We present a theory study of the physisorption of the series of methylbenzenes (toluene, xylene and mesitylene), as well as benzene, on graphene. This is relevant for the basic understanding of graphene used as a material for sensors and as an ideali
zed model for the carbon in active carbon filters. The molecules are studied in a number of positions and orientations relative graphene, using density functional theory with the van der Waals functional vdW-DF. We focus on the vdW-DF1 and vdW-DF-cx functionals, and find that the binding energy of the molecules on graphene grows linearly with the number of methyl groups, at the rate of 0.09 eV per added methyl group.
To increase public awareness of theoretical materials physics, a small group of high school students is invited to participate actively in a current research projects at Chalmers University of Technology. The Chalmers research group explores methods
for filtrating hazardous and otherwise unwanted molecules from drinking water, for example by adsorption in active carbon filters. In this project, the students use graphene as an idealized model for active carbon, and estimate the energy of adsorption of the methylbenzene toluene on graphene with the help of the atomic-scale calculational method density functional theory. In this process the students develop an insight into applied quantum physics, a topic usually not taught at this educational level, and gain some experience with a couple of state-of-the-art calculational tools in materials research.
Chlorinated hydrocarbon compounds are of environmental concerns, since they are toxic to humans and other mammals, are widespread, and exposure is hard to avoid. Understanding and improving methods to reduce the amount of the substances is important.
We present an atomic-scale calculational study of the adsorption of chlorine-based substance chloroform (CHCl3) on graphene oxide, as a step in estimating the capacity of graphene oxide for filtering out such substances, e.g., from drinking water. The calculations are based on density functional theory (DFT), and the recently developed consistent-exchange functional for the van der Waals density-functional method (vdW-DF-cx) is employed. We obtain values of the chloroform adsorption energy varying from roughly 0.2 to 0.4 eV per molecule. This is comparable to previously found results for chloroform adsorbed directly on clean graphene, using similar calculations. In a wet environment, like filters for drinking water, the graphene will not stay clean and will likely oxidize, and thus adsorption onto graphene oxide, rather than clean graphene, is a more relevant process to study.
The dispersion interaction between a pair of parallel DNA double-helix structures is investigated by means of the van der Waals density functional (vdW-DF) method. Each double-helix structure consists of an infinite repetition of one B-DNA coil with
10 base pairs. This parameter-free density functional theory (DFT) study illustrates the initial step in a proposed vdW-DF computational strategy for large biomolecular problems. The strategy is to first perform a survey of interaction geometries, based on the evaluation of the van der Waals (vdW) attraction, and then limit the evaluation of the remaining DFT parts (specifically the expensive study of the kinetic-energy repulsion) to the thus identified interesting geometries. Possibilities for accelerating this second step is detailed in a separate study. For the B-DNA dimer, the variation in van der Waals attraction is explored at relatively short distances (although beyond the region of density overlap) for a 360 degrees rotation. This study highlights the role of the structural motifs, like the grooves, in enhancing or reducing the vdW interaction strength. We find that to a first approximation, it is possible to compare the DNA double strand at large wall-to-wall separations to the cylindrical shape of a carbon nanotube (which is almost isotropic under rotation). We compare our first-principles results with the atom-based dispersive interaction predicted by DFT-D2 [J. Comp. Chem. 27, 1787 (2006)] and find agreement in the asymptotic region. However, we also find that the differences in the enhancement that occur at shorter distances reveal characteristic features that result from the fact that the vdW-DF method is an electron-based (as opposed to atom-based) description.
The adsorption energies and orientation of methanol on graphene are determined from first-principles density functional calculations. We employ the well-tested vdW-DF method that seamlessly includes dispersion interactions with all of the more close-
ranged interactions that result in bonds like the covalent and hydrogen bonds. The adsorption of a single methanol molecule and small methanol clusters on graphene are studied at various coverages. Adsorption in clusters or at high coverages (less than a monolayer) is found to be preferable, with the methanol C-O axis approximately parallel to the plane of graphene. The adsorption energies calculated with vdW-DF are compared with previous DFT-D and MP2-based calculations for single methanol adsorption on flakes of graphene (polycyclic aromatic hydrocarbons). For the high coverage adsorption energies we also find reasonably good agreement with previous desorption measurements.
Large biomolecular systems, whose function may involve thousands of atoms, cannot easily be addressed with parameter-free density functional theory (DFT) calculations. Until recently a central problem was that such systems possess an inherent sparsen
ess, that is, they are formed from components that are mutually separated by low-electron-density regions where dispersive forces contribute significantly to the cohesion and behavior. The introduction of, for example, the van der Waals density functional (vdW-DF) method [PRL 92, 246401 (2004)] has addressed part of this sparse-matter system challenge. However, while a vdW-DF study is often as computationally efficient as a study performed in the generalized gradient approximation, the scope of large-sparse-matter DFT is still limited by computer time and memory. It is costly to self-consistently determine the electron wavefunctions and hence the kinetic-energy repulsion. In this paper we propose and evaluate an adaption of the Harris scheme [PRB 31, 1770 (1985)]. This is done to speed up non-selfconsistent vdW-DF studies of molecular-system interaction energies. Also, the Harris-type analysis establishes a formal link between dispersion-interaction effects on the effective potential for electron dynamics and the impact of including selfconsistency in vdW-DF calculations [PRB 76, 125112 (2007)].
A calculational study of the trihalomethanes chloroform (CHCl_3) and bromoform (CHBr_3) adsorbed on graphene is presented. The study uses the van der Waals density functional method vdW-DF to obtain adsorption energies and adsorption structures for t
hese molecules of environmental concern. In this study chloroform is found to adsorb with the H atom pointing away from graphene, with adsorption energy 357 meV (34.4 kJ/mol). For bromoform the calculated adsorption energy is 404 meV (39.0 kJ/mol). The corrugation of graphene as seen by chloroform is small, the difference in adsorption energy along the graphene plane is less than 6 meV.
Detailed physisorption data from experiment for the H_2 molecule on low-index Cu surfaces challenge theory. Recently, density-functional theory (DFT) has been developed to account for nonlocal correlation effects, including van der Waals (dispersion)
forces. We show that the functional vdW-DF2 gives a potential-energy curve, potential-well energy levels, and difference in lateral corrugation promisingly close to the results obtained by resonant elastic backscattering-diffraction experiments. The backscattering barrier is found selective for choice of exchange-functional approximation. Further, the DFT-D3 and TS-vdW corrections to traditional DFT formulations are also benchmarked, and deviations are analyzed.
The adsorption of an adenine molecule on graphene is studied using a first-principles van der Waals functional (vdW-DF) [Dion et al., Phys. Rev. Lett. 92, 246401 (2004)]. The cohesive energy of an ordered adenine overlayer is also estimated. For the
adsorption of a single molecule, we determine the optimal binding configuration and adsorption energy by translating and rotating the molecule. The adsorption energy for a single molecule of adenine is found to be 711 meV, which is close to the calculated adsorption energy of the similar-sized naphthalene. Based on the single molecular binding configuration, we estimate the cohesive energy of a two-dimensional ordered overlayer. We find a significantly stronger binding energy for the ordered overlayer than for single-molecule adsorption.
The past few years has brought renewed focus on the physics behind the class of materials characterized by long-range interactions and wide regions of low electron density, sparse matter. There is now much work on developing the appropriate algorithm
s and codes able to correctly describe this class of materials within a parameter-free quantum physical description. In particular, van der Waals (vdW) forces play a major role in building up material cohesion in sparse matter. This work presents an application to the vanadium pentoxide (V2O5) bulk structure of t
