Interactions of pyridoxine (Vitamin B6) with squaric acid and water. Experimental and theoretical studies

• Published in: Journal of molecular structure 2022-03, Vol.1251, p.131773, Article 131773
• Main Authors: Komasa, Anna, Babijczuk, Karolina, Dega-Szafran, Zofia, Gołdyn, Mateusz, Bartoszak-Adamska, Elżbieta, Szafran, Mirosław, Cofta, Grzegorz
• Format: Article
• Language: English
• Subjects: DFT calculations; FTIR and NMR spectroscopy; Hydrogen bonds; Microbial activity; Pyridoxine; Squaric acid
• ISSN: 0022-2860; 1872-8014
• DOI: 10.1016/j.molstruc.2021.131773

•The structure of pyridoxinium hydrogen squarate monohydrate is determined by X-ray diffraction.•Two molecules form a centrosymmetrical dimer.•The structures of dimer and monomers are optimized at APF-D/6–311++G(d,p) level.•Two dimensional techniques are applied to explain the H-1 and C-13 NMR spectra.•The O−H⋅⋅⋅O, N−H⋅⋅⋅O interactions are characterized using QTAIM method. Pyridoxine (Vitamin B6, 3‑hydroxy-4,5-bis(hydroxymethyl)-2-methylpyridine) forms a hydrate adduct with squaric acid (3,4-dihydroxy-3-cyclobuten-1,2‑dione). The proton from squaric acid is transferred to the pyridoxine nitrogen atom. Two hydrogen squarate anions form a centrosymmetric α-dimer, which interacts symmetrically with two pyridoxinium cations and two water molecules, through several hydrogen bonds of the lengths from 2.498(3) to 2.843(3) Å. The molecular structure of the 2:2:2 adduct (dimer) was studied by a single-crystal X-ray diffraction, DFT calculations, FTIR and NMR spectroscopies. Structures of three models of the monomer of pyridoxinium hydrogen squarate monohydrate (1:1:1) were optimized at the APF-D/6–311++G(d,p) level of theory. Their molecular geometries, hydrogen bond distances, IR spectra, natural atomic charges, frontier molecular orbitals (HOMO and LUMO) were analyzed. The quantum theory of atoms in molecule (QTAIM) was used to classify the strength of the hydrogen bonds in the dimer and monomers of the optimized adducts. The studied compound was screened for antifungal activities and showed inhibiting properties against A. niger and P. placenta. [Display omitted]