Structural studies on two new phosphoramides with the same [OC4H8N]P(O) segment by means of single-crystal X-ray diffraction, Hirshfeld surface analysis and 3D energy framework approach

Elucidating the Role of Atomically Dilute Copper Centers Impregnating a Phosphamide Polymer for the Preferential Hydrogen Evolution Reaction over CO2 Reduction

Organic polymers have attracted considerable interest in designing a multifunctional electrocatalyst. However, the inferior electro-conductivity of such metal-free polymers is often regarded as a shortcoming. Herein, a nitrogen- and phosphorus-rich polymer with phosphamide functionality (PAP) in the repeating unit has been synthesized from diaminopyridine (DAP) and phenylphosphonic dichloride (PPDC) precursors. The presence of phosphamide oxygen and pyridine nitrogen in the repeating unit of PAP leads to the coordination of the CuII ion and the incorporation of 3.29 wt % in the polymer matrix (Cu30@PAP) when copper salt is used to impregnate the polymer. Combined with a spectroscopic, microscopic, and DFT study, the coordination and geometry of copper in the PAP matrix has been established to be a distorted square planar CuII in a N2O2 ligand environment where phosphamide oxygen and pyridine nitrogen of the PAP coordinate to the metal center. The copper incorporation in the PAP modulates its electrocatalytic activity. On the glassy carbon electrode, PAP shows inferior activity toward the hydrogen evolution reaction (HER) in 0.5 M H2SO4 while 3 wt % copper incorporation (Cu30@PAP) significantly improves the HER performance with an overpotential of 114 mV at 10 mA cm-2. The notable electrochemical activity with Cu30@PAP occurs due to the impregnation of Cu(II) in PAP, improved electro-kinetics, and better charge transfer resistance (Rct). When changing the electrolyte from H2SO4 to CO2-saturated bicarbonate solution at nearly neutral pH, PAP shows HER as the dominant pathway along with the partial reduction of CO2 to formate. Moreover, the use of Cu30@PAP as an electrolcatalyst could not alter the predominant HER path, and only 20% Faradaic efficiency for the CO2 reduced products has been achieved. Post-chronoamperometric characterization of the recovered catalyst suggests an unaltered valence state of the copper ion and the intact chemical structure of PAP. DFT studies unraveled that the copper sites of Cu30@PAP promote water adsorption while phosphamide-NH of the PAP can weakly hold the CO2 adduct via a hydrogen bonding interaction. A detailed calculation has pointed out that the tetra-coordinated copper centers present in the PAP frame are the reactive sites and that the formation of the [CuI-H] intermediate is the rate-limiting step for both HER and its competitive side reaction, i.e., CO2 reduction to formate or CO formation. The high proton concentration in the electrolyte of pH < 7 leads to HER as the predominant pathway. This combined experimental and theoretical study has highlighted the crucial role of copper sites in electrocatalysis, emphasizing the plausible reason for electrocatalytic selectivity.

Structural and Molecular Packing study of Three New Amidophosphoric Acid Esters and Assessment of Their Inhibiting Activity Against SARS-CoV-2 by Molecular Docking

Three new compounds of amidophosphoric acid esters with a [OCH2C(CH3)2CH2O]P(O)[X] segment (where X=cyclopentylamido (1), 2-aminopyridinyl (2) and pyrrolidinyl (3)) were synthesized and studied using FT-IR and 31P/13C/1H NMR spectroscopies and single-crystal X-ray diffraction analysis. The compounds crystallize in the triclinic space groups P 1 ‾ for 1 and 3 and in the orthorhombic space group Pca21 for 2, where the asymmetric unit consists of three symmetrically-independent molecules for 1 and one molecule for 2 and 3. The intermolecular interactions and supramolecular assemblies are assessed by Hirshfeld surface analysis and enrichment ratios. The results reveal that the substituent effect plays an important role in directing the supramolecular structures. The presence of the aromatic substituent aminopyridine in 2 providing the C-H…π interactions leads to a larger variety in interactions including H…H, H…O/O…H, H…C/C…H and H…N/N…H contacts, whereas the packings of the compounds 1 and 3 bearing aliphatic substituents only include H…H and H…O/O…H contacts. The enrichment ratios affirm the importance of O…H/H…O contacts reflecting the hydrogen bond N-H…O interactions to be the enriched contacts. Compounds 1-3 were also investigated along with five similar reported structures with a [OCH2C(CH3)2CH2O]P(O) segment for their inhibitory behavior against SARS-CoV-2. The molecular docking results illustrate that the presence of the aromatic amido substituent versus the aliphatic type provides a more favorable condition for their biological activities.

Experimental and theoretical study of novel amino-functionalized P(V) coordination compounds suggested as inhibitor of MPro of SARS-COV-2 by molecular docking study

Amino-functionalized P(V) derivatives providing both N- and O-donor modes have attracted interest owing to their potential to form interesting coordination assemblies with applications such as biological drugs. Novel coordination modes of two- and four-dentate tris (pyridin-2-yl)phosphoric triamide OP[NH-2Py]3 as ([Co(II){[O][NH-2Py]P(O)[Ph]}2(DMF)2], 1) and ([Cu(II)Cl{[NH-2Py]2P(O)[N-2Py]}].DMF, 2) have been synthesized and structurally studied. The metal center environment is distorted octahedral for 1 and distorted square pyramidal for 2. The crystal structure of a new complex of Cu(II) with a Cu[N]4[Cl]2 environment ([Cu(II)Cl2(Pyrazole)4], 3) is also investigated. An evaluation of the inhibitory effect against the coronavirus (Main Protease [MPro] of SARS-CoV-2) was carried out by a molecular docking study and illustrates that these compounds have a good interaction tendency with CoV-2, where 1 has the best binding affinity with the biological target comparable with other SARS-CoV-2 drugs. Moreover, theoretical QTAIM and natural bond orbital (NBO) calculations are used to evaluate the metal-oxygen/-nitrogen bonds suggesting that they are mainly electrostatic in nature with a slight covalent contribution. A molecular packing analysis using Hirshfeld surface (HS) analysis shows that N-H … O (in 1 and 2) and N-H … Cl (in 3) hydrogen bonds are the dominant interactions that contribute to the crystal packing cohesion. The semi-empirical PIXEL method indicates that the electrostatic and repulsion energy components in the structures of 1 and 2 and the dispersion and electrostatic components in that of 3 are the major contributors to the total lattice energy.

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

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 ) ${R}_{2}^{1}\left(6\right)$ , C(4) and R 2 2 ( 10 ) / R 2 1 ( 6 ) ${R}_{2}^{2}\left(10\right)/{R}_{2}^{1}\left(6\right)$ motifs, respectively, for 1–3) or dimeric (the R 2 2 ( 8 ) ${R}_{2}^{2}\left(8\right)$ 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.