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Weak C-H···X (X = O, N) hydrogen bonds in the crystal structure of dihydroberberine.

ABSTRACT: Dihydroberberine (systematic name: 9,10-dimethoxy-6,8-dihydro-5H-1,3-dioxolo[4,5-g]isoquinolino[3,2-a]isoquinoline), C20H19NO4, a reduced form of pharmacologically important berberine, crystallizes from ethanol without interstitial solvent. The molecule shows a dihedral angle of 27.94 (5)° between the two arene rings at the ends of the molecule, owing to the partial saturation of the inner quinolizine ring system. Although lacking classical O-H or N-H donors, the packing in the crystalline state is clearly governed by C-H···N and C-H···O hydrogen bonds involving the two acetal-type C-H bonds of the 1,3-dioxole ring. Each dihydroberberine molecule is engaged in four hydrogen bonds with neighbouring molecules, twice as donor and twice as acceptor, thus forming a two-dimensional sheet network that lies parallel to the (100) plane.

SUBMITTER: Pingali S

PROVIDER: S-EPMC4165590 | biostudies-literature | 2014 Apr

REPOSITORIES: biostudies-literature

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Weak C-H···X (X = O, N) hydrogen bonds in the crystal structure of dihydroberberine.

Pingali Subramanya S Donahue James P JP Payton-Stewart Florastina F

Acta crystallographica. Section C, Structural chemistry 20140311 Pt 4

Dihydroberberine (systematic name: 9,10-dimethoxy-6,8-dihydro-5H-1,3-dioxolo[4,5-g]isoquinolino[3,2-a]isoquinoline), C20H19NO4, a reduced form of pharmacologically important berberine, crystallizes from ethanol without interstitial solvent. The molecule shows a dihedral angle of 27.94 (5)° between the two arene rings at the ends of the molecule, owing to the partial saturation of the inner quinolizine ring system. Although lacking classical O-H or N-H donors, the packing in the crystalline state ...[more]

PMID: 24705054

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Project description:Pyrimidinone scaffolds are present in a wide array of molecules with synthetic and pharmacological utility. The inherent properties of these compounds may be attributed to intermolecular interactions analogous to the interactions that molecules tend to establish with active sites. Pyrimidinones and their fused derivatives have garnered significant interest due to their structural features, which resemble nitrogenous bases, the foundational building blocks of DNA and RNA. Similarly, pyrimidinones are predisposed to forming N-H···O hydrogen bonds akin to nitrogenous bases. Given this context, this study explored the supramolecular features and the predisposition to form hydrogen bonds in a series of 18 substituted 4-(trihalomethyl)-2(1H)-pyrimidinones. The formation of hydrogen bonds was observed in solution via nuclear magnetic resonance (NMR) spectroscopy experiments, and subsequently confirmed in the crystalline solid state. Hence, the 18 compounds were crystallized through crystallization assays by slow solvent evaporation, followed by single-crystal X-ray diffraction (SC-XRD). The supramolecular cluster demarcation was employed to evaluate all intermolecular interactions, and all crystalline structures exhibited robust hydrogen bonds, with an average energy of approximately -21.64 kcal mol-1 (∼19% of the total stabilization energy of the supramolecular clusters), irrespective of the substituents at positions 4, 5, or 6 of the pyrimidinone core. To elucidate the nature of these hydrogen bonds, an analysis based on the quantum theory of atoms in molecules (QTAIM) revealed that the predominant intermolecular interactions are N-H···O (average of -16.55 kcal mol-1) and C-H···O (average of -6.48 kcal mol-1). Through proposing crystallization mechanisms based on molecular stabilization energy data and contact areas between molecules and employing the supramolecular cluster and retrocrystallization concepts, it was determined that altering the halogen (F/Cl) at position 4 of the pyrimidinone nucleus modifies the crystallization mechanism pathway. Notably, the hydrogen bonds present in the initial proposed steps were confirmed by 1H NMR experiments using concentration-dependent techniques.

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Weak C-H···X (X = O, N) hydrogen bonds in the crystal structure of dihydroberberine.

Publications

Weak C-H···X (X = O, N) hydrogen bonds in the crystal structure of dihydroberberine.

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