New organotin(IV)-phosphoramidate complexes: Breaking of the PO⋯HN hydrogen bonds and its influence on the molecular packing

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 Sn^IV 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.

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).

Weak functional group interactions revealed through metal-free active template rotaxane synthesis

Modest functional group interactions can play important roles in molecular recognition, catalysis and self-assembly. However, weakly associated binding motifs are often difficult to characterize. Here, we report on the metal-free active template synthesis of [2]rotaxanes in one step, up to 95% yield and >100:1 rotaxane:axle selectivity, from primary amines, crown ethers and a range of C=O, C=S, S(=O)2 and P=O electrophiles. In addition to being a simple and effective route to a broad range of rotaxanes, the strategy enables 1:1 interactions of crown ethers with various functional groups to be characterized in solution and the solid state, several of which are too weak - or are disfavored compared to other binding modes - to be observed in typical host-guest complexes. The approach may be broadly applicable to the kinetic stabilization and characterization of other weak functional group interactions.