Optimal Atomistic Modifications of Material Surfaces: Design of Selective Nesting Sites for Biomolecules

In recent years, enormous progress has been made in understanding the structures and functions of biological molecules. This effort is largely focused on deciphering the nature of biosystems, designing novel drugs, and treating diseases. In numerous research areas, proteins, enzymes, and various organic or inorganic molecules are attached to materials surfaces. The goals of these challenging studies range from the realization of molecular-electronic and bioelectronic systems to the building of bionetworks functioning outside cells. 10] The material substrates should allow stable nesting of the attached biomolecules in water and provide rich possibilities for their activation or sensing. Carbon compounds, such as diamond or graphene-based nanostructures, are ideal biosubstrates since they are water resistant, could be modified to be hydrophobic or hydrophilic, conducting or isolating, and allow activation of the biomolecules. It is often crucial to attach the biomolecules to the substrates in specific configurations, in order to preserve and control their activity. 17] To minimize the molecule–surface interaction, one could covalently bind a selected atom in the biomolecule to the surface. A robust and universal possibility, allowing the control of numerous molecular activities, is to position the molecules in selective nesting sites preACHTUNGTRENNUNGdesigned on the material surfaces. In this work, we develop the methodology of “optimal modifications” of material surfaces, with the goal of designing highly selective nesting sites for the adsorbed molecules. We resort to optimization approaches, based on genetic algorithms, using similar principles to biological evolution. These universal methods have been widely applied in the design of proteins and drugs, nanostructures, and in optical control of chemical reactions and nanoscale processes. This methodology is first developed in the absence of polar solvents and electrolytes. In such cases, one could build the selective molecular nests by doping the surfaces using carefully designed patterns of suitable atoms, which become partially charged upon doping. Their positions can be arranged in such a way that the local electrostatic potential formed above the doped surface selectively binds the chosen molecule. The methodology is illustrated on a graphene layer, 14] substitutionally doped with B and N atoms, which are often used to change free-carrier concentrations in carbon systems. Nesting of the molecules on these modified surfaces is controlled by Coulombic and van der Waals coupling. The nesting sites are designed by genetic algorithms that minimize the potential energy of the docked molecules. First, the local charges of each dopant and its neighbors is required. Ab initio calculations, done with the B3LYP exchange-correlation functional in the Gaussian03 software package, show that when a single C atom in the graphene layer is substituted by an isolated B or N atom, it carries the charge QB 1.2 e or QN 1.0 e, respectively. We assume that this charge is neutralized within the first three neighboring C atoms, each carrying the charge QC= QB(N)/3. When several dopants have a single C neighbor between them, the C atom is charged by summing contributions from those dopants. The same dopants are not allowed to be first neighbors. However, when different types of dopants (B and N) are first neighbors, we find that their charges are QB 1.0 e and QN 1.0 e. To simplify the simulations, it can be assumed that the charges of dopants are always QB 1.1 e and QN 1.1 e. This approximation allows implementation of simple genetic algorithms. The total Coulombic interaction energy between the adsorbed molecule and the graphene layer doped by an isolated B (or N) atom is given by