Cyclodipeptides: Structure and conformation of cyclo(tyrosyl-prolyl)

The structure and conformation of the cyclodipeptide, cyclo(Tyrosyl-Prolyl), cyclo(Tyr-Pro) have been investigated with X-ray crystallographic and spectroscopic methods. Two conformations of cyclo(Tyr-Pro) crystallized in the space groupP2₁2₁2 with cell dimensionsa=11.890(3),b=12.057(1),c=18.528(4). Both these conformations are uncommon for cyclodipeptides containing a proline residue. The tyrosyl side chains of these conformers are folded towards the diketopiperazine (DKP) ring. The DKP ring adopts a flattened chair conformation in contrast to the typical boat conformation generally observed for DKP rings. The conformation of the pyrrolidine ring can be described as a pseudo C₂ symmetrical twist. One intermolecular hydrogen bond was observed for each of the two conformations of cyclo(Tyr-Pro). The hydrogen of the hydroxyl group of the tyrosyl residue is hydrogen bonded to the oxygen of the carbonyl group of the diketopiperazine ring, i.e., the carbonyl group originating from the tyrosyl residue. NMR spectroscopic studies indicated a different conformation for cyclo(Tyr-Pro) in solution similar to the generally observed conformation of cyclodipeptides, i.e., extended aromatic side chain and boat conformation for the DKP ring.     

A twist boat: Structure and conformation oftrans-2,4,6-tris(trichloromethyl)-1,3,5-trithian

Trans-2,4,6-tris(trichloromethyl)-1,3,5-trithian, (CCl₃·CHS)₃, has been prepared free from persistent impurification bycis-trans-2,4,6-tris(trichloromethyl)-1,3,5-oxadithian and its conformation determined by single crystal x-ray crystallography. The title compound is orthorhombic,Pbca, a=10.479(10),b=27.957(14),c=11.093(3) Å,V=3250 ų,Z=8. The structure was solved by direct methods, from data collected at room temperature on an Enraf-Nonius CAD4 diffractometer, and refined by full-matrix least squares to a finalR value at 0.074 using 1186 reflections. The molecule exhibits a twist boat conformation with the –CCl₃ groups occupying pseudoequatorial positions. The torsion angles in the trithian ring are successively 29(1), –79(1), 41(1), 41(1), –84(1), 39(1)°. Average values are: S-C 1.82(2), C(ring)-C(Cl₃) 1.56(4), C-Cl 1.76(2) Å, S-C-S 112.7(2)°. The C-S-C angles are 97.4(7), 101.4(7), 97.3(7)°.     

Structure and conformation of 6-nitro-2,4-bis(dichloromethyl)-1,3-benzdioxin

6-Nitro-2,4-bis(dichloromethyl)-1,3-benzdioxin is monoclinic,P2₁/c, witha=8.514(1),b=22.187(3),c=7.931(1) Å,=117.96(1)°,Z=4. The structure was solved, from data collected with MoK radiation on an Enraf-Nonius CAD4 diffractometer, by direct methods and refined by full-matrix least squares using 2170 unique reflections to give a finalR factor of 0.032. The heterocyclic ring in the title compound has an envelope conformation with thecis-dichloromethyl groups in pseudoequatorial positions. The average C-C(HCl₂) distance is 1.516(4) Å. A comparison is given with the structure of the analogous compound 6-nitro-2,4-bis(trichloromethyl)-1,3-benzdioxin (Irving, A., and Irving, H. M. N. H. (1986)J. Crystallogr. Spectrosc. Res. 16, 703) which also containscis-halogenoalkyl groups but in which the –CCl₃ group at the 4-position occupies a pseudoaxial position.     

Structure and conformation of 6,8-dinitro-2,4-bis(trichloromethyl)-1,3-benzdioxin: X-ray crystallographic determination

6,8-dinitro-2,4-bis(trichloromethyl)-1,3-benzdioxin is monoclinic,P2₁/c,Z=4,a=12.348(2),b=11.575(3),c=12.183(4) Å,=107.48(2)°. The structure was solved by direct methods, from data collected at room temperature on an Enraf-Nonius CAD4 diffractometer, and refined by least-squares to a finalR value of 0.032 using 2192 reflections. The heterocyclic ring is an envelope structure, the dihedral angle between the plane of the aromatic ring and that containing five of the atoms of the heterocycle being 4.98(6)°. One -CCl₃ group is pseudoequatorial while the (Ar-C)CCl₃ group is pseudoaxial. C-C_eq 1.526(3) Å; C-C_ax 1.537(3) Å; C-C(C_ax)-O 112.4(2)°; C(C_ax)-O-C(C_eq) 115.2(2)°.     

Structure and conformation of 6-nitro-2,4-bis(trichloromethyl)-1,3-benzdioxin: X-ray crystallographic determination

6-Nitro-2,4-bis(trichloromethyl)-1,3-benzdioxin is triclinic,P¯1;a=6.604(2),b=7.678(6),c=15.201(4) Å; =91.57(5),=99.39(2), =90.50(5)°;Z=2. The structure was solved by direct methods from data collected at room temperature on an Enraf-Nonius CAD4 diffractometer and refined by least squares to a finalR value of 0.035 using 2092 reflections.The molecule consists of a heterocycle in a distorted screw boat conformation fused to a significantly nonplanar aromatic ring. One-CCl₃ group is pseudoequatorial while the (Ar-C)CCl₃ group is pseudoaxial. The C_Ar-C-O-C side of the ring is much flatter than the C_Ar-C_Ar-O-C side, the distortion being caused by the necessity of the-C_axCl₃ group to bend away from the heterocycle. C-C_eq 1.532(4) Å; C-C_ax 1.550(4) Å; C-C(C_ax)-O 113.0(3)°; C(C_ax)-O-C(C_eq) 115.5(2)°.     

Structure and conformation of the 6-carboxylic acid and the 6-methylsulfonate of 2,4-bis(trichloromethyl)-1,3-benzdioxin

The 6-methylsulfonate (I) and the 6-carboxylic acid (II) of 2,4-bis(trichloromethyl)-1,3-benzdioxin both crystallize in the space groupP2₁/n withZ=4. Unit cell parameters of I are:a=13.398(7),b=14.553(2),c=8.945(2) Å, =99.16(2)°; those of II are:a=6.010(16),b=25.741(16),c=10.505(10) Å, =100.05(16)°. The structures were solved by direct methods and refined by full-matrix least squares, from room-temperature data obtained with an Enraf-Nonius CAD4 diffractometer, to conventionalR factors of 0.035 for I and 0.041 for II. The methylsulfonate group of I is disordered except for the sulfur atom and in II, which forms hydrogen-bonded dimers through the –COOH group, the hydrogen atom of the –COOH group is distributed equally between two positions.The conformation and molecular parameters of the 2,4-bis(trichioromethyl)-1,3-benzdioxin fragment for both compounds is very similar to that in 6-nitro-2,4-bis(trichloromethyl)-1,3-benzdioxin (Irving A., and Irving H. M. N. H. (1986)J. Cryst. Spectrosc. Res. 16, 703). The dioxin ring has an approximate envelope conformation with a pseudoequatorial –CCl₃ group in the 2-position and a pseudoaxial –CC1₃ group in the 4-position. C(ring)-C_eq(Cl₃) is 1.525(5) Å for I and 1.536(6) Å for II, whereas the C(ring)-C_ax(Cl₃) bond length is 1.547(5) Å for I and 1.550(4) Å for II. The chemical shifts of the two protons in the heterocyclic ring do not appear to be altered by these changes in the 6-substituent.     

Structure and conformation of the sodium chloride salt of N-t-Boc-Phenylalanyl-Proline (Boc-Phe-Pro·NaCl) and the dihydrate of N-t-Boc-Tyrosyl-Proline (Boc-Tyr-Pro·2H2O)

The structure and conformation of the salt of N-t-Boc-Phenylalanyl-Proline (Boc-Phe-Pro·NaCl) (C₁₉H₂₆N₂O₅NaCl) (compound 2) and the dihydrate of N-t-Boc-Tyrosyl-Proline (Boc-Tyr-Pro·2H₂O) (C₁₉H₃₀O₈N₂) (compound 1) have been investigated with X-ray crystallographic and spectroscopic methods. Boc-Phe-Pro·NaCl crystallizeds in an extended trans conformation in the space groupP2₁ with cell dimensionsa=7.961 (3),b=10.045(2), andc=13.495(4). One intermolecular hydrogen bond and one intramolecular hydrogen bond was observed for the dipeptide salt. Boc-Tyr-Pro·2H₂O crystallized in an extended trans conformation in the space group P2₁ with cell dimensionsa=7.964(1),b=10.011(1), andc=13.853(2). Six intermolecular hydrogen bonds were observed for Boc-Tyr-Pro·2H₂O. The conformation of both dipeptides reflect collagen-type of proline-compounds. The puckering mode of the pyrrolidine ring of the proline residues can be described as an approximate C₂ half-chair symmetry having an A conformation with the Cγ atom located exo and Cβ atom located endo relative to the carboxamide group, i.e., γ/β T.Cis-trans isomerism was observed in the NMR spectra of both dipeptides with a predominance for the extended side chain for the phenylalanyl and tyrosyl residues, respectively.     

Unusual solid-state conformation of D-glucitol hexa(p-chlorobenzoate)

The carbon atom chain in the molecule ofd-glucitol hexa (p-chlorobenzoate) adopts a planar, zigzag conformation in the solid state, as determined by X-ray crystallography. The preference for such conformation in the crystal can be ascribed to the stacking interactions in which an infinite number of p-chlorobenzoyloxy substituents is involved.     

Crystal structure and conformation of N-(t-butoxycarbonyl)-L-isoleucyl-L-alanine benzylester

C₂₂N₂O₅H₃₂,M _r =404.5, monoclinic,C2,a=21.781(5),b=5.065(1),c=22.333(4)Å,=112.81(2)°,V=2271.1(9)ų,D _calc=1.148 g cm³, (CuK )=1.5418 Å,=5.89 cm^–1,F(000)=848, room temperature,R=0.058 for 2178 unique reflections [I2.5(I)]. The peptide linkage is in thetrans conformation. The molecule adopts the-sheet structure. The crystal structure is stabilized by a three-dimensional network of N-HO and C-HO hydrogen bonds.DCB Contribution No. 813.     

Structure, absolute configuration, and conformation of the antimalarial drug artesunate

The crystal and molecular structure of the antimalarial compound artesunate has been determined by direct methods. Crystals are orthorhombic, P2₁2₁2₁, a = 9.8371(12), b = 10.517(2), c = 18.7594(5) Å, Z = 4, D _c = 1.316 mg/mL. The molecule is comprised of a fused ring system containing a six-membered ring C which includes an oxygen bridge and a peroxy bridge. The 9-atom oxygen–carbon chain from O(5)—C(12)... to ... O(2)—C(6) displays a striking sequence of short, long, short, long ... bonds while these distances are all within the ranges of a normal single bond or partial double bond. It is proposed that this pattern is caused by the delocalization of the lone pair electrons on the oxygen atoms. The ring C has a distorted boat conformation and the C—O—O—C torsion angle is 46.3(2)°. Rings A and D have ideal chair conformations. Ring junctions A/B and A/D are cis junctions, B/D and C/D are trans. Packing of the molecules is stabilized by one strong hydrogen bond involving the hydroxyl group on the ester linkage and the oxygen atom of the lactone ring.     

Structure, absolute configuration, and conformation of the antimalarial compound, Artemisinin

The crystal and molecular structure of the antimalarial compound Artemisinin (formerly known as Qinghaosu), C₁₅H₂₂O₅ has been determined by direct methods. Crystals are orthorhombic colorless needles, space group P2₁2₁2₁, Z = 4. D _c = 1.299 g cm ^–3, with unit cell parameters a = 6.3543(9), b = 9.439(3), c= 24.066(4) Å. The molecule incorporates a fused ring system containing a six-membered ring C which includes an oxygen bridge and a peroxy-bridge. The ring C has a distorted boat conformation and the C - O - O - C torsion angle is 47.8(2)°. Rings A and D have symmetrical chair and distorted chair conformations, repectively. Ring junctions A/B, A/D, and C/D are cis, junction B/D is trans. All inter-molecular contacts are van der Waals. The absolute configuration of Artemisinin was determined from the refined value of the Flack x parameter. [The atomic coordinates given in a previous structure analysis, Crystal Structure and Absolute Configuration of Qinghaosu, Qinghaosu Research Group, Institute of Biophysics, Academica Sinica, Scientia Sinica, Vol. XXIII No. 3, 380 (1980), do not display the molecule in its absolute configuration.]     

Structure,absolute configuration,and conformation of a fused complex cyclic carbohydrate from a cameroon plant extract (CAMT2)

The crystal and molecular structure of the natural product C₂₉H₃₈O₉, an extract from a Cameroonian plant, has been determined by direct methods. Crystals are orthorhombic, P2₁2₁2₁,a=24.571(4),b=16.398(3),c=13.778(4) Å,Z-8,D _c=1.270 mg/m³. The final R-factor for 2892 reflections withI>2(I) is 0.0531. The two molecules forming the asymmetric unit have very similar molecular geometry. each molecule comprising a nucleus of six fused rings B to G: where B=pyranyl, C=pyranyl, D=furanyl, E=cyclohexene, F=pyranyl, G=cyclohexyl. Ring B also has a furanyl side-group (ring A). The ring conformations in both molecules are: A (1/2-chair/envelope); B(envelope); C(envelope); D(1/2-chair); E(1/2-chair); F(envelope); G(chair). In the cyclohexene ring E the substitution pattern is 2-hydroxy 3-methyl 5-dimethyl. The two molecules in the asymmetric unit are linked by two OH...O hydrogen bonds to form the crystal structure.     

(TMTSF)2(2,5-Tcnqbr2): Structure and Physical Properties

The 2:1 charge-transfer salt (TMTSF)₂(2,5-TCNQBr2) has been prepared and its physical properties investigated. Its crystal structure consists of segregated stacks of TMTSF donors (ring-over-bond overlap pattern; mean interplanar spacing of 3.6A) and chains of edge-on and disordered 2,5-TCNQBr2 acceptors. Infrared data are suggestive of unit charge on the 2,5-TCNQBr2 molecule and, therefore, half charge on the TMTSF donor. Resistivity data are successfully interpreted on the basis of a percolation construction. Magnetic data are also presented.     

Molecular conformation and electronic structure. II: Crystal and molecular structure ofN-(p-bromobenzylidene)-p-bromoaniline

The structure of the title compound C₁₃H₉Br₂N has been determined with MoKα₁ diffractometer data, and refined by full-matrix least squares toR = 0.061 for 888 observed reflections. The crystals are monoclinic: space groupP2₁/a,a = 24.912(13),b = 5.877(1),c = 4.046(1) Å,β = 92.42(3) °Z = 2. The uv absorption spectrum indicates a nonplanar conformation in solution. In the solid, the molecule is disordered about a crystallographic inversion center and is planar to within 0.045 Å.     

Structure of dichloroethanolaminecopper(II) and dibromoethanolaminecopper(II)

CuCl₂(NH₂CH₂CH₂OH) is monoclinic, space group C2/c, witha+11.092(2),b+10.012(2),c+6.401(1) Å, =121.71(1)°, andV=604.8(2)ų withZ+4. The structure was refined to a final value ofR+0.27 for 518 unique observed reflections with |F|>3. The ethanolamine and halide ions coordinate to the copper(II) ion forming a pseudoplanar four-coordinate monomeric CuCl₂L² complex (L²+bidentate ligand). The copper ion also interacts with the halides of neighboring complexes through the formation of semi-coordinate Cu-Cl linkages (2.926(1) Å) between oligomers. The copper thus attains a 4+2 elongated octahedral coordination geometry. In this space group, the ligand is statisticallydisordered The Cu-Cl distance is 2.267(1)Å while the Cu-N/O distances are 2.025(2)Å. The dibromide structure is isomorphous with the dichloride structure, with space group C2/c, anda+11.285(2),b+10.218(2),c+6.715(1) Å, =121.65(1)°, andV=659.2(2)ų.     

Structure and conformation of 6-nitro-2-trichloromethyl-4-dichloromethylene-1,3-benzdioxin: X-ray crystallographic determination

6-Nitro-trichloromethy1-4-dichloromethylene-1,3-benzdioxin is monoclinic,C2/c,a=12.906(2) Å,b=19.957(2) Å,c=19.992(2) Å,=99.05(1)°,Z=8. The structure was solved by direct methods, from data collected at room temperature on an Enraf-Nonius CAD4 diffractometer, and refined by least squares to a finalR value of 0.032 using 1838 reflections.The compound exhibits a distorted envelope structure in the dioxin ring, and the trichloromethyl group is in the equatorial position. The angle between the planes each containing a group of three atoms from either end of the double bond of the:C(ring)=CCl₂ moiety is 3.8(2)°: a short discussion of deformations found in other compounds which contain:C(ring)=CC1₂ in light atom structures is given. The benzene ring is slightly puckered and planarity has been retained about the carbon atoms which are common to both rings.     

Structure and conformation of 6-nitro-2-trichloromethyl-1,3-benzdioxin-4-one: X-ray crystallographic determination

6-nitro-2-trichloromethyl-1,3-benzdioxin-4-one is monoclinic,P2₁/n;a=5.969(2),b=11.646(1),c=16.953(1) Å;=98.03(2)°;Z=4. The structure was solved by direct methods, from data collected at room temperature on an Enraf-Nonius CAD4 diffractometer, and refined by least squares to a finalR value of 0.030 using 1530 reflections.The heterocyclic ring is a distorted half-boat and is substituted equatorially by a trichloromethyl group. Dihedral angles are (a) 4.87(7)° between the mean plane of the aromatic ring and the plane containing the two carbon atoms common to both rings plus the two atoms bonded to these, and (b) 16.8(2)° between the carbonyl group and the aromatic ring. The conformation is discussed with reference to the two previously reported X-ray structures of 1,3-benzdioxin-4-ones and to two isocoumarins.     

Structure and conformation of 6,8-dinitro-2-trichloromethyl-4-dichloromethylene-1,3-benzdioxin

6,8-Dinitro-2-trichloromethyl-4-dichloromethylene-1,3-benzdioxin is orthorhombic,Pccn,a=18.850(3),b=18.404(3),c=8.849(2) Å,Z=8. The structure was solved by direct methods, from data collected at room temperature on an Enraf-Nonius CAD4 diffractometer, and refined by least squares to a finalR value of 0.036 using 1889 reflections. The heterocyclic ring has an envelope conformation and is substituted pseudo-equatorially by a trichloromethyl group. The molecular parameters and conformation of the title compound are discussed with reference to the 6-nitro analog and with reference to 6-nitro and 6,8-dinitro-2, 4-bis(trichloromethyl)-1,3-benzdioxin.     

The Crystal and Molecular Structure of the Complex Diaquatetrakis(imidazole)copper(II) Terephthalate Crystal Structure Containing Cu(II) Him and TA

The title compound has been synthesized and its crystals structure determined at room temperature. MW = 536.01, monoclinic, space group C2/c, Z = 4, a = 22.193(5) Å, b = 8.038(2) Å, c = 15.699(4) Å, β = 119.64(2)°. The crystal structure consists of repeated [Cu(Him)₄(H₂O)₂] (Him = imidazole) cations and non-coordinated terephthalato dianions. The copper(II) ion displays an elongated octahedral coordination being linked to the four nitrogen atoms of the four imidazole ligands and to the two oxygen atoms of the two water molecules. The terephthalato dianions are hydrogen bonded to the four water molecules and four imidazole groups.