Synthesis, spectroscopic (FT–IR and UV–Vis), crystallographic and theoretical studies, and a molecular docking simulation of an imatinib-like template

2019 ◽  
Vol 75 (12) ◽  
pp. 1681-1689
Author(s):  
Rodolfo Moreno-Fuquen ◽  
Kevin Arango-Daraviña ◽  
Esteban Garcia ◽  
Juan-C. Tenorio ◽  
Javier Ellena
Keyword(s):  
Crystal Growth ◽  
Hydrogen Bonds ◽  
Docking Simulation ◽  
Myelogenous Leukemia ◽  
Amino Group ◽  
Protein Residues ◽  
Function Analyzer ◽  
Stretching Vibration ◽  
Donor Acceptor ◽  
Ft Ir

The aim of the present study was to report the crystal structure and spectroscopic, electronic, supramolecular and electrostatic properties of a new polymorph of 4-(pyridin-2-yl)pyrimidin-2-amine (C9H8N4). The compound was synthesized under microwave irradiation. The single-crystal X-ray structure analysis revealed an angle of 13.36 (8)° between the planes of the rings, as well as molecules linked by Nsp 2—H...N hydrogen bonds forming dimers along the crystal. The material was analyzed by FT–IR vibrational spectroscopy, while a computational approach was used to elucidate the vibrational frequency couplings. The existence of Nsp 2—H...N hydrogen bonds in the crystal was confirmed spectroscopically by the IR peaks from the N—H stretching vibration shifting to lower wavenumbers in the solid state relative to those in the gas phase. The supramolecular studies confirmed the formation of centrosymmetric R 2 2(8) rings, which correspond to the formation of dimers that stack parallel to the b direction. Other weak C—H...π interactions, essential for crystal growth, were found. The UV–Vis spectroscopic analysis showed a donor–acceptor process, where the amino group acts as a donor and the pyridine and pyrimidine rings act as acceptors. The reactive sites of the molecule were identified and their quantitative values were defined using the electrostatic potential model proposed in the multifunctional wave function analyzer multiwfn. The calculated interaction energies between pairs of molecules were used to visualize the electrostatic terms as the leading factors against the dispersion factors in the crystal-growth process. The docking results showed that the amino group of the pyrimidine moiety was simultaneously anchored by hydrogen-bonding interactions with the Asp427 and His407 protein residues. This compound could be key for the realization of a series of syntheses of molecules that could be used as possible inhibitors of chronic myelogenous leukemia.

FT-IR Solution Spectra of Propyl Sulfide, Propyl Sulfoxide, and Propyl Sulfone

1995 ◽  
Vol 49 (12) ◽  
pp. 1772-1775 ◽  
Author(s):  
R. Louis Staggs ◽  
William G. Lyon
Keyword(s):  
Organic Acids ◽  
Ir Spectra ◽  
Stretching Vibration ◽  
Donor Acceptor ◽  
Ft Ir ◽  
Stretching Vibrations ◽  
Acidic Solvents ◽  
Sulfoxide Group

FT-IR spectra were obtained of 0.5% volumetric solutions of propyl sulfide, propyl sulfoxide, and propyl sulfone in hexane, CCl4, CS2, and CHCl3 to assist in the assignment of FT-IR-PAS spectra of propyl sulfoxide sorbed within the structure of several peats and onto cellulose. The C-H stretching bands of all three compounds showed a 10-fold larger solvent sensitivity than did analogous aliphatic bands in a comparable series of n-alkanes in solution. The S=O stretching bands of alkyl sulfoxides are known to be quite sensitive to solvent environments because of donor-acceptor interactions involving the oxygen of the sulfoxide group and the slightly acidic protons of generalized organic acids; the expected decreases in frequency were seen with propyl sulfoxide and acidic solvents like chloroform. The frequencies of asymmetric and symmetric stretching vibrations of the -SO2 group of propyl sulfone both exhibit smaller decreases in Old, than does the sulfoxide S=O stretching vibration.

The effect of partial methylation of the glycine amino group on crystal structure inN,N-dimethylglycine and its hemihydrate

2012 ◽  
Vol 68 (8) ◽  
pp. o283-o287 ◽  
Author(s):  
Vasily S. Minkov ◽  
Elena V. Boldyreva
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Water Molecules ◽  
Amino Group ◽  
Asymmetric Unit ◽  
Partial Methylation ◽  
Space Groups ◽  
Carboxylate Groups ◽  
Anhydrous Compound ◽  
Additional Hydrogen

N,N-Dimethylglycine, C4H9NO2, and its hemihydrate, C4H9NO2·0.5H2O, are discussed in order to follow the effect of the methylation of the glycine amino group (and thus its ability to form several hydrogen bonds) on crystal structure, in particular on the possibility of the formation of hydrogen-bonded `head-to-tail' chains, which are typical for the crystal structures of amino acids and essential for considering amino acid crystals as mimics of peptide chains. Both compounds crystallize in centrosymmetric space groups (PbcaandC2/c, respectively) and have twoN,N-dimethylglycine zwitterions in the asymmetric unit. In the anhydrous compound, there are no head-to-tail chains but the zwitterions formR44(20) ring motifs, which are not bonded to each other by any hydrogen bonds. In contrast, in the crystal structure ofN,N-dimethylglycinium hemihydrate, the zwitterions are linked to each other by N—H...O hydrogen bonds into infiniteC22(10) head-to-tail chains, while the water molecules outside the chains provide additional hydrogen bonds to the carboxylate groups.

scholarly journals Potential Mitochondrial Isocitrate Dehydrogenase R140Q Mutant Inhibitor from Traditional Chinese Medicine against Cancers

2014 ◽  
Vol 2014 ◽  
pp. 1-10 ◽  
Author(s):  
Wen-Yuan Lee ◽  
Kuan-Chung Chen ◽  
Hsin-Yi Chen ◽  
Calvin Yu-Chian Chen
Keyword(s):  
Isocitrate Dehydrogenase ◽  
Point Mutations ◽  
Docking Simulation ◽  
Myelogenous Leukemia ◽  
Mutant Protein ◽  
Binding Affinities ◽  
Isocitrate Dehydrogenase 1 ◽  
Lead Compounds ◽  
Arginine Residues ◽  
Acute Myelogenous

A recent research of cancer has indicated that the mutant of isocitrate dehydrogenase 1 and 2 (IDH1and2) genes will induce various cancers, including chondrosarcoma, cholangiocarcinomas, and acute myelogenous leukemia due to the effect of point mutations in the active-site arginine residues of isocitrate dehydrogenase (IDH), such as IDH1/R132, IDH2/R140, and IDH2/R172. As the inhibition for those tumor-associated mutant IDH proteins may induce differentiation of those cancer cells, these tumor-associated mutant IDH proteins can be treated as a drug target proteins for a differentiation therapy against cancers. In this study, we aim to identify the potent TCM compounds from the TCM Database@Taiwan as lead compounds of IDH2 R140Q mutant inhibitor. Comparing to the IDH2 R140Q mutant protein inhibitor, AGI-6780, the top two TCM compounds, precatorine and abrine, have higher binding affinities with target protein in docking simulation. After MD simulation, the top two TCM compounds remain as the same docking poses under dynamic conditions. In addition, precatorine is extracted fromAbrus precatoriusL., which represents the cytotoxic and proapoptotic effects for breast cancer and several tumor lines. Hence, we propose the TCM compounds, precatorine and abrine, as potential candidates as lead compounds for further study in drug development process with the IDH2 R140Q mutant protein against cancer.

Synthese und Kristallstrukturen einiger Tetramethylstibonium-Hydrogendicarboxylate / Synthesis and Crystal Structures of Some Tetramethylstibonium Hydrogendicarboxylates

1982 ◽  
Vol 37 (11) ◽  
pp. 1393-1401 ◽  
Author(s):  
Beatrix Milewski-Mahrla ◽  
Hubert Schmidbaur
Keyword(s):  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Spectroscopic Data ◽  
Molar Ratio ◽  
Ionic Structure ◽  
X Ray Diffraction ◽  
X Ray ◽  
Carboxylate Oxygen ◽  
Donor Acceptor ◽  
New Compounds

Reactions of pentamethylantimony (CH3)5Sb with carboxylic acids in the molar ratio 1:2 afford one equivalent of methane and essentially quantitative yields of crystalline tetramothylstibonium hydrogendicarboxylates. Six new compounds of this series have been synthesized using benzoic, o-phthalic, salicylic, 4-ethoxy-salicylic, oxalic, and malic acid, and characterized by analytical and spectroscopic data. An ionic structure with strong hydrogen bonds in the anionic components is proposed.The crystal structures of the hydrogen-dibenzoato (1), hydrogen-ortho-plithalato (2) and 4-ethoxy-hydrogen-salicylate (3) were determined by single crystal X-ray diffraction. The compounds can be described as having ionic lattices with some donor-acceptor inter­actions between the stibonium centers and the carboxylate oxygen atoms. The anions are characterized by strong hydrogen bonds O...H...O. Thus, the (CH3)4Sb-tetrahedron in 1 is distorted by two benzoate oxygon atoms (at 304(2) and 340(2) pin). The cation in 2 is largely undistorted and the anion has a hydrogenphthalate hydrogen bond of d(O...H...O) = 232 pm. The cation-anion contact in 3 is as short as d(Sb-O) = 289 pm rendering the Sb atom pentacoordinate.

Mono- and dinuclear CuII complexes of the benzyldipicolylamine (BDPA) ligand: crystal structure, synthesis and characterization

2017 ◽  
Vol 73 (11) ◽  
pp. 1024-1029
Author(s):  
Dharmalingam Sivanesan ◽  
Min Hye Youn ◽  
Ki Tae Park ◽  
Hak Joo Kim ◽  
Andrews Nirmala Grace ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Reaction Medium ◽  
Bound Water ◽  
Dinuclear Complex ◽  
Residual Moisture ◽  
Structure Synthesis ◽  
Distorted Octahedral ◽  
Vis Spectroscopy ◽  
Ft Ir ◽  
Solvent Molecules

The crystal structures of mono- and dinuclear CuII trifluoromethanesulfonate (triflate) complexes with benzyldipicolylamine (BDPA) are described. From equimolar amounts of Cu(triflate)2 and BDPA, a water-bound CuII mononuclear complex, aqua(benzyldipicolylamine-κ3 N,N′,N′′)bis(trifluoromethanesulfonato-κO)copper(II) tetrahydrofuran monosolvate, [Cu(CF3SO3)2(C19H19N3)(H2O)]·C4H8O, (I), and a triflate-bridged CuII dinuclear complex, bis(μ-trifluoromethanesulfonato-κ2 O:O′)bis[(benzyldipicolylamine-κ3 N,N′,N′′)(trifluoromethanesulfonato-κO)copper(II)], [Cu2(CF3SO3)4(C19H19N3)2], were synthesized. The presence of residual moisture in the reaction medium afforded water-bound complex (I), whereas dinuclear complex (II) was synthesized from an anhydrous reaction medium. Single-crystal X-ray structure analysis reveals that the CuII centres adopt slightly distorted octahedral geometries in both complexes. The metal-bound water molecule in (I) is involved in intermolecular O—H...O hydrogen bonds with triflate ligands and tetrahydrofuran solvent molecules. In (II), weak intermolecular C—H...F(triflate) and C—H...O(triflate) hydrogen bonds stabilize the crystal lattice. Complexes (I) and (II) were also characterized fully using FT–IR and UV–Vis spectroscopy, cyclic voltammetry and elemental analysis.

scholarly journals Synthesis of some Heterocyclic Compounds Derived from

2013 ◽  
Vol 10 (3) ◽  
pp. 525-536
Author(s):  
Baghdad Science Journal
Keyword(s):  
Spectroscopic Data ◽  
Heterocyclic Compounds ◽  
Sulfonyl Chloride ◽  
Starting Material ◽  
Amino Group ◽  
Thiazole Derivatives ◽  
Ft Ir ◽  
Bromo Compound

The 4-(?-bromo acetyl)-4?-toluene sulfonanilide (2) was used as key intermediate to synthesize new heterocyclic compounds. This bromo compound was synthesized via sulfonation of amino group of p-amino acetophenone using Hinsburg method with 4-toluene sulfonyl chloride to form 4-acetyl-4?-toluene sulfonanilide (1) which is used as a starting material in this work. This compound was brominated to yield compound (2) which is used as a precursor to synthesize new five and seven membered heterocyclic compounds such as substituted 1,3-oxazoles (3,4), 1,3-thiazole derivatives (5-7), thiourea compounds (8a,b), 1,3-Thiazoline-2-thione compounds (9a-f) and 1,2,5-triazepine compounds (11a-d). The synthesized compounds were identified depending upon physical, FT-IR and UV spectroscopic data.

scholarly journals Crystal structure and Hirshfeld surface analysis of 2,4-diamino-6-phenyl-1,3,5-triazin-1-ium 4-methylbenzenesulfonate

2018 ◽  
Vol 74 (8) ◽  
pp. 1159-1162
Author(s):  
Ramalingam Sangeetha ◽  
Kasthuri Balasubramani ◽  
Kaliyaperumal Thanigaimani ◽  
Savaridasson Jose Kavitha
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Intermolecular Interactions ◽  
Hirshfeld Surface ◽  
Amino Group ◽  
Asymmetric Unit ◽  
Graph Set ◽  
Molecular Salt ◽  
Sulfonate Anion ◽  
Hydrogen Bonded

In the title molecular salt, C9H10N5 +·C7H7O3S−, the asymmetric unit consists of a 2,4-diamino-6-phenyl-1,3,5-triazin-1-ium cation and a 4-methylbenzenesulfonate anion. The cation is protonated at the N atom lying between the amine and phenyl substituents. The protonated N and amino-group N atoms are involved in hydrogen bonding with the sulfonate O atoms through a pair of intermolecular N—H...O hydrogen bonds, giving rise to a hydrogen-bonded cyclic motif with R 2 2(8) graph-set notation. The inversion-related molecules are further linked by four N—H...O intermolecular interactions to produce a complementary DDAA (D = donor, A = acceptor) hydrogen-bonded array, forming R 2 2(8), R 4 2(8) and R 2 2(8) ring motifs. The centrosymmetrically paired cations form R 2 2(8) ring motifs through base-pairing via N—H...N hydrogen bonds. In addition, another R 3 3(10) motif is formed between centrosymetrically paired cations and a sulfonate anion via N—H...O hydrogen bonds. The crystal structure also features weak S=O...π and π–π interactions. Hirshfeld surface and fingerprint plots were employed in order to further study the intermolecular interactions.

Crystal growth and characterization of solvated organic charge-transfer complexes built on TTF and 9-dicyanomethylenefluorene derivatives

CrystEngComm ◽  
2015 ◽  
Vol 17 (32) ◽  
pp. 6227-6235 ◽  
Author(s):  
Amparo Salmerón-Valverde ◽  
Sylvain Bernès
Keyword(s):  
Charge Transfer ◽  
Crystal Growth ◽  
Charge Transfer Complexes ◽  
Organic Complexes ◽  
Donor Acceptor ◽  
Degree Of Charge Transfer

A series of solvated donor–acceptor organic complexes were shown to slowly release the lattice solvent while the degree of charge transfer decreases steadily. This behavior is not observed in the case of a hydrate.

Hydrogen-bonding patterns in the cocrystal 2,4-diamino-6-phenyl-1,3,5-triazine–sorbic acid (1/1)

2007 ◽  
Vol 63 (11) ◽  
pp. o4450-o4451 ◽  
Author(s):  
Kaliyaperumal Thanigaimani ◽  
Packianathan Thomas Muthiah ◽  
Daniel E. Lynch
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Sorbic Acid ◽  
Carboxyl Group ◽  
Amino Group ◽  
Acid Molecule ◽  
Asymmetric Unit ◽  
Graph Set ◽  
Bonding Patterns

In the title cocrystal, C9H9N5·C6H8O2, the asymmetric unit contains one 2,4-diamino-6-phenyl-1,3,5-triazine molecule and a sorbic acid molecule. The triazine molecules are base-paired [with a graph set of R 2 2(8)] on either side via N—H...N hydrogen bonds, forming a supramolecular ribbon along the c axis. Each triazine molecule interacts with the carboxyl group of a sorbic acid molecule via N—H...O and O—H...N hydrogen bonds, generating R 2 2(8) motifs. The supramolecular ribbons are interlinked by N—H...O hydrogen bonds involving the 2-amino group of the triazine molecules and the carboxyl O atom of the sorbic acid molecule.

Sign in / Sign up

Export Citation Format

Share Document