Accurate Prediction of Adsorption Energies on Graphene, Using a Dispersion-Corrected Semiempirical Method Including Solvation

Investigating the interplay between charge transfer and CO2 insertion in the adsorption of a NiFe catalyst for CO2 electroreduction on a graphite support through DFT computational approaches

This article describes a density functional theory (DFT) study to explore a bio-inspired NiFe complex known for its experimental activity in electro-reducing CO2 to CH4 when adsorbed on graphite. The coordination properties of the complex are investigated in isolated form and when physisorbed on a graphene surface. A comparative analysis of DFT approaches for surface modeling is conducted, utilizing either a finite graphene flake or a periodic carbon surface. Results reveal that the finite model effectively preserves all crucial properties. By examining predicted structures arising from CO2 insertion within the mono-reduced NiFe species, whether isolated or adsorbed on the graphene flake, a potential species for subsequent electro-reduction steps is proposed. Notably, the DFT study highlights two positive effects of complex adsorption: facile electron transfers between graphene and the complex, finely regulated by the complex state, and a lowering of the thermodynamic demand for CO2 insertion.

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.

Binding and optical characteristics of polycyclic aromatic hydrocarbons and their nitroderivatives adsorbed on the C3N monolayer

Carbon–nitrogen based two dimensional frameworks have attracted significant attention due to their great potential for environmental applications.

e-Graphene: A Computational Platform for the Prediction of Graphene-Based Drug Delivery System by Quantum Genetic Algorithm and Cascade Protocol

Graphene, as a novel category of carbon nanomaterials, has attracted a great attention in the field of drug delivery. Due to its large dual surface area, graphene can efficiently load drug molecules with high capacity via non-covalent interaction without chemical modification of the drugs. Hence, it ignites prevalent interests in developing a new graphene/graphene oxide (GO)-based drug delivery system (GDDS). However, current design of GDDS primarily depends on the prior experimental experience with the trial-and-error method. Thus, it is more appealing to theoretically predict possible GDDS candidates before experiments. Toward this end, we propose to fuse quantum genetic algorithm (QGA) and quantum mechanics (QM)/semi-empirical quantum mechanics (SQM)/force field (FF) to globally search the optimal binding interaction between the graphene/GO and drug in a given GDDS and develop a free computational platform “e-Graphene” to automatically predict/screen potential GDDS candidates. To make this platform more pragmatic for the rapid yet relatively accurate prediction, we further propose a cascade protocol via firstly conducting a fast QGA/FF calculation with fine QGA parameters and automatically passing the best chromosomes from QGA/FF to initialize a higher level QGA/SQM or QGA/QM calculation with coarse QGA parameters (e.g., small populations and short evolution generations). By harnessing this platform and protocol, systematic tests on a typical GDDS containing an anticancer drug SN38 illustrate that high fabrication rates of hydroxyl, epoxy, and carboxyl groups on a pristine graphene model will compromise the stability of GDDS, implying that an appropriate functionalization rate is crucial for the delicate balance between the stability and solubility/biocompatibility of GDDS. Moreover, automatic GDDS screen in the DrugBank database is performed and elicits four potential GDDS candidates with enhanced stability than the commonly tested GDDS containing SN38 from the computational point of view. We hope that this work can provide a useful program and protocol for experimental scientists to rationally design/screen promising GDDS candidates prior to experimental tests.

Modelling the adsorption of natural organic matter on Ag (111) surface: Insights from dispersion corrected density functional theory calculations

Understanding the nature of the interactions between natural organic matter (NOM) and engineered nanoparticles (ENPs) is of crucial importance in understanding the fate and behaviour of engineered nanoparticles in the environment. In the present study, dispersion-corrected density functional theory (DFT-D) has been used to elucidate the molecule-surface interactions of higher molecular weight (HMW) NOM ambiguously present in the aquatic systems, namely: humic acid (HA), fulvic acid (FA) and protein Cryptochrome (Cry) on Ag (111) surface. Investigations were done in the gas phase and to mimic real biological environment, water has been used as a solvent within the conductor-like screening model (COSMO) framework. The calculated adsorption energies for HA, FA and Cry on Ag (111) surface were -27.90 (-18.45) kcal/mol, -38.28 (-18.68) kcal/mol and -143.89 (-150.82) kcal/mol respectively in the gas (solvent) phase and the equilibrium distances between the surface and HA, FA and Cry molecules were 1.87 (2.18) Å, 2.31(2.31) Å and 1.91 (1.70) Å respectively in the gas (solvent) phase. In both gas and water phase Cry showed stronger adsorption which means it has a stronger interaction with Ag (111) surface compared to HA and FA. The results for adsorption energy, solvation energy, isosurface of charge deformation difference, total density of state and partial density of states indicated that indeed these chosen adsorbates do interact with the surface and are favourable on Ag (111) surface. In terms of charge transfer, one of many calculated descriptors in this study, electrophilicity (ω) concur that charge transfer will take place from the adsorbates to Ag (111) surface.

Initial Studies Directed toward the Rational Design of Aqueous Graphene Dispersants

This study presents preliminary experimental data suggesting that sodium 4-(pyrene-1-yl)butane-1-sulfonate (PBSA), 5, an analogue of sodium pyrene-1-sulfonate (PSA), 1, enhances the stability of aqueous reduced graphene oxide (RGO) graphene dispersions. We find that RGO and exfoliated graphene dispersions prepared in the presence of 5 are approximately double the concentration of those made with commercially available PSA, 1. Quantum mechanical and molecular dynamics simulations provide key insights into the behavior of these molecules on the graphene surface. The seemingly obvious introduction of a polar sulfonate head group linked via an appropriate alkyl spacer to the aromatic core results in both more efficient binding of 5 to the graphene surface and more efficient solvation of the polar head group by bulk solvent (water). Overall, this improves the stabilization of the graphene flakes by disfavoring dissociation of the stabilizer from the graphene surface and inhibiting reaggregation by electrostatic and steric repulsion. These insights are currently the subject of further investigations in an attempt to develop a rational approach to the design of more effective dispersing agents for rGO and graphene in aqueous solution.

Chemical sensors based on N-substituted polyaniline derivatives: reactivity and adsorption studies via electronic structure calculations

Conjugated organic polymers represent an important class of materials for varied technological applications including in active layers of chemical sensors. In this context, polyaniline (PANI) derivatives are promising candidates, mainly due to their high chemical stability, good processability, versatility of synthesis, polymerization, and doping, as well as relative low cost. In this study, electronic structure calculations were carried out for varied N-substituted PANI derivatives in order to investigate the potential sensory properties of these materials. The opto-electronic properties of nine distinct compounds were evaluated and discussed in terms of the employed substituents. Preliminary reactivity studies were performed in order to identify adsorption centers on the oligomer structures via condensed-to-atoms Fukui indexes (CAFI). Finally, adsorption studies were carried out for selected derivatives considering five distinct gaseous analytes. The influence of the analytes on the oligomer properties were investigated via the evaluation of average binding energies and changes on the structural features, optical absorption spectra, frontier orbitals distribution, and total density of states in relation to the isolated oligomers. The obtained results indicate the derivatives PANI-NO₂ and PANI-C₆H₅ as promising materials for the development of improved chemical sensors.

Combined molecular and periodic DFT analysis of the adsorption of co macrocycles on graphene

The molecular doping of graphene with π-stacked conjugated molecules has been widely studied during the last 10 years, both experimentally or using first-principle calculations, mainly with strongly acceptor or donor molecules. Macrocyclic metal complexes have been far less studied and their behavior on graphene is less clear-cut. The present density functional theory study of cobalt porphyrin and phthalocyanine adsorbed on monolayer or bilayer graphene allows to compare the outcomes of two models, either a finite-sized flake of graphene or an infinite 2D material using periodic calculations. The electronic structures yielded by both models are compared, with a focus on the density of states around the Fermi level. Apart from the crucial choice of calculation conditions, this investigation also shows that unlike strongly donating or accepting organic dopants, these macrocycles do not induce a significant doping of the graphene sheet and that a finite size model of graphene flake may be confidently used for most modeling purposes. © 2017 Wiley Periodicals, Inc.

Approximate quantum chemical methods for modelling carbohydrate conformation and aromatic interactions: β-cyclodextrin and its adsorption on a single-layer graphene sheet

Adsorption of carbohydrates on graphene has the potential to improve graphene dispersibility in water. Here we assess the ability of DFTB-based and NDDO-based quantum chemical methods to model β-cyclodextrin conformations and interactions with graphene.

Shielding the chemical reactivity using graphene layers for controlling the surface properties of carbon materials

Graphene can efficiently shield chemical interactions and gradually decrease the binding to reactive defect areas. In the present study, we have used the observed graphene shielding effect to control the reactivity patterns on the carbon surface. The experimental findings show that a surface coating with a tiny carbon layer of 1-2 nm thickness is sufficient to shield the defect-mediated reactivity and create a surface with uniform binding ability. The shielding effect was directly observed using a combination of microscopy techniques and evaluated with computational modeling. The theoretical calculations indicate that a few graphene layers can drastically reduce the binding energy of the metal centers to the surface defects by 40-50 kcal mol(-1). The construction of large carbon areas with controlled surface reactivity is extremely difficult, which is a key limitation in many practical applications. Indeed, the developed approach provides a flexible and simple tool to change the reactivity patterns on large surface areas within a few minutes.

Recent Progress in Treating Protein-Ligand Interactions with Quantum-Mechanical Methods

We review the first successes and failures of a “new wave” of quantum chemistry-based approaches to the treatment of protein/ligand interactions. These approaches share the use of “enhanced”, dispersion (D), and/or hydrogen-bond (H) corrected density functional theory (DFT) or semi-empirical quantum mechanical (SQM) methods, in combination with ensemble weighting techniques of some form to capture entropic effects. Benchmark and model system calculations in comparison to high-level theoretical as well as experimental references have shown that both DFT-D (dispersion-corrected density functional theory) and SQM-DH (dispersion and hydrogen bond-corrected semi-empirical quantum mechanical) perform much more accurately than older DFT and SQM approaches and also standard docking methods. In addition, DFT-D might soon become and SQM-DH already is fast enough to compute a large number of binding modes of comparably large protein/ligand complexes, thus allowing for a more accurate assessment of entropic effects.

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.

Theoretical study of adsorption of amino acids on graphene and BN sheet in gas and aqueous phase with empirical DFT dispersion correction

Suitability of BN nanosheet/graphene towards the adsorption of amino acids established by dispersion corrected DFT calculations.

Modelling of graphene functionalization

This perspective describes the available theoretical methods and models for simulating graphene functionalization based on quantum and classical mechanics.

Benchmark calculations of the adsorption of aromatic molecules on graphene

Selecting the saturated graphene fragment as a model of graphene, we have investigated seven popular density functionals, including ωB97X-D, B97-D, B-LYP-D3, M05-2X, M06-2X, M11-L, and N12, for their performance in describing the adsorption of aromatic molecules on graphene. The best performing functionals are B97-D, B-LYP-D3, and ωB97X-D. M05-2X, M06-2X, and M11-L significantly underestimate the adsorption strengths, while N12 fails completely in this respect. The effects of the basis sets and size of the saturated graphene fragments on the geometries, energies, and properties for the adsorption of aromatic molecules on graphene have also been studied. It was found that the small basis sets such as 6-31G(d) and jun-cc-pVDZ are not suitable for the accurate description of the adsorption of aromatic molecules on graphene. The size of selected graphene fragments has a little effect on both the ωB97X-D and SCS-SAPT0 interaction energies, but the effects of the size of selected graphene fragments on the energy components are significant in some cases of the adsorption of aromatic molecules on graphene. The surprising weakness of electrostatic interactions by F substitution for the adsorption of F-substituted benzenes on graphene was explained using the energy component analysis.

Enhanced semiempirical QM methods for biomolecular interactions

Recent successes and failures of the application of 'enhanced' semiempirical QM (SQM) methods are reviewed in the light of the benefits and backdraws of adding dispersion (D) and hydrogen-bond (H) correction terms. We find that the accuracy of SQM-DH methods for non-covalent interactions is very often reported to be comparable to dispersion-corrected density functional theory (DFT-D), while computation times are about three orders of magnitude lower. SQM-DH methods thus open up a possibility to simulate realistically large model systems for problems both in life and materials science with comparably high accuracy.