The 1:2 co-crystal formed between N,N'-bis(pyridin-4-ylmeth-yl)ethanedi-amide and benzoic acid: crystal structure, Hirshfeld surface analysis and computational study

Synthesis, Structure, Hirshfeld Surface Analysis, Non-Covalent Interaction, and In Silico Studies of 4-Hydroxy-1-[(4-Nitrophenyl)Sulfonyl]Pyrrolidine-2-Carboxyllic Acid

The new compound 4-hydroxy-1-[(4-nitrophenyl)sulfonyl]pyrrolidine-2-carboxyllic acid was obtained by the reaction of 4-hydroxyproline with 4-nitrobenzenesulfonyl chloride. The compound was characterized using single crystal X-ray diffraction studies. Spectroscopic methods including NMR, FTIR, ES-MS, and UV were employed for further structural analysis of the synthesized compound. The title compound was found to have crystallized in an orthorhombic crystal system with space group P212121. The S1-N1 bond length of 1.628 (2) Å was a strong indication of the formation of the title compound. The absence of characteristic downfield 1H NMR peak of pyrrolidine ring and the presence of S-N stretching vibration at 857.82 cm-1 on the FTIR are strong indications for the formation of the sulfonamide. The experimental study was complemented with computations at the B3LYP/6-311G +  + (d,p) level of theory to gain more understanding of interactions in the compound at the molecular level. Noncovalent interaction, Hirsfeld surface analysis and interaction energy calculations were employed in the analysis of the supramolecular architecture of the compound. Predicted ADMET parameters, awarded suitable bioavailability credentials, while the molecular docking study indicated that the compound enchants promising inhibition prospects against dihydropteroate synthase, DNA topoisomerase, and SARS-CoV-2 spike.

Graphical Abstract

Herein we present the solid state structure, noncovalent interaction and spectroscopic analysis of a prospective bioactive compound 4-hydroxy-1-[(4-nitrophenyl)sulphonyl]pyrrolidine-2-carboxyllic acid.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10870-023-00978-0.

Crystal structure, Hirshfeld surface and computational study of 1-(9,10-dioxo-9,10-dihydroanthracen-1-yl)-3-propanoylthiourea

In the title compound, the thio­urea chromophore is planar to an r.m.s deviation of 0.032 Å with the thiol­ate sulfur atom being the most deviated. Bifurcated N—H⋯O intra­molecular hydrogen bonds result in an S(6) supra­molecular synthon. In the crystal, mol­ecules are linked by N—H⋯O inter­molecular hydrogen-bonding inter­actions and stabilized by C—H⋯π and π–π inter­actions.

The title compound, C₁₈H₁₄N₂O₃S, crystallizes in the ortho­rhom­bic crystal system and Pbca space group. The thio­urea chromophore is planar to an r.m.s deviation of 0.032 Å with the thiol­ate sulfur atom being the most deviated. Bifurcated N—H⋯O intra­molecular hydrogen bonds result in an S(6) supra­molecular synthon. In the crystal, mol­ecules are linked by N—H⋯O inter­molecular hydrogen-bonding inter­actions and stabilized by C—H⋯π and π–π inter­actions. Hirshfeld surface analysis and fingerprint plot indicate the H⋯H inter­molecular contacts as the highest contributor to the overall surface contacts (38%) and this is supported by the high dispersive and electrostatic inter­action energies.

Non-covalent interactions involving remote substituents influence the topologies of supramolecular chains featuring hydroxyl-O–H⋯O(hydroxyl) hydrogen bonding in crystals of (HOCH2CH2)2NC(S)N(H)(C6H4Y-4) for Y = H, Me, Cl and NO2

Secondary non-covalent interactions prove crucial in determining the topology of supramolecular chains sustained by conventional O–H⋯O hydrogen bonding.

Crystal structure, Hirshfeld surface analysis and computational study of the 1:2 co-crystal formed between N,N'-bis-[(pyridin-4-yl)meth-yl]ethanedi-amide and 3-chloro-benzoic acid

The asymmetric unit of the title 1:2 co-crystal, C₁₄H₁₄N₄O₂·2C₇H₅ClO₂, comprises a half-mol-ecule of oxalamide (⁴ LH₂), being located about a centre of inversion, and a mol-ecule of3-chloro-benzoic acid (3-ClBA) in a general position. From symmetry, the ⁴ LH₂ mol-ecule has a (+)anti-periplanar conformation with the 4-pyridyl residues lying to either side of the central, planar C₂N₂O₂ chromophore with the dihedral angle between the core and pyridyl ring being 74.69 (11)°; intra-molecular amide-N-H⋯O(amide) hydrogen bonds are noted. The 3-ClBA mol-ecule exhibits a small twist as seen in the C₆/CO₂ dihedral angle of 8.731 (12)°. In the mol-ecular packing, three-mol-ecule aggregates are formed via carb-oxy-lic acid-O-H⋯N(pyrid-yl) hydrogen bonding. These are connected into a supra-molecular tape along [111] through amide-N-H⋯O(carbon-yl) hydrogen bonding. Additional points of contact between mol-ecules include pyridyl and benzoic acid-C-H⋯O(amide), methyl-ene-C-H⋯O(carbon-yl) and C-Cl⋯π(pyrid-yl) inter-actions so a three-dimensional architecture results. The contributions to the calculated Hirshfeld surface are dominated by H⋯H (28.5%), H⋯O/O⋯H (23.2%), H⋯C/C⋯H (23.3%), H⋯Cl/Cl⋯H (10.0%) and C⋯Cl/C⋯Cl (6.2%) contacts. Computational chemistry confirms the C-Cl⋯π inter-action is weak, and the importance of both electrostatic and dispersion terms in sustaining the mol-ecular packing despite the strong electrostatic term provided by the carb-oxy-lic acid-O-H⋯N(pyrid-yl) hydrogen bonds.

Crystal structure, Hirshfeld surface analysis and computational study of the 1:2 co-crystal formed between N,N'-bis-(pyridin-4-ylmeth-yl)ethane-diamide and 4-chloro-benzoic acid

The asymmetric unit of the title 1:2 co-crystal, C14H14N4O2·2C7H5ClO2, comprises two half mol-ecules of oxalamide (4 LH2), as each is disposed about a centre of inversion, and two mol-ecules of 4-chloro-benzoic acid (CBA), each in general positions. Each 4 LH2 mol-ecule has a (+)anti-periplanar conformation with the pyridin-4-yl residues lying to either side of the central, planar C2N2O2 chromophore with the dihedral angles between the respective central core and the pyridyl rings being 68.65 (3) and 86.25 (3)°, respectively, representing the major difference between the independent 4 LH2 mol-ecules. The anti conformation of the carbonyl groups enables the formation of intra-molecular amide-N-H⋯O(amide) hydrogen bonds, each completing an S(5) loop. The two independent CBA mol-ecules are similar and exhibit C6/CO2 dihedral angles of 8.06 (10) and 17.24 (8)°, indicating twisted conformations. In the crystal, two independent, three-mol-ecule aggregates are formed via carb-oxy-lic acid-O-H⋯N(pyrid-yl) hydrogen bonding. These are connected into a supra-molecular tape propagating parallel to [100] through amide-N-H⋯O(amide) hydrogen bonding between the independent aggregates and ten-membered {⋯HNC2O}2 synthons. The tapes assemble into a three-dimensional architecture through pyridyl- and methyl-ene-C-H⋯O(carbon-yl) and CBA-C-H⋯O(amide) inter-actions. As revealed by a more detailed analysis of the mol-ecular packing by calculating the Hirshfeld surfaces and computational chemistry, are the presence of attractive and dispersive Cl⋯C=O inter-actions which provide inter-action energies approximately one-quarter of those provided by the amide-N-H⋯O(amide) hydrogen bonding sustaining the supra-molecular tape.