Crystal Structures of Dipeptides Derived from the β-Amino Acids (1R,2S)-2-Aminocyclopentanecarboxylic Acid and (1S,2R,3S)-2-Amino-3-methylcyclopentanecarboxylic Acid

Abstract  

Crystals of the dimeric β-peptides 13 and 20, derived from (1R,2S)-2-aminocyclopentanecarboxylic acid and (1S,2R,3S)-2-amino-3-methylcyclopentanecarboxylic acid, respectively, were synthesised and studied by X-ray diffraction in order to establish their solid state secondary structural characteristics. Compound 13 crystallises in the monoclinic space group P 2 ₁ with cell parameters of a = 5.2682(1) ?, b = 9.1211(2) ?, c = 22.4467(6) ?, β = 91.3855(9)°, V = 1078.29(4) ?³ and Z = 2. Compound 20 crystallizes in the orthorhombic space group P 2 ₁ 2 ₁ 2 ₁ with cell parameters of a = 5.0968(1) ?, b = 11.5546(2) ?, c = 43.5414(8) ?, V = 2564.22(8) ?³ and Z = 4. In both cases adjacent molecules are linked by a series of N–H···O=C hydrogen bonds to form β-sheet like structures.     

Synthesis and Structure of cis-Dioxo(3-Methoxysalicylaldehyde 4-Methylthiosemicarbazonato-N,O,S)(γ-Picoline-N)Molybdenum(VI)

Abstract  Red crystals of cis-dioxo(3-methoxysalicylaldehyde 4-methylthiosemicarbazonato-N,O,S)(γ-picoline-N)molybdenum(VI), [MoO₂L(γ-pic)], [L²⁻=CH₃OC₆H₄(O)CH=NN=C(S)NHCH₃, 3-methoxysalicylaldehyde 4-methylthiosemicarbazonato] were prepared by the reaction of [MoO₂L] _n with γ-picoline in dry methanol. The title compound crystallized in the monoclinic space group P2₁/n, a = 6.7984(7) ?, b = 15.9760(12) ?, c = 17.1466(14) ?, β = 93.613(8)°, V = 1858.6(3) ?³, Z = 4. The coordination geometry around the molybdenum center is distorted octahedral with the tridentate thiosemicarbazonato ligand (L²⁻) bonded meridionally to the [MoO₂]²⁺ core. The sixth coordination site is occupied by a weakly bound γ-picoline molecule. The adjacent molecules are joined by the N–H···O hydrogen bonds between their amino and methoxy groups thus forming infinite molecular chains. The three-dimensional solid-state structure is achieved by the additional C–H···O, C–H···π and van der Waals interactions. Graphical Abstract  In the title compound, [MoO₂L(γ-pic)], the tridentate thiosemicarbazonato ligand (L²⁻) is meridionally bound to the [MoO₂]²⁺ core, while a molecule of γ-picoline completes the distorted octahedral coordination around the metal atom.      

Absolute Configuration Determination of Two Optically Active Cyclopropyl-Ketoacids: (1′S, 3S) 3-(2′,2′-Dichloro-1′-methyl-cyclopropyl)-6-oxo-heptanoic acid and (1′S, 3S) 3-(2′,2′-Dibromo-1′-methyl-cyclopropyl)-6-oxo-heptanoic acid

Abstract  

The title compounds C₁₁H₁₆Cl₂O₃ (III) and C₁₁H₁₆Br₂O₃ (IV) have been prepared from (S)-Limonen. Their crystal structure and absolute configuration have been determined by X-ray analysis which confirmed the 1′S absolute configuration at the cyclopropyl moiety, in agreement with the known absolute configuration of the starting material. Both (III) and (IV) are orthorhombic, space group P2₁2₁2₁ with a = 7.2558(4) ? (for III) 7.4058(6) ? (for IV), b = 9.7885(5) ? (for III) 9.7459(7) ? (for IV), c = 17.7551(10) ? (for III) 18.0354(14) ? (for IV), α = 90°, β = 90°, γ = 90° and Z = 4.     

Stereospecific Ligands and Their Complexes. III. Oxalato and Malonato-(ethylenediamine- N , N ′-di- S , S -2-propionato)-Chromate(III) Complexes. Crystal Structure of the Δ-(–)589- s - cis -K[Cr( S , S -eddp)(ox)]?·?0.5H2O

Abstract  The s-cis-[Cr(S,S-eddp)L]⁻ complexes (S,S-eddp = S,S-ethylenediamine-N,N′-di-2-propionate ion; L = oxalate or malonate ions) were prepared. The complexes were purified by ion-exchange chromatography. The geometry of the complexes has been supposed on the basis of the electronic absorption spectra, and the absolute configurations of the isolated s-cis-[Cr(S,S-eddp)L]⁻ complexes have been predicted on the basis of their circular dichroism (CD) spectra and confirmed by X-ray analysis of the crystal structure of the Δ-(–)₅₈₉-s-cis-K[Cr(S,S-eddp)(ox)] 0.5H₂O complex. Index Abstract  The title compound, s-cis-potassium-(ethylenediamine-N,N’-di-S,S-2-propionato) (oxalato)chromate(III) semihydrate was synthesized by passing the corresponding sodium salt through cation exchange-resin Merck I in potassium form and its crystal structure determined. Single crystal X-ray diffraction analysis reveals s-cis geometry of the complex cation. For Part II see Glodjović VV, Trifunović SR (2008) J Serb Chem Soc 73:541.     

Crystal structures and properties of catena-μ-nitrato (7-amino-5-aza-4-methyl-3-hepten-2-onato) copper(II) and μ3-hydrox-otris(μ-8-amino-5-aza-4-methyl-3-octen-2-onato) tricopper(II) dinitrate

The products of monocondensation of penta-2,4,-dione with 1,2-diaminoethane, HAE, and with 1,3-diaminopropane, HAT, react with copper nitrate hemipentahydrate to give catena--nitrato (7-amino-5-aza-4-methyl-3-hepten-2-onato) copper(II), [Cu(AE)NO₃]_n and a mixture of ₃-hydroxo-tris (-8-amino-5-aza-4-methyl-3-octen-2-onato) tricopper(II) dinitrate [Cu₃(AT)₃OH]-(NO₃)₂ and [Cu(AT)NO₃]_x, respectively. The structure of [Cu(AE)NO₃]_n has been determined from 1601 diffractometer data and refined by least squares methods toR=0.0306. The compound crystallizes in the monoclinic space groupP2₁/a witha=16.856(3)Å,b=8.109(4)Å,c=7.518(3)Å,=90.15(2)°,D _c =1.725 g cm^–3,D _o=1.72 g cm^–3 andZ=4. Copper atoms in [Cu(AE)NO₃]_n are in a 4+1+1^* environment and are linked by the pseudobidentate and bridging nitrato group into infinite chains. The structure of [Cu₃(AT)₃OH](NO₃)₂ has been determined from 3178 diffractometer data and refined toR=0.0544. The compound crystallizes in the triclinic space groupP¯1 witha=11.918(2)Å,b=14.478(2)Å,c=11.501(3)Å,=98.04(2)°,=117.72(2)°, =99.80(1)°,D _c =1.580 g cm^–3,D _o=1.59 g cm^–3 andZ=2. The compound is associated in hexanuclear clusters due to hydrogen bonding interactions. Coordination about Cu is best described as square pyramidal. Magnetic susceptibility data indicate a weak antiferromagnetic exchange within the trinuclear core withJ=–14 cm^–1.     

Synthesis, Characterization and X-Ray Structure of Bis(O-propyldithiocarbonato-κ2S,S′)bis(4-cyanopyridine-κN)nickel(II)

Abstract  

The [Ni(S₂COCH₂CH₂CH₃)₂(C₆H₄N₂)₂] adduct of 4-cyanopyridine with [Ni(S₂COCH₂CH₂CH₃)₂] was synthesized and characterized by elemental analysis, magnetic susceptibility measurement, IR, electronic spectral data, Thermogravimetric analysis/DTA techniques and X-ray diffraction analysis. The Ni atom in the title complex is octahedrally coordinated within a trans-N₂S₄ donor set, with the Ni atom located on a centre of inversion. The title complex crystallizes in the monoclinic space group P2 ₁ /c with unit cell parameters a = 11.75(4), b = 11.62(3), c = 9.20(2) ?, β = 104.99(3)°. Crystal structure was solved by direct methods and refined by full matrix least squares procedures to a final R-value of 0.0294 for 1895 observed reflections. The packing of layers of molecules is stabilized by weak C–H···N and C–H···π interactions.     

Crystal structure of (4α,4aα,8aα)-(±)-octahydro-2-(phenylmethyl)-2H-1,2-benzoxazin-4-ol, 4-methylbenzenesulfonate(ester)

The title compound, a bicyclic tetrahydro-1,2-oxazine, crystallizes in a monoclinic lattice, space group P2₁/c, with a = 12.9809(18)Å, b = 12.920(2)Å, c = 13.631(2)Å, = 110.713(12)°, and Z = 4. The structure found in the solid state for this conformationally mobile molecule shows the tosyl group in an axial position and a benzyl group in an equatorial position of the bicyclic system.     

Synthesis and Crystal Structure of Benzoyloxymethyl (4α,8β,13β)-13-methyl-16-oxo-17-norkauran-18-carbonate Ester

Abstract  Isosteviol derivative: benzoyloxymethyl (4α,8β,13β)-13-methyl-16-oxo-17-norkauran-18-carbonate ester was synthesized by esterification of isosteviol with chloromethyl benzoate and its crystal structure was determined by X-ray diffraction method. The compound crystallizes in the triclinic space group P1 with unit cell parameters: a = 8.784(3) ?, b = 9.079(3) ?, c = 15.950(6) ?, α = 79.343(6)°, β = 79.061(5)°, γ = 89.849(5)°, Z= 2. The conformation of rings A and B is chair, whereas the conformation of ring C is unsymmetrical twist chair. The carbonyl group at the C20 is coplanar with the benzene ring. The fragment of the ester group occupying the pseudoaxial site of C1 position adopts a zigzag conformation. Index Abstract  Isosteviol derivative: benzoyloxymethyl (4α,8β,13β)-13-methyl-16-oxo-17-norkauran -18-carbonate ester was synthesized and its crystal structure was determined by X-ray diffraction method.      

Synthesis and crystal structures of cis- and trans-1-(3′-N, N-dimethylthiocarbamoyl-4′-methoxy)-2-(3″, 4″, 5″trimethoxyphenyl) ethene

The combretastatin A-4 analogue cis-1-(3-N,N-dimethylthiocarbamoyl-4-methoxy)-2-(3,4, 5-trimethoxyphenyl) ethene (1) and its trans stereoisomer (2) were synthesized. The molecular structures of these compounds were obtained by single-crystal X-ray diffraction. Crystallization of 1 occurs in the centrosymmetric monoclinic space group C2/c (No. 15) with a = 21.468(5), b = 7.932(1), c = 23.949(3); and = 100.75(1) and Z = 8. Crystallization of 2 occurs in the centrosymmetric monoclinic space group P2₁/n (No. 14) with a = 11.7825(7), b = 11.562(1), c = 14.911(1) and = 93.294(6); and Z = 4. Details of the synthesis and the structural characterization of the title compounds are presented and discussed.     

Crystal and molecular structures of 1,4-dihydro-6-methyl-5-N,N-diethylcarbamoyl-4-phenyl-2(3H)-pyrimidinethione (1) and 1,4-dihydro-6-methyl-5-N-methyl carbamoyl-4-(2′-nitrophenyl)-2(3H)-pyrimidinethione hemihydrate (2)

The crystal structure of 1,4-dihydro-6-methyl-5-N,N-diethylcarbamoyl-4-phenyl-2(3H)-pyrimidinethione, C₁₆ H ₂₁ N ₃OS (1), is monoclinic, space group P2₁/n, a = 6.818(1), b = 13.211(2), c = 18.807(3) Å, = 99.53(1)°, V = 1670.6(4) ų, Z = 4 and d _cal = 1.206 Mg/m³, R = 0.042 (wR = 0.119) for 190 parameters and 2560 observations with I 2(I) and 1,4-dihydro-6-methyl-5-N-methyl carbamoyl-4-(2-nitrophenyl)-2(3H)-pyrimidinethione hemihydrate, C₁₃ H ₁₄N₄O₃S 0.5H₂O, (2), is triclinic, space group P1, a = 7.513(1), b = 14.381(2), c = 15.506(2)Å, = 114.95(2), = 98.11(1), = 93.55(1)°, V = 1490.0(3) ų, Z = 4 and d _cal = 1.406 Mg/m³, R = 0.062 (wR = 0.165) for 388 parameters and 3094 observations with I 2(I).The compound 2 crystallized having two molecules in the asymmetric unit, which can be regarded as monohydrated dimers, and forming a hydrate. The conformation of the central heterocyclic ring (1,4-dihydropyrimidine) in both compounds was found to be close to a half-chair conformation. The 2-nitrophenyl substituent in 2 is in the axial synperiplanar orientation. In both compounds, the conformation of the 3-substituted carbamoyl group appears to be influenced by hydrogen bonding with anticlinal orientation observed for carbonyl groups serving as hydrogen bonding acceptors.     

The Synthesis and Crystal Structure of (4α,8β,13β,16β)-13-Methyl-16,18-diol-17-Norkaurane: A Simultaneous Reduction Product of Isosteviol

Abstract  

(4α,8β,13β,16β)-13-methyl-16,18-diol-17-norkaurane was synthesized by esterification and reduction of isosteviol, respectively. The structure of the title compound was established by spectral analysis and X-ray diffraction studies. The compound crystallizes in the orthorhombic space group P2₁2₁2₁ with unit cell parameters: a = 7.3705 (14) ?, b = 13.508 (3) ?, c = 20.139 (4) ?, V = 2005.1 (7) ?³, Z = 4. The conformation of rings A and B is chair, whereas the conformation of ring C is unsymmetrical distorted chair. The stereochemistry of the A/B and B/C ring junctions is trans, while the five-membered ring D adopts an envelope conformation.     

Synthesis, Characterization, and Crystal Structures of 3-bromo-N′-(2-methoxybenzylidene)benzohydrazide and N′-(2-methoxybenzylidene)-3,4-methylenedioxybenzohydrazide

Abstract  

Two new hydrazone compounds, 3-bromo-N′-(2-methoxybenzylidene)benzohydrazide (1) and N′-(2-methoxybenzylidene)-3,4-methylenedioxybenzohydrazide (2), have been synthesized and characterized by elemental analysis, IR, and single crystal X-ray diffractions. Compound (1) crystallizes in the triclinic space group P1 with unit cell dimensions a = 8.4088(5) ?, b = 8.5398(5) ?, c = 10.6572(6) ?, α = 90.356(3)°, β = 102.868(3)°, γ = 97.987(3)°, V = 738.28(7) Ǻ³, Z = 2, R ₁ = 0.0406, and wR ₂ = 0.0804. Compound (2) crystallizes in the tetragonal space group P4₁ with unit cell dimensions a = b = 9.792(4) ?, c = 15.788(6) ?, V = 1513.8(10) Ǻ³, Z = 4, R ₁ = 0.0415, and wR ₂ = 0.0818. The molecules of both compounds display E configurations with respect to the C=N double bonds. In the crystal structure of (1), molecules are linked through N–H···O hydrogen bonds, forming chains running along the b axis. In the crystal structure of (2), molecules are linked through N–H···O hydrogen bonds, forming chains running along the c axis.     

Crystal Structure?4-(2,4-Dihydroxybenzylideneamino)-5-methyl-2H-1,2,4-triazol-3(4H)-one

Abstract  

The title compound (I), 4-(2,4-dihydroxybenzlideneamino)-5-methyl-2H-1,2,4-triazol-3(4H)-one was characterized by single crystal X-ray diffraction. This crystal is monoclinic, space group P2₁/c with a = 10.1447(7) ?, b = 7.0972(3) ?, c = 14.6726(10) ?, β = 98107(5)°, V = 1045.85(11) ?³, Z = 4, D _c = 1.487 g/cm³, F ₀₀ = 488, R = 0.039 and wR = 0.1025, S = 1.003, T = 293 (2) K. The title molecule is planar: the angle between the triazole ring and benzene ring is 179.1(1)°. The crystal structure contains two intramolecular (O–H···N and C–H···O) and three intermolecular interaction (O–H···N, N–H···O, and C–H···O). In addition, there is also π–π interactions.     

Novel manganese(III) oxidation chemistry: X-ray crystal structures of (1α,2α,4β)-1,2-diacetoxy-4-(4-methoxyphenyl)-6-methoxy-1,2,3,4-tetrahydronaphthalene (compound A) and (1α,2α,4β)-1,2-diacetoxy-4-(2-methoxyphenyl)-8-methoxy-1,2,3,4-tetrahydronaphthalene (compound B)

CompoundA is (1,2,4)-1,2-diacetoxy-4-(4-methoxyphenyl)-6-methoxy-l,2,3,4-tetrahydronaphthalene, C₂₂H₂₄O₆,M _r=384.43, monoclinic, P2₁/n, witha=11.074(3),b=10.353(4),c=17.616(4)Å,=94.96(2)°,V=2012.1ų,D _calc=1.27 g cm^–3 and=0.55 cm^–1 forZ=4. Least-squares refinement of 1371 observed [F ₀5 (F ⁰)] reflections led to the final agreement index ofR=0.052. A twofold disorder was observed for the 1-acetoxy group whereas the 2-acetoxy group was ordered. CompoundB, (1,2,4)-1,2-diacetoxy-4-(2-methoxyphenyl)-8-methoxy-l,2,3,4-tetrahydronaphthalene, C₂₂H₂₄O₆,M _r=384.43, crystallizes in the monoclinic space group, P2₁/c, witha=16.209(2),b=10.076(1),c=13.357(4)Å,=111.41(2)°,V=2030.9ų,D _calc=1.26 g cm^–3 and=0.54 cm^–1 forZ=4. A final agreement index ofR=0.045 was realized by least-squares refinement of 1486 observed [F _o5 (F _o)] reflections. Intermolecular interactions in the cell lattices of compoundsA andB are noted. The title compoundsA andB were prepared by manganese(III) acetate oxidative dimerization of two molecules of 4-methoxystyrene and 2-methoxystyrene, respectively.     

Crystal and molecular structure of 17-β-methyl-α-isolupanineN-(16)-oxide perchlorate monohydrate

[C₁₆H₂₇N₂O₂]⁺·ClO ₄ ^– ·H₂O,M _r=396.87, orthorhombicP2₁2₁2₁ a=13.708(4),b=16.930(7),c=8.311(3) Å,V=1928.3(13) ų,Z=4,D _x=1.367(2) g cm^–3,(MoK)=0.71068 Å,(MoK)=1.95 cm^–1,F(000)=848,T=292 K,R=0.061 for 1324 unique reflections. RingsA,B,C,D have half-chair, chair, chair and chair conformations, respectively; the quinolizidone moietyA/E has a quasi-trans and the quinolizidine moietyC/D has a trans configuration. The cations are connected into chains along the crystallographic direction [001] by strong hydrogen bonds utilizing the water molecule: C(2)=O(5)O(W)O(6)-N(16) of 2.623(7) and 2.574(7) Å, respectively. The water molecule is also hydrogen-bonded to one oxygen atom of the perchlorate anion: O(W)O(2) is 3.106(10) Å. A very short intramolecular distance between N(1) and O(6) of 2.696(7) Å, due to the quasitrans-trans configuration of the-isolupanine skeleton, is observed.     

Synthesis and crystal structure of N-(1-phenyl-3-methyl-4-benzal-pyrazolone-5)- N′-salicylidene hydrazine

A novel Schiff base compound, N-(1-phenyl-3-methyl-4-benzal-pyrazolone-5)-salicylidene hydrazine (PMBP-SAH), has been synthesized and characterized by X-ray diffraction: monoclinic, space group C2/c with a = 21.796(5) Å, b = 18.370(3) Å, c = 20.843(3) Å, = 95.440(10)°, V = 8308(3) ų, and Z = 16. The title compound contains two kinds of tautomers: the red compound is the keto form and the other is the enol form. Changes in color are due to the isomerization of the enol and keto forms by the intramolecular proton transfer.     

Crystal and molecular structure of CI Solvent Yellow 18, 4-(2′,4′-dimethyl phenyl hydrazono)-5-methyl-2-phenyl-3H-pyrazol-3-one

The crystal structure of CI Solvent Yellow 18, C₁₈H₁₈N₄O, has been determined by single crystal X-ray diffraction techniques. It crystallizes in the monoclinic system witha=7.480(2) Å,b=19.184(3) Å,c=11.260(1) Å,=98.00(3)°, space groupP2₁/n andZ=4. The structure has been solved by direct methods, and least-squares refinement has been completed on three-dimensional data (2310 reflections, CuK radiation). The hydrogen atoms have been found, but only their positional parameters refined. Final residual 0.085 (all positive intensity data). The molecule exists as the hydrazone tautomer and intramolecular hydrogen bonding keep the molecule approximately planar. The molecules are packed in layers parallel to the (¯202) plane and in columns parallel tob. Alternate molecules within the columns are in antiparallel. The molecules are linked by van der Waals' forces.     

Crystal and molecular structure of 2-(7-cyanonorcaran-7-yl)-5-(ethoxycarbonyl)-4,5,6,11b-tetrahydro(Δ4-1,2,4-oxadiazolino)-[2,3-a]-β-carboline,C23H24N4O3

The structure of the title compound, C₂₃H₂₄N₄O₃, was determined by X-rays.M _r =404.47, orthorhombic, space groupPna2₁; unit cell dimensionsa=9.0386(4),b=28.0249(14),c=7.8936(9) Å,V _c =1999.49(3) ų,Z=4,D _x =1.344 Mg m^–1. CuK radiation (graphite crystal monochromator, =1.54178 Å),(CuK)=0.699 mm^–1,F(000)=856,T=295 K. Final conventionalR-factor=0.030,R _w =0.037 for 3215 unique reflections and 366 variables. The structure was solved by automated rotation functions in vector space, usingDirdif. The absolute configuration of the structure is reported.     

X-ray diffraction studies of 6-methyl-5-acetyl-4-α-furyl-2-keto-1,2,3,6-tetrahydropyrimidine and 6-methyl-5-acetyl-4-γ-bromophenyl-2-thio-1,2,3,6-tetrahydropyrimidine

6-Methyl-5-acetyl-4-α-furyl-2-keto-1,2,3,6-tetrahydropyrimidine (I) and 6-methyl-5-acetyl-4-γ-bromophenyl-2-thio-1,2,3,6-tetrahydropyrimidine (II) are prepared by the modified Biginelli reaction, and their crystal and molecular structures are studied. It is shown that, in crystals I and II, the pyrimidine ring has an amide tautomeric form and adopts a sofa conformation. The IR absorption spectra are analyzed, and the stability of the tautomers of the pyrimidine fragments is evaluated using quantum-chemical calculations.     

Crystal structure ofβ-C.I. Solvent Yellow 18, 4(2′,4′-dimethylphenyl hydrazono)-5-methyl-2-phenyl-3H-pyrazol-3-one

The crystal structure of-C.I. Solvent Yellow 18, C₁₈H₁₈N₄O, has been determined by single crystal X-ray diffraction techniques. It crystallizes in the monoclinic system witha=30.948(18)Å,b=4.918(4)Å,c=20.861(9)Å,=91.68(4)°, space groupC2/c,Z=8. The structure has been solved by direct methods and least-squares refinement has been completed on three dimensional data (1237 reflections MoK radiation). The hydrogen atoms have been found but only their positional parameters refined. Final residual 0.092 (all intensity data). The molecule exists as the hydrazone tautomer and intramolecular hydrogen bonding keeps the molecule approximately planar. The molecules are packed in columns parallel to theb axis, while the molecule lies approximately parallel to the (51¯3) plane. The molecules are linked by van der Waals' force.