium intercalation in both structures is: C3′ endo (3′-5′) C2′ endo. This mixed sugar-puckering pattern has been observed in all previous studies of ethidium intercalation and is a feature common to other drug-nucleic acid structural studies carried out in our laboratory. We discuss this further in this paper and in the accompanying papers.  相似文献   

18.
The structures of (4-bipyH)2[(μ-4-bipy)Nd2(NO3)8(H2O)4]·3(4-bipy) (4-bipy = 4,4′-bipyridine; P21/c, a = 18.723(10), b = 10.720(6), c = 18.027(10) Å, β = 94.43(5)°, Z = 2; R = 0.066 for 4931 (diffractometer data) and of a second monoclinic form of [Ho(NO3)3(H2O)3]·2(4-bipy) (P21/c, a = 15.830(10), b = 21.44(3), c = 15.70(3) Å, β = 100.4(2)°, Z = 8; R = 0.091 for 2335 film data) are reported. In the first compound pairs of Nd atoms are bridged across a crystal inversion centre by a 4-bipy ligand, and 10-coordination is completed by one monodentate NO3, three bidentate NO3, and two H2O ligands, with bond lengths Nd---N 2.70, Nd---OH2(av.) 2.44, Nd---O(NO3, av.) 2.56 Å. The second compound has a variant of the previously-reported monoclinic [Y(NO3)3(H2O)3]·2(4-bipy) structure, with doubling of the unit cell on a but with essentially no change in the geometry and orientation of the nine-coordinate complex. In both compounds the non-coordinated, non-protonated 4-bipy N atoms form hydrogen bonds with ligand H2O.  相似文献   

19.
The crystal and molecular structures of the complexes MoO2((SCH2CH2)2NCH2CH2SCH3), I and MoO2((SCH2CH2)2NCH2CH2N(CH3)2), II, have been determined from X-ray intensity data collected by counter methods. Compound I crystallizes in two forms, Ia and Ib. In form Ia the space group is P21/n with cell parameters a = 7.235(2), b = 7.717(2), c = 24.527(6) Å, β = 119.86(2)°, V = 1188(1) Å3, Z = 4. In form Ib the space group is P21/c with cell parameters a = 14.945(5), b = 11.925(5), c = 14.878(4) Å, β = 114.51(2)°, V = 2413(3) Å3, Z = 8. The molecules of I in Ia and Ib are very similar having an octahedral structure with cis oxo groups, trans thiolates (cis to both oxo groups) and N and thioether sulfur atoms trans to oxo groups. Average ditances are MoO = 1.70, MoS (thiolate) = 2.40, MoN = 2.40 and MoS (thioether) = 2.79 Å. Molecule II crystallizes in space group P212121 with a = 7.188(1), b = 22.708(8), c = 7.746(2) Å, V = 1246(1) Å3 and Z = 4. The coordination about Mo is octahedral with cis oxo groups, trans thiolates and N atoms trans to oxo. Distances in the first coordination sphere are MoO = 1.705(2), 1.699(2), MoS = 2.420(1), 2.409(1) and MoN = 2.372(2), 2.510(2) Å. The conformational features of the complexes are discussed. Complex I displays MoO and MoS distances which are very similar to those found by EXAFS in sulfite oxidase. This similarity is discussed.  相似文献   

20.
A structural investigation of the marine algal polysaccharide poly-α-L -guluronic acid is described. The molecular chains consist of 1 → 4 diaxially linked L -guluronic acid residues in the 1C chair conformation and are stabilized in a twofold helix conformation by an intra-molecular O(2)H … O(6)D hydrogen-bond. The X-ray fiber diffraction photograph has been indexed to an orthorhombic unit cell in which a = 8.6 Å, b (fiber axis) = 8.7 Å, c = 10.7 Å. A structure corresponding to the space group P212121 is proposed, in which all intermolecular hydrogen bonds interact with water molecules and in which all oxygen atoms except for the inaccessible bridge oxygens are involed. The relationship between the shape and structure of the polyguluronic acid molecule and its biological function is discussed.  相似文献   

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