Crystal structure, Hirshfeld surface analysis, DFT and molecular docking studies of 4′-(benzyloxy)-[1,1′-biphenyl]-3-carboxylic acid

IF 0.5 Q4 CRYSTALLOGRAPHY

Acta Crystallographica Section E: Crystallographic Communications Pub Date : 2025-03-01 DOI:10.1107/S2056989025001021

M. Harish Kumar , M. Vinduvahini , H. T. Srinivasa , H. C. Devarajegowda , B. S. Palakshamurthy

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引用次数: 0

Abstract

The title molecule was studied by single-crystal X-ray analysis to determine its molecular structure and investigate the interactions present. Theoretical (obtained by DFT) and experimental parameters were compared. In addition, Hirshfeld surface analysis and molecular docking studies were performed for the title compound as a ligand and the SARS-Covid-2 (PDB ID:8BEC) protein, specifically the Omicron variant.

In the title compound, C₂₀H₁₆O₃, intramolecular C— H⋯O hydrogen bonds are observed. The dihedral angles between the aromatic benzoic acid ring and the two adjacent aromatic rings are 26.09 (4) and 69.93 (8)°, while the dihedral angle between the aromatic rings connected by the C—O—C—C [torsion angle = −175.9 (2)°] link is 89.11 (3)°. In the crystal, inversion dimers linked by pairs of O—H⋯O hydrogen bonds generate R₂²(8) ring motifs. These dimers are further linked by C—H⋯π interactions, forming molecular sheets along (010). The molecular structure was optimized by density functional theory (DFT) at the B3LYP/6–311+ G(d,p) level and the bond lengths, angles and torsion angles were compared with experimental values obtained by X-ray diffraction. The HOMO and LUMO were calculated, the energy gap between them being 4.3337 eV. Further, the intermolecular interactions were quantified using Hirshfeld surface analysis and fingerprint plots and energy frameworks were generated. The two-dimensional fingerprint plots indicate that the major contributions to the crystal packing are from H⋯H (39.7%), H⋯C (39.0%) and H⋯O (18.0%) interactions. The energy framework calculations reveal that the dispersion energy (E_dis= 201.0 kJ mol⁻¹) dominates the other energies. Molecular docking studies were carried out for the title compound as a ligand and the SARS-Covid-2 (PDB ID:8BEC) protein, specifically the Omicron variant, was used as a receptor giving a binding affinity of −7.6 kcal mol⁻¹.

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在标题化合物C20H16O3中，观察到分子内的C- H⋯O氢键。芳香族苯甲酸环与相邻的两个芳环之间的二面角分别为26.09(4)和69.93(8)°，而由C-O-C-C[扭角= -175.9(2)°]连接的芳环之间的二面角为89.11(3)°。在晶体中，由一对O- h⋯O氢键连接的倒置二聚体产生r22(8)环基序。这些二聚体通过C-H⋯π相互作用进一步连接，沿着（010）形成分子片。利用密度泛函理论（DFT）在B3LYP/6-311+ G（d,p）水平上对分子结构进行优化，并将键长、键角和扭角与x射线衍射实验值进行比较。计算了HOMO和LUMO的能级，两者之间的能差为4.3337 eV。利用Hirshfeld表面分析对分子间相互作用进行了定性分析，生成了指纹图谱和能量框架。二维指纹图谱表明，对晶体堆积的主要贡献是H⋯H（39.7%）、H⋯C（39.0%）和H⋯O（18.0%）相互作用。能量框架计算表明，色散能（E dis= 201.0 kJ mol-1）占主导地位。标题化合物作为配体进行了分子对接研究，SARS-Covid-2 （PDB ID:8BEC）蛋白，特别是Omicron变体，被用作结合亲和力为-7.6 kcal mol-1的受体。

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来源期刊

Acta Crystallographica Section E: Crystallographic Communications Chemistry-Chemistry (all)

CiteScore

1.90

自引率

0.00%

发文量

351

审稿时长

3 weeks

期刊介绍： Acta Crystallographica Section E: Crystallographic Communications is the IUCr''s open-access structural communications journal. It provides a fast, simple and easily accessible publication mechanism for crystal structure determinations of inorganic, metal-organic and organic compounds. The electronic submission, validation, refereeing and publication facilities of the journal ensure rapid and high-quality publication of fully validated structures. The primary article category is Research Communications; these are peer-reviewed articles describing one or more structure determinations with appropriate discussion of the science.

Crystal structure, Hirshfeld surface analysis, DFT and mol­ecular docking studies of 4′-(benz­yloxy)-[1,1′-biphen­yl]-3-carb­oxy­lic acid

Abstract

Crystal structure, Hirshfeld surface analysis, DFT and molecular docking studies of 4′-(benzyloxy)-[1,1′-biphenyl]-3-carboxylic acid