Systematic study on crystal-contact engineering of diphthine synthase: influence of mutations at crystal-packing regions on X-ray diffraction quality

A novel Zn complex [Zn (C12H8N2)(C4H4O5)(H2O)](H2O) has been synthesized from a hydrothermal reaction and the crystal structure has been determined by means of single-crystal X-ray diffraction. The Zn atom is six-coordinated by two phenanthroline N atoms, three O atoms from malic acid anion and one O atom from water. The crystal packing is stabilized by O-H...O hydrogen bonding interactions.

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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

Acta Crystallographica Section C Structural Chemistry ◽

10.1107/s2053229618013980 ◽

2018 ◽

Vol 74 (11) ◽

pp. 1427-1433 ◽

Cited By ~ 3

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.

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Accurate H-atom parameters for the two polymorphs of L-histidine at 5, 105 and 295 K

Acta Crystallographica Section B Structural Science Crystal Engineering and Materials ◽

10.1107/s205252062100740x ◽

2021 ◽

Vol 77 (5) ◽

pp. 785-800

Author(s):

Giulia Novelli ◽

Charles J. McMonagle ◽

Florian Kleemiss ◽

Michael Probert ◽

Horst Puschmann ◽

...

Keyword(s):

Neutron Diffraction ◽

Single Crystal ◽

Diffraction Data ◽

Crystal Packing ◽

Basis Sets ◽

X Ray Diffraction ◽

X Ray ◽

Refinement Method ◽

Primary Amino ◽

Precision And Accuracy

The crystal structure of the monoclinic polymorph of the primary amino acid L-histidine has been determined for the first time by single-crystal neutron diffraction, while that of the orthorhombic polymorph has been reinvestigated with an untwinned crystal, improving the experimental precision and accuracy. For each polymorph, neutron diffraction data were collected at 5, 105 and 295 K. Single-crystal X-ray diffraction experiments were also performed at the same temperatures. The two polymorphs, whose crystal packing is interpreted by intermolecular interaction energies calculated using the Pixel method, show differences in the energy and geometry of the hydrogen bond formed along the c direction. Taking advantage of the X-ray diffraction data collected at 5 K, the precision and accuracy of the new Hirshfeld atom refinement method implemented in NoSpherA2 were probed choosing various settings of the functionals and basis sets, together with the use of explicit clusters of molecules and enhanced rigid-body restraints for H atoms. Equivalent atomic coordinates and anisotropic displacement parameters were compared and found to agree well with those obtained from the corresponding neutron structural models.

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

10.26434/chemrxiv.12646655.v1 ◽

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 NdPc2 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 NdPc2 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 NdPc2+ and NdPc2- are easily obtained through weak oxidizing and reducing agents, respectively. Additionally, we show that the protonated form of the NdPc2- complex has a nearly identical UV-Vis spectra to that of neutral NdPc2, explaining some of the confusion over chemical composition in previously published literature.

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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

Acta Crystallographica Section B Structural Science ◽

10.1107/s0108768105004106 ◽

2005 ◽

Vol 61 (2) ◽

pp. 207-217 ◽

Cited By ~ 11

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.

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Study on Novel Structure of Praseodymium Complex, C5H13O11Pr

Advanced Materials Research ◽

10.4028/www.scientific.net/amr.834-836.515 ◽

2013 ◽

Vol 834-836 ◽

pp. 515-518

Author(s):

Hai Xing Liu ◽

Qing Liu ◽

Ting Ting Huang ◽

Yang Xu ◽

Lin Tong Wang ◽

...

Keyword(s):

Crystal Structure ◽

Hydrogen Bonding ◽

Single Crystal ◽

Hydrothermal Reaction ◽

Crystal Packing ◽

X Ray Diffraction ◽

X Ray ◽

Hydrogen Bonding Interactions ◽

Novel Structure ◽

Praseodymium Complex

A novel praseodymium complex C5H13O11Pr has been synthesized from hydrothermal reaction and the crystal structure has been determined by means of single-crystal X-ray diffraction. The Pr1 atom is nine coordinated by nine O atoms. The crystal packing is stabilized by O-H...O hydrogen bonding interactions.

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Synthesis, growth, structure and characterization of molybdenum zinc thiourea complex crystals

Acta Crystallographica Section B Structural Science Crystal Engineering and Materials ◽

10.1107/s2052520615005922 ◽

2015 ◽

Vol 71 (3) ◽

pp. 285-292 ◽

Cited By ~ 1

Author(s):

M. Rajasekar ◽

K. Muthu ◽

A. Aditya Prasad ◽

R. Agilandeshwari ◽

SP Meenakshisundaram

Keyword(s):

Single Crystal ◽

Diffraction Analysis ◽

Intermolecular Interactions ◽

Crystal Packing ◽

Second Harmonic ◽

Morphological Changes ◽

Strong Interactions ◽

X Ray Diffraction ◽

X Ray ◽

Cell Parameters

Single crystals of molybdenum-incorporated tris(thiourea)zinc(II) sulfate (MoZTS) are grown by the slow evaporation solution growth technique. Crystal composition as determined by single-crystal X-ray diffraction analysis reveals that it belongs to the orthorhombic system with space groupPca21and cell parametersa= 11.153 (2),b= 7.7691 (14),c= 15.408 (3) Å,V= 1335.14 (4) Å3andZ= 4. The surface morphological changes are studied by scanning electron microscopy. The vibrational patterns in FT–IR are used to identify the functional group and TGA/DTA (thermogravimetric analysis/differential thermal analysis) indicates the stability of the material. The structure and the crystallinity of the material were confirmed by powder X-ray diffraction analysis and the simulated X-ray diffraction (XRD) closely matches the experimental one with varied intensity patterns. The band gap energy is estimated using diffuse reflectance data by the application of the Kubelka–Munk algorithm. The relative second harmonic generation (SHG) efficiency measurements reveal that MoZTS has an efficiency comparable to that of tris(thiourea)zinc(II) sulfate (ZTS). Hirshfeld surfaces were derived using single-crystal X-ray diffraction data. Investigation of the intermolecular interactions and crystal packingviaHirshfeld surface analysis reveal that the close contacts are associated with strong interactions. Intermolecular interactions as revealed by the fingerprint plot and close packing could be the possible reasons for facile charge transfer leading to SHG activity.

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

Zeitschrift für Kristallographie - Crystalline Materials ◽

10.1515/zkri-2018-2100 ◽

2019 ◽

Vol 234 (3) ◽

pp. 155-164 ◽

Cited By ~ 7

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.

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

RSC Advances ◽

10.1039/c8ra08063a ◽

2018 ◽

Vol 8 (67) ◽

pp. 38445-38454 ◽

Cited By ~ 5

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.

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Reaction of 2-[(2-aminoethyl)amino]ethanol with pyridine-2-carbaldehyde and complexation of the products with CuII and CdII along with docking studies

Acta Crystallographica Section C Structural Chemistry ◽

10.1107/s2053229619008258 ◽

2019 ◽

Vol 75 (7) ◽

pp. 951-959 ◽

Cited By ~ 1

Author(s):

Zahra Mardani ◽

Mohammad Hakimi ◽

Keyvan Moeini ◽

Fabian Mohr

Keyword(s):

Crystal Packing ◽

Docking Studies ◽

Molar Ratio ◽

Distorted Octahedral Geometry ◽

X Ray Diffraction ◽

Donor Ligand ◽

X Ray ◽

H Nmr ◽

Distorted Octahedral ◽

Ft Ir

The reaction between 2-[2-(aminoethyl)amino]ethanol and pyridine-2-carbaldehyde in a 1:2 molar ratio affords a mixture containing 2-({2-[(pyridin-2-ylmethylidene)amino]ethyl}amino)ethanol (PMAE) and 2-[2-(pyridin-2-yl)oxazolidin-3-yl]-N-(pyridin-2-ylmethylidene)ethanamine (POPME). Treatment of this mixture with copper(II) chloride or cadmium(II) chloride gave trichlorido[(2-hydroxyethyl)({2-[(pyridin-2-ylmethylidene)amino]ethyl})azanium]copper(II) monohydrate, [Cu(C10H16N3O)Cl3]·H2O or [Cu(HPMAE)Cl3]·H2O, 1, and dichlorido{2-[2-(pyridin-2-yl)oxazolidin-3-yl]-N-(pyridin-2-ylmethylidene)ethanamine}cadmium(II), [CdCl2(C16H18N4O)] or [CdCl2(POPME)], 2, which were characterized by elemental analysis, FT–IR, Raman and 1H NMR spectroscopy and single-crystal X-ray diffraction. PMAE is potentially a tetradentate N3O-donor ligand but coordinates to copper here as an N2 donor. In the structure of 1, the geometry around the Cu atom is distorted square pyramidal. In 2, the Cd atom has a distorted octahedral geometry. In addition to the hydrogen bonds, there are π–π stacking interactions between the pyridine rings in the crystal packing of 1 and 2. The ability of PMAE, POPME and 1 to interact with ten selected biomolecules (BRAF kinase, CatB, DNA gyrase, HDAC7, rHA, RNR, TrxR, TS, Top II and B-DNA) was investigated by docking studies and compared with doxorubicin.

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