Influence of 3-{5-[4-(diethylamino)benzylidene]rhodanine}propionic acid on the conformation of 5-(4-chlorobenzylidene)-2-(4-methylpiperazin-1-yl)-3H-imidazol-4(5H)-one

2018 ◽  
Vol 74 (11) ◽  
pp. 1427-1433 ◽  
Author(s):  
Ewa Żesławska ◽  
Wojciech Nitek ◽  
Waldemar Tejchman ◽  
Jadwiga Handzlik
Keyword(s):  
Crystal Structures ◽  
Crystal Packing ◽  
Protonated Form ◽  
Acid Form ◽  
Asymmetric Unit ◽  
X Ray Diffraction ◽  
Basic Form ◽  
Piperazine Ring ◽  
X Ray ◽  
Intermolecular Contacts

The arylidene–imidazolone derivatives are a group of compounds of great interest in medicinal chemistry due to their various pharmacological actions. In order to study the possible conformations of an arylidene–imidazolone derivative, two new crystal structures were determined by X-ray diffraction, namely (Z)-5-(4-chlorobenzylidene)-2-(4-methylpiperazin-1-yl)-3H-imidazol-5(4H)-one, C15H17ClN4O, (6), and its salt 4-[5-(4-chlorobenzylidene)-5-oxo-4,5-dihydro-3H-imidazol-2-yl]-1-methylpiperazin-1-ium 3-{5-[4-(diethylamino)benzylidene]-4-oxo-2-thioxothiazolidin-3-yl}propionate, C15H18ClN4O+·C17H19N2O3S2 −, (7). Both compounds crystallize in the space group P\overline{1}. The basic form (6) crystallizes with two molecules in the asymmetric unit. In the acid form of (6), the N atom of the piperazine ring is protonated by proton transfer from the carboxyl group of the rhodanine acid derivative. The greatest difference in the conformations of (6) and its protonated form, (6c), is observed in the location of the arylidene–imidazolone substituent at the N atom. In the case of (6c), the position of this substituent is close to axial, while for (6), the corresponding position is intermediate between equatorial and axial. The crystal packing is dominated by a network of N—H...O hydrogen bonds. Furthermore, the crystal structures are stabilized by numerous intermolecular contacts of types C—H...N and C—H...Cl in (6), and C—H...O and C—H...S in (7). The geometry with respect to the location of the substituents at the N atoms of the piperazine ring was compared with other crystal structures possessing an N-methylpiperazine moiety.

Structural Studies of Some o- and p-Nitrophenylcarbamates by IR Spectroscopy and X-Ray Diffraction

2008 ◽  
Vol 63 (12) ◽  
pp. 1402-1406
Author(s):  
Monika Simon ◽  
Carol Csunderlik ◽  
G. Jones
Keyword(s):  
Ir Spectroscopy ◽  
Crystal Structures ◽  
Ir Spectrum ◽  
Structural Studies ◽  
Asymmetric Unit ◽  
X Ray Diffraction ◽  
X Ray

N-Alkyl-o-nitrophenylcarbamates as solids present two carbonyl stretching bands in the region 1700 - 1800 cm−1 but similar N-alkyl-p-nitrophenylcarbamates have only one such band in the IR spectrum. In solution both kinds of carbamate present one carbonyl stretching band, but for the former, the splittings occur when the carbamates crystallize. Four crystal structures were analyzed by X-ray diffraction. The two ortho derivatives have more than one molecule in the asymmetric unit, which is consistent with the IR observations.

scholarly journals Selective Crystallization of Four Bis(phthalocyaninato)neodymium(III) Polymorphs

2020 ◽  
Author(s):  
Maegan Dailey ◽  
Claire Besson
Keyword(s):  
Crystal Packing ◽  
Detailed Comparison ◽  
Protonated Form ◽  
Slow Evaporation ◽  
X Ray Diffraction ◽  
Acid Base ◽  
Initial Oxidation ◽  
X Ray ◽  
Secondary Interactions ◽  
Selective Crystallization

Four polymorphs of bis(phthalocyaninato)neodymium(III) were reproducibly and selectively crystallized by the slow evaporation of saturated solutions. The obtained phase depended on the initial oxidation state of the NdPc<sub>2</sub> molecule and the choice of solvent. Single-crystal X-ray diffraction studies were used to correct previous mis-identifications and provide missing coordinates for the γ-phase as well as a detailed comparison of molecular structure and crystal packing in all NdPc<sub>2</sub> polymorphs. The primary feature in all phases is columnar stacking based on parallel π π interactions, with a variety of slip angles within those stacks as well as secondary interactions between them. Chemical redox and acid-base titrations, performed on re-dissolved crystals demonstrate that NdPc<sub>2</sub><sup>+</sup> and NdPc<sub>2</sub><sup>-</sup> are easily obtained through weak oxidizing and reducing agents, respectively. Additionally, we show that the protonated form of the NdPc<sub>2</sub><sup>-</sup> complex has a nearly identical UV-Vis spectra to that of neutral NdPc<sub>2</sub>, explaining some of the confusion over chemical composition in previously published literature.<br>

Intermolecular hydrogen bonding H···Cl in crystal structure of palladium(II)-bis(diaminocarbene) complex

2019 ◽  
Vol 234 (3) ◽  
pp. 155-164 ◽  
Author(s):  
Mikhail A. Kinzhalov ◽  
Sergey V. Baykov ◽  
Alexander S. Novikov ◽  
Matti Haukka ◽  
Vadim P. Boyarskiy
Keyword(s):  
Crystal Packing ◽  
Solid Phase ◽  
Topological Analysis ◽  
X Ray Diffraction ◽  
Intermolecular Hydrogen Bonds ◽  
X Ray ◽  
Intermolecular Contacts ◽  
Organometallic Cations ◽  
Supramolecular Contacts ◽  
Moderate Yield

Abstract The reaction of bis(isocyanide)palladium complex cis-[PdCl2(CNXyl)2] (Xyl=2,6-Me2C6H3) with excess of 4,5-dichlorobenzene-1,2-amine in a C2H4Cl2/MeOH mixture affords monocationic bis(diaminocarbene) complex cis-[PdClC{(NHXyl)=NHC6H2Cl2NH2}{C(NHXyl)=NHC6H2Cl2NH2}]Cl (3) in moderate yield (42%). Complex 3 exists in the solid phase in the H-bonded dimeric associate of two single charged organometallic cations and two chloride anions according to X-ray diffraction data. The Hirshfeld surface analysis for the X-ray structure of 3 reveals that the crystal packing is determined primarily by intermolecular contacts H–Cl, H–H, and H–C. The intermolecular hydrogen bonds N–H···Cl and C–H···Cl in the H-bonded dimeric associate of 3 were studied by DFT calculations and topological analysis of the electron density distribution within the framework of QTAIM method, and estimated energies of these supramolecular contacts vary from 1.6 to 9.1 kcal/mol. Such non-covalent bonding means that complex 3 is an anionic receptor for the chloride anions.

Dimethyl-, Disilyl- and Digermylsulfide: Different Intermolecular Contacts in the Solid State

2004 ◽  
Vol 59 (6) ◽  
pp. 635-638 ◽  
Author(s):  
Norbert W. Mitzel ◽  
Udo Losehand
Keyword(s):  
Solid State ◽  
Low Temperature ◽  
Crystal Structures ◽  
X Ray Diffraction ◽  
X Ray ◽  
Intermolecular Contacts

The compounds (H3C)2S, (H3Si)2S and (H3Ge)2S have been crystallised in situ on a diffractometer and their crystal structures determined by low-temperature X-ray diffraction. The molecules are present as monomers in the crystals. The aggregation of the molecules through secondary intermolecular contacts in the crystal is different: (H3C)2S is weakly associated into dimers by S···S contacts, whereas (H3Si)2S and (H3Ge)2S form Si···S and Ge···S contacts in an ice-analogous aggregation motif. Important geometry parameters are (H3C)2S: C-S 1.794(av) Å , C-S-C 99.2(1)°; (H3Si)2S: Si- S 2.143(1) Å , Si-S-Si 98.4°; (H3Ge)2S Ge-S 2.223(2) and 2.230(2) Å , Ge-S-Ge 98.2(1)◦.

scholarly journals A variable-temperature X-ray diffraction and theoretical study of conformational polymorphism in a complex organic molecule (DTC)

RSC Advances ◽  
2018 ◽  
Vol 8 (67) ◽  
pp. 38445-38454 ◽  
Author(s):  
Andrea Gionda ◽  
Giovanni Macetti ◽  
Laura Loconte ◽  
Silvia Rizzato ◽  
Ahmed M. Orlando ◽  
...  
Keyword(s):  
Theoretical Study ◽  
Crystal Packing ◽  
Variable Temperature ◽  
Asymmetric Unit ◽  
X Ray Diffraction ◽  
X Ray ◽  
Complex Organic Molecule ◽  
Non Covalent Interactions ◽  
Complex Organic ◽  
Covalent Interactions

A small conformational change in the asymmetric unit has a significant effect on how non-covalent interactions determine (i) the crystal packing and (ii) the effect of T on the relative balance of electrostatics and dispersion–repulsions.

Conformational study of the 3,6-dihydro-2H-1,4-oxazin-2-one fragment in 8-tert-butyl-7-methoxy-8-methyl-9-oxa-6-azaspiro[4.5]decane-2,10-dione stereoisomers

2017 ◽  
Vol 73 (7) ◽  
pp. 556-562
Author(s):  
Ewa Żesławska ◽  
Anna Jakubowska ◽  
Wojciech Nitek
Keyword(s):  
Amino Acids ◽  
Crystal Structures ◽  
Stereoselective Synthesis ◽  
Biologically Active ◽  
Asymmetric Unit ◽  
Conformational Study ◽  
X Ray Diffraction ◽  
X Ray ◽  
Natural Amino Acids ◽  
Heterocyclic Moiety

Unnatural cyclic α-amino acids play an important role in the search for biologically active compounds and macromolecules. Enantiomers of natural amino acids with a D configuration are not naturally encoded, but can be chemically synthesized. The crystal structures of two enantiomers obtained by a method of stereoselective synthesis, namely (5R,8S)-8-tert-butyl-7-methoxy-8-methyl-9-oxa-6-azaspiro[4.5]decane-2,10-dione, (1), and (5S,8R)-8-tert-butyl-7-methoxy-8-methyl-9-oxa-6-azaspiro[4.5]decane-2,10-dione, (2), both C14H21NO4, were determined by X-ray diffraction. Both enantiomers crystallize isostructurally in the space group P21, with one molecule in the asymmetric unit and with the same packing motif. The crystal structures are stabilized by C—H...O hydrogen bonds, resulting in the formation of chains along the [100] and [010] directions. The conformation of the 3,6-dihydro-2H-1,4-oxazin-2-one fragment was compared with other crystal structures possessing this heterocyclic moiety. The comparison showed that the title compounds are not exceptional among structures containing the 3,6-dihydro-2H-1,4-oxazin-2-one fragment. The planar moiety was more frequently observed in derivatives in which this fragment was not condensed with other rings.

scholarly journals Crystal structures of 5,12-dimethyl-1,4,8,11-tetraazacyclotetradecane cobalt(III) mono-phenylacetylide and bis-phenylacetylide

2018 ◽  
Vol 74 (4) ◽  
pp. 522-529 ◽  
Author(s):  
Benjamin M. Oxley ◽  
Brandon Mash ◽  
Matthias Zeller ◽  
Susannah Banziger ◽  
Tong Ren
Keyword(s):  
Crystal Structures ◽  
Symmetry Operator ◽  
Asymmetric Unit ◽  
X Ray Diffraction ◽  
Weak Base ◽  
Monoclinic Symmetry ◽  
X Ray ◽  
Independent Molecules ◽  
Solvent Molecules ◽  
Occupancy Rates

Reported in this contribution are the synthesis and crystal structures of new mono- and bis-phenylacetylides based on CoIII(DMC) (DMC is 5,12-dimethyl-1,4,8,11-tetraazacyclotetradecane). Chlorido(5,12-dimethyl-1,4,8,11-tetraazacyclotetradecane)(phenylethynyl)cobalt(III) chloride–acetonitrile–methanol (1/1/1), [Co(C8H5)Cl(C12H28N4)]Cl·CH3CN·CH3OH, 1, and (5,12-dimethyl-1,4,8,11-tetraazacyclotetradecane)bis(phenylethynyl)cobalt(III) trifluoromethanesulfonate–dichloromethane (2/1), [Co(C8H5)2(C12H28N4)]2(CF3SO3)2·CH2Cl2, 2, were prepared under weak-base conditions in satisfactory yields. Single-crystal X-ray diffraction studies revealed that both 1 and 2 adopt a pseudo-octahedral symmetry in which the Cl—Co—C angles of 1 and C—Co—C of 2 range from 177.7 (2) to 178.0 (2)° and from 177.67 (9) to 179.67 (9)°, respectively. In both structures, the CoIII metal center is coordinated in the equatorial plane by four N atoms, in which the N—Co—N angles range from 85.6 (3) to 94.4 (3)°. The structure of 1 features two crystallographically independent molecules in its triclinic cell (Z′ = 2), which are related to each other by pseudo-monoclinic symmetry. The crystal investigated was twinned by a symmetry operator of the approximate double-volume C-centered cell (180° rotation around [201] of the actual triclinic cell), with a refined twin ratio of 0.798 (3) to 0.202 (3). Both methanol solvent molecules in 1 are disordered, the major occupancy rates refined to 0.643 (16) and 0.357 (16). Compound 2 also contains two molecules in the asymmetric unit, together with two trifluoromethanesulfonate anions [of which one is disordered; occupancy values of 0.503 (16) and 0.497 (16)] and a disordered dichloromethane [occupancy values of 0.545 (12) and 0.455 (12)].

scholarly journals Crystal structures of cristobalite-type and coesite-type PON redetermined on the basis of single-crystal X-ray diffraction data

2015 ◽  
Vol 71 (11) ◽  
pp. 1325-1327 ◽  
Author(s):  
Maxim Bykov ◽  
Elena Bykova ◽  
Vadim Dyadkin ◽  
Dominik Baumann ◽  
Wolfgang Schnick ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Single Crystal ◽  
Single Crystals ◽  
Crystal Structures ◽  
Rotation Axis ◽  
Asymmetric Unit ◽  
X Ray Diffraction ◽  
X Ray ◽  
Structure Determinations ◽  
Anisotropic Displacement Parameters

Hitherto, phosphorus oxonitride (PON) could not be obtained in the form of single crystals and only powder diffraction experiments were feasible for structure studies. In the present work we have synthesized two polymorphs of phosphorus oxonitride, cristobalite-type (cri-PON) and coesite-type (coe-PON), in the form of single crystals and reinvestigated their crystal structures by means of in house and synchrotron single-crystal X-ray diffraction. The crystal structures ofcri-PON andcoe-PON are built from PO2N2tetrahedral units, each with a statistical distribution of oxygen and nitrogen atoms. The crystal structure of thecoe-PON phase has the space groupC2/cwith seven atomic sites in the asymmetric unit [two P and three (N,O) sites on general positions, one (N,O) site on an inversion centre and one (N,O) site on a twofold rotation axis], while thecri-PON phase possesses tetragonalI-42dsymmetry with two independent atoms in the asymmetric unit [the P atom on a fourfold inversion axis and the (N,O) site on a twofold rotation axis]. In comparison with previous structure determinations from powder data, all atoms were refined with anisotropic displacement parameters, leading to higher precision in terms of bond lengths and angles.

Crystal Structures of the Pentacoordinate Bromo, Isocyanato, Iodo, Acetato and Isothiocyanato Complexes of the meso-Tetraphenylporphyrinatomanganese Cation

1998 ◽  
Vol 51 (9) ◽  
pp. 835 ◽  
Author(s):  
Peter Turner ◽  
Maxwell J. Gunter ◽  
Brian W. Skelton ◽  
Allan H. White
Keyword(s):  
Crystal Structures ◽  
Metal Ion ◽  
Crystal Packing ◽  
Carbonyl Oxygen ◽  
Unit Cell ◽  
X Ray Diffraction ◽  
Complex Molecules ◽  
X Ray ◽  
Rigid Body Model ◽  
Pyrrole Nitrogen

The room-temperature single-crystal X-ray diffraction determined structures of the Mn(tpp)Br.C7H8, Mn(tpp)(NCO), Mn(tpp)I.C7H8, Mn(tpp)(CO2CH3).0·5C7H8, and Mn(tpp)(NCS).0·5C7H8 complexs are described. The monoclinic P21/c unit cell of Mn(tpp)(NCO) has a 14·82(1), b 17·136(5), c 14·576(5) Å, β 111·41(5)°, V 3446(3) Å3, Z 4. The refinement converged with conventional R(|F|) 0·053 for No 3199 (I > 3·0σ(I)) ‘observed’ reflections. The monoclinic P 21/m unit cell of Mn(tpp)Br.C7H8 has a 9·984(1), b 15·453(6), c 13·583(3) Å, β 103·99(2)°, V 2033(1) Å3, Z 2, R 0·039 for No 2668. The Mn(tpp)I.C7H8 structure is triclinic, P-1, with a 22·28(1), b 14·466(4), c 13·555(6) Å, α 76·32(3), β 81·74(4), γ 74·75(3)°, V 4079(3) Å3, Z 4, R 0·050 for No 9039. The triclinic P-1 crystal structures of the Mn(tpp)(CO2CH3).0·5C7H8 and Mn(tpp)(NCS).0·5C7H8 complexes are isomorphous. The Mn(tpp)(CO2CH3).0·5C7H8 structure has a 26·18(1), b 13·503(3), c 12·074(6) Å, α 66·08(4), β 81·36(4), γ 86·71(5)°, V 3858(3) Å3, Z 4, R 0·075 for No 6388. Solvate disorder, requiring a rigid body model, islargely responsible for the relatively high residuals. The Mn(tpp)(NCS).0·5C7H8 structure has a 25·442(6), b 13·746(3), c 12·182(5) Å, α 66·97(3), β 78·59(3), γ 87·90(2)°, V 3839(2) Å3, Z 4, R 0·061 for No 5506. The asymmetric units of the iodo, acetato and isothiocyanato structures each contain two crystallographically independent complex molecules that are sensitive to crystal packing forces. The metal ion displacements from the least-squares planes formed by the pyrrole nitrogen atoms are 0·299(1) and 0·274(1) Å for the Mn(tpp)(NCO) and Mn(tpp)Br.C7H8complexes, and 0·240(1) and 0·252(1), 0·281(1) and 0·278(1), and 0·243(1) and 0·244(1) Å for the independent (a) and (b) complex molecules of Mn(tpp)I.C7H8, Mn(tpp)(CO2CH3).0·5C7H8, and Mn(tpp)(NCS).0·5C7H8 respectively. The axial Mn–X bond lengths are 2·029(5) and 2·490(1) Å for the Mn(tpp)(NCO) and Mn(tpp)Br.C7H8 complexes, and 2·767(1) and 2·730(1), 2·028(5) and 2·010(5), and 2·067(6) and 2·072(5) Å for the (a) and (b) complex molecules of Mn(tpp)I.C7H8, Mn(tpp)(CO2CH3).0·5C7H8, and Mn(tpp)(NCS).0·5C7H8. One of the independent complex molecules in the Mn(tpp)(CO2CH3).0·5C7H8 structure appears to exhibit acetate coordination through a carbonyl oxygen.

Comparison of the crystal structures and thermochemistry of a novel soluble guanylate cyclase stimulator riociguat and its solvates

2017 ◽  
Vol 73 (5) ◽  
pp. 891-898 ◽  
Author(s):  
Xinbo Zhou ◽  
Xiurong Hu ◽  
Jianming Gu ◽  
Jianrong Zhu
Keyword(s):  
Crystal Structure ◽  
Thermogravimetric Analysis ◽  
Crystal Structures ◽  
Guanylate Cyclase ◽  
Soluble Guanylate Cyclase ◽  
Crystal Packing ◽  
X Ray Diffraction ◽  
Scanning Calorimetry ◽  
X Ray ◽  
Soluble Guanylate Cyclase Stimulator

Riociguat (Rio) is the first oral soluble guanylate cyclase stimulator to be approved for pulmonary arterial hypertension. In this study, form (II) of riociguat and three solvates with acetonitrile [form (III)],N,N-dimethylformamide [form (IV)] and ethyl acetate [form (V)] were crystallized. They were identified and characterized by differential scanning calorimetry, thermogravimetric analysis, X-ray powder diffraction, and their crystal structures were determined by single-crystal X-ray diffraction. No crystal structure has previously been reported for the known form (II) of riociguat. Crystal structure determination of Rio and its new solvates revealed that the dimericR22(14) motif is common in both structures. The crystal packing of solvates adopts channel-like patterns, whereas form (II) of riociguat adopts sheet-like patterns. Strong π–π interactions exist in the above four forms. The conformation of the riociguat in one molecule of 0.5-DMF solvate was found to be significantly different from the conformations found in the other solvates. Desolvation of the three solvates was studied by thermogravimetric analysis and X-ray diffraction, and was shown to transform them into form (I) of riociguat.

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