Electrostatic interactions are important for understanding molecular interactions, since they are long-range interactions and can guide binding partners to their correct binding positions. To investigate the role of electrostatic forces in molecular recognition, we calculated electrostatic forces between binding partners separated at various distances. The investigation was done on a large set of 275 protein complexes using recently developed DelPhiForce tool and in parallel, evaluating the total electrostatic force via electrostatic association energy. To accomplish the goal, we developed a method to find an appropriate direction to move one chain of protein complex away from its bound position and then calculate the corresponding electrostatic force as a function of separation distance. It is demonstrated that at large distances between the partners, the electrostatic force (magnitude and direction) is consistent among the protocols used and the main factors contributing to it are the net charge of the partners and their interfaces. However, at short distances, where partners form specific pair-wise interactions or de-solvation penalty becomes significant, the outcome depends on the precise balance of these factors. Based on the electrostatic force profile (force as a function of distance), we group the cases into four distinctive categories, among which the most intriguing is the case termed “soft landing.” In this case, the electrostatic force at large distances is favorable assisting the partners to come together, while at short distance it opposes binding, and thus slows down the approach of the partners toward their physical binding.

Graphene’s adhesive and charge delocalization properties offer the opportunity for the direct study of biological molecule in the nanoscale regime. The inherent charge on DNA base pairs and the associated phosphate backbone can be probed by non-covalent interactions with graphene, which is a useful platform for the creation of anisotropic nanopatterned biological assemblies. Here, we report the graphene nanoribbon (GNR) supported anisotropic supramolecular self-assembly of single stranded adenine (A), cytosine (C), guanine (G), thymine (T), AT, and GC 20mer oligonucleotides, as well as the unique ordering of double stranded plasmid (circular) and Herring sperm (linear) DNA. The GNRs serve as a double sided adhesive platform for attachment to the SiO2 substrate, as well as DNA oligomers and polymers. The self-assembly is attributed to donor-acceptor interactions between DNA and graphene. These findings demonstrate that the DNA-GNR assembly yields a prospective route to novel bio-relevant nanostructures.

Noncovalent functionalization provides an effective way to modulate the electronic properties of graphene. Recent experimental work has demonstrated that hybrids of dipolar phototransductive molecules tethered to graphene are reversibly tunable in doping. We have studied the electronic structure characteristics of chromophore/graphene hybrids using dispersion-corrected density functional theory. The Dirac point of noncovalently functionalized graphene shifts upward via cis–trans isomerism, which is attributed to a change in the chromophore’s dipole moment. Our calculation results reveal that the experimentally observed reversible doping of graphene is attributed to the change in charge transfer between the light-switchable chromophore and graphene via isomerization. Furthermore, we show that by varying the electric field perpendicular to the supramolecular functionalized graphene, additional tailoring of graphene doping can be accomplished.

Recent experimental work has demonstrated production of quasi-free-standing graphene by methane intercalation. The intercalation weakens the coupling of adjacent graphene layers and yields Dirac fermion behaviour of monolayer graphene. We have investigated the electronic characteristics of a methane intercepted graphene bilayer under a perpendicularly applied electric field. Evolution of the band structure of intercalated graphene as a function of the bias is studied by means of density-functional theory including interlayer van der Waals interactions. The implications of controllable band gap opening in methane-intercalated graphene for future device applications are discussed.

Fluorinated epitaxial graphene has potential applications in organic electronics. We present the calculation results by means of first-principles density-functional-theory for various fluorination patterns. Our results indicate that semi-fluorinated graphene conformations follow the same energetic order as the corresponding hydrogenated graphene counterparts. The distinctive electronic properties between semi-hydrogenated graphene and semi-fluorinated graphene are attributed to the polar covalent C-F bond in contrast to the covalent C-H bond. The partial ionic character of the C-F bond results in the hyperconjugation of C-F σ-bonds with an sp(2) network of graphene. Resonant orbitals stabilize the stirrup conformation via the gauche effect. Resonant orbitals also lead to electron doping of the sp(2) network and enhanced excitonic effect. The implications of resonant-orbital-induced doping for the electronic and magnetic properties of fluorinated epitaxial graphene are discussed.