Insights into the non-covalent interaction between modified nucleobases and graphene nanoflake from first-principles

Abstract

The four new modified nucleobases (NBs), 5-mC, 5-hmC, 5-fC and 5-caC, besides the regular adenine, thymine, cytosine, guanine and uracil, are important in expression and regulation of genetic information. These four new major NBs are all derived from base cytosine by adding various functional groups, and their identification from the regular ones are much desired currently. However, the four new major NBs interacted with graphene on its surface have not been well considered, though a number of studies of regular NBs adsorbed on low-dimensional carbon materials are available to identify different NBs. This work reveals the interaction between the four new major NBs and graphene nanoflake substrate by using first-principle calculations based on density functional theory. The structure, energy and non-covalent interaction of the graphene/NBs complex are calculated and explored in details. The energy decomposition analysis, reduced density gradient, charge transfer and projected density of states are also performed to investigate the nature of the interaction between NBs and graphene nanoflake. Electrostatic and orbital interaction are found to be important to stabilize the interaction between NBs and graphene nanoflake, though orbital interaction is less significant. It is very noticed that the proportion of dispersion interaction could be more than half of the sum attractive contributions. Thus, dispersion interaction is the most dominating factor in stabilizing graphene/NBs complexes. The results of reduced density gradient further confirm that the interaction between the graphene nanoflake and NBs is mainly the van der Waals type. Besides, much attention is paid to the interaction differences between the four new major NBs and the pristine cytosine, and the impact of the introduced functional groups of the four new major NBs on the structure, energy and interaction is also discussed.