On the Performance of Local Density Approximation in Describing the Adsorption of Electron Donating/Accepting Molecules on Graphene

Adsorption of Tunable aryl alkyl ionic liquids (TILs) on the graphene and Defective graphene nanosheets: A DFT Study

Optical and electronic characteristics of the graphene nanosheets (GNS) could be altered by some structural defects such as double-vacancy and Stone-Wales ones. The physisorption manner of [MPI][BF4], [MPT1][BF4], [MPT2][BF4], and [MPTT][BF4] ionic liquids on intact and defective GNS surfaces were investigated using M06-2X/cc-pVDZ computational method. Capability for adsorption on the DV and SW graphene surfaces by TILs is increased by about 1.0-4.3 and 0.4-2.0 kcal/mol respectively. The electrostatic potential of the GNS-DV surface is more negative than the GNS-SW one which enables it to interact with cation parts of the adsorbed TILs so extensively. The highest adsorption energy belongs to the [MPI][BF4]/GNS-DV system. Adsorption of the TILs on the GNS surfaces leads to a decrease in the energy of the LUMO molecular orbital as well as their energy gap of them. Results revealed that the electrical conductivity, as well as absorption spectra of the GNS surfaces, are affected by TILs adsorption and defect nature.

A Comprehensive DFT Investigation of the Adsorption of Polycyclic Aromatic Hydrocarbons onto Graphene

To better understand graphene and its interactions with polycyclic aromatic hydrocarbons (PAHs), density-functional-theory (DFT) computations were used. Adsorption energy is likely to rise with the number of aromatic rings in the adsorbates. The DFT results revealed that the distance between the PAH molecules adsorbed onto the G ranged between 2.47 and 3.98 Å depending on the structure of PAH molecule. The Non-Covalent Interactions (NCI) plot supports the concept that van der Waals interactions were involved in PAH adsorption onto the Graphene (G) structure. Based on the DFT-calculated adsorption energy data, a rapid and reliable method employing an empirical model of a quantitative structure–activity relationship (QSAR) was created and validated for estimating the adsorption energies of PAH molecules onto graphene.

Adsorption of Transition-Metal Clusters on Graphene and N-Doped Graphene: A DFT Study

Using the dispersion-corrected density functional theory (DFT-D3) method, we systematically studied the adsorption of 15 kinds of transition-metal (TM) clusters on pristine graphene (Gr) and N-doped graphene (N-Gr). It has been found that TM_n (n = 1-4) clusters adsorbed on the N-Gr surface are much stronger than those on the pristine Gr surface, while 3d series clusters present similar geometries on Gr and N-Gr surfaces. The most preferred sites of TMs migrate from hollow to bridge to the top site on the Gr surface along the d series in the periodic table, while the preferred sites of TMs migrate in a much more complex manner on the N-Gr surface. It has also been found that charge transfer decreases along the d series for adsorbed clusters on both surfaces, but adsorbed clusters present less charge transfer on the N-Gr surface than on the Gr surface. What is more interesting is that some TM (Tc, Ru, and Re) clusters change the growth mechanism from the three-dimensional (3D) growth mode on the Gr surface to the two-dimensional (2D) growth mode on the N-Gr surface. At last, it has been found that adsorbed clusters are more dispersed on the N-Gr surface than on the pristine Gr surface due to growth and average aggregation energies.

Targeting Beta-Blocker Drug-Drug Interactions with Fibrinogen Blood Plasma Protein: A Computational and Experimental Study

In this work, one of the most prevalent polypharmacology drug–drug interaction events that occurs between two widely used beta-blocker drugs—i.e., acebutolol and propranolol—with the most abundant blood plasma fibrinogen protein was evaluated. Towards that end, molecular docking and Density Functional Theory (DFT) calculations were used as complementary tools. A fibrinogen crystallographic validation for the three best ranked binding-sites shows 100% of conformationally favored residues with total absence of restricted flexibility. From those three sites, results on both the binding-site druggability and ligand transport analysis-based free energy trajectories pointed out the most preferred biophysical environment site for drug–drug interactions. Furthermore, the total affinity for the stabilization of the drug–drug complexes was mostly influenced by steric energy contributions, based mainly on multiple hydrophobic contacts with critical residues (THR22: P and SER50: Q) in such best-ranked site. Additionally, the DFT calculations revealed that the beta-blocker drug–drug complexes have a spontaneous thermodynamic stabilization following the same affinity order obtained in the docking simulations, without covalent-bond formation between both interacting beta-blockers in the best-ranked site. Lastly, experimental ultrasound density and velocity measurements were performed and allowed us to validate and corroborate the computational obtained results.

Polycyclic Aromatic Hydrocarbons Adsorption onto Graphene: A DFT and AIMD Study

Density functional theory (DFT) calculations and ab-initio molecular dynamics (AIMD) simulations were performed to understand graphene and its interaction with polycyclic aromatic hydrocarbons (PAHs) molecules. The adsorption energy was predicted to increase with the number of aromatic rings in the adsorbates, and linearly correlate with the hydrophobicity of PAHs. Additionally, the analysis of the electronic properties showed that PAHs behave as mild n-dopants and introduce electrons into graphene; but do not remarkably modify the band gap of graphene, indicating that the interaction between PAHs and graphene is physisorption. We have also discovered highly sensitive strain dependence on the adsorption strength of PAHs onto graphene surface. The AIMD simulation indicated that a sensitive and fast adsorption process of PAHs can be achieved by choosing graphene as the adsorbent. These findings are anticipated to shed light on the future development of graphene-based materials with potential applications in the capture and removal of persistent aromatic pollutants.

Modulating the electronic and optical properties of monolayer arsenene phases by organic molecular doping

Recently, arsenene monolayer structure of the arsenic with two phases has displayed semiconducting behavior. We have systematically investigated the electronic and optical properties of single-layer arsenene with two types of functionalized organic molecules; an electrophilic molecule [tetracyanoquinodimethane (TCNQ)] and a nucleophilic molecule [tetrathiafulvalene (TTF)], as an electron acceptor and electron donor, respectively. The interfacial charge transfer between the arsenene monolayer and TCNQ/TTF molecules extensively reduces the band gap of arsenene and accordingly resulted in a p- or n-type semiconducting behavior, respectively. We have also performed the interfacial charge transfer from organic molecules to monolayer arsenene and vice versa. The interfacial surface molecular modification has established an efficient way to develop the light harvesting of arsenene in different polarization directions. Our theoretical investigation suggests that such n- and p-type arsenene semiconductors would broaden the applications in the field of nanoelectronic and optoelectronic devices such as photodiodes and it is also useful for constructing functional electronic systems.

The effect of defect types on the electronic and optical properties of graphene nanoflakes physisorbed by ionic liquids

Defect engineering and non-covalent interaction strategies allow for dramatically tuning the optoelectronic properties of graphene. Using ab initio density functional theory (M06-2X/cc-pVDZ), we find that the nature of defects on the graphene nanoflakes (GNFs) and the size of defective GNF (DGNF) surfaces affect the binding energy (ΔE_b) of ionic liquids (ILs) and the UV-Vis absorption spectra of DGNFIL complexes. Further, our results indicate that increasing the size of DGNFs affects the geometrical structure of the surfaces and increases the binding energy of ILs by about 10%. Analysis based on AIM and EDA shows that the interactions between ILs and DGNFs are non-covalent in nature (dispersion energy being dominant) and associated with charge transfer between the IL and nanoflakes. A comparison between the ΔE_b values of ILs on DGNFs, GNFs, and h-BN nanoflakes (h-BNNF) shows that the presence of defects on the GNF surfaces increases the binding energy values as follows: DGNFIL > pristine GNFIL > h-BNNFIL. Our calculations indicate that increasing the size of DGNF surfaces leads to a decrease in the HOMO-LUMO energy gap (E_g) of the DGNF surfaces. Orbital energy and density of state calculations show that the E_g of DV(SW)-GNFs decreases upon IL adsorption and their Fermi energy level is shifted depending on the type of IL, thus enabling better conductivity. Reactivity descriptors generally indicate that the chemical potential (μ) and chemical hardness (η) of nanoflakes decrease upon IL adsorption, whereas the electrophilicity index (ω) increases. The UV-Vis absorption spectrum of DV-GNF and SW-GNF shows four bands in the visible spectrum which correspond to π → π* transitions with the absorption bands of SW-GNF appearing at higher wavelengths than those of DV-GNF. The most intense absorption bands in DV-GNF (λ = 348 nm) and SW-GNF (λ = 375 nm) are associated with electronic transitions HOMO-1 → LUMO+2 and HOMO → LUMO+1, respectively. In addition, these absorption bands undergo a red-shift by both increasing the size of the DV(SW)-GNF surfaces and IL adsorption. We also observe that the energy gaps and absorption spectra can be altered by varying the defect types and the type of IL adsorbate, where the defect types affect the spectral shapes of the bands and adsorbates at the first absorption peak, thus having potential application for light-emitting devices.

Organic molecules deposited on graphene: a computational investigation of self-assembly and electronic structure

We use ab initio simulations to investigate the adsorption and the self-assembly processes of tetracyanoquinodimethane (TCNQ), tetrafluoro-tetracyanoquinodimethane (F4-TCNQ), and tetrasodium 1,3,6,8-pyrenetetrasulfonic acid (TPA) on the graphene surface. We find that there are no chemical bonds at the molecule-graphene interface, even at the presence of grain boundaries on the graphene surface. The molecules bond to graphene through van der Waals interactions. In addition to the molecule-graphene interaction, we performed a detailed study of the role played by the (lateral) molecule-molecule interaction in the formation of the, experimentally verified, self-assembled layers of TCNQ and TPA on graphene. Regarding the electronic properties, we calculate the electronic charge transfer from the graphene sheet to the TCNQ and F4-TCNQ molecules, leading to a p-doping of graphene. Meanwhile, such charge transfer is reduced by an order of magnitude for TPA molecules on graphene. In this case, it is not expected a significant doping process upon the formation of self-assembled layer of TPA molecules on the graphene sheet.