Molecular structures and hydrogen-bond networks in crystals of synthetic 1-D-galactosamide bolaamphiphiles

The crystal structures of synthetic 1-galactosamide bolaamphiphiles, N,N'-bis(beta-D-galactopyranosyl)decane-1,10-dicarboxamide (1) and N,N'-bis(beta-D-galactopyranosyl)dodecane-1,12-dicarboxamide (2), were determined by single-crystal X-ray analysis. The space groups are P21, Z = 2 with cell dimensions: a = 13.624(2), b = 4.832(3), c = 21.178(3) Angstroms, beta = 98.57(1) degrees for 1; a = 13.521(2), b = 4.838(1), c = 23.706(2) Angstroms, beta = 104.945(10) degrees for 2. The galactopyranosyl rings of 1 and 2 are in a 4C1 chair conformation. The bolaamphiphile molecules are arranged in a layered structure for 1 and 2, with the alkylene chains packed parallel all over the layers. The hydroxyl groups of the galactopyranosyl rings in 1 and 2 form identical three-dimensional hydrogen-bond networks. The connecting decamethylene spacer of 1 has a kink conformation, while the dodecamethylene chain of 2 an all-trans zigzag conformation.     

Physicochemical characterization of deflazacort: thermal analysis, crystallographic and spectroscopic study

The solid state properties of deflazacort (1-(1beta,16alpha)-21-(acetyloxy)-11-hydroxy-2'-methyl-5'H-pregna-1,4-dieno[17,16-d]oxazole-3,20-dione, 1) were investigated using differential scanning calorimetry (DSC), thermogravimetry (TG), single-crystal X-ray diffraction, solid and liquid nuclear magnetic resonance spectroscopy ((13)C NMR), Fourier transform infrared and Raman spectroscopy (FTIR and FT Raman). From the trends observed in the crystal structure and spectral data some conclusions can be made about hydrogen bonding, molecular conformation and crystal packing. Compound 1 crystallizes in an orthorhombic cell, space group P2(1)2(1)2(1) and the following lattice parameters: a=11.2300(5), b=12.8161(8), c=16.171(1)A, V: 2327.4(2)A(3), D(c): 1.260g/cm(3), R1=0.0479, wR2=0.1012. The crystal structure is stabilized by intra and intermolecular interactions, which provides for a very closely packed form. The NMR data indicated that 1 shows a similar conformation in solid and liquid state; while, thermal data revealed that 1 follows a monophasic pattern with a DSC melting peak at 258.4 degrees C (DeltaH 99.7Jg(-1), n=3), indicating that 1 is thermally stable as solid; but, as liquid is unstable to undergo a thermal decomposition reaction. The reactivity of 1 toward light and moisture was examined via DSC and TLC. The data indicated that 1 do not interact with water to give hydrated forms or decomposition products; however, light degrades 1.     

Identification and synthesis of novel alkaloids from the root system of Nicotiana tabacum: affinity for neuronal nicotinic acetylcholine receptors

A novel pyridine derivative, 3,5-bis-(1-methyl-pyrrolidin-2-yl)-pyridine, and a pair of diastereomers of 1,1'-dimethyl-[2,3']bipyrrolidinyl were isolated from the root of Nicotiana tabacum plants and identified as novel alkaloids by GC-MS analysis. The structures of these new alkaloids were confirmed by total synthesis. The affinities of these novel alkaloids, and other structurally related compounds for alpha4beta2*, alpha7* neuronal nicotinic acetylcholine receptors (nAChRs), and for nAChRs mediating nicotine-evoked dopamine release from rat striatum were also assessed. The results indicate that these compounds do not interact with alpha7* nAChRs, but inhibit [3H]nicotine binding to the alpha4beta2* nAChR subtype. The results also demonstrate that these compounds act as antagonists at nAChRs mediating nicotine-evoked dopamine release from rat striatum.     

Photodimerization in pyrimidine-substituted dipeptides.

Ten N(epsilon)-glycylornithineamide derivatives have been synthesized containing various N(alpha)-linked pyrimidine-1-ylacetyl groups which can undergo (2pi + 2pi) photodimerization on irradiation with UV light at 254 nm. The dimerization efficiency of the free and bound pyrimidine groups was compared in aqueous solution: it was dependent on the substitution of the pyrimidine ring. N(alpha),N(alpha')-bis-(uracil-1-ylacetyl)-(N(epsilon)-glycylornithineamide) and N(alpha),N(alpha')-bis-(5-bromouracil-1-ylacetyl)-(N(epsilon)-glycylornithineamide) were identified as possible candidates for optical data storage.     

Successful prediction of the hydrogen bond network of the 3-oxo-12alpha-hydroxy-5beta-cholan-24-oic acid crystal from resolution of the crystal structure of deoxycholic acid and its three 3,12-dihydroxy epimers

Crystal structures of p-xylene-crystallized deoxycholic acid (3alpha,12alpha-dihydroxy-5beta-cholan-24-oic acid) and its three epimers (3beta,12alpha-; 3alpha,12beta-; and 3beta,12beta-) have been solved. Deoxycholic acid forms a crystalline (P21) complex with the solvent with a 2:1 stoichiometry whereas crystals of the three epimers do not form inclusion compounds. Crystals of the 3beta,12beta-epimer are hexagonal, whereas the 3alpha,12beta-and 3beta,12alpha-epimers crystallize in the P2(1)2(1)2(1) orthorhombic space group. The three hydrogen bond sites (two hydroxy groups, i. e. O3-H, and O12-H, and the carboxylic acid group of the side chain, O24bO24a-H) simultaneously act as hydrogen bond donors and acceptors. The hydrogen bond network in the crystals was analyzed and the following sequences have been observed: two chains (abcabc... or acbacb... ) and two rings (abc or acb), which constitute a complete set of all the possible sequences which can be drawn for an intermolecular hydrogen bond network formed by three hydrogen bond donor/acceptor sites forming crossing hydrogen bonds. The orientation of O3-H (alpha or beta) determines the sequence of the acceptor and the donor groups involved in the pattern: O24a --> O12 --> O3 --> O24b when it is alpha and O24a --> O3 --> O12--> O24B when it is beta. These observations were used to predict the hydrogen bond network of p-xylene-crystallized 3-oxo,12alpha-hydroxy-5beta-cholan-24-oic acid. This compound has two hydrogen bond donor and three potential hydrogen bond acceptor sites. According to the previous sequence set, this compound should crystallize in the monoclinic P21 system, should form a complex with the solvent, O24b should not participate in the hydrogen bond network, and the chain sequence O24a --> O12 --> O3 would be followed. All predictions were confirmed experimentally.     

Design, synthesis, and crystal structure of self-assembling norbornene (NBE)-supported two-helix bundles: a unique example of Janus helicity in the solid-state structure of NBE(Aib(5))(2)

Norbornene-supported bis-helical peptides with the general structure NBE(Aib(n) )(2) (NBE: 2,3-trans-norbornene dicarbonyl unit; Aib: alpha,alpha'-dimethyl glycine unit; n = 4,5) have been synthesized and examined for self-assembly preferences in the solid state. An x-ray study has revealed a phenomenon of Janus helicity in the solid state structure of NBE(Aib(5))(2). The lower homologue NBE(Aib(4))(2), however, shows an identical screw sense for both the helical arms. The difference in the handedness of left and right arms is reflected in the self-assembly patterns. Thus, while the NBE(Aib(4))(2) molecule self-assembles to form an infinite hydrogen-bonded superhelical ladder, the Janus molecule NBE(Aib(5))(2) crystallizes as individual units surrounded by water molecules. The structures of Z-Aib(4)-OMe and Z-Aib(5)-OMe are also presented to compare their conformations with the helical arms of the title compound and also to the already known structures of other X-Aib(n) -Y compounds. The helices in all the molecules are the 3(10)-type.     

观光木酚性成分研究

从观光木(Tsoongiodendron odorum Chun)茎枝的80％乙醇提取物中分离得到11个酚性化合物,经波谱鉴定为:对羟基苯甲醛(1)、香草醛(2)、1,3,5-三甲氧基苯(3),丁香醛(4)、香草酸(5)、苏式-2,3-二-(4-羟基-3-甲氧基苯)-3-甲氧基丙醇(6)、赤式-2,3-二-(4-羟基-3-甲氧基苯)-3-甲氧基丙醇(7)、丁香酸(8)、3-羟基-1-(4-羟基-3,5-二甲氧基苯)-1-丙酮(9)、对羟基苯乙醇(10)和C-veratroylglycol( 11).其中,化合物1～4和6～ 11为首次从该植物中分离得到.     

Synthesis and structural characterization of two monomeric potassium phenolates

Reaction of 2,6-dibenzylphenol and 2,6-bis-(2-methoxybenzyl)phenol with potassium hexamethyldisilazide in the presence of 18-crown-6 yielded [K(18-crown-6)(Odbp)] and [K(18-crown-6)(OdbpOMe)], respectively. Both compounds were mononuclear with seven-coordinate potassium and displayed C-H?O and C-H?π intermolecular hydrogen bonding.     

The effect of hydrogen bonding in two crystal modifications of aquabis(N,N-dimethylglycinato-κN,κO)copper(II): Experimental and theoretical study

From the crystals of trans aquabis(N,N-dimethylglycinato-κN,κO)copper(II) dihydrate (compound 1, space group P2₁2₁2₁) novel crystal structure of trans aquabis(N,N-dimethylglycinato-κN,κO)copper(II) (compound 2, space group Pbca) was obtained and analysed by X-ray diffraction. In the crystal structure 1, the O-H?O hydrogen bonds form three-dimensional network. In the crystal structure 2, two-dimensional layers stacking to each other are formed, with non-polar N,N-dimethyl groups placed on the opposite sides of the layers, and with the polar part in the middle forming CO?O-H and C-H?O hydrogen bonds. Different hydrogen bonding patterns in 1 and 2 do not pronouncedly affect molecular geometry of the title compound. Molecular mechanics force field suited for studying the properties of bis(amino acidato)copper(II) complexes in the solid state can follow the differences between the experimental molecular structures in the two diverse crystalline surroundings. To make possible direct comparison between crystal lattices, the force field was applied to predict unit cell packing of supposed anhydrous bis(N,N-dimethylglycinato)copper(II) in space group Pbca. Relative intermolecular energies of hypothetic anhydrous crystal and simulated 1 and 2 crystals are discussed. On the basis of experimental and theoretical results we conclude that the main effect of two water molecules of crystallisation in 1 is to stabilise the crystal packing via hydrogen bonding, whilst similar pyramidal copper(II) coordination geometry in 1 and 2 is due to axially coordinated water molecule and its intermolecular interactions.     

Somatic antigens of Pseudomonas aeruginosa. The structure of O-specific polysaccharide chains of P. aeruginosa O:3a, b and O:3a, d lipopolysaccharides

On mild acid degradation of Pseudomonas aeruginosa O:3a,b and O:3a,d lipopolysaccharides O-specific polysaccharides were isolated. Both polysaccharides were found to contain 2-acetamido-2,6-dideoxy-D-galactose, identified as fucosamine hydrochloride formed after hydrolysis with a very low yield. The other two components of the trisaccharide repeating unit, 2,3-diacetamido-2,3-dideoxy-D-mannuronic acid and 2,3-(1-acetyl-2-methyl-2-imidazolino-5,4)-2,3-dideoxy-D-mannuronic acid, were identified without isolation in their free state directly in the course of structural investigation of the polysaccharides. Both these monosaccharides have never before been found in nature. Solvolysis of either O:3a,b or O:3a,d polysaccharides with liquid hydrogen fluoride resulted in the formation of the same trisaccharide, N-acetylfucosamine residue being the reducing end. The structure of this trisaccharide, which is the repeating unit of both polysaccharides, was deduced from the results of successive chemical modifications and 13C-nuclear magnetic resonance spectra recorded for every oligosaccharide formed. As a result, the acidic diaminosugars were converted into 2,3-diacetamido-2,3-dideoxy-D-mannose indistinguishable from authentic sample. The O-specific polysaccharides O:3a,b and O:3a,d differed in the configuration of the glycosidic bond of N-acetylfucosamine residue only and had the following structures: leads to 4)DManImU(beta 1 leads to 4)DMan(NAc)2U (beta 1 leads to 3)DFucNAc(beta 1- leads to 4)DManImU(beta 1 leads to 4)DMan(NAc)2U (beta 1 leads to 3)DFucNAc(alpha 1- where DManImU = 2.3-(1-acetyl-2-methyl-2-imidazolino-5,4)-2, 3-dideoxy-D-mannuronic acid, DMan(NAc)2U = 2,3-diacetamido-2,3-dideoxy-D-mannuronic acid, DFucNAc = 2-acetamido-2,6-dideoxy-D-galactose. The structures established were in agreement with optical rotations and assignments of all the signals in the 13C-nuclear magnetic resonance spectra of the polysaccharides.     

Stereoselective synthesis and X-ray structure of 1-(4-O-benzyl-1,5-anhydro-2,3-dideoxy-D-arabino-hex-1-enitol-3-yl )-4-me thoxy-1H-pyrimidin-2-one

The intramolecular glycosylation of a 6-O-(4-methoxypyrimidin-2-yl) derivative of phenyl 2,3-didehydrohex-2-eno-1-thiopyranoside afforded 3-deoxy-3-(4-methoxypyrimidin-2-on-1-yl)glycal as the major product in a stereoselective manner. The isolated 3'-deoxyglycal nucleoside was characterized by X-ray and NMR spectral analyses.     

Synthesis and crystal structures of mono- and dinuclear silver(I) complexes bearing 1,8-naphthyridine ligand

Mononuclear and dinuclear silver(I) complexes bearing 1,8-naphthyridine (napy) were prepared. The crystal structures of [Ag(napy-κN)₂](PF₆) (1) and [Ag₂(μ-napy)₂](PF₆)₂ · 3CH₃CN (2 · 3CH₃CN) were determined by X-ray diffraction studies. In complex 1, intermolecular π-π interaction of napy ligands between neighboring molecules forms left-handed hexagonal columns in the solid state. On the other hand, two napy ligands bridging two Ag ions in the dinuclear complex 2 shape a face-to-face π-π stacking with those of the neighboring molecule to form the dimeric unit. Besides, two of four napy ligands, which are located in a diagonal position in the dimeric unit, build intermolecular back-to-back π-π stackings with those of the adjacent dimeric unit, and a ladder-like stairway structure is generated in the solid state. Irrespective of such characteristic structures of 1 and 2 in the solid state, both complexes show very rapid dynamic behavior in solutions. No conversion between 1 and 2 took place even in the presence of excess amounts of Ag⁺ or napy in solutions.     

Solid and solution state conformation of 1L-1-O-acetyl-2,3:5,6-di-O-isopropylidene-chiro-inositol

The X-ray crystal structure of 1L-1-O-acetyl-2,3:5,6-di-O-isopropylidene-chiro-inositol is described. The inositol ring deviates considerably from the ideal chair conformation to a flattened chair. A comparison of its conformation in solution with that in solid was made by the use of 1H NMR. This conformational analysis revealed that the title compound adopts similar conformations in solid state and in solution states irrespective of solvent polarity.     

Theoretical conformation analysis of specific O-antigenic polysaccharides. Polysaccharide of Shigella dysenteriae of serotype 2

Theoretical conformational analysis of Shigella dysenteriae serotype 2 polysaccharide containing repeating unit: -4Gal beta 1-3GalNAc alpha 1-3(GlcNAc alpha 1-4)GalNAc alpha 1-4Glc alpha 1- has been carried out. It is shown that spatial forms of the polymer are determined by conformational states of Glc alpha 1-4Gal links which form the internal bends of the chain. The structures of low energy are shown to be left three-fold helices with an axially projected repeat of approximately 12 A. N-Acetamide groups of side residues alpha-D-GlcNAc are the most accessible for intermolecular interactions and may determine immunological specificity of the polysaccharide.     

Two biflavonoids from Ouratea flava stem bark

In a chemical investigation on the stem bark of Ouratea flava, two biflavonoids: 1-[3-(2,4-dihydroxy-benzoyl)-4,5,6-trihydroxy-2-(4-hydroxy-phenyl)-benzofuran-7-yl] -3-(4-hydroxy-phenyl) -propenone (flavumone A) and 3-(2,4-dihydroxy-benzoyl)-4-hydroxy-2,7-bis-(4-hydroxy-phenyl) -7,8- dihydro-furo[2,3-f]chromen-9-on (flavumone B) were isolated along with five known flavonoids. Their structures were established by various analyses including 2D-NMR spectroscopy.     

The presence of novel glucuronic acid-containing, type-specific glycolipid antigens within Mycobacterium spp. Revision of earlier structures

Previously, we had described the structures of the haptenic oligosaccharides of the surface glycopeptidolipid antigens from serotypes 9 and 25 of the Mycobacterium avium complex and had synthesized these units as putative antigenic probes. The lack of chemical concordance between the synthetic products and the haptens has prompted a re-examination of these structures utilizing the instrumental techniques not previously available of fast atom bombardment-mass spectrometry, Fourier transform infra-red, and high resolution NMR spectroscopy. With the additional information thus available, more extensive chemical fragmentations by base degradation, followed by alkylation, have furnished supportive evidence to allow formulation of revised and novel structures, all of which contain glucuronic acid: serotype 9, 2,3-di-O-Me-L-Fucp(alpha 1----4)-D-GlcAp(beta 1----4)-2,3-di-O-Me-L-Fucp(alpha 1----3)-L-Rhap(alpha 1----2)-6dTal; and serotype 25, 4-acetamido-4,6-dideoxy-2-O-Me-hexosyl(alpha 1----4)-D- GlcAp(beta 1----4)2-O-Me-L-Fucp(alpha 1----3)-L-Rhap(alpha 1----2)6dTal. Glucuronic acid, acetamido sugars, and other novel sugars appear to be widespread in the glycopeptidolipid antigens of Mycobacterium spp. The revised structures will allow renewed synthesis of artificial antigen probes and rational approaches to preparing monoclonal antibodies, both necessary for the new diagnostics required to trace the sources of widespread infections due to M. avium and Mycobacterium intracellulare.     

(13)C CP MAS NMR and crystal structure of methyl glycopyranosides

The X-ray diffraction analysis, (13)C CP MAS NMR spectra and powder X-ray diffraction patterns were obtained for selected methyl glycosides: alpha- and beta-d-lyxopyranosides (1, 2), alpha- and beta-l-arabinopyranosides (3, 4), alpha- and beta-d-xylopyranosides (5, 6) and beta-d-ribopyranoside (7) and the results were confirmed by GIAO DFT calculations of shielding constants. In X-ray diffraction analysis of 1 and 2, a characteristic shortening and lengthening of selected bonds was observed in molecules of 1 due to anomeric effect and, in crystal lattice of 1 and 2, hydrogen bonds of different patterns were present. Also, an additional intramolecular hydrogen bond with the participation of ring oxygen atom was observed in 1. The observed differences in chemical shifts between solid state and solution come from conformational effects and formation of various intermolecular hydrogen bonds. The changes in chemical shifts originating from intermolecular hydrogen bonds were smaller in magnitude than conformational effects. Furthermore, the powder X-ray diffraction (PXRD) performed for 4, 5 and 7 revealed that 7 existed as a mixture of two polymorphs, and one of them probably consisted of two non-equivalent molecules.     

Crystal structure and vibrational spectra of rubidium salts of bis(dicyanomethylene)croconate (croconate violet)

The crystal structures and vibrational spectra of two alkaline salts of 3,5-bis-(dicyanomethylene)cyclopentane-1,2,4-trionate , known as croconate violet, are described: 1-rubidium and potassium croconate violet (RbKCV), and 2-rubidium croconate violet (Rb₂CV). These compounds are isostructural and crystallize in triclinic space group. The stoichiometries of the salts show two water molecules to each M₂C₁₁N₄O₃ unit. The anions are displayed in layers linked to water molecules by hydrogen bonds, therefore forming an extended structure with two-dimensional arrangement (2D). Crystal structure shows two different metal sites (M1 and M2) that present different types of coordination: monodentate, quelate and bidentate in M1; and monodentate and bidentate in M2. In RbKCV the rubidium cation is predominant in M1 and M2 sites, presenting total occupation of 70% and the molecular formula of this salt is Rb_1.4K_0.6C₁₁N₄O₃ · 2H₂O. Vibrational spectra of RbKCV and Rb₂CV are similar to the spectra of potassium croconate violet (K₂CV). In the Raman spectrum of RbKCV some small wavenumber shifts are observed when compared K₂CV and Rb₂CV spectra. The structural difference in RbKCV salt is due to the interionic interactions between CV anion and potassium and rubidium cations; this effect could be responsible to spectral differences observed in RbKCV Raman spectra. However, the exchange between potassium and rubidium ions in the solid state structure does not alter croconate violet anion crystal packing, which can be observed in the vibrational spectra.     

Two neolignans from Perilla frutescens and their inhibition of nitric oxide synthase and tumor necrosis factor-alpha expression in murine macrophage cell line RAW 264.7

Two neolignans were isolated from leaves of Perilla frutescens (Labiatae) as inhibitors of nitric oxide syntheses (IC50 5.9 microM and 53.5 microM, respectively) and tumor necrosis factor-alpha in lipopolysaccharide-activated RAW 264.7 cells. Their structures were identified as 1beta,2alpha,3beta,4alpha-1,2-dimethyl-3,4-bis-(2,4,5-trimethoxyphenyl)-cyclobutane (magnosalin), and 1alpha,2beta,3beta,4alpha-1,2-dimethyl-3,4-bis-(2,4,5-trimethoxyphenyl)-cyclobutane (andamanicin), and their activities were confirmed as resulted from the suppressed expression of inducible nitric oxide synthase enzyme and from the secretion of tumor necrosis factor-alpha from activated macrophages.     

Interaction between beta-cyclodextrin and 1,10-phenanthroline: uncommon 2:3 inclusion complex in the solid state

The crystallographic structure of the complex formed by beta-cyclodextrin with 1,10-phenanthroline has been studied by X-ray diffraction. The result shows that the complex adopts an uncommon 2:3 stoichiometry in solid state, that is, every complex unit contains three 1,10-phenanthroline molecules and two beta-cyclodextrin molecules, where two 1,10-phenanthroline molecules individually occupy two cyclodextrin cavities, and the third guest molecule is located in the interstitial space between two head-to-head cyclodextrin molecules. The intermolecular hydrogen bonds between the adjacent complex units further link these individual monomers to a channel-type assembly. Furthermore, 1H and 2D NMR spectroscopy has been employed to investigate the inclusion behavior between the host beta-cyclodextrin and guest 1,10-phenanthroline in aqueous solution.