Electrostatic properties of beta-cytidine and cytosine monohydrate from Bragg diffraction.

Abstract

The charge-density distribution in the crystal structure of the nucleoside beta-cytidine at 123 K has been determined from X-ray diffraction data (Ag K alpha, lambda = 0.5608 A) using all 7233 reflections with sin theta/lambda < or = 1.14 A-1. Maps of electrostatic potential for the cytosine base in cytidine are similar to those derived from previous charge-density studies of cytosine monohydrate and 1-beta-D-arabinosyl-cytosine, after taking chemical differences into account. These results were obtained from pseudoatom multipole refinements including kappa as a variable to describe the expansion or contraction of the spherical valence shell for each atom type. A new structure refinement of this type has also been carried out for cytosine monohydrate. A survey of kappa values for hydrogen indicates that this is a variable which is not well determined experimentally. Variations in kappa H are relayed into the population parameters obtained for other pseudoatoms and can have a small but significant effect on molecular properties, such as the dipole moment. Assuming an average theoretical value of kappa H = 1.24, the molecular dipole moments calculated from the monopole and dipole pseudoatom population parameters are 17 (4) and 8.2 (15) Debye for cytidine nucleoside and cytosine in the monohydrate, respectively. Systems of atomic point charges are presented for cytidine, cytosine and water. These are generally satisfactory in reproducing the experimentally determined molecular electrostatic potentials and dipole moments.