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.     

Preliminary crystallographic data and primary sequence for anti-peptide Fab' B13I2 and its complex with the C-helix peptide from myohemerythrin

Crystals of the Fab' fragment from the monoclonal anti-peptide antibody B1312 and of the Fab'-peptide antigen complex have been characterized. The monoclonal antibodies were raised against a synthetic homologue of the C-helix of myohemerythrin (residues 69-87 in myohemerythrin). The Fab'-peptide complex crystallizes in space group P6322 with unit cell dimensions a = b = 142.5 A, c = 101.5 A, alpha = beta = 90 degrees, gamma = 120 degrees, and Z = 1. The native Fab' crystallizes in space group P212121 with unit cell dimensions a = 98.0 A, b = 151.7 A, c = 80.8 A, alpha = beta = gamma = 90 degrees, and Z = 2. Both crystal forms diffract to beyond 2.6 A resolution. We also report the cDNA and predicted amino acid sequences for the variable regions of both the light and heavy chains of this anti-peptide antibody.     

Model for interactions of amino acid side chains with Watson-Crick base pair of guanine and cytosine: crystal structure of 9-(2-carbamoylethyl)guanine and 1-methylcytosine complex

As a model of interaction between the guanine-cytosine base pair and carbamoyl group, the crystal structure of 9-(2-carbamoylethyl)guanine-1-methylcytosine complex has been studied by X-ray method. The crystal data are a = 8.540 (1) A, b = 12.693 (3) A, c = 14.249 (2) A, beta = 94.02 (1) degrees, space group P21/c, Z = 4, dm = 1.50, dc = 1.49 g cm-3, and R = 0.10 for 1035 reflections. The bases form a Watson-Crick pair, and the carbamoyl group is hydrogen bonded with O(6) of guanine and N(4) of cytosine in the adjacent pairs. A structural correlation has been found between the hydrogen-bonding pattern and the secondary structural fitting of alpha-helical segment with B-form DNA.     

Crystallization of Bowman-Birk type protease inhibitor (peanut) and its complex with trypsin

Crystallization and preliminary crystallographic study of Bowman-Birk type protease inhibitors, A-I, A-II, and B-III from peanut seeds (Arachis hypogaea), and of the A-II + trypsin complex were carried out. A-II, with 70 amino acid residues, crystallizes in a trigonal system, P3(1)21 (or P3(2)21), a = 71.8, c = 65.9 A, Z = 12 or 18. The A-I crystal is isomorphous with that of A-II, indicating that the N-terminal residues are in a disordered state in both crystals. The B-III crystal is monoclinic, C2, a = 119.6, b = 69.6, c = 94.2 A, beta = 115.1 degrees, Z is about 40. The A-II + trypsin complex crystallizes in an orthorhombic system, P2(1)2(1)2(1), a = 55.5, b = 56.0, c = 182.1 A, Z = 4.     

Preparation, X-ray crystal structure, and 195Pt NMR spectra of platinum(II) with dipeptides and dipeptide methyl esters

Three dipeptide complexes of the form K[M(dipeptide)Cl] (H2dipeptide=glycylbeta-alanine, beta-alanylglycine, beta-alanylbeta-alanine) and four dipeptide methyl ester complexes of the form K[M(dipeptideOMe)Cl2] (HdipeptideOMe=glycylalpha-alanine methyl ester, alpha-alanylglycine methyl ester, dialpha-alanine methyl ester) were newly prepared. The K[Pt(glybeta-ala)Cl] complex crystallizes in the monoclinic space group C2/c with unit cell dimensions of a=25.77(1) A, b=4.09(2) A, c= 16.432(9) A, beta=103.74(4) degrees, and Z=8. The K[Pt(glyalpha-alaOMe)Cl2] complex crystallizes in the monoclinic space group P1 with unit cell dimensions of a=7.195(2) A, b=7.977(5) A, c=10.326(3) A, alpha=72.49(3) degrees, beta=103.74(4) degrees, gamma=88.27(4) degrees and Z=2. The 195Pt NMR peaks of the complexes containing the beta-alanine moiety appeared significantly more upfield than those of the complexes containing diglycine. The ratios of the species of the platinum complexes containing the dipeptide ester in neutral solution were significantly different from those in alkaline solution at 40 degrees C for a short time.     

Synthesis,structural characterization and in vitro cytotoxicity of organotin(IV) derivatives of heterocyclic thioamides, 2-mercaptobenzothiazole, 5-chloro-2-mercaptobenzothiazole, 3-methyl-2-mercaptobenzothiazole and 2-mercaptonicotinic acid

Five new organotin(IV) molecules with the heterocyclic thioamides; 2-mercaptobenzothiazole (Hmbzt), 5-chloro-2-mercaptobenzothiazole (Hcmbzt), 3-methyl-2-mercaptobenzothiazole (mmbzt) and 2-mercaptonicotinic acid (H(2)mna) of formulae [(n-C(4)H(9))(2)Sn(mbzt)(2)] (1), [(C(6)H(5))(2)Sn(mbzt)(2)] (2), [(CH(3))(2)Sn(cmbzt)(2)].1.7(H(2)O)] (3), [(n-C(4)H(9))(2)SnCl(2)(mmbzt)(2).(CH(2)Cl(2))] (4) and [[(C(6)H(5))(3)Sn](2)(mna).[(CH(3))(2)CO]] (5) have been synthesized and characterized by elemental analysis, 1H-, 13C-NMR, FT-IR and M?ssbauer spectroscopic techniques. Crystal structures of molecules 1, 3 and 5 have been determined by X-ray diffraction at 173(1) K (1 and 5) and 293(2) K (3). Compound 1 C(22)H(26)N(2)S(4)Sn, is monoclinic, space group C2/c, a=44.018(2), b=8.8864(5), c=12.8633(7) A, beta=104.195(5) degrees, Z=8. Compound 3 is also monoclinic, space group P2(1)/c and a=17.128(2) A, b=17.919(2) A, c=7.3580(10) A, beta=98.290(10) degrees, Z=4. In both molecules 1 and 3, two carbon atoms from aryl groups, two sulfur and two nitrogen atoms from thione ligands form a distorted octahedral geometry around tin(IV) with trans-C(2), cis-N(2), cis-S(2) configurations. Compound 5 C(45)H(39)NO(3)SSn(2) is monoclinic, space group P2(1)/n, a=9.1148(2) A, b=29.2819(6), c=15.5556(4) A, beta=106.2851(9) degrees, Z=4. Complex 5 contains two [(C(6)H(5))(3)Sn(IV)] moieties linked by a double deprotonated 2-mercaptonicotinic acid (H(2)mna). Both tin(IV) ions are five coordinated. This complex is the an example of a pentacoordinated Ph(3)SnXY system with an axial-equatorial arrangement of the phenyl groups at Sn(1) atom. Compounds 1, 3 and 5 were tested for in vitro cytotoxicity against the cancer cell line of sarcoma cells (mesenchymal tissue) from the Wistar rat, polycyclic aromatic hydrocarbons (benzo[a]pyrene) carcinogenesis. Compound 5 exhibits strong cytotoxic activity, while complexes 1 and 3 show less cytotoxic activity.     

N-Salicylidenehydrazides as versatile tridentate ligands for dioxovanadium(V) complexes

The Schiff base ligand derived from salicylaldehyde and benzoic acid hydrazide (H2salhyph) reacts with potassium metavanadate in methanol solution to yield the potassium salt of the corresponding cis-dioxovanadium(V) complex K[VO2(salhyph)] (1). 1 crystallizes with one molecule of methanol in the monoclinic space group P2(1)/c with a = 1332.3(7), b = 669.9(2), c = 1809.0(8) pm, beta = 100.96(4) degrees, and Z = 4. The reactions of 1 with several proton acidic compounds including water, methanol, ethane-1,2-diol (H2ed), and proton acids lead to neutral monooxovanadium(V) and cis-dioxovanadium(V) complexes ([VO2(Hsalhyph)] (2); [V2O3(salhyph)2] (3); [VO(OMe)(salhyph)(HOMe)] (4); [VO(Hed)(salhyph)] (5)). The crystal structure of 2 (triclinic space group P1 with a = 677.79(5), b = 842.89(7), c = 1214.66(9) pm, alpha = 79.931(1), beta = 75.466(1), gamma = 73.391(1) degrees, and Z = 2) reveals that the protonation of the cis-dioxovanadium(V) complex 1 occurs at the hydrazide nitrogen atom of the ligand system. This was confirmed by the spectroscopic properties of the deuterium derivative.     

Palladium(II) complexes of 2-benzoylpyridine-derived thiosemicarbazones: spectral characterization, structural studies and cytotoxic activity

Palladium(II) complexes of 2-benzoylpyridine thiosemicarbazone (H2Bz4DH) and its N4-methyl (H2Bz4M) and N4-phenyl (H2Bz4Ph) derivatives were obtained and fully characterized. [Pd(2Bz4DH)Cl] (1) crystallizes in the monoclinic space group P21/c with a=11.671(1), b=10.405(1), c=13.124(1), beta=115.60(1) degrees and Z=4; [Pd(2Bz4M)Cl] (2) in the monoclinic space group P21/c with a=9.695(1), b=15.044(1), c=10.718(1) A, beta=105.38(1) degrees and Z=4 and [Pd(2Bz4Ph)Cl] (3) in the triclinic space group P1 with a=9.389(1), b=13.629(1), c=15.218(1) A, alpha=70.25(1), beta=73.46(1), gamma=83.57(1) degrees and two independent molecules per asymmetric unit (Z=4). All complexes show a quite similar planar fourfold environment around palladium(II). A negatively charged organic molecule acts as a tridentate ligand and binds to the metal through the pyridine nitrogen, the imine nitrogen and the sulfur atom. A chloride ion occupies the fourth coordination site. The planar complexes stack nearly parallel to one another in the lattice conforming a layered crystal structure. The cytotoxic activity of the thiosemicarbazones and their metal complexes was tested against the MCF-7, TK-10 and UACC-62 human tumor cell lines. The ligands exhibit lower values of GI50 and LC50 than the complexes, H2Bz4Ph being the most active with GI50<0.003 microM; LC50=13.4 microM; GI50=9.3 microM, LC50=12.9 microM; GI50<0.003, LC50=13.8 microM in the MCF-7, TK-10 and UACC-62 cell lines, respectively. Among the complexes, [Pd(2Bz4Ph)Cl] (3) exhibited the lowest values of GI50 in the three studied cell lines.     

C9 conformation of N-(N alpha-[(tert.-butyloxy)-carbonyl]-L-alanyl)-N,N'-dicyclohexylu rea in solid and solution.

An X-ray diffraction study was carried out on a single crystal of N-(N alpha-[(tert.-butyloxy)-carbonyl]-L-alanyl)-N,N'-dicyclohexylur ea belonging to the tetragonal space group P4(1)2(1)2, having cell dimensions a = b = 10.102(3) A, c = 46.067(7) A, V = 4701.2 A3, Z = 8. The crystal structure was solved by direct methods and refined to an R value of 0.056 for 1602 unique reflections with I greater than 2.5 sigma(I). Crystal structure analysis shows the presence of an intramolecular N-H ... O=C H-bond stabilizing the molecule in a folded form similar to that of a beta turn, forming a nine-membered ring. IR and 1H-NMR studies in CDCl3 solution confirm the stable folded conformation found in the crystalline state, as well as the existence of N-H ... O=C H-bonds in the title compound, as in peptides.     

The crystal structure and physicochemical characteristics of 2-hydroxy-N-[3(5)-pyrazolyl]-1,4-naphthoquinone-4-imine,a new antitrypanosomal compound

This study was designed to investigate the physical characteristics and crystalline structure of 2-hydroxy-N-[3(5)-pyrazolyl]-1,4-naphthoquinone-4-imine (PNQ), a new active compound against Trypanosoma cruzi, the causative agent of American trypanosomiasis. Methods used included differential scanning calorimetry, thermogravimetry, hot stage microscopy, polarized light microscopy (PLM), Fourier-transform infrared (FTIR) spectroscopy, and high-resolution X-ray powder diffraction (HR-XRPD). According to PLM and HR-XRPD data, PNQ crystallized as red oolitic crystals (absolute methanol) or prisms (dimethyl sulfoxide [DMSO]-water) with the same internal structure. The findings obtained with HR-XRPD data (applying molecular location methods) showed a monoclinic unit cell [a = 18.4437(1) A, b = 3.9968(2) A, c = 14.5304(1) A, alpha = 90 degrees , beta = 102.71(6) degrees , gamma = 90 degrees , V = 1044.9(1) A(3), Z = 4, space group P2(1)/c], and a crystal structure (excluding H-positions) described by parallel layers in the direction of the b-axis, with molecules held by homochemical (phenyl-phenyl and pyrazole-pyrazole) van der Waals interactions. In addition, FTIR spectra displayed the NH-pyrazole stretch overlapped with the OH absorption at 3222 cm(-1), typical of -NH and -OH groups associated through H-bondings; and a carbonyl stretching absorption at 1694 cm(-1), indicating a nonextensively H-bonded quinonic C=O, which was in accordance with the solved crystal structure of PNQ. The existence of such cohesive forces shed light on the thermoanalytical data, which revealed that PNQ is a stable solid, unaffected by oxygen that decomposed without melting above 260 degrees C.     

X-ray and conformational investigations of a 4:1 mixture of 6-(N-benzyl-N-tert-butoxycarbonylamino)-2,3,6,7-tetradeoxy-alpha- DL-ery thro- and -beta-DL-threo-hept-2-enopyranos-4-uloses

The crystals of a 4:1 mixture of 6-(N-benzyl-N-tert-butoxycarbonylamino)-2,3,6,7-tetradeoxy-a-DL-er ythro- and -beta-DL-threo-hept-2-enopyranos-4-ulose were monoclinic, space group P2(1)/c, with cell dimensions: a = 9.490(2), b = 21.516(5), c = 10.279(2) A, beta = 115.31(1) degrees, Z = 4. The ulose ring had a half-chair conformation deformed towards the sofa (envelope) form.     

Interactions of metal ions with a 2,4-diaminopyrimidine derivative (trimethoprim). Antibacterial studies

The interaction of copper (II), zinc(II) and cadmium(II) with Trimethoprim (2,4-diamino-5-(3',4',5'-trimethoxybenzyl) pyrimidine) has been studied. The crystal structures of [Zn(Trim)2Cl2] (2) and [Cd(Trim)Cl2(CH3OH)]n (4) are reported. Compound (2) exhibits a distorted tetrahedral environment around the metal center and crystallizes in the triclinic space group P1 with a=10.2397(6), b=10.4500(6), c=16.3336(16) A, alpha=96.141(8), beta=106.085(5), gamma=96.551(5) degrees and Z=2. In complex (4), the Cd(II) centers are bridged sequentially by two chlorine ions to form infinite chains and present a six-coordinated environment; the compound crystallizes in the monoclinic P2(1)/C space group with a=13.958(5), b=7.532(2), c=18.390(2) A, alpha=90, beta=97.32(5), gamma=90 degrees and Z=4. In both structures the Trimethoprim acts as a monodentate ligand through the pyrimidinic nitrogen N(1) atom. The characterization of the Cu(Trim)2(CH3O)(ClO4) complex through EPR and magnetic measurements suggests a binuclear or polinuclear nature, with bridging methoxo groups. The complexes were screened for their activity against several bacteria, showing activity similar to that of trimethoprim.     

Crystallization and preliminary X-ray analysis of a fungal endoglucanase I.

An endoglucanase I (EG1) from a fungal source (Humicola insolens) has been crystallized in a number of forms suitable for X-ray diffraction analysis. Four crystal forms have been grown from various precipitants using vapour phase diffusion methods in hanging drops. Three of these crystal forms diffract to beyond 2.5 A resolution. Two forms, obtained from ammonium sulphate at pH 5.4, or 8.0, grow as tetragonal bipyramids in space group P4(1)22 or P4(3)22, with approximate cell dimensions a = b = 102 A, c = 282 A. The other crystal forms were grown from polyethylene glycol 8000 at pH 8.0. One grows as monoclinic plates, space group P2(1), with cell dimensions a = 66.9 A, b = 75.2 A, c = 86.9 A and beta = 102.9 degrees and the other as long hexagonal rods in space group P6(1)22 or P6(5)22, with cell dimensions a = b = 119 A, c = 83 A.     

Crystal structure of cholesteryl decanoate.

Cholesteryl decanoate (C37H64O2) is monoclinic, space group P2I, with cell dimensions a = 12.931 (6), b = 9.066 (2), c = 30.22 (1) A, beta = 91.14 (4) degrees, and Z = 4. The atomic coordinates from cholesteryl laurate were used in an initial trial structure which was refined by block diagonal least-squares methods with 1846 observed X-ray reflections (R = 0.129). Molecules A and B have almost fully extended conformations, except at the ester bonds and towards the end of the decanoate B chain. The molecules are arranged in antiparallel array forming monolayers of thickness d001 = 30.22 A, with the molecular long axis making an angle of about 67 degrees with the layer interface. The crystal structure is very similar to that of cholesteryl nonanoate and cholesteryl laurate.     

Crystallization and preliminary X-ray analysis of flavocytochrome c(3), the fumarate reductase from Shewanella frigidimarina.

The fumarate reductase (flavocytochrome c(3)) from Shewanella frigidimarina (formerly S. putrefaciens) NCIMB400 has been crystallized in the space group P2(1), with cell dimensions of a = 45.447 A, b = 92.107 A, c = 78.311 A, and beta = 91.038 degrees and one molecule per asymmetric unit. A native data set has been collected to 1.8 A. The gene encoding Fcc(3) from the S. frigidimarina type strain ACAM591 has been cloned and sequenced and the protein crystallized in space group P2(1) with cell dimensions of a = 45.359 A, b = 88.051 A, c = 77.473 A, and beta = 104.499 degrees. Anomalous data have also been collected from the NCIMB400 crystal allowing the heme iron positions to be identified.     

Drug-metal interactions: copper(II) complex of the antidiabetic drug acetohexamide and pyridine

The preparation, spectral properties, and crystal structure of a copper(II) complex of 4-acetyl-N-[(cyclohexylamino)carbonyl]benzenesulfonamide, which is known as acetohexamide, and pyridine are reported. The complex Cu(AH)2(py)2, where AH = acetohexamide and py = pyridine, was prepared and characterized by X-ray and ESR. The complex is monoclinic, space group P2(1)/a, with a = 17.412(6), b = 9.039(2), c = 26.531(10) A, beta = 102.24(2) degrees, and Z = 4. The final refinement used 3892 unique reflections and gave an R value of 0.0646. The copper atom is surrounded by four nitrogen atoms in a square-planar arrangement, two from the acetohexamide ligands (Cu-N = 2.009 A) and two from the pyridine molecules (Cu-N = 2.016 A) in a trans geometry. The ESR data support a similar coordination behavior of the copper (g parallel greater than g perpendicular greater than ge) with the unpaired electron in the dx2-y2 orbital.     

Crystallization and preliminary diffraction analysis of cholesterol esterase from Candida cylindracea

Cholesterol esterase (EC 3.1.1.13) from the microorganism Candida cylindracea has been crystallized in two forms. Crystals, typically 0.30 x 0.15 x 0.10 mm in size, diffract rotating anode generated x-rays to beyond 3 A are suitable for data collection for an x-ray crystallographic investigation. A monoclinic crystal form in the space group P2(1) was found to have cell dimensions of a = 122.9 A, b = 101.0 A, c = 95.2 A and beta = 108.3 degrees. The asymmetric unit of the cell contains two dimers of 129 kDa each. A second crystal form, in the triclinic space group P1, has cell dimensions of a = 58.6 A, b = 88.7 A, c = 58.6 A, alpha = 93.3 degrees, beta = 113.8 degrees and gamma = 96.0 degrees, and has one dimer per asymmetric unit.     

Synthetic peptide helices in crystals: structure and antiparallel and skewed packing motifs for alpha-helices in two isomeric decapeptides

The isomeric decapeptides Boc-Aib-Ala-Leu-Ala-Aib-Aib-Leu-Ala-Leu-Aib-OMe (II) and Boc-Aib-Ala-Aib-Ala-Leu-Ala-Leu-Aib-Leu-Aib-OMe (III), are predominantly alpha-helical with little effect on the conformation with interchange of Aib/Ala residues or Aib/Leu residues. The packing motif of helices in crystal II is antiparallel, whereas the helices pack in a skewed fashion in crystal III, with a 40 degrees angle between neighboring helix axes. Crystal III contains a water molecule in a hydrophobic hole that forms hydrogen bonds with two carbonyl oxygens that also participate in 5----1 type hydrogen bonds. Values for helical torsional angles phi and psi assume a much wider range than anticipated. Crystal II: C49H88N10O13, space group P2(1), with a = 16.625 (2) A, b = 9.811 (5) A, c = 18.412 (3) A, beta = 99.79 (1) degrees, Z = 2, R = 5.7% for 4338 data with magnitude of F0' greater than 3 sigma(F). Crystal III: C49H88N10O13 x 1/2H2O, space group P2(1) with a = 11.072 (2) A, b = 34.663 (5) A, c = 16.446 (3) A, beta = 107.85 (1) degrees, Z = 4, R = 8.3% for 6087 data with [F0[ greater than 3 sigma(F).     

NMR conformational analysis of p-tolyl furanopyrimidine 2'-deoxyribonucleoside and crystal structure of its 3',5'-di-O-acetyl derivative

The conformation of a representative molecule of a new, potent class of antiviral-active modified nucleosides is determined. A bicyclic nucleoside, 3-(2'-deoxy-beta-D-ribofuranosyl)-6-(4-methylphenyl)-2,3-dihydrofuro[2,3-d]pyrimidin-2-one, shows C2'-endo and C3'-endo ribose conformations in solution (63:37, 37 degrees C; DMSO-d6), as determined by 1H NMR studies. The crystal structure of a 3',5'-di-O-acetyl-protected derivative (monoclinic, P21, a/b/c= 6.666(1)/12.225(1)/24.676(2) A, beta=90.24(1) degrees , Z=4) shows exclusively C2'-endo deoxyribose puckering. The base is found in the anti position both in solution and in crystalline form.     

Molecular structure of antitumor drug steffimycin and modelling of its binding to DNA.

The molecular and crystal structure of steffimycin have been determined by single crystal X-ray diffraction to 0.9 angstrom resolution. The triclinic crystals are in the space group P1, with the unit cell dimensions of a = 8.606(3) angstrom, b = 22.168(7) angstrom, c = 8.448(2) angstrom, alpha = 97.56(3) degrees, beta = 95.97(2) degrees, gamma = 87.94(3) degrees, Z = 2. The structure was solved by direct methods and refined by the full-matrix least-squares method to a final R value of 0.065 with 3405 (Inet greater than 2.0 sigma (Inet] observed reflections using the NRCVAX software package. The crystal lattice includes 2 independent steffimycin, 3 water and one 2-methyl-2,4-pentanediol molecules. The conformation of steffimycin is grossly similar to other anthracycline antibiotics including daunorubicin. The crystal packing interactions of steffimycin suggest a preferred stacking of the aglycone chromophore of the antibiotic which resembles the intercalative interactions seen in the daunorubicin-d(CGTACG) (Wang et al., Biochemistry 26, 1152 (1987] and nogalamycin-d(CGT(pS)ACG) (Liaw et al., Biochemistry 28, 9913 (1989] complexes. The atomic coordinates data from these complexes were used to model the intercalative binding of steffimycin to DNA. The models were then stereochemically idealized by the constraint refinement program NUCLSQ. Subsequently XPLOR software package was used for energy minimization of these models in vacuo. The model building studies suggest that steffimycin has a higher CpG base sequence specificity over the TpA step, similar to that of daunorubicin and nogalamycin.