scholarly journals Structural Insights of Three 2,4-Disubstituted Dihydropyrimidine-5-carbonitriles as Potential Dihydrofolate Reductase Inhibitors

Molecules ◽  
2021 ◽  
Vol 26 (11) ◽  
pp. 3286
Author(s):  
Lamya H. Al-Wahaibi ◽  
Althaf Shaik ◽  
Mohammed A. Elmorsy ◽  
Mohammed S. M. Abdelbaky ◽  
Santiago Garcia-Granda ◽  
...  
Keyword(s):  
Water Molecule ◽  
Dihydrofolate Reductase ◽  
Crystal Packing ◽  
Docking Simulation ◽  
X Ray Diffraction ◽  
Space Groups ◽  
Reductase Inhibitors ◽  
Inhibitory Potential ◽  
Human Dihydrofolate Reductase

In this report, we describe the structural characterization of three 2,4-disubstituted-dihydropyrimidine-5-carbonitrile derivatives, namely 2-{[(4-nitrophenyl)methyl]sulfanyl}-6-oxo-4-propyl-1,6-dihydropyrimidine-5-carbonitrile 1, 4-(2-methylpropyl)-2-{[(4-nitrophenyl)methyl]sulfanyl}-6-oxo-1,6-dihydropyrimidine-5-carbonitrile 2, and 2-[(2-ethoxyethyl)sulfanyl]-6-oxo-4-phenyl-1,6-dihydropyrimidine-5-carbonitrile monohydrate 3. An X-ray diffraction analysis revealed that these compounds were crystallized in the centrosymmetric space groups and adopt an L-shaped conformation. One of the compounds (3) crystallized with a water molecule. A cyclic motif (R22(8)) mediated by N–H···O hydrogen bond was formed in compounds 1 and 2, whereas the corresponding motif was not favorable, due to the water molecule, in compound 3. The crystal packing of these compounds was analyzed based on energy frameworks performed at the B3LYP/6-31G(d,p) level of theory. Various inter-contacts were characterized using the Hirshfeld surface and its associated 2D-fingerprint plots. Furthermore, a molecular docking simulation was carried out to assess the inhibitory potential of the title compounds against the human dihydrofolate reductase (DHFR) enzyme.

scholarly journals 4-METHYL HYPPURIC ACID: A CASE OF POLYMORPHISM AND SOLVATOMORPHISM

2019 ◽  
Vol 16 (32) ◽  
pp. 812-819
Author(s):  
G. DELGADO ◽  
M. GUILLEN ◽  
A. J. MORA
Keyword(s):  
Pharmaceutical Industry ◽  
Physical Properties ◽  
Crystal Packing ◽  
Solid Material ◽  
Monoclinic Space Group ◽  
X Ray Diffraction ◽  
Space Group ◽  
Pharmaceutical Ingredients ◽  
Orthorhombic Cell

Polymorphism is known as the ability of a solid material to exist in more than one form or crystal structure, with important applications in the preparation of active pharmaceutical ingredients. Characterization of different polymorphs of the specific metabolite of 4-xylene can contribute to the chemical and pharmaceutical industry. Polymorphism is of particular importance in industrial processes, where different physical properties of polymorphic forms can substantially alter the viability and quality of a manufactured product. This is particularly so for the design and production of drugs in the pharmaceutical industry, as varying physical properties between different polymorphs can affect shelf life and durability, solubility, as well as bioavailability and manufacturing of the drug. The crystallization, spectroscopic and X-ray diffraction characterization of two polymorph and one solvatomorph of 4-methylhippuric acid are presented. These compounds crystallizes in different crystalline systems. Polymorph I (4mH-I) crystalize in an orthorhombic cell with space group P212121. Polymorph II (4mHII) crystallizes in a monoclinic space group P21/c. Solvatomorph (4mH-S) crystallizes in a triclinic P-1 cell. All polymorphs crystallize in neutral form. The crystal packing of the three compounds are governed by hydrogen bonds intermolecular interactions of the type N--H···O and O--H···O forming tridimensional networks.

scholarly journals Crystal structure of a mononuclear copper(II) complex with 2-methoxy-N,N-bis(quinolin-2-ylmethyl)ethylamine (DQMEA)

2018 ◽  
Vol 74 (8) ◽  
pp. 1138-1141
Author(s):  
Steven T. Frey ◽  
Jason Li ◽  
Manpreet Kaur ◽  
Jerry P. Jasinski
Keyword(s):  
Hydrogen Bonding ◽  
Crystal Packing ◽  
Complex Cation ◽  
Axial Position ◽  
Charge Balance ◽  
X Ray Diffraction ◽  
Pyramidal Geometry ◽  
Square Pyramidal Geometry ◽  
Monodentate Coordination

Structural characterization of the compound [Cu(C2H3N)(C23H23N3O)](ClO4)2] or [Cu(C2H3N)(DQMEA)](ClO4)2] [DQMEA = 2-methoxy-N,N-bis(quinolin-2-ylmethyl)ethylamine] {systematic name: (acetonitrile)[2-methoxy-N,N-bis(quinolin-2-ylmethyl)ethylamine]copper(II) diperchlorate} by single-crystal X-ray diffraction reveals a complex cation with a tetradentate coordination of the DQMEA ligand along with monodentate coordination of a CH3CN ligand to a single CuII center, with two perchlorate anions providing charge balance. The CuII center has a distorted square-pyramidal geometry in which the nitrogen atoms of the DQMEA and CH3CN ligands occupy the equatorial positions, while the oxygen atom of the DQMEA ligand resides in the axial position with an elongated Cu—O bond. The quinoline ring systems are nearly co-planar in the structure, while the linear CH3CN ligand is tilted significantly below this plane, and the central nitrogen of DQMEA is above it. Within the complex, weak C—H...N hydrogen bonding takes place between the nitrogen of CH3CN and a neighboring quinolyl group. The perchlorate ions are disordered within the structure, but undergo a number of weak intermolecular C—H...O hydrogen-bonding interactions. Additional weak π-stacking interactions between the quinolyl groups of neighboring complexes further stabilize the crystal packing.

scholarly journals Syntheses and crystal structures of 2-(p-tolyl)-1H-perimidine hemihydrate and 1-methyl-2-(p-tolyl)-1H-perimidine

2022 ◽  
Vol 78 (2) ◽  
Author(s):  
Paulina Kalle ◽  
Sergei V. Tatarin ◽  
Marina A. Kiseleva ◽  
Alexander Yu. Zakharov ◽  
Daniil E. Smirnov ◽  
...  
Keyword(s):  
Water Molecule ◽  
Crystal Structures ◽  
Crystal Packing ◽  
Rotation Axis ◽  
Point Group ◽  
Group Symmetry ◽  
X Ray Diffraction ◽  
Hydrogen Atoms ◽  
H Nmr ◽  
Rotation Axes

The title compounds, 2-(4-methylphenyl)-1H-perimidine hemihydrate (1, C18H14N2·0.5H2O) and 1-methyl-2-(4-methylphenyl)-1H-perimidine (2, C19H16N2), were prepared and characterized by 1H NMR and single-crystal X-ray diffraction. The organic molecule of the hemihydrate lies on a twofold rotation axis while the water molecule lies on the intersection of three twofold rotation axes (point group symmetry 222). As a consequence, the hydrogen atoms that are part of the N—H group and the water molecule as well as the CH3 group of the p-tolyl ring are disordered over two positions. In compound 1, the perimidine and the 2-aryl rings are slightly twisted while its N-methylated derivative 2 has a more distorted conformation because of the steric repulsion between the N-methyl group and the 2-aryl ring. In the crystal structures, molecules of perimidine 2 are held together only by C—H...π contacts while the parent perimidine 1 does not exhibit this type of interaction. Its crystal packing is established by intermolecular N—H...O hydrogen bonds with the solvent water molecules and additionally stabilized by π–π stacking.

scholarly journals SYNTHESIS AND STRUCTURAL CHARACTERIZATION OF THE 1:1 PROTON TRANSFER SALT OF MALONIC ACID WITH P-CHLOROANILINE

2017 ◽  
Vol 14 (28) ◽  
pp. 66-71
Author(s):  
Gerson E. DELGADO ◽  
Lusbely BELANDRIA ◽  
Asiloé J. MORA ◽  
Julia BRUNO-COLMENÁREZ ◽  
Gustavo MARROQUÍN
Keyword(s):  
Hydrogen Bonds ◽  
Malonic Acid ◽  
Crystal Packing ◽  
Chemical Properties ◽  
Supramolecular Assembly ◽  
X Ray Diffraction ◽  
Monoclinic System ◽  
X Ray ◽  
Cell Parameters

The design of multicomponent crystals offers a means to modify the physicochemical properties of crystals without altering the chemical properties of a particular molecule. In this study, a multicomponent crystal, the salt of malonic acid with p-chloroaniline, was synthetized and structurally characterized. The title compound wasprepared by grinding in an agate mortar, and its structure was studied by powder and single-crystal X-ray diffraction. This compound crystallize in the monoclinic system with space group P21/c, Z = 4, and unit cell parameters a = 12.9776(7)Å, b = 9.2308(5)Å, c = 8.5170(5)Å, β = 93.474(3)°. The multicomponent compound, p-chloroanilinium semi-malonate, can be described as an ionic ensemble assisted by hydrogen bonds established between p-chloroanilinium cations and semi-malonate anions. The molecular structure and crystal packing are stabilized mainly by intermolecular O-H•••O and N-H•••O hydrogen bonds interactions. The molecules construct a supramolecular assembly with a two-dimensional hydrogen bonded network along the ca plane.

scholarly journals 16α-Hydroxyfriedelin and 3-Oxo-16-methylfriedel-16-ene as Building Blocks: Crystal Structure and Hirshfeld Surfaces Decoding Intermolecular Contacts

2013 ◽  
Vol 2013 ◽  
pp. 1-6
Author(s):  
Rodrigo S. Corrêa ◽  
Lucienir P. Duarte ◽  
Grácia D. F. Silva ◽  
Djalma M. de Oliveira ◽  
Javier Ellena ◽  
...  
Keyword(s):  
Crystal Packing ◽  
Building Blocks ◽  
Chair Conformation ◽  
X Ray Diffraction ◽  
Central Ring ◽  
Intermolecular Hydrogen Bonds ◽  
Space Groups ◽  
Hirshfeld Surfaces ◽  
Crystallographic Study ◽  
Intermolecular Contacts

In this paper the importance of C–H⋯O intermolecular hydrogen bonds and van der Waals forces in crystal packing stabilization of 16α-hydroxyfriedelin (1) and 3-oxo-16-methylfriedel-16-ene (2) is described. Compound 1 is a natural product isolated from the hexane extract of Salacia elliptica branches, whereas compound 2 is obtained from compound 1 after dehydration accompanied by methyl migration of C-17 to C-16. The single-crystal X-ray diffraction experiments for 1 and 2 were carried out at 150 K, and the crystallographic study demonstrated that these compounds crystallize in noncentrosymmetric space groups, with 1 showing an orthorhombic P212121 space group and 2 a monoclinic P21 one. Compounds 1 and 2 are composed of five fused six-membered rings presenting a chair conformation, except for the central ring of 2, which adopts a half-chair conformation. In addition, the intra- and intermolecular parameters were studied using CCDC MOGUL analyses and Hirshfeld surfaces.

scholarly journals Purification, crystallization and preliminary X-ray diffraction analysis of inner membrane complex (IMC) subcompartment protein 1 (ISP1) fromToxoplasma gondii

2012 ◽  
Vol 68 (7) ◽  
pp. 832-834 ◽  
Author(s):  
Michelle L. Tonkin ◽  
Shannon Brown ◽  
Josh R. Beck ◽  
Peter J. Bradley ◽  
Martin J. Boulanger
Keyword(s):  
Diffraction Analysis ◽  
X Ray Diffraction ◽  
Inner Membrane ◽  
Crystal Forms ◽  
X Ray ◽  
Space Groups ◽  
Membrane Complex ◽  
Specific Proteins ◽  
Inner Membrane Complex

The protozoan parasites of the Apicomplexa phylum are devastating global pathogens. Their success is largely due to phylum-specific proteins found in specialized organelles and cellular structures. The inner membrane complex (IMC) is a unique apicomplexan structure that is essential for motility, invasion and replication. The IMC subcompartment proteins (ISP) have recently been identified inToxoplasma gondiiand shown to be critical for replication, although their specific mechanisms are unknown. Structural characterization ofTgISP1 was pursued in order to identify the fold adopted by the ISPs and to generate detailed insight into how this family of proteins functions during replication. An N-terminally truncated form ofTgISP1 was purified fromEscherichia coli, crystallized and subjected to X-ray diffraction analysis. Two crystal forms ofTgISP1 belonging to space groupsP4132 orP4332 andP212121diffracted to 2.05 and 2.1 Å resolution, respectively.

scholarly journals Crystal and molecular structure of bis(N-(diethylcarbamothioyl)cyclohexane carboxamido)copper(II) complex

2020 ◽  
Vol 11 (4) ◽  
pp. 319-323
Author(s):  
Cemal Koray Ozer ◽  
Gun Binzet ◽  
Hakan Arslan
Keyword(s):  
Crystal Structure ◽  
Crystal Packing ◽  
Chair Conformation ◽  
Planar Geometry ◽  
X Ray Diffraction ◽  
Structural Index ◽  
Cell Parameters ◽  
Square Planar ◽  
Puckering Parameters

Herein, we describe the synthesis and characterization of bis(N-(diethylcarbamothioyl)cyclohexane carboxamido)copper(II) complex, cis-[Cu(L-κ2S,O)2], has been prepared by the reaction of N-(diethyl carbamothioyl)cyclohexanecarboxamide ligand with copper(II) acetate. The green colored crystals of the complex were obtained by slow evaporation of their dichloromethane:ethanol solution (2:1, v:v). The crystal structure of cis-[Cu(L-κ2S,O)2] was obtained by single-crystal X-ray diffraction. The crystal structure reveals an monoclinic C2 (no. 5) space group with cell parameters a = 14.848(3) Å, b = 10.543(2) Å, c = 10.511(2) Å, β = 123.84(3)°, V = 1366.7(7) Å3, Z = 2, T = 153(2) K, μ(MoKα) = 0.979 mm-1, Dcalc = 1.327 g/cm3, 4979 reflections measured (6.6° ≤ 2Θ ≤ 50.68°), 2243 unique (Rint = 0.0223, Rsigma = 0.0444) which were used in all calculations. The final R1 was 0.0225 (>2sigma(I)) and wR2 was 0.0490 (all data). The angular structural index parameter, τ4, is equal to 0.40, which confirms the distorted square planar geometry for the title compound. The puckering parameters (q2 = 0.015(3) Å, q3 = 0.576(3) Å, QT = 0.577(3) Å, θ = 1.6(3)° and φ = 20(11)°) of the title complex show that the cyclohexane ring adopts a chair conformation. The two ethyl groups of the diethyl amine group have anti-orientation with respect to one another. The crystal packing shows the molecules stacked in parallel sheets along [010], accompanied by C3-H3A···O1ⁱ (i -x, +y, 1-z) intermolecular contact.

scholarly journals Synthesis and structural characterization of new polyether complexes of germanium(II) and tin(II)

2018 ◽  
Vol 96 (6) ◽  
pp. 570-577 ◽  
Author(s):  
Alina M. Secara ◽  
Justin F. Binder ◽  
Ala’aeddeen Swidan ◽  
Charles L.B. Macdonald
Keyword(s):  
Crystal Structure ◽  
Crown Ether ◽  
Water Molecule ◽  
Single Crystal ◽  
Structural Characterization ◽  
X Ray Diffraction ◽  
X Ray

A series of germanium(II) and tin(II) bromide polyether complexes have been synthesized. Specifically, [GeBr([15]crown-5)][GeBr3], [GeBr([18]crown-6)][GeBr3], [GeBr(triglyme)][GeBr3], [GeBr(tetraglyme)][GeBr3], [SnBr([18]crown-6)][SnBr3], [Sn([15]crown-5)2][SnBr3]2, [SnBr(triglyme)][SnBr3], and [SnBr(tetraglyme)][SnBr3] have been fully characterized including by single crystal X-ray diffraction. The synthesis of [GeBr(dibenzo[24]crown-8)][GeBr3] and [GeCl(dibenzo[24]crown-8)][GeCl3] are also reported, along with the crystal structure of the latter’s water adduct, which features a water molecule adjacent to the GeCl+ ion within the cavity of the crown ether.

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