First principles studies on the adsorption of rare base-pairs on the surface of B/N atom doped γ-graphyne

Rare base-pairs consists of guanine (G) paired with rare bases, such as 5-methylcytosine (5-meCyt), 5-hydroxymethylcytosine (5-hmCyt), 5-carboxylcytosine (5-caCyt), and 5-formylcytosine (5-fCyt), have become the focus of epigenetic research because they can be used as markers to detect some chronic diseases and cancers. However, the correlation detection of these rare base-pairs is limited, which in turn limits the development of diagnostic tests and devices. Herein, the interaction of rare base-pairs adsorbed on pure and B/N-doped γ-graphyne (γ-GY) nanosheets was explored using the density functional theory. The calculated adsorption energy showed that the system of rare base-pairs on B-doped γ-GY is more stable than that on pure γ-GY or N-doped γ-GY. Translocation time values indicate that rare base-pairs can be successfully distinguished as the difference in their translocation times is very large for pure and B/N-doped γ-GY nanosheets. Meanwhile, sensing response values illustrated that pure and B-doped γ-GY are the best for G-5-hmCyt adsorption, while the N-doped γ-GY is the best for G-Cyt adsorption. The findings indicate that translocation times and sensing response can be used as detection indexes for pure and B/N doped γ-GY, which will provide a new way for experimental scientists to develop the biosensor components.

First-Principles Investigation of Nucleobase Detection by Tetranitrogen Coordinated Transition Metal Doped Graphene Nanoribbons

Detection of nucleobases is of great significance in DNA sequencing, which is one of the main goals of the Human Genome Project. By employing the nonequilibrium Green function method combined with density functional theory, we proposed a biosensor based on the TMN4 (TM = Ni, Cu) embedded graphene nanoribbons for nucleobase detection. The adsorption energy calculations show that all five nucleobases are physisorbed on the TMN4-doped graphene nanoribbons. Utilizing the distinction of current, the bases T, C, and U can be gradually detected at the biases of 0.4, 0.6, and 0.8 V by NiN4-doped graphene nanoribbons, respectively. The bases A and G can be finally distinguished by CuN4-doped graphene nanoribbons under an external bias of not less than 0.8 V. The identification of individual nucleobases at specific biases could provide a novel mechanism for the further development of biosensors in rapid genome sequencing applications.

Review of research of nanocomposites based on graphene quantum dots

Graphene quantum dots (GQDs) belong to the vast and versatile family of carbon nanomaterials. Their unique position amongst versatile carbon nanoparticles (NPs) originates from the properties of quantum confinement and edge effects. GQDs are similar to conventional semiconductor QDs due to their tunable band gaps and high photoluminescence activity. However, GQDs have superior characteristics due to their excellent biocompatibility, low toxicity, good water dispersibility, large optical absorptivity, high fluorescence activity and photostability. These properties have generated significant interest in GQDs applications in various fields: nanosensor fabrication, drug delivery, photocatalysis, photovoltaics, and photodynamic therapy. Numerous GQD-based nanocomposites/nanohybrides have been synthesized and/or studied computationally. This review focuses on recent computational studies of various GQD-based nanocomposites/nanohybrides and systems which can be related to them.

Research of weak interaction between water and different monolayer graphene systems

Weak interactions play a very important role in the fields of supramolecular chemistry, molecular physics, materials science, etc. They have a great impact on the structure of the compounds in the gas, liquid and solid phases and the mechanism of some reaction processes. In this study, we visualized the intermolecular interactions between H₂O and different graphene systems through density functional theory. Because the surface of Graphene oxide (GO) has epoxy groups, hydroxyl groups, and other oxygen-containing groups. These groups are prone to hydrogen bonding with hydrogen atoms of H₂O, and we further explain some of them based on the acid-base theory. Also, we obtained the components of interactions between different graphene complex and H₂O by energy decomposition. Then we found that for systems with moderate strength hydrogen bonding, such as hydroxyl functional group systems, electrostatic attraction is dominant while the dispersion attraction and induction function play an auxiliary role together.

Towards developing a criterion to characterize non-covalent bonds: a quantum mechanical study

Chemical bonds are central to chemistry, biology, and allied fields, but still, the criterion to characterize an interaction as a non-covalent bond has not been studied rigorously.

Density Functional Study on the Adsorption of 5-Membered N-Heterocycles on B/N/BN-Doped Graphene: Coronene as a Model System

Adsorption of seven 5-membered N-heterocycles on B/N/BN-doped graphene (with coronene as a model system) has been studied using density functional theory (DFT). The geometry of the complexes validated the involvement of both π···π stacking and N-H···π interaction in the adsorption process. The stability of the complexes is measured in terms of stabilization energy, and the results suggested that the complexes are stable enough (stabilization energies are in the range of 7.61-14.77 kcal mol^-1). Studies confirmed the stability of complexes in the solvent phase too irrespective of the dielectric of the solvent. Dispersive force is the major mode of interaction in stabilizing the complexes. Natural bond orbital analysis indicated a small contribution from electrostatic and covalent interactions. Thermochemical analysis revealed that the complexation is exothermic in nature and favorable at a lower temperature. Adsorption of N-heterocycles exerts a nominal impact on the electronic properties of the undoped/doped graphene. The study presents a simple approach to introduce an arbitrary functionality to undoped/doped graphene by preserving its electronic properties.

Host-guest interactions between octa acid and cations/nucleobases

The nature of host-guest interaction in between octa acid cavitand (OA) and some representative cationic guests (Li⁺ , Na⁺ , K⁺ , Be⁺² , Mg⁺² , Ca⁺² , Li₃ O⁺ , Na₃ O⁺ , K₃ O⁺ ) as well as heterocyclic moieties like [adenine (A), guanine (G), cytosine (C), thymine (T), uracil (U), and tetrathiafulvalene (TTF)] has been examined with the aid of density functional theory (DFT)-based computations. Thermochemical results indicate that all the guests bind with OA in a thermodynamically favorable fashion at 298.15 K temperature and one atmospheric pressure. OA exhibits high selectivity in binding the lighter cations/metal cluster cations as compared to the heavier congeners along each given series. Moreover, OA exhibits enhanced affinity as well as selectivity in binding A/G/TTF molecules as compared to C/T/U. Noncovalent interaction and energy decomposition analyses reveal that in addition to the van der Waals interaction, significant contribution from electrostatic as well as orbital interactions dictate the outcome in all the host-guest complexes. Time dependent DFT calculations have been carried out to assess the role of the guests in tuning the electronic properties as well as absorption spectrum of OA. © 2017 Wiley Periodicals, Inc.

Tunable electronic and magnetic properties of graphene-like XYBe3 (XY = BN, AlN, SiC, GeC) nanosheets with carrier doping: a first-principles study

Graphyne-like ternary beryllide nanosheets are found to be promising host materials because of their carrier-induced tunable magnetism and half-metallicity.

Nitrogen doped nanographene structures; study on the adsorption of nucleobases, nucleotides, and their triphosphate derivatives using mixed docking, MD, and QM/MM approaches

The interactions of the nucleobases, nucleotides, and their triphosphate derivatives in both neutral and anionic forms with the nitrogen doped graphenes (NG) were studied using docking and molecular dynamic simulation methods. In docking studies, based on binding energy results, the anionic species and nucleobases were showing the most and the least tendency toward the surface of the NG, respectively. The molecular mechanic/Poisson-Boltzmann surface area results revealed similar results, except for the anionic species; in these studies, the anionic species showed a lesser affinity toward the NG. The time-dependent density functional theory studies were carried out to investigate the effects of the NG on the electronic nature of the investigated ligands; a red-shift in all of the cases was observed. The results of binding energy decomposition and atoms in molecules studies showed that the interactions are van der Waals in nature. The graphitic, pyridinic, and pyrrolic nitrogen atoms which were considered in this study behaved similar to each other.

Noncovalent Interaction of Graphene with Heterocyclic Compounds: Benzene, Imidazole, Tetracene, and Imidazophenazines

Noncovalent functionalization of graphene with organic molecules offers a direct route to multifunctional modification of this nanomaterial, leading to its various possible practical applications. In this work, the structures of hybrids formed by linear heterocyclic compounds such as imidazophenazine (F1) and its derivatives (F2-F4) with graphene and the corresponding interaction energies are studied by using the DFT method. Special attention is paid to the hybrids where the attached molecule is located along the graphene zigzag (GZZ ) and armchair (GAC ) directions. The interaction energies corresponding to the graphene hybrids of the F1-F4 compounds for the two directions are found to be distinct, while tetracene (being a symmetrical molecule) shows a small difference between these binding energies. It is found that the back-side CH3 and CF3 groups have an important influence on the arrangements of F1 derivatives on graphene and on their binding energies. The contribution of the CF3 group to the total binding energy of the F3 molecule with graphene is the largest (3.4 kcal mol(-1) ) (the GZZ direction) while the CH3 group increases this energy of F2 only by 2.0 kcal mol(-1) (the GAC direction). It is shown that replacing the carbons with other atoms or adding a back-side group enables one to vary the polarizability of graphene.