Crystal structures of propanediamine complexed with L and DL- glutamic acid: effect of chirality on propanediamine.

The structures of complexes of 1,3-diaminopropane With L- and DL-glutamic acid have been determined. L-Glutamic acid complex: C3H12N22+.2C5H8NO4-, M(r) = 368.4, orthorhombic. P2(1)2(1)2(1), a = 5.199 (1), b = 16.832 (1). c = 20.076 (3) angstrom, V = 1756.6 (4) angstrom3, z = 4, D(x) = 1.39 g cm-3, lambda(Mo K-alpha) = 0.7107 angstrom, mu = 1.1 cm-1, F(000) = 792. T = 296 K, R = 0.044 for 1276 observed reflections. DL-Glutamic acid complex: C3H12N22+.2C5H8NO4-, M(r) = 368.4, orthorhombic, Pna2(1), a = 15.219(2), b = 5.169 (1), c 22.457 (4) angstrom, V = 1766.6 (5) angstrom3 Z = 4, D(x) = 1.38 g cm-3, lambda(Mo K-alpha) = 0.7107 angstrom, mu = 1.1 cm F(000) = 792, T = 296 K, R = 0.056 for 993 observed reflections. The conformation of diaminopropane is all-trans in the DL complex but trans-gauche in the L complex. The main packing feature in the L complex is the arrangement of diaminopropane around dimers of antiparallel L-glutamic acid molecules. The diaminopropane in the DL complex is sandwiched between two antiparallel glutamic acid molecules of the same chirality and this forms the basic packing unit. This might be the dominant form of interaction between L-glutamic acid and diaminopropane in solution. The structures reveal the adaptability of the polyamine backbone to different environments and the probable reasons for their choice as biological cations.

Reactivity Of Pph3 Toward Ruiiruiiicl(O2car)4 - Syntheses, Molecular-Structures, And Spectroscopic And Electrochemical Properties Of Ruiiruiii(Oh2)Cl(Mecn)(O2car)4(Pph3)2 And Ruii2(Oh2)(Mecn)2(O2car)4(Pph3)2

By the reaction of Ru2Cl(O2CAr)4 (1) and PPh3 in MeCN-H2O the diruthenium(II,III) and diruthenium(II) compounds of the type Ru2(OH2)Cl(MeCN)(O2CAr)4(PPh3)2 (2) and Ru2(OH2)(MeCN)2(O2CAr)4(PPh3)2 (3) were prepared and characterized by analytical, spectral, and electrochemical data (Ar is an aryl group, C6H4-p-X; X = H, OMe, Me, Cl, NO2). The molecular structure of Ru2(OH2)Cl(MeCN)(O2CC6H4-p-OMe)4(PPh3)2 was determined by X-ray crystallography. Crystal data are as follows: triclinic, P1BAR, a = 13.538 (5) angstrom, b = 15.650 (4) angstrom, c = 18.287 (7) angstrom, alpha = 101.39 (3)-degrees, beta = 105.99 (4)-degrees, gamma = 97.94 (3)-degrees, V = 3574 angstrom 3, Z = 2. The molecule is asymmetric, and the two ruthenium centers are clearly distinguishable. The Ru(III)-Ru(II), Ru(III)-(mu-OH2), and Ru(II)-(mu-OH2) distances and the Ru-(mu-OH2)-Ru angle in [{Ru(III)Cl(eta-1-O2CC6H4-p-OMe)(PPh3)}(mu-OH2)(mu-O2CC6H4-p-OMe)2{Ru(II)(MeCN)(eta-1-O2CC6H4-p-OMe)(PPh3)}] are 3.604 (1), 2.127 (8), and 2.141 (10) angstrom and 115.2 (5)-degrees, respectively. The compounds are paramagnetic and exhibit axial EPR spectra in the polycrystalline form. An intervalence transfer (IT) transition is observed in the range 900-960 nm in chloroform in these class II type trapped mixed-valence species 2. Compound 2 displays metal-centered one-electron reduction and oxidation processes near -0.4 and +0.6 V (vs SCE), respectively in CH2Cl2-TBAP. Compound 2 is unstable in solution phase and disproportionates to (mu-aquo)diruthenium(II) and (mu-oxo)diruthenium(III) complexes. The mechanistic aspects of the core conversion are discussed. The molecular structure of a diruthenium(II) compound, Ru2(OH2)(MeCN)2(O2CC6H4-p-NO2)4(PPh3)2.1.5CH2Cl2, was obtained by X-ray crystallography. The compound crystallizes in the space group P2(1)/c with a = 23.472 (6) angstrom, b = 14.303 (3) angstrom, c = 23.256 (7) angstrom, beta = 101.69 (2)-degrees, V = 7645 angstrom 3, and Z = 4. The Ru(II)-Ru(II) and two Ru(II)-(mu-OH2) distances and the Ru(II)-(mu-OH2)-Ru(II) angle in [{(PPh3)-(MeCN)(eta-1-O2CC6H4-p-NO2)Ru}2(mu-OH2)(mu-O2CC6H4-p-NO2)2] are 3.712 (1), 2.173 (9), and 2.162 (9) angstrom and 117.8 (4)-degrees, respectively. In both diruthenium(II,III) and diruthenium(II) compounds, each metal center has three facial ligands of varying pi-acidity and the aquo bridges are strongly hydrogen bonded with the eta-1-carboxylato facial ligands. The diruthenium(II) compounds are diamagnetic and exhibit characteristic H-1 NMR spectra in CDCl3. These compounds display two metal-centered one-electron oxidations near +0.3 and +1.0 V (vs SCE) in CH2Cl2-TBAP. The overall reaction between 1 and PPh3 in MeCN-H2O through the intermediacy of 2 is of the disproportionation type. The significant role of facial as well as bridging ligands in stabilizing the core structures is observed from electrochemical studies.

Structure of a monochloro bridged polymeric copper(II)-di-2-pyridylamine complex: [Cu(dipyam)Cl(NO3)].0.5H2O

Di-2-pyridylaminechloronitratocopper(II) hemihydrate, [CuCl(NO3)(C10H9N3)].0.5H2O, M(r) = 341.21, monoclinic, P2(1)/a, a = 7.382 (1), b = 21.494 (4), c = 8.032 (1) angstrom, beta = 94.26 (1)-degrees, V = 1270.9 angstrom 3, Z = 4, D(m) = 1.78, D(x) = 1.782 g cm-3, lambda(Mo K-alpha) = 0.7107 angstrom, mu(Mo K-alpha) = 19.47 cm-1, F(000) = 688. The structure was solved by the heavy-atom method and refined to a final R value of 0.034 for 2736 reflections collected at 294 K. The structure consists of polymeric [Cu(dipyam)Cl(NO3)] units bridged by a chloride ion.

Studies in crystal engineering. Photochemical and crystallographic investigations of bromocoumarins and (±)-7-(p-bromobenzylidene)piperitone

Studies in crystal engineering. Photochemical and crystallographic investigations of bromocoumarins and (±)-7-(p-bromobenzylidene)piperitone

The identification of 14 alpha,17 beta-dihydroxyandrost-4-en-3-one monohydrate and 14 alpha,17 beta-dihydroxyandrosta-1,4-dien-3-one monohydrate, metabolites of androstenedione in Mucor piriformis

The microorganism Mucor piriformis transforms androst-4-ene-3,17-dione into a major and several minor metabolites. X-ray crystallographic analysis of two of these metabolites was undertaken to determine unambiguously their composition and chirality. Crystals belong to the orthorhombic space-group P2(1)2(1)2(1), with a = 7.199(4) angstrom and a = 6.023(3) angstrom, b = 11.719(3) angstrom and b = 13.455(4) angstrom, c = 20.409(3) angstrom and c = 20.702(4) angstrom for the two title compounds, respectively. The structures have been refined to final R values of 0.060 and 0.040, respectively.

The influence of lone-pair repulsions on C–C bond lengths: a critical evaluation of the experimental and theoretical evidence

X-Ray structural data, as well as semiempirical and ab initio molecular orbital calculations, reveal no systematic and substantial difference between the C–C bond lengths of cis and trans 1,2-diketones. Additional results on various conformations of 1,2-diimines and 1,2-dithiones follow the same pattern. Therefore, lone-pair repulsions cannot be implicated in the observed lengthening of C–C bonds in isatin and several related molecules. Conjugation in these systems occurs peripherally avoiding the participation of the central C–C bond. Negative hyperconjugative interaction between the oxygen lone pairs and the adjacent C–C σ* orbital is suggested to be the principal reason for the relatively long C–C bond in diketones. This effect is found in both the cis and trans conformations.

Crystal and Molecular Structure of N-acetyl-L-glutamine

The crystal and molecular structure of the title compound has been determined by direct methods from diffractometer data. Crystals are orthorhombic, with Z= 4 in a unit cell of dimensions : a= 13.811 (10), b= 5.095(5), c= 12.914(10)Å, space group P212121. The structure was refined by least-squares to R 3.31% for 868 observed reflections. There is significant non-planarity of the peptide group and its nitrogen atom is significantly pyramidal. There is no correlation between the double-bond character and reactivity of the C–N bond of the terminal amide group in glutamine and acetamide

The crystal structure of the dipotassium salt of uridine 5'-diphosphate

C9H12N2Ot2P22-. 2K + .3H20 is orthorhombic, P2~2~2p with a = 18.977 (5), b - 22.597 (6), c = 8.995 (2) A, Z = 8. The structure was refined to R = 0.059 for 2587 observed reflexions. The two molecules of the asymmetric unit have very similar conformations with a 2'- endo sugar pucker and a folded pyrophosphate chain. They form a dimer, coordinated by the K + ions but without direct bridging between the base and the pyrophosphate within each individual molecule. One uracil base has the keto-enol and the other the diketo form. The extended structure shows alternating hydrophobic and hydrophilic regions.

Conformational studies of the triphenylphosphazenyl side chain in cyclophosphazenes. I. Crystal and molecular structure of N3P3C15(NPPh3)

The title compound, C t8H~sC15NaP4, crystallizes in the monoclinic space group P2~/n with a = 20.14 (2), b = 8.69 (1), c = 14.92 (2) A, fl = 98.8 (3) ° , Z = 4. The structure was determined from visual data and refined to R = 0-069 for 1450 reflections. The cyclophosphazene ring is non-planar. The exocyclic NPPh 3 group exhibits type I conformation [R. A. Shaw (1975). Pure Appl. Chem. 44, 317-341] in which the N-P bond is perpendicular to the adjacent P-CI bond.

X-ray studies on crystalline complexes involving amino acids and peptides. XXV. Structures of DL-proline hemisuccinic acid and glycyl-L-histidinium semisuccinate monohydrate and a comparative study of amino-acid and peptide complexes of succinic acid

DL-Proline hemisuccinic acid, C5H9NO2.1/2C4H6O4, M(r) = 174.2, P2(1/c) a = 5.254 (1), b = 17.480 (1), c = 10.230 (i) angstrom, beta = 119.60 (6)-degrees Z = 4, D(m) = 1.41 (4), D(x) = 1.42 g cm-3, R = 0.045 for 973 observed reflections. Glycyl-L-histidinium semisuccinate monohydrate, C8H13N4O3+.C4H5O4-.H2O, M(r) = 348.4, P2(1), a = 4.864 (1), b = 17.071 (2), c = 9.397 (1) angstrom, beta = 90.58-degrees, Z = 2, D(m) = 1.45 (1), D(x) = 1.48 g cm-3, R = 0.027 for 1610 observed reflections. Normal amino-acid and dipeptide aggregation patterns are preserved in the structures in spite of the presence of succinic acid/semisuccinate ions. In both the structures, the amino-acid/dipeptide layers stack in such a way that the succinic acid molecules/semisuccinate ions are enclosed in voids created during stacking. Substantial variability in the ionization state and the stoichiometry is observed in amino-acid and peptide complexes of succinic acid. Succinic acid molecules and succinate ions appear to prefer a planar centro-symmetric conformation with the two carboxyl (carboxylate) groups trans with respect to the central C=C bond. Considerable variation is seen in the departure from and modification of normal amino-acid aggregation patterns produced by the presence of succinic acid. Some of the complexes can be described as inclusion compounds with the amino acid/dipeptide as the 'host' and succinic acid/semisuccinate/succinate as the 'guest'. The effects of change in chirality, though very substantial, are not the same in different pairs of complexes involving DL and L isomers of the same amino acid.

Structural features of B-DNA dodecamer crystal structures: Influence of crystal packing versus base sequence

We have analyzed the set of inter and intra base pair parameters for each dinucleotide step in single crystal structures of dodecamers, solved at high and medium resolution and all crystallized in P2(1)2(1)2(1) space group. The objective was to identify whether all the structures which have either the Drew-Dickerson (DD) sequence d[CGCGAATTCGCG] with some base modification or related sequence (non-DD), would display the same sequence dependent structural variability about its palindromic sequence, despite the molecule being bent at one end because of similar crystal lattice packing effect. Most of the local doublet parameters for base pairs steps G2-C3 and G10-C11 positions, symmetrically situated about the lateral twofold, were significantly correlated between themselves. In non-DD sequences, significant correlations between these positional parameters were absent. The different range of local step parameter values at each sequence position contributed to the gross feature of smooth helix axis bending in all structures. The base pair parameters in some of the positions, for medium resolution DD sequence, were quite unlike the high-resolution set and encompassed a higher range of values. Twist and slide are the two main parameters that show wider conformational range for the middle region of non-DD sequence structures in comparison to DD sequence structures. On the contrary, the minor and major groove features bear good resemblance between DD and non-DD sequence crystal structure datasets. The sugar-phosphate backbone torsion angles are similar in all structures, in sharp contrast to base pair parameter variation for high and low resolution DD and non-DD sequence structures, consisting of unusual (epsilon =g(-), xi =t) B-II conformation at the 10(th) position of the dodecamer sequence. Thus examining DD and non-DD sequence structures packed in the same crystal lattice arrangement, we infer that inter and intra base pair parameters are as symmetrically equivalent in its value as the symmetry related step for the palindromic DD sequence about lateral two-fold axis. This feature would lead us to agree with the conclusion that DNA conformation is not substantially affected by end-to-end or lateral inter-molecular interaction due to crystal lattice packing effect. Non-DD sequence structures acquire step parameter values which reflect the altered sequence at each of the dodecamer sequence position in the orthorhombic lattice while showing similar gross features of DD sequence structures

Kinetics of ceric ion oxidation of naphthalene and its derivatives. Formation of the radical cation intermediate in the rate limiting step

Ceric ammonium sulfate, CAS, oxidizes naphthalene to 1,4-naphthoquinone in essentially quantitative yield in CH3CN-dil. H2SO4. Stoichiometric studies indicate that 6 mol of CAS are required for the oxidation of 1 mol of naphthalene to 1,4-naphthoquinone. Kinetic investigations reveal that the reaction takes place through initial formation of a 1:1 complex of naphthalene and cerium(IV) in an equilibrium step followed by slow decomposition of the complex to naphthalene radical cation. Kinetic results on the effects of acid strength, polarity of the medium, temperature and substituents are in accordance with this mechanism. Further conversion of the radical cation into 1,4-naphthoquinone takes place in fast steps involving a further 5 mol of cerium(IV) and 2 mol of H2O.

Palladium(II) chloride complexes of bis(pyrazolyl)cyclotriphosphazenes

Reactions of the bis(3,5-dimethylpyrazolyl)cyclotriphosphazene derivatives gem-N3P3(MeNCH(2)CH(2)O)(2)(dmp)(2) (1) and nongeminal cis-N3P3(OPh)(4)(dmp)(2) (2) with PdCl2 afford complexes of the type [PdCl2.(L)] (L = 1 or 2). In these complexes, the phosphazenes act as bidentate NN-donor ligands with the two pyrazolyl pyridinic nitrogen atoms bonded to the metal, thus forming a six- and an eight-membered chelate ring, respectively. The structures of 2 and [PdCl2.(2)] (4) have been confirmed by single-crystal X-ray diffraction. Crystal data for 2: a = 16.759(2) Angstrom, b = 10.788(3) Angstrom, c = 19.635(9) Angstrom, beta = 101.61(3)degrees, P2(1/c), Z = 4, R = 0.038 for 4688 reflections with F > 5 sigma(F). Crystal data for 4: a = 9.701(3) Angstrom, b = 24.853(4) Angstrom, c = 15.794(4) Angstrom, beta = 101.46(2)degrees, P2(1/n), Z = 4, R = 0.030 for 5416 reflections with F > 5 sigma(F).

Stereochemistry of 2'-5' linked nucleic acids: crystal and molecular structure of ammonium adenylyl-2',5'-adenosine tetrahydrate: a core fragment of 2'-5' oligo A's produced by interferon induced adenylate synthetase

The preponderance of 3'-5' phosphodiester links in nucleic acids is well known. Albeit less prevalent, the 2'-5' links are specifically utilised in the formation of 'lariat' in group II introns and in the msDNA-RNA junction in myxobacterium. As a sequel to our earlier study on cytidylyl-2',5'-adenosine we have now obtained the crystal structure of adenylyl-2',5'-adenosine (A2'p5'A) at atomic resolution. This dinucleoside monophosphate crystallizes in the orthorhombic space group P2(1)2(1)2(1) with a = 7.956(3) A, b = 12.212(3) A and c = 36.654(3) A. CuK alpha intensity data were collected on a diffractometer. The structure was sloved by direct methods and refined by full matrix least squares methods to R = 10.8%. The 2' terminal adenine is in the commonly observed anti (chi 2 = 161 degrees) conformation and the 5' terminal base has a syn (chi 1 = 55 degrees) conformation more often seen in purine nucleotides. A noteworthy feature of A2'p5'A is the intranucleotide hydrogen bond between N3 and O5' atoms of the 5' adenine base. The two furanose rings in A2'p5'A show different conformations - C2' endo, C3' endo puckering for the 5' and 2' ends respectively. In this structure too there is a stacking of the purine base on the ribose O4' just as in other 2'-5' dinucleoside structures, a feature characteristically seen in the left handed Z DNA. In having syn, anti conformation about the glycosyl bonds, C2' endo, C3' endo mixed sugar puckering and N3-O5' intramolecular hydrogen bond A2'p5'A resembles its 3'-5' analogue and several other 2'-5' dinucleoside monophosphate structures solved so far. Striking similarities between the 2'-5' dinucleoside monophosphate structures suggest that the conformation of the 5'-end nucleoside dictates the conformation of the 2' end nucleoside. Also, the 2'-5' dimers do not favour formation of miniature classical double helical structures like the 3'-5' dimers. It is conceivable, 2-5(A) could be using the stereochemical features of A2'p5'A which accounts for its higher activity.

Aromatic claisen rearrangements in carbohydrates: stereocontrol of rearrangement rates in unsaturated sugar substrates

A remarkable difference is observed in the rates of [3,3]-sigmatropic rearrangement of aryl 4,6-di-O-acetyl-2,3-dideoxy-D-erythro-hex-2-enopyranosides 1 and 2; the slower reactivity of the alpha-isomers is consistent with AM1 calculated transition state energetics of model systems.