Assessment of Density Functional Theory in Predicting Interaction Energies between Water and Polycyclic Aromatic Hydrocarbons: from Water on Benzene to Water on Graphene

Exploring the mechanism of graphene-oxide reduction by hydrazine in a multi-epoxide environment with DFT calculations

Reduction mechanisms between hydrazine and a multi-epoxide arrangement were investigated on a finite-sized graphene-oxide model with density functional theory. Three multistep reaction pathways were explored to examine different graphene-oxide (GO) deoxygenation scenarios. Epoxides sharing the same hexagonal ring show the typical one-by-one elimination of the oxygen functional groups through two protonation steps and the formation of cis-diazine and water. Nevertheless, the migration of one of the epoxy groups to an out-of-ring position has to precede the reduction. When a hexagonal ring separates two epoxy groups, forming a partially reduced surface with two hydroxyl groups is energetically favoured. This reduction product is so stable that it may remain on the surface after the termination of the reduction process. If further deoxygenation occurs, it can lead to surface fragmentation due to the ring opening of the remaining epoxides. The formation of nitrogen-containing functional groups at the edge of the graphene-oxide flake is also considered, and their surface presence is evaluated based on their thermodynamic stabilities.

Structure and thermodynamics of water adsorption in NU-1500-Cr

Metal-organic frameworks (MOFs) are a class of materials with diverse chemical and structural properties, and have been shown to effectively adsorb various types of guest molecules. The mechanism of water adsorption in NU-1500-Cr, a high-performance atmospheric water harvesting MOF, is investigated using a combination of molecular dynamics simulations and infrared spectroscopy. Calculations of thermodynamic and dynamical properties of water as a function of relative humidity allow for following the adsorption process from the initial hydration stage to complete filling of the MOF pores. Initial hydration begins at the water molecules that saturate the open Cr³⁺ sites of the framework, which is then followed by the formation of water chains that extend along the channels connecting the hexagonal pores of the framework. Water present in these channels gradually coalesces and fills the hexagonal pores sequentially after the channels are completely hydrated. The development of hydrogen-bond networks inside the MOF pores as a function of relative humidity is characterized at the molecular level using experimental and computational infrared spectroscopy. A detailed analysis of the OH-stretch vibrational band indicates that the low-frequency tail stems from strongly polarized hydrogen-bonded water molecules, suggesting the presence of some structural disorder in the experimental samples. Strategies for designing efficient water harvesting MOFs are also proposed based on the mechanism of water adsorption in NU-1500-Cr.

Development of accurate potentials for the physisorption of water on graphene

From coupled-cluster singles and doubles model including connected triples corrections [CCSD(T)] calculations on the water dimer and B97D/CC on the water-circumcoronene complex at a large number of randomly generated conformations, interaction potentials for the physisorption of water on graphene are built, accomplishing almost sub-chemical accuracy. The force fields were constructed by decomposing the interaction into electrostatic and van der Waals contributions, the latter represented through improved Lennard-Jones potentials. Besides, a Chemistry at Harvard Macromolecular Mechanics (CHARMM)-like term was included in the water-water potential to improve the description of hydrogen bonds, and an induction term was added to model the polarization effects in the interaction between water and polyaromatic hydrocarbons (PAHs) or graphene. Two schemes with three and six point charges were considered for the interactions water-water and water-PAH, as Coulomb contributions are zero in the water-graphene system. The proposed fitted potentials reproduce the ab initio data used to build them in the whole range of distances and conformations and provide results for selected points very close to CCSD(T) benchmarks. When applied to the water-graphene system, the obtained results are in excellent agreement with p-CCSD(T), revised symmetry-adapted perturbation theory based on density functional theory monomer properties (DFT-SAPT), and diffusion Monte Carlo reference values. Furthermore, the stability of the various conformers water-PAH and water-graphene, as well as the different trends observed between these systems are rationalized in terms of the modifications of the electrostatic contribution.

Interactions between large molecules pose a puzzle for reference quantum mechanical methods

Quantum-mechanical methods are used for understanding molecular interactions throughout the natural sciences. Quantum diffusion Monte Carlo (DMC) and coupled cluster with single, double, and perturbative triple excitations [CCSD(T)] are state-of-the-art trusted wavefunction methods that have been shown to yield accurate interaction energies for small organic molecules. These methods provide valuable reference information for widely-used semi-empirical and machine learning potentials, especially where experimental information is scarce. However, agreement for systems beyond small molecules is a crucial remaining milestone for cementing the benchmark accuracy of these methods. We show that CCSD(T) and DMC interaction energies are not consistent for a set of polarizable supramolecules. Whilst there is agreement for some of the complexes, in a few key systems disagreements of up to 8 kcal mol^-1 remain. These findings thus indicate that more caution is required when aiming at reproducible non-covalent interactions between extended molecules.

How do the doping concentrations of N and B in graphene modify the water adsorption?

Understanding the interaction of water and graphene is crucial for various applications such as water purification, desalination, and electrocatalysis. Experimental and theoretical studies have already investigated water adsorption on N- and B-doped graphene. However, there are no reports available that elucidate the influences of the N and B doping content in graphene on the microscopic geometrical structure and the electronic properties of the adsorbed water. Thus, this work is devoted to solving this problem using self-consistent van der Waals density functional theory calculations. The N and B doping contents of 0.0, 3.1, 6.3, and 9.4% were considered. The results showed that the binding energy of water increases almost linearly as a function of doping content at all concentrations for N-doped graphene but below 6.3% for B-doped graphene. In the linear range, the binding energy increases by approximately 30 meV for each increment of the doping ratio. Analyses of the geometric and electronic structures explained the enhancement of the water-graphene interaction with the variation in doping percentage.

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.

Computational Investigations of Dispersion Interactions between Small Molecules and Graphene-like Flakes

We investigate dispersion interactions in a selection of atomic, molecular, and molecule-surface systems, comparing high-level correlated methods with empirically corrected density functional theory (DFT). We assess the efficacy of functionals commonly used for surface-based calculations, with and without the D3 correction of Grimme. We find that the inclusion of the correction is essential to get meaningful results, but there is otherwise little to distinguish between the functionals. We also present coupled-cluster quality interaction curves for H₂, NO₂, H₂O, and Ar interacting with large carbon flakes, acting as models for graphene surfaces, using novel absolutely localized molecular orbital based methods. These calculations demonstrate that the problems with empirically corrected DFT when investigating dispersion appear to compound as the system size increases, with important implications for future computational studies of molecule-surface interactions.

X-ray Photoionization Cross Section Spectra of Water and Ammonia Bonded on Polycyclic Aromatic Hydrocarbons: A Quantum Mechanical Interpretation to the Absorption Spectra on Graphene

A theoretical study of the K-shell total photoabsorption and photoionization cross section spectra of water and ammonia bonded to benzene (C₆H₆) and the polycyclic aromatic hydrocarbons (PAHs) naphthalene (C₁₀H₈), coronene (C₂₄H₁₂) and circumcoronene (C₅₄H₁₈) by van der Waals (vdW) forces is presented. The discretized electronic pseudospectra at the oxygen and nitrogen K-edges, covering the discrete and the continuum spectral regions, were obtained at the time-dependent density functional theory (TDDFT) level with dispersion correction. An analytic continuation procedure based on the Padé approximants was used in order to obtain the K-shell cross sections of the structures at the discrete and the continuum regions of the spectra. By examining the electronic spectra of water and ammonia bonded to coronene and circumcoronene, we observed that our results agree well with the experiments performed with graphene. This work provides a quantum mechanical interpretation to the NEXAFS experiments of water and ammonia adsorbed on graphene in terms of a physisorption model of these molecules by van der Waals forces.

Transparent proton transport through a two-dimensional nanomesh material

Molecular sieving is of great importance to proton exchange in fuel cells, water desalination, and gas separation. Two-dimensional crystals emerge as superior materials showing desirable molecular permeability and selectivity. Here we demonstrate that a graphdiyne membrane, an experimentally fabricated member in the graphyne family, shows superior proton conductivity and perfect selectivity thanks to its intrinsic nanomesh structure. The trans-membrane hydrogen bonds across graphdiyne serve as ideal channels for proton transport in Grotthuss mechanism. The free energy barrier for proton transfer across graphdiyne is ~2.4 kJ mol-1, nearly identical to that in bulk water (2.1 kJ mol-1), enabling "transparent" proton transport at room temperature. This results in a proton conductivity of 0.6 S cm-1 for graphdiyne, four orders of magnitude greater than graphene. Considering its ultimate pore size of 0.55 nm, graphdiyne membrane blocks soluble fuel molecules and exhibits superior proton selectivity. These advantages endow graphdiyne a great potential as proton exchange material.