Protonated nucleobases are not fully ionized and may form stable base pairs in the crystalline state

The following paper presents experimental charge density studies of cytosinium chloride, adeninium chloride hemihydrate, and guanine dichloride crystals based on ultra-high resolution X-ray diffraction data and extensive theoretical calculations. Results confirm that the cohesive energies of the studied systems are dominated by contributions from intermolecular electrostatic interactions, as expected for ionic crystals. Electrostatic interactions energies (Ees) usually constitute 95% of total interaction energies. The Ees energies were several times larger in absolute value when compared, for example, to pairs of neutral nucleobases. However, they were not as big as some of the theoretical calculations predicted. This was because the molecules appeared not to be fully ionized in the studied crystals. Apart from chlorine to protonated nucleobase charge transfer, small but visible, charge redistribution within nucleobase cations was observed. Some pairs of single protonated bases in the studied crystals exhibited attractive interactions (negative values of Ees) or unusually low repulsion despite identical molecular charges. This was because strong hydrogen bonding between bases overcompensated overall cation-cation repulsion, the latter being weakened due to charge transfer and molecular charge density polarization.