Synthesis and structural study of five new phosphoric triamides: interplay between classical and non-classical intermolecular interactions

Author(s):  
Bahar Bakhshipour ◽  
Atekeh Tarahhomi ◽  
Arie van der Lee

Abstract Phosphoric triamides are attractive to investigate because of their extensive applications in various fields, especially in medicine. Five new phosphoric triamides with the main parts [N]P(O)[NH]2 and [C(O)NH]P(O)[N]2 have been structurally analyzed by single crystal MoKα/synchrotron-based X-ray diffraction and characterized by spectroscopic methods (FT-IR and 1H, 13C, 31P NMR). Compounds crystallize in orthorhombic (1 with space group Pnma) and monoclinic (2 (P21/a), 3 (C2/c), 4 (P21/n) and 5 (P21/c)) crystal systems. The asymmetric unit of all structures consists of one phosphoric triamide molecule, except for 1 with one half of molecule. X-ray crystallography data reveal that the molecular architectures constructed by classical N—H … O hydrogen bonds are as 1D linear (building the R 2 1 ( 6 ) ${R}\_{2}^{1}(6)$ , C(4) and R 2 2 ( 10 ) / R 2 1 ( 6 ) ${R}\_{2}^{2}(10)/{R}\_{2}^{1}(6)$ motifs, respectively, for 1–3) or dimeric (the R 2 2 ( 8 ) ${R}\_{2}^{2}(8)$ ring motif for 4 and 5). A detailed investigation of the intermolecular interactions using Hirshfeld surface (HS) analysis illustrates that the H … H, O … H/H … O and C … H/H … C contacts for all compounds, and Cl … H/H … Cl and F … H/H … F contacts for 3–5, are the most significant contributors to the crystal packing. Moreover, based on the calculated enrichment ratios (E), the O … H/H … O contacts including the classical N—H … O hydrogen bonds for all structures are considered as favoured contacts.

2016 ◽  
Vol 72 (3) ◽  
pp. 251-259 ◽  
Author(s):  
Mojtaba Keikha ◽  
Mehrdad Pourayoubi ◽  
Atekeh Tarahhomi ◽  
Arie van der Lee

Phosphoric triamides have extensive applications in biochemistry and are also used asO-donor ligands. Four new mixed-amide phosphoric triamide structures, namelyrac-N-tert-butyl-N′,N′′-dicyclohexyl-N′′-methylphosphoric triamide, C17H36N3OP, (I),rac-N,N′-dicyclohexyl-N′-methyl-N′′-(p-tolyl)phosphoric triamide, C20H34N3OP, (II),N,N′,N′′-tricyclohexyl-N′′-methylphosphoric triamide, C19H38N3OP, (III), and 2-[cyclohexyl(methyl)amino]-5,5-dimethyl-1,3,2λ5-diazaphosphinan-2-one, C12H26N3OP, (IV), have been synthesized and studied by X-ray diffraction and spectroscopic methods. Structures (I) and (II) are the first diffraction studies of acyclic racemic mixed-amide phosphoric triamides. The P—N bonds resulting from the different substituent –N(CH3)(C6H11), (C6H11)NH–, 4-CH3-C6H4NH–, (tert-C4H9)NH– and –NHCH2C(CH3)2CH2NH– groups are compared, along with the different molecular volumes and electron-donor strengths. In all four structures, the molecules form extended chains through N—H...O hydrogen bonds.


2020 ◽  
Vol 76 (1) ◽  
pp. 30-36 ◽  
Author(s):  
Ewa Żesławska ◽  
Justyna Kalinowska-Tłuścik ◽  
Wojciech Nitek ◽  
Henryk Marona ◽  
Anna M. Waszkielewicz

Aminoalkanol derivatives have attracted much interest in the field of medicinal chemistry as part of the search for new anticonvulsant drugs. In order to study the influence of the methyl substituent and N-oxide formation on the geometry of molecules and intermolecular interactions in their crystals, three new examples have been prepared and their crystal structures determined by X-ray diffraction. 1-[(2,6-Dimethylphenoxy)ethyl]piperidin-4-ol, C15H23NO2, 1, and 1-[(2,3-dimethylphenoxy)ethyl]piperidin-4-ol, C15H23NO2, 2, crystallize in the orthorhombic system (space groups P212121 and Pbca, respectively), with one molecule in the asymmetric unit, whereas the N-oxide 1-[(2,3-dimethylphenoxy)ethyl]piperidin-4-ol N-oxide monohydrate, C15H23NO3·H2O, 3, crystallizes in the monoclinic space group P21/c, with one N-oxide molecule and one water molecule in the asymmetric unit. The geometries of the investigated compounds differ significantly with respect to the conformation of the O—C—C linker, the location of the hydroxy group in the piperidine ring and the nature of the intermolecular interactions, which were investigated by Hirshfeld surface and corresponding fingerprint analyses. The crystal packing of 1 and 2 is dominated by a network of O—H...N hydrogen bonds, while in 3, it is dominated by O—H...O hydrogen bonds and results in the formation of chains.


2018 ◽  
Vol 74 (11) ◽  
pp. 1427-1433 ◽  
Author(s):  
Ewa Żesławska ◽  
Wojciech Nitek ◽  
Waldemar Tejchman ◽  
Jadwiga Handzlik

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.


Author(s):  
M. Rajasekar ◽  
K. Muthu ◽  
A. Aditya Prasad ◽  
R. Agilandeshwari ◽  
SP Meenakshisundaram

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.


2018 ◽  
Vol 74 (1) ◽  
pp. 31-36
Author(s):  
Resul Sevinçek ◽  
Duygu Barut Celepci ◽  
Serap Köktaş Koca ◽  
Özlem Akgül ◽  
Muittin Aygün

In order to determine the impact of different substituents and their positions on intermolecular interactions and ultimately on the crystal packing, unsubstituted N-phenyl-2-phthalimidoethanesulfonamide, C16H14N2O4S, (I), and the N-(4-nitrophenyl)-, C16H13N3O6S, (II), N-(4-methoxyphenyl)-, C16H16N3O6S, (III), and N-(2-ethylphenyl)-, as the monohydrate, C18H18N2O4S·H2O, (IV), derivatives have been characterized by single-crystal X-ray crystallography. Sulfonamides (I) and (II) have triclinic crystal systems, while (III) and (IV) are monoclinic. Although the molecules differ from each other only with respect to small substituents and their positions, they crystallized in different space groups as a result of differing intra- and intermolecular hydrogen-bond interactions. The structures of (I), (II) and (III) are stabilized by intermolecular N—H...O and C—H...O hydrogen bonds, while that of (IV) is stabilized by intermolecular O—H...O and C—H...O hydrogen bonds. All four structures are of interest with respect to their biological activities and have been studied as part of a program to develop anticonvulsant drugs for the treatment of epilepsy.


RSC Advances ◽  
2018 ◽  
Vol 8 (67) ◽  
pp. 38445-38454 ◽  
Author(s):  
Andrea Gionda ◽  
Giovanni Macetti ◽  
Laura Loconte ◽  
Silvia Rizzato ◽  
Ahmed M. Orlando ◽  
...  

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.


2019 ◽  
Vol 75 (4) ◽  
pp. 451-461 ◽  
Author(s):  
Avantika Hasija ◽  
Deepak Chopra

The concomitant occurrence of dimorphs of diphenyl (3,4-difluorophenyl)phosphoramidate, C18H14F2NO3P, was observed via a solution-mediated crystallization process with variation in the symmetry-free molecules (Z′). The existence of two forms, i.e. Form I (block, Z′ = 1) and Form II (needle, Z′ = 2), was characterized by single-crystal X-ray diffraction, differential scanning calorimetry and powder X-ray diffraction. Furthermore, a quantitative analysis of the energetics of the different intermolecular interactions was carried out via the energy decomposition method (PIXEL), which corroborates with inputs from the energy framework and looks at the topology of the various intermolecular interactions present in both forms. The unequivocally distinguished contribution of strong N—H...O hydrogen bonds along with other interactions, such as C—H...O, C—H...F, π–π and C—H...π, mapped on the Hirshfeld surface is depicted by two-dimensional fingerprint plots. Apart from the major electrostatic contribution from N—H...O hydrogen bonds, the crystal structures are stabilized by contributions from the dispersion energy. The closely related melting points and opposite trends in the calculated lattice energies are interesting to investigate with respect to the thermodynamic stability of the observed dimorphs. The significant variation in the torsion angles in both forms helps in classifying them in the category of conformational polymorphs.


2019 ◽  
Vol 75 (7) ◽  
pp. 951-959 ◽  
Author(s):  
Zahra Mardani ◽  
Mohammad Hakimi ◽  
Keyvan Moeini ◽  
Fabian Mohr

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.


Author(s):  
Piyush Panini ◽  
K. N. Venugopala ◽  
Bharti Odhav ◽  
Deepak Chopra

A new polymorph belonging to the tetrahydropyrimidinium class of compounds, namely 6-(4-chlorophenyl)-5-(methoxycarbonyl)-4-methyl-2-(3-(trifluoromethylthio)phenylamino)-3,6-dihydropyrimidin-1-ium chloride, and a hydrate of 2-(3-bromophenylamino)-6-(4-chlorophenyl)-5-(methoxycarbonyl)-4-methyl-3,6-dihydropyrimidin-1-ium chloride, have been isolated and characterized using single-crystal X-ray diffraction (XRD). A detailed comprehensive analysis of the crystal packing in terms of the associated intermolecular interactions and a quantification of their interaction energies have been performed for both forms of the two different organic salts (AandB) using X-ray crystallography and computational methods such as density functional theory (DFT) quantum mechanical calculations, PIXEL lattice-energy calculations (with decomposition of total lattice energy into the Coulombic, polarization, dispersion and repulsion contribution), the calculation of the Madelung constant (the EUGEN method), Hirshfeld and two-dimensional fingerprint plots. The presence of ionic [N—H]+...Cl−and [C—H]+...Cl−hydrogen bonds mainly stabilizes the crystal packing in both formsAandB, while in the case ofB·H2O [N—H]+...Owaterand Owater—H...Cl−hydrogen bonds along with [N—H]+...Cl−and [C—H]+...Cl−provide stability to the crystal packing. The lattice-energy calculations from both PIXEL and EUGEN methods revealed that in the case ofA, form (I) (monoclinic) is more stable whereas forBit is the anhydrous form that is more stable. The analysis of the `Madelung mode' of crystal packing of two forms ofAandBand its hydrates suggest that differences exist in the position of the charged ions/atoms in the organic solid state. TheR/E(distance–energy) plots for all the crystal structures show that the molecular pairs in their crystal packing are connected with either highly stabilizing (due to the presence of organicR+and Cl−) or highly destabilizing Coulombic contacts. The difference in crystal packing and associated intermolecular interactions between polymorphs (in the case ofA) or the hydrates (in the case ofB) have been clearly elucidated by the analysis of Hirshfeld surfaces and two-dimensional fingerprint plots. The relative contributions of the various interactions to the Hirshfeld surface for the cationic (dihydropyrimidinium) part and anionic (chloride ion) part for the two forms ofAandBand its hydrate were observed to be different.


2021 ◽  
Vol 77 (1) ◽  
pp. 11-19
Author(s):  
Damian Rosiak ◽  
Andrzej Okuniewski ◽  
Jarosław Chojnacki

By the reaction of benzoyl chloride, potassium isothiocyanate and the appropriate halogenoaniline, i.e. 2/3/4-(bromo/iodo)aniline, we have obtained five new 1-benzoyl-3-(halogenophenyl)thioureas, namely, 1-benzoyl-3-(2-bromophenyl)thiourea and 1-benzoyl-3-(3-bromophenyl)thiourea, C14H11BrN2OS, and 1-benzoyl-3-(2-iodophenyl)thiourea, 1-benzoyl-3-(3-iodophenyl)thiourea and 1-benzoyl-3-(4-iodophenyl)thiourea, C14H11IN2OS. Structural and conformational features of the compounds have been analyzed using X-ray diffraction and theoretical calculations. The novel compounds were characterized by solid-state IR and 1H/13C NMR spectroscopy. The conformations and intermolecular interactions, such as hydrogen bonds, π–π and S(6)...π stacking, and X...O (X = I or Br), I...S and I...π, have been examined and rationalized, together with four analogous compounds described previously in the literature. The set of nine compounds was chosen to examine how a change of the halogen atom and its position on the phenyl ring affects the molecular and crystal structures.


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