Structural and computational insights into two novel organic salts: XRD, hirshfeld analysis, DFT, and molecular docking studies

Soudani S., Demir Kanmazalp S., ÖZDEMİR M., YALÇIN B., Mi J., Nasr C. B.

Journal of Molecular Structure, vol.1338, 2025 (SCI-Expanded) identifier

  • Publication Type: Article / Article
  • Volume: 1338
  • Publication Date: 2025
  • Doi Number: 10.1016/j.molstruc.2025.142263
  • Journal Name: Journal of Molecular Structure
  • Journal Indexes: Science Citation Index Expanded (SCI-EXPANDED), Scopus, Academic Search Premier, Chemical Abstracts Core, Chimica, Compendex, INSPEC
  • Keywords: Crystal structure, DFT, Hirshfeld surface, Molecular docking, X-ray diffraction
  • Marmara University Affiliated: Yes

Abstract

Two new salts, 1-phenylpiperazinium nitrate (I) and 2,4 diamino-6-hydroxypyrimidinium perchlorate (II), were synthesized and characterized using single-crystal X-ray diffraction and DFT calculations. Compound (I) forms layers of NO₃⁻ anions and organic cations linked via N–H···O, N–H···N, and C–H···O hydrogen bonds. Compound (II) exhibits porous structures, with organic moieties (C₄H₇N₄O) and perchlorate anions connected by N–H···O and C–H···O hydrogen bonds, creating pores along the b-axis at (0, 0, 0) and (1/2, 1/2, 0). Hirshfeld surface and 2D fingerprint analyses revealed intermolecular interactions, while energy frameworks identified stabilization contributions. DFT calculations showed compound (II) to be more stable, polar, and with a larger band gap than (I), attributed to its hydrogen bonding and electronic structure. Both compounds exhibited HOMO-LUMO charge separation. Molecular docking against HIV-II protease demonstrated effective interactions with key amino acids, suggesting drug potential. Despite their smaller size, the salts formed interactions akin to Indinavir, a known HIV protease inhibitor.