The conformational analyses of 2-amino-N-[2-(dimethylphenoxy)ethyl]propan-1-ol derivatives in different environments

2020 ◽  
Vol 76 (7) ◽  
pp. 681-689
Author(s):  
Wojciech Nitek ◽  
Agnieszka Kania ◽  
Henryk Marona ◽  
Anna M. Waszkielewicz ◽  
Ewa Żesławska
Keyword(s):  
Crystal Packing ◽  
Picolinic Acid ◽  
Structural Studies ◽  
Asymmetric Unit ◽  
X Ray Diffraction ◽  
Ether Group ◽  
Space Group ◽  
X Ray ◽  
Hirshfeld Surfaces ◽  
Hydrogen Bonded

Four crystal structures of 2-amino-N-(dimethylphenoxyethyl)propan-1-ol derivatives, characterized by X-ray diffraction analysis, are reported. The free base (R,S)-2-amino-N-[2-(2,3-dimethylphenoxy)ethyl]propan-1-ol, C13H21NO2, 1, crystallizes in the space group P21/n, with two independent molecules in the asymmetric unit. The hydrochloride, (S)-N-[2-(2,6-dimethylphenoxy)ethyl]-1-hydroxypropan-2-aminium chloride, C13H22NO2 +·Cl−, 2c, crystallizes in the space group P21, with one cation and one chloride anion in the asymmetric unit. The asymmetric unit of two salts of 2-picolinic acid, namely, (R,S)-N-[2-(2,3-dimethylphenoxy)ethyl]-1-hydroxypropan-2-aminium pyridine-2-carboxylate, C13H22NO2 +·C6H4NO2 −, 1p, and (R)-N-[2-(2,6-dimethylphenoxy)ethyl]-1-hydroxypropan-2-aminium pyridine-2-carboxylate, C13H22NO2 +·C6H4NO2 −, 2p, consists of one cation and one 2-picolinate anion. Salt 1p crystallizes in the triclinic centrosymmetric space group P\overline 1, while salt 2p crystallizes in the space group P41212. The conformations of the amine fragments are contrasted and that of 2p is found to have an unusual antiperiplanar arrangement about the ether group. The crystal packing of 1 and 2c is dominated by hydrogen-bonded chains, while the structures of the 2-picolinate salts have hydrogen-bonded rings as the major features. In both salts with 2-picolinic acid, the specific R 1 2(5) hydrogen-bonding motif is observed. Structural studies have been enriched by the generation of fingerprint plots derived from Hirshfeld surfaces.

A new polymorph of bis(2-aminopyridinium) fumarate–fumaric acid (1/1) from powder X-ray diffraction

2013 ◽  
Vol 69 (8) ◽  
pp. 896-900 ◽  
Author(s):  
Shuichao Dong ◽  
Yaqiu Tao ◽  
Xiaodong Shen ◽  
Zhigang Pan
Keyword(s):  
Hydrogen Bonds ◽  
Fumaric Acid ◽  
Diffraction Method ◽  
Monoclinic Space Group ◽  
Asymmetric Unit ◽  
X Ray Diffraction ◽  
Acta Cryst ◽  
Space Group ◽  
X Ray ◽  
Hydrogen Bonded

A new polymorph of bis(2-aminopyridinium) fumarate–fumaric acid (1/1), 2C5H7N2+·C4H2O42−·C4H4O4, was obtained and its crystal structure determined by powder X-ray diffraction. The new polymorph (form II) crystallizes in the triclinic system (space groupP\overline{1}), while the previous reported polymorph [form I; Ballabh, Trivedi, Dastidar & Suresh (2002).CrystEngComm,4, 135–142; Büyükgüngör, Odabaşoğlu, Albayrak & Lönnecke (2004).Acta Cryst.C60, o470–o472] is monoclinic (space groupP21/c). In both forms I and II, the asymmetric unit consists of one 2-aminopyridinium cation, half a fumaric acid molecule and half a fumarate dianion. The fumarate dianion is involved in hydrogen bonding with two neighbouring 2-aminopyridinium cations to form a hydrogen-bonded trimer in both forms. In form II, the hydrogen-bonded trimers are interlinked across centres of inversionviapairs of N—H...O hydrogen bonds, whereas such trimers are joinedviasingle N—H...O hydrogen bonds in form I, leading to different packing modes for forms I and II. The results demonstrate the relevance and application of the powder diffraction method in the study of polymorphism of organic molecular materials.

Supramolecular architecture in azaheterocyclic phosphonates. III. Structures of an ethyl phosphonamidate and an ethyl phosphonate

2018 ◽  
Vol 74 (8) ◽  
pp. 907-916
Author(s):  
Anna Pietrzak ◽  
Jakub Modranka ◽  
Jakub Wojciechowski ◽  
Tomasz Janecki ◽  
Wojciech M. Wolf
Keyword(s):  
Hydrogen Bond ◽  
Diffraction Analysis ◽  
Crystal Packing ◽  
Supramolecular Architecture ◽  
The Novel ◽  
Structural Studies ◽  
X Ray Diffraction ◽  
X Ray ◽  
Hirshfeld Surfaces ◽  
Independent Molecules

The novel crystal structures of ethyl (S)-P-(4-oxo-4H-benzo[4,5]thiazolo[3,2-a]pyrimidin-3-yl)-N-[(R)-1-phenylethyl]phosphonamidate, C20H20N3O3PS, I, and diethyl (4-isopropyl-2-oxo-3,4-dihydro-2H-benzo[4,5]thiazolo[3,2-a]pyrimidin-3-yl)phosphonate, C18H25N2O4PS, II, were characterized by X-ray diffraction analysis. The crystal packing of I is dominated by two infinite stacks composed of symmetry-independent molecules linked by distinctively different hydrogen-bond systems. The structure of II shows a ladder packing topology similar to those observed in related phosphorylated azaheterocycles. Structural studies are supplemented by calculations on the interactions stabilizing the molecular assemblies using the PIXEL method. Additionally, fingerprint plots derived from the Hirshfeld surfaces were generated for each structure to characterize the crystal packing arrangements in detail. The aromaticities of the heterocyclic moieties have been investigated using HOMA and HOMHED parametrization and compared with structures reported previously.

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.

scholarly journals Crystallization and X-ray diffraction analysis of native and selenomethionine-substituted PhyH-DI fromBacillussp. HJB17

2017 ◽  
Vol 73 (11) ◽  
pp. 607-611
Author(s):  
Fang Lu ◽  
Bei Zhang ◽  
Yong Liu ◽  
Ying Song ◽  
Gangxing Guo ◽  
...  
Keyword(s):  
Unit Cell ◽  
Diffusion Method ◽  
Data Sets ◽  
Asymmetric Unit ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
Solvent Content ◽  
Space Group ◽  
X Ray ◽  
Cell Parameters

Phytases are phosphatases that hydrolyze phytates to less phosphorylatedmyo-inositol derivatives and inorganic phosphate. β-Propeller phytases, which are very diverse phytases with improved thermostability that are active at neutral and alkaline pH and have absolute substrate specificity, are ideal substitutes for other commercial phytases. PhyH-DI, a β-propeller phytase fromBacillussp. HJB17, was found to act synergistically with other single-domain phytases and can increase their efficiency in the hydrolysis of phytate. Crystals of native and selenomethionine-substituted PhyH-DI were obtained using the vapour-diffusion method in a condition consisting of 0.2 Msodium chloride, 0.1 MTris pH 8.5, 25%(w/v) PEG 3350 at 289 K. X-ray diffraction data were collected to 3.00 and 2.70 Å resolution, respectively, at 100 K. Native PhyH-DI crystals belonged to space groupC121, with unit-cell parametersa = 156.84,b = 45.54,c = 97.64 Å, α = 90.00, β = 125.86, γ = 90.00°. The asymmetric unit contained two molecules of PhyH-DI, with a corresponding Matthews coefficient of 2.17 Å3 Da−1and a solvent content of 43.26%. Crystals of selenomethionine-substituted PhyH-DI belonged to space groupC2221, with unit-cell parametersa = 94.71,b= 97.03,c= 69.16 Å, α = β = γ = 90.00°. The asymmetric unit contained one molecule of the protein, with a corresponding Matthews coefficient of 2.44 Å3 Da−1and a solvent content of 49.64%. Initial phases for PhyH-DI were obtained from SeMet SAD data sets. These data will be useful for further studies of the structure–function relationship of PhyH-DI.

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.

Inclusion compounds of plant growth regulators in cyclodextrins. V. 4-Chlorophenoxyacetic acid encapsulated in β-cyclodextrin and heptakis(2,3,6-tri-O-methyl)-β-cyclodextrin

2005 ◽  
Vol 61 (2) ◽  
pp. 207-217 ◽  
Author(s):  
Frantzeska Tsorteki ◽  
Kostas Bethanis ◽  
Nikos Pinotsis ◽  
Petros Giastas ◽  
Dimitris Mentzafos
Keyword(s):  
Guest Molecule ◽  
Crystal Packing ◽  
Host Molecule ◽  
X Ray Diffraction ◽  
Guest Molecules ◽  
Space Group ◽  
X Ray ◽  
Dimeric Complexes ◽  
The Mean ◽  
Chlorophenoxyacetic Acid

The crystal structures of 4-chlorophenoxyacetic acid (4CPA) included in β-cyclodextrin (β-CD) and heptakis(2,3,6-tri-O-methyl)-β-cyclodextrin (TMβCD) have been studied by X-ray diffraction. The 4CPA/β-CD complex crystallizes as a head-to-head dimer in the space group C2 in the Tetrad packing mode. The packing modes of some β-CD dimeric complexes, having unique stackings, are also discussed. The 4CPA/TMβCD inclusion complex crystallizes in the space group P21 and its asymmetric unit contains two crystallographically independent complexes, complex A and complex B, exhibiting different conformations. The host molecule of complex A is significantly distorted, as a glucosidic residue rotated about the O4′—C1 and C4—O4 bonds forms an aperture where the guest molecule is accommodated. The phenyl moiety of the guest molecule of complex B is nearly perpendicular to the mean plane of the O4n atoms. The conformations of the guest molecules of the two complexes are similar. The crystal packing consists of antiparallel columns as in the majority of the TMβCD complexes published so far.

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.

Structural studies of technetium complexes. V. The preparation and crystal structure of Dichlorobis(diethyldithiocarbamato)thionitrosyltechnetium(III)

1984 ◽  
Vol 37 (4) ◽  
pp. 751 ◽  
Author(s):  
J Baldas ◽  
J Bonnyman ◽  
MF Mackay ◽  
GA Williams
Keyword(s):  
Crystal Structure ◽  
Positive Charge ◽  
Mirror Plane ◽  
Structural Studies ◽  
Asymmetric Unit ◽  
X Ray Diffraction ◽  
Orthorhombic Space Group ◽  
Data Set ◽  
Coordination Environment ◽  
X Ray

Dichlorobis(diethyldithiocarbamato)thionitrosyltechnetium(III), [Tc(S2CNEt2)2Cl2(NS)], has been prepared by the reaction of [Tc(S2CNEt2)2N] with either disulfur dichloride or thionyl chloride. The crystal structure of [TC(S2CNEt2)2Cl2(NS)] has been determined by single-crystal X-ray diffraction methods at 15�C. Crystals are orthorhombic, space group Pcmn, with a 8.936(1), b 15.681(1), c 28.445(7) �, and Z 8. Automatic diffractometry has provided significant Bragg intensities for 2078 independent reflections, and the structure has been refined by full-matrix least-squares methods to R 0.078. The crystal lattice is disordered across a non-crystallographic mirror plane, the degree of disorder being 4.0(2)% for the crystal described above, and 21.9(7)% for another crystal initially used to obtain an intensity data set. There are two independent molecules of [Tc(S2CNEt2)2Cl2(NS)] in the asymmetric unit, and in each the technetium atom is seven-coordinate with a pentagonal-bipyramidal coordination environment. The Tc=N=S bonding is linear with Tc=N c. 1.75 and N=S c. 1.52 �, which indicates that the thionitrosyl group is a three-electron donor with a formal positive charge. This is only the third crystal structure of a complex containing the thionitrosyl group to be determined, and the first for technetium.

scholarly journals Crystallization and preliminary X-ray diffraction analysis of human DNA primase

2014 ◽  
Vol 70 (2) ◽  
pp. 206-210 ◽  
Author(s):  
Andrey G. Baranovskiy ◽  
Jianyou Gu ◽  
Nigar D. Babayeva ◽  
Vinod B. Agarkar ◽  
Yoshiaki Suwa ◽  
...  
Keyword(s):  
Active Site ◽  
Large Subunit ◽  
Structural Studies ◽  
Asymmetric Unit ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
X Ray ◽  
Cell Parameters ◽  
Human Dna ◽  
Structural Details

Human primase synthesizes RNA primers and transfers them to the active site of Pol α with subsequent extension with dNTPs. Human primase is a heterodimer of two subunits: a small catalytic subunit (p49) and a large subunit (p58). The structural details of the initiation and elongation steps of primer synthesis, as well as primer length counting, are not known. To address these questions, structural studies of human primase were initiated. Two types of crystals were obtained. The best diffracting crystals belonged to space groupP1, with unit-cell parametersa= 86.2,b= 88.9,c= 94.68 Å, α = 93.82, β = 96.57, γ = 111.72°, and contained two heterodimers of full-length p49 and p59 subunits in the asymmetric unit.

Crystal data for ternary compounds of the system Cu–As2Se3

1987 ◽  
Vol 20 (4) ◽  
pp. 323-323
Author(s):  
C. A. Majid ◽  
M. A. Hussain
Keyword(s):  
Diffraction Data ◽  
Lattice Parameters ◽  
Structural Studies ◽  
Crystal Data ◽  
X Ray Diffraction ◽  
Space Group ◽  
X Ray ◽  
Ternary Compounds

Structural studies of polycrystalline CuAsSe2, Cu3AsSe4 and Cu3AsSe3 are reported. These were found to be cubic with space group Pm{\bar 3}m and lattice parameters as follows: (1) CuAsSe2: a = 5.513(4) Å, V = 167.47(1) Å3, Z = 2; Dm = 5.56(6), Dx = 5.88 g cm−3. (2) Cu3AsSe4: a = 5.530(5) Å; V = 169.11(2) Å3; Z = 1; Dm = 5.51(5), Dx = 5.75 g cm−3. (3) Cu3AsSe3: a = 5.758(9) Å, V = 190.87(3) Å3, Z = 1, Dm = 5.03(9), Dx = 4.45 g cm−3. X-ray diffraction data using a Rigaku DMAX-IIIA diffractometer and Cu Kα radiation.

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