Phosphoric Triamide Ligand Research Articles

Structural, Hirshfeld surface and molecular docking studies of a new organotin(IV)-phosphoric triamide complex and an amidophosphoric acid ester proposed as possible SARS-CoV-2 and Monkeypox inhibitors

Phosphoramides and their complexes are attractive compounds due to their significant inhibiting functionality in biological medicine. In this paper, a novel organotin(IV)-phosphoramide complex (Sn(CH3)2Cl2{[(3-Cl)C6H4NH]P(O)[NC4H8O]2}2, 1), derived from a reaction between phosphoric triamide ligand with dimethyltin dichloride, and a new amidophosphoric acid ester ([OCH2C(CH3)2CH2O]P(O)[N(CH3)CH2C6H5], 2), prepared from the condensation of a cyclic chlorophosphate reagent with N-methylbenzylamine, are structurally characterized and in silico investigated as potential SARS-CoV-2 and Monkeypox inhibitors by molecular docking simulation. Both compounds crystallize in the monoclinic crystal system with space group P21/c. The asymmetric unit of the complex 1 consists of one-half molecule, where SnIV is located on an inversion center, while the asymmetric part of 2 consists of one whole molecule. In the complex 1, the tin atom adopts a six-coordinate octahedral geometry with trans groups of (Cl)2, (CH3)2 and (PO)2 (PO = phosphoric triamide ligand). The molecular architecture consists of the N–H⋯Cl hydrogen bonds stretching as a 1D linear arrangement along the b axis with intermediate R22(12) ring motifs, whereas in the case of 2, the crystal packing is devoid of any classical hydrogen bond interaction. Furthermore, a graphical analysis by using Hirshfeld surface method identifies the most important intermolecular interactions being of the type H⋯Cl/Cl⋯H (for 1) and H⋯O/O⋯H (for 1 and 2), covering the hydrogen bond interactions N–H⋯Cl and C–H⋯O═P, respectively, which turn out to be favoured. A biological molecular docking simulation on the studied compounds provides evidence to suggest a significant inhibitory potential against SARS-COV-2 (6LU7) and Monkeypox (4QWO) especially for 6LU7 with a binding energy around −6 kcal/mol competing with current effective drugs against this virus (with a binding energy around −5 and −7 kcal/mol). It is worth noting that this report is the first case of an inhibitory potential evaluation of phosphoramide compounds on Monkeypox.

Effect of SBA-15-based immobilization of a new phosphoric triamide Ag (I) complex on its catalytic activity: Synthesis, characterization, crystallography and catalytic investigation

A new Ag (Ⅰ) complex (C) containing phosphoric triamide ligand (L) with a formula of [Ag ((C5H4NC (O) NHP (O) (NC6H12)2)2NO3] 2 was synthesized by the reaction of AgNO3 with N-nicotinyl –N′, N″-bis (hexamethylenyl) phosphoric triamide. The complex (C) was characterized by Fourier transform infrared spectroscopy (FT-IR), molar conductivity, thermal gravimetric analysis (TGA), and X-ray crystallography techniques. Results showed that complexation occurred via the nitrogen atom of the pyridine ring. The molecular structure of C, refined from single-crystal X-ray diffraction, is triclinic with a P-1 space group. The complex was immobilized on SBA-15 and the produced compound (C@SBA-15) was identified by BET, AAS, FT-IR, XRD, and TGA methods. Successful loading of the complex on SBA-15 was determined by the BET method. According to AAS findings, the amount of silver in the C@SBA-15 composition was 18%. FT-IR and XRD results showed that the complex was absorbed on the support physically and the hexagonal structure of the support was retained after immobilization. Thermal stability of C@SBA-15 was confirmed by TGA analysis. The homogeneous complex (C) and heterogeneous C@SBA-15 were used as catalysts in the oxidation reaction of aromatic aldehydes and sulfides and their catalytic properties compared. H2O2 was used as a green oxidant, some effective parameters (reaction temperature, substrate to oxidant molar ratio, catalyst amount, and solvent type) were optimized, and the conversion percentages of 70% (for C catalyst) and 50% (for C@SBA-15 catalyst) obtained. The reusability of C@SBA-15 and the generality of both catalysts were evaluated and confirmed. The results showed that when the complex was immobilized on SBA-15, its catalytic efficiency decreased, and its recoverability increased. A comparison with other published reports showed that the catalytic efficiency of the catalysts in the oxidation reaction of aldehydes and sulfides was within acceptable limits.

Conformational analysis of two new organotin(IV) structures completed with a CSD survey.

The conformational flexibilities are studied in two new organotin(IV) complexes, namely, trans-dichloridodimethylbis[N,N',N''-tris(2-chlorobenzyl)phosphoric triamide]tin(IV), [Sn(CH3)2(C21H21Cl3N3OP)2Cl2] or Sn(CH3)2Cl2{OP[NHCH2C6H4(2-Cl)]3}2, (I), and bis(dipropylammonium) tetrachloridodimethylstannate(IV), [(CH3CH2CH2)2NH2]2[Sn(CH3)2Cl4], (II), and their analogous structures from the Cambridge Structural Database (CSD). The conformations are considered based on the N-P=O-Sn torsion angles for (I) and the C-C-C-N, C-C-N-C, C-N-C-C and N-C-C-C torsion angles for the two symmetry-independent [CH3CH2CH2NH2CH2CH2CH3]+ cations in (II), and the ±ac±sp±ac (ac = anticlinal and sp = synperiplanar) and ±ap±ap±ap±ap (ap = antiperiplanar) conformations are observed, respectively. In both structures, the four atoms in the corners of the square-planar segment of the octahedral shape around the Sn atom participate in normal hydrogen-bonding interactions as acceptors, which include two O and two Cl atoms for (I), and four Cl atoms for (II). However, the phosphoric triamide ligands block the environment around the Sn atom and limit the hydrogen-bond pattern to form a supramolecular ribbon assembly, while in the presence of small organic cations in (II), a two-dimensional hydrogen-bonded architecture is achieved. The weak interactions π-π, C-H...π and C-Cl...π in (I), and C-H...Cl in (II) do not change the dimensionality of the hydrogen-bond pattern. The 62 CSD structures analogous to (I), i.e. with an SnOPN3 segment (including 83 entries) fall into four categories of conformations based on the N-P=O-Sn torsion angles. The 132 [(CH3CH2CH2)2NH2]+ cations from 85 CSD structures are classified into seven groups based on the torsion angles noted for (II). Most of the CSD structures adopt the same associated conformations noted for (I) and (II). 15 [Sn(CH3)2Cl4]2- anions extracted from the CSD are compared with the structure of (II).

Evaluation of structural, spectroscopic, bonding and electronic properties of some organotin(IV)-phosphoric triamide complexes by using help of DFT, QTAIM and Hirshfeld surface investigations

Different computational investigations by using help of DFT (density functional theory), QTAIM (quantum theory of atom in molecule) and HS (Hirshfeld surface) approaches are carried out to evaluate the various properties, especially Sn…O interactions, of some organotin(IV)-phosphoric triamide (OP is introduced as the phosphoric triamide ligand with a segment (O═)P[N]3) complexes. Among the most important results of this study is the absence of a net Sn-O bond between Sn(IV) center and O atom of P═O group (of OP ligand) in the segment Sn(CH3)2Cl2(OP)2, where no bond critical point (BCP) is found along the path connecting tin and oxygen atoms. However, a survey of other connectivities (such as Sn…C and C/Cl…O contacts) suggests a weak non-covalent interaction (with ionic in nature) for Sn…O(═P) in the studied complexes. DFT studies show that orientation of OP ligands around tin (trans or cis) is important for the strength of Sn…O interactions; so that a slightly higher strength is found in trans(OP)-form six-coordinate complexes of 1 – 3. Furthermore, a precise exploration of the intermolecular interactions by using Hirshfeld surface analysis reveals that the H…O/O…H (for 1 – 4) and H…Cl/Cl…H (for 1 – 5) contacts are favoured. A characteristic Sn….Cl contact with a high enrichment ratio is explored in five-coordinate complex 5. Finally, the presence of normal intermolecular interactions in the crystal structures of 3 and 4 is aligned with the lower chemical reactivities of these structures.

The first coordination compounds of OP[NC4H8O]3 phosphoric triamide ligand: structural study and Hirshfeld surface analysis of SnIV and MnII complexes

The first X-ray crystal structures of coordination compounds of OP[NC4H8O]3 phosphoric triamide (L) are investigated in Cl2(CH3)2Sn(trans-L)2 (1) and [Mn(H2O)4(trans-L)2]Cl2·2H2O (2) as models of molecular and salt complexes for Hirshfeld surface (HS)-based analysis. The crystal packing of 1 includes weak interactions, while in the salt complex 2, a 2-D aggregate, along the (001) plane, is mediated by normal O–H⋯Cl and O–H⋯O hydrogen bonds. In the Hirshfeld study, the crystal cohesions of 1 and 2 are recognized via H⋯H, O⋯H/H⋯O, and Cl⋯H/H⋯Cl contacts. Among these interactions, hydrogen bonds O–H⋯Cl occur in the salt structure of 2, as well as some weaker hydrogen interactions as C–H⋯O (1 and 2), C–H⋯Cl (1), and O–H⋯O (2). The full fingerprint plots have nearly symmetric shapes for two independent molecules of 1, while an asymmetric shape appears for the cationic component of 2. To extract more detailed information on close intermolecular contacts, the molecular surface of the previously reported structure L was also mapped. The structure 2 is the first monomeric octahedral Mn(II)–phosphoric triamide complex reported so far. Furthermore, the HS analysis of 2 is the first such study on a cation–anion complex structure including phosphoric triamide ligand.

Two new organotin(IV)-phosphoryl complexes: crystal structure and Hirshfeld surface analysis

Hirshfeld surfaces and two-dimensional fingerprint plots are used to visualize and analyse intermolecular interactions in two new organotin(IV)-phosphoryl complexes: [Sn(CH3)2[OP(O)(OCH3)2]2]n (I) and {[(4-CH3)C6H4NH][C5H9(4-CH3)N]2P(O)}Sn(CH3)2Cl2 (II). In (I), the asymmetric unit is composed of the Sn(CH3)2[OP(O)(OCH3)2]2 segment bonded to the neighbouring segment through Sn–O bonds thus constructing a coordination polymer. The tin centre has an Sn[C]2[O]4 environment with the axial positions occupied by methyl groups and with the oxygen atoms of Sn–O bonds located at the equatorial plane, while the oxygen atoms of OCH3 groups do not take part in the coordination interaction. In (II), the asymmetric unit contains one complete molecule and the tin centre has an Sn[C]2[Cl]2O trigonal bipyramid coordination environment, where the phosphoric triamide ligand and one of the chlorine atoms are placed in axial positions. Hirshfeld surface analysis on the asymmetric unit of (I) shows a contribution of 5.9 % of total interactions in crystal for Sn…O contacts related to involving of four-coordinated Sn site of asymmetric unit with two oxygen atoms of two neighbouring phosphates in the coordination polymer. The Sn centre in the asymmetric unit of (II) receives a second interaction from chlorine atom that, however, has negligible contribution portion in the total interactions (evaluated by fingerprint plot) in the crystal. On the other hand, this chlorine affects the geometry at the Sn atom and causes the open C–Sn–C bond angle (of 140.18(24)°). For both structures, the contribution of H…H contacts to the total interaction is decisive, being 59.1 % for (I) and 73.9 % for (II); so that the one distinct spike observed in each of the fingerprint plots is related to H…H contacts. The O…H (34.1 %) in (I) and the H…Cl (20.2 %) in (II) are the characteristic intermolecular contacts in the corresponding structures, monitoring as two pairs of H-bond spikes for O…H and two sharp spikes for H…Cl. Furthermore, the structure (I) does not show the C…H interaction, whereas (II) including unsaturated carbon atoms manifests such interaction (5.7 %) as two very short spikes.

Synthesis, structural determination, theoretical studies and catalytic activity of Mn(II) complex of N-isonicotinyl phosphoric triamide ligand

A new N-isonicotinyl phosphoric triamide ligand with the formula 4-NC5H4C(O)NHP(O)(NC4H8)2 (L) was synthesized and characterized by 1H, 13C, 31P NMR and IR spectroscopies. The reaction of MnCl2·4H2O with L led to the formation of a new 3D system {MnL2Cl2}n·34CH3OH (C1). X-ray crystallographic data revealed that the ligand binds to the neighboring manganese ions through the nitrogen atom of pyridine (Npy) and the oxygen atom of phosphoryl (OP) in a bidentate manner. The Mn(II) centers showed a distorted cis(Npy, Npy) cis(OP, OP) cis(Cl, Cl) octahedral configuration. In order to compare the relative stability of C1 (with all-cis configuration) and its possible all-trans isomer, C′1, density functional theory (DFT) calculations were performed and the results showed the preference of C1 over C′1 from energy point of view. Quantum theory of atoms in molecules (QTAIM) analysis was applied to elucidate the nature of interactions, and the results suggested an ionic character (closed-shell interaction) for Mn–OP bond, and a partial covalent contribution for Mn–Npy interaction. Natural bond orbital (NBO) analysis was also used to calculate the charge distribution on atoms in the complex. The complex C1 showed efficient catalytic activity in the oxidation reaction of some alkenes to their corresponding epoxides. In addition, the effect of temperature and reaction time on the conversion and selectivity of cyclohexene epoxidation reaction in the presence of C1 as catalyst was investigated.

A novel Zn(II) complex of N-nicotinyl phosphoramide: Combined experimental and computational studies

Abstract A novel Zn(II) coordination polymer of N-nicotinyl phosphoric triamide ligand, {[Zn(L)2(H2O)2]⋅(NO3)2}n C1 (L = 3-NC5H4C(O)NHP(O)(NC6H12)2), has been synthesized and characterized by IR and 1H, 13C, 31P NMR spectroscopy. Crystal structure analysis of C1 demonstrates a distorted octahedral geometry for Zn(II) ions. The oxygen atom of phosphoryl group (Ophosphoryl) and the nitrogen atom of pyridine ring (Npyridine) of ligand take part in coordination to Zn(II) centers in a bidentate bridging mode. This coordination pattern results in infinite 1D polymeric chains along c axis, which are composed of metal shared 16-membered puckered rings. Structural data show that despite binding through Ophosphoryl, the P O bond distance unexpectedly shortens in C1 when compared to that of the ligand, conceivably due to the steric factors in the solid state. This is confirmed by comparing the structural and electronic properties of C1 and L in the gas phase by using density functional theory (DFT) calculations. Natural bond orbital (NBO) analysis reveals the metal–ligand interaction for C1 as donor–acceptor type delocalizations (charge transfer). Besides, on the basis of the quantum theory of atoms in molecules (QTAIM) analysis, the nature of Zn O and Zn N bondings is found to be mainly electrostatic with a small amount of covalent character.

Disperse dyeing and antibacterial properties of nylon and wool fibers using two novel nanosized copper(II) complexes bearing phosphoramide ligands

Disperse dyeing of nylon and wool fibers with two new nanosized copper(II) complexes including phosphoric triamide ligands with formula Cu(NO3)2L2 (1) and Cu(CH3COO)2L2 (2) where L=4-NO2C6H4NHP(O)(NC4H8O)2 (A) was performed successfully. Both complexes 1 and 2 produced yellow and green colored nylon and wool fabrics, respectively. The complexes were synthesized by ultrasonic method and characterized by 1H, 13C, 31P NMR, Fourier-transform infrared, photoluminescence, ultraviolet–visible spectroscopy, X-ray diffraction, field-emission microscopy and elemental analysis. The FE-SEM micrographs revealed that the nanoparticles of these compounds are spherical in morphology and ∼17–20nm in size. Very appropriate washfastness while poor lightfastness results were deduced for the dyed fibers. The in vitro antibacterial activities of the dyes 1, 2 and dyed wool/nylon fibers against the Gram-positive Bacillus subtilis bacterium illustrated increasing in the antibacterial effect by increasing the dye concentration from 0.1% to 0.5% o.w.f. on both wool and nylon dyed fibers.

Discrete and Polymeric Coordination Assemblies Derived from 3-Pyridyl Attached Flexible Phosphoric Triamide Ligand and Copper Salts

A new example of phosphonium cation, [P(NH3Py)4]+, (2) featuring 3-pyridyl substituents has been reported. Reactivity of 2 with KOH in methanol have resulted in the formation of a neutral phosphine imine [P(N3Py)(NH3Py)3], 2-H. Treatment of 2 with various metal salts of copper have resulted in a P–N bond cleavage in which the in situ generated phosphoramide ligand [PO(NH3Py)3], 1, has shown to yield interesting kinds of self-assembled structures in macrocyclic, cage and 2D-coordination polymers. Thus, the reaction of 2 with Cu(NO3)2 in methanol gave the supramolecular [M6L8]12+ type cage reported earlier with the phosphoramide 1. Treatment of 2 with a Cu(I) salt in CHCl3 under ambient conditions have lead to the formation of a 20-membered macrocyclic Cu(II) compound [(PO(NH3Py)3)CuCl2]2, 3, via the in situ oxidation of Cu(I). In another reaction, treatment of 1 or 2 with Cu(NO3)2 in a reducing solvent such as dimethylformamide (DMF) under hydrothermal conditions gave a Cu(I) coordination polymer {[Cu2(PO(NH3Py)3)3](NO3)2}n, 4. Crystallographic studies on all these newly synthesized compounds have shown interesting kinds of supramolecular organization for these molecules. New examples of a phosphonium cation, [P(NH3Py)4]+, and a phosphine imine, [P(N3Py)(NH3Py)3] featuring 3-pyridyl substituents have been reported. Treatment of the phosphonium cation with various metal salts of copper have resulted in a P–N bond cleavage in which the in situ generated phosphoramide ligand [PO(NH3Py)3], has shown to yield interesting kinds of self-assembled structures in macrocyclic, cage and 2D-coordination polymers.

Nanoparticles of novel organotin(IV) complexes bearing phosphoric triamide ligands

Four novel organotin(IV) complexes containing phosphoric triamide ligands were synthesized and characterized by multinuclear (1H, 31P, 13C) NMR, infrared, ultraviolet and fluorescence spectroscopy as well as elemental analysis. The 1H NMR spectra of complexes 1–4 proved that the Sn atoms adopt octahedral configurations. The nanoparticles of the complexes were also prepared by ultrasonication, and their SEM micrographs indicated identical spherical morphologies with particles sizes about 20–25 nm. The fluorescence spectra exhibited blue shifts for the maximum wavelength of emission upon complexation.

A CSD analysis on H-bond patterns from phosphoric triamides to their coordination compounds, new complexes with (tBuNH)3PO ligand (PO): Cl2Ph2Sn(PO)2 and Fe(PO)2(NO3)3

The phosphoryl donor ligand (tBuNH)3PO (PO) was used for preparation of new tin(IV), Cl2Ph2Sn(PO)2 (1), and iron(III), Fe(PO)2(NO3)3 (2), complexes. These complexes are the first examples of using a phosphoric triamide containing a secondary nitrogen atom, [RNH]3P(O), for preparation of an organotin(IV) complex of the type ([RNH]3P(O))2X2Ph2Sn, X = halide, and an iron(III) complex. In 1, the Sn coordination geometry is octahedral with the pair of similar ligands in a trans orientation. The Fe center in 2 is seven-coordinated with the two phosphoramide ligands in a trans fashion, too. This article also reviews the structures of analogous complexes with phosphoric triamide ligands, deposited in the CSD, aiming to classify hydrogen bond patterns in this category of compounds. Moreover, it is tried to find a relationship between the H-bond patterns in complexes and the related free ligands.

New N-nicotinyl and N-isonicotinyl, N′,N″-diaryl phosphorictriamides with new Er(III) complex: synthesis, spectroscopic study and crystal structures

Ten new N-nicotinyl and N-isonicotinyl phosphoramidates with formula XP(O)R2, X = Nicotinamide(nia), R = NHCH2Ph (1), N(CH3)CH2Ph (2), NHCH(CH3)Ph (3), NH-CH2C4H3O (4), NHCH2(C5H4N) (5), 3-NH-C5H4N (6), and YP(O)R2, Y = isonicotinamide(iso), R = NHCH2Ph (7), N(CH3)CH2Ph (8), NHCH(CH3)Ph (9), NH-CH2C4H3O (10) plus one new Er(III) complex with formula Er(L)2(NO3)3 (11), L = (iso)PO(NHCH2C4H3O)2 (10), were synthesized and characterized by elemental analysis and 1H, 13C, 31P NMR, IR, UV–vis spectroscopy. Crystal structures of compounds 10 and 11 were also determined by X-ray crystallography. Interestingly, the 1H NMR spectra of compounds 1, 2, 6, 7, 9 indicated long-range n J P,H (n = 5,6,7) coupling constants, in the range of 1.4–1.9 Hz, for the splitting of pyridine ring protons with phosphorus atom. IR results showed that the ν(C=O) values of compounds 7–10 are greater than those of compounds 1–5 which means that isonicotinyl moiety is more electron withdrawing than nicotinyl group. X-ray outcomes revealed that in complex 11 three phosphoric triamide ligands have been connected to each Er(III); one from Npyridine and two from P=O donor sites. One of the P=O donor ligands is mono dentate while the other one acts as a bidentate ligand and coordinates to another Er atom via its Npyridine site. By forming complex 11 the P=O and C–Namide bond lengths of ligand is increased in both, mono and bi dentate, ligands while the C=O bond length is decreased to lower values. These variations are in good agreement with IR results. All H-bonds and electrostatic interactions lead to form a three-dimensional polymeric cluster in the crystal lattice of 10 and 11.