Conformers and hydrogen bonds in cytidine 5′-diphosphocholine sodium single crystals grown from a mixture of ethanol and water

Abstract

The molecular structure of cytidine 5′-diphosphocholine sodium (CDPC) grown from a mixture of ethanol and water was determined by X-ray diffraction (XRD). CDPC was found to have an orthorhombic structure with confirmed lattice parameters of a = 6.978 Å, b = 12.406 Å and c = 29.326 Å. This nucleotide coenzyme was highly folded and net-like. Each crystallographic unit consisted of one sodium atom, one pyrophosphate group, one cytosine group, one coordinated water molecule, one pentose molecule, and three lattice water molecules. The interspaces of neighboring CDPC molecules were filled with water molecules and methyl groups. Although the coordinated water was connected to sodium atoms, the lattice water molecules formed chair-shaped water hexamers. The hydrogen bonds which played an important role in maintaining the structure included O H···O, N H···O and C H···O and ranged in length from 2.682 (17) to 3.349 (17) Å. Fourier transform infrared spectroscopy (FTIR) showed a broad absorption in the 400–2000 cm −1 region characteristic of short hydrogen bonds. So for industrial crystallization, methods which could eliminate the influence of hydrogen bonds should be taken, and it would be beneficial for the process of crystallization.