Ab Initio Van Der Waals Research Articles

First-principles study of benzene and its homologues upon graphene-metal surfaces: Comparison of London dispersion corrections

We perform a comparative theoretical study of benzene and its homologues (toluene, para-xylene, and mesitylene) adsorbed on Cu/Al/Pd(111)-supported graphene using density functional theory (DFT). The long-range attraction is handled by semiempirical dispersion correction method (PBE-D3) and ab initio van der Waals density functionals (vdW-DF2, optB86b-vdW, optB88-vdW, and SCAN-rVV10). Our results show a systematic increase in the adsorption energy of organic molecules on graphene in the presence of underlaying metal substrates. In the case of strong metal-graphene contact, such as Pd(111)-graphene, the adsorption energy of benzene even increases 0.44 eV, which presents suitable platform for filtering harmful molecules such as benzene. Besides, we find out that the dispersion-corrected functionals play a fundamental role in the structure and adsorption energy. Furthermore, the adsorption energy increases linearly with the number of methyl groups on the benzene ring.

Study of the stability and interwall distance of (6,0)@(n,0) double-walled silicon carbide nanotubes by the vdW-DFT method

In this work, the stability and electronic structure of zigzag double-walled silicon carbide nanotubes (DWSiCNTs) (6,0)@(n,0) (with n=11-17) were investigated by using ab initio Van der Waals density functional. By calculating the formation energy and the binding energy of each double walled nanotube, the best interwall distance for the outer nanotube was indicated. The results revealed that (13,0) nanotube could be the best external nanotube for the (6,0) internal nanotube with 3.53 Ainterwall distance to make (6,0)@(13,0) DWSiCNT. The structural calculations also revealed that all studied silicon carbide nanotubes were semiconductors and their energy gap decreased from the single one to the double-walled one. Moreover, with raising the nanotube diameter, the energy gap increased, such that at the most stable double-walled nanotube, its value was about 0.216 eV.

Ab-initio study of structural and electronic properties of WS2/h-BN van der Waals heterostructure

First-principle calculations with different exchange-correlation functionals, including LDA, GGA, semi-empirical and ab-initio van der Waals in the forms of vdW-DF2B86R and vdW-DF2 were performed to evaluate the performance of different functionals in describing the bonding mechanism, adsorption energy and interlayer distance of WS2 monolayer on and between h-BN layers. The finding was that the vdW-DF2B86R seems to be the approach best lending itself to this purpose. In order to include the van der Waals (vdW) interactions in our calculations, we used the DFT-D2 and vdW methods, which gave rise to a physical adsorption with no net charge transfer between the WS2 layer and the corresponding substrates. In addition, we investigated the electronic and structural properties of WS2 and h-BN heterolayers, using vdW-DF2B86R functional. Based on density functional theory calculations, WS2 on and between h-BN layers showed a direct band gap at the K-point, which was experimentally observed.

Remediation of phenol-contaminated water by pristine and functionalized SWCNTs: Ab initio van der Waals DFT investigation

Despite known toxic properties of phenol and its derivatives, their man-caused release into nature continues. Their importance as building blocks in polymers, pesticides, pharmaceuticals and other industrial chemicals remains a barrier for reducing their introduction into ecosystems. Hence, a considerable effort has been devoted to these organic contaminates removal from water sources. In the present work, we have employed functionalized (5, 5) carbon nanotubes (f-CNTs) for adsorption and remidiation of phenol pollutant from water. Several binding sites (incloding hydroxyl and phenyl groups) were considered due to their ability in π-π stacking and H-bonding interactions with phenol. The adsorption modes and energies of both water and phenol to these sites are evaluated using a general dispersion-corrected density functional (DFT-D3) method. We showed that both water and phenol molecules are weakly bound (weak physisorption) to the outer surface of pristine CNT while they can be adsorbed stronger on the functionalized CNTs. It was found that phenol bound stronger to the CNT-OH than water molecule which was due to the existence of simultaneous π-π stacking and H-bonding in the system. Also, we have prepared a brief report about the solvent effect in the adsorption nature of the more stable systems.The results show that the absorption energy sequence for the absorbing/carbon nanotube complexes in the aqueous phase is similar to the calculated absorption energy for in the gas phase, but adsorption decreased in the aqueous phase. We have also provided a succinct report about the reactivity, energy gap and polarity of the considered systems for all systems. For comparison, we evaluated the adsorption behavior for zigzag OH-CNT (8, 0).The calculation reveal that difference of the binding energy of phenol and water molecules on a zigzag is alike to the armchair CNT system. The phenol adsorption properties onto CNT-OH system in periodic and cluster SWCNT have compared and we were found that the results predicted by the CNT saturated with hydrogen can be comparable to periodic SWCNT. Furthermore, our first-principles calculations demonstrated the importance of dispersion corrections based on weak intermolecular interactions in designing absorbents. Our study offers molecular level understanding of the interactions between water/phenol molecule and CNTs surface and may be informative for toxicity agent adsorption and remediation from environment.

Structural and electronic properties of supramolecular C60:RU(II)(bipy)3:C60 triad: Ab initio van der Waals calculations

We have investigated the influence of non-local dispersion interactions and temperature on the structure and electronic properties of Ru(bipy)3-(C60)2 triad using the ab initio van der Waals density functional (vdW-DF) calculations. It was found that non-local dispersion interactions affects slightly on the structural geometry and charge transfer property of the system under study. Therefore, it's not necessary to consider dispersion interactions which are computationally more expensive than the conventional DFT calculations for the presented supramolecules.The obtained results from the ab initio MD simulations indicated that structural property of respected molecule varies at various temperatures. The Mulliken charge analyses show a remarkable charge transfer about 0.64 electrons between Ru (bipy)3-bridges as donors and fullerenes as acceptors entities in the isolated molecule by increasing the temperature, the charge transfer was also increased.Our first-principles results for the isolated complex showed that the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) states were located on the fullerene spheroid and thus the charge separation (orbital localization) is not desirable. However, increasing of temperature causes the LUMO's to localize on the acceptor moieties (fullerenes) and the HOMO's on the donor moieties (Ru(bipy)3). From the results obtained for the molecular orbitals we found that the best distribution is occurred at ambient condition (300K).

Aluminum nitride graphene for DMMP nerve agent adsorption and detection

Using ab initio van der Waals density functional (vdW-DF) calculations, we investigate the adsorption of DMMP nerve agent on graphene, BN and AlN graphenes, involving full geometry optimization. Several active sites for both the interacting systems were considered in the adsorption process. The detailed analysis of the structural and electronical properties of energetically favorable configurations is carried out. The results show that adsorption of DMMP molecule on the Al site of the AlN graphene is energetically preferable. The calculated binding energy and equilibrium distance are about −0.74 eV (−72.34 kJ mol−1) and 2.035 Å, respectively, accompanying with charge transfer of 0.23 e. In addition, the P–O bond is rather significantly elongated when DMMP is adsorbed on AlN graphene. Compared to carbon graphene or BN graphene, the AlN graphene has stronger interaction with the DMMP molecule and can provide more sensitive signal for a single DMMP molecule. In particular, the semiconducting AlN graphene would become metallic after adsorption DMMP. Consequently, the AlN graphene is a promising candidate for the DMMP sensing and detection. Our ab initio vdW-DF findings present evidence for a rational benchmark for the applicability of the AlN graphene for DMMP adsorption and detection.

Doping of carbon nanotubes with aluminum atom to improve Pt adsorption

We implement the ab initio van der Waals (vdW) calculations at the density functional level of theory (vdW-DF) for the investigation of Pt adsorption ability of Al-doped carbon nanotubes (Al-CNTs). We present and discuss the energetically favorable sites for a single Pt atom adsorbed on the surface of Al-CNTs. Our results show significantly increment in the binding energy of Pt on the Al-CNT compared with pristine CNTs. We also find that Pt adsorption ability of Al-CNTs is more stronger than that of B- and N-doped CNTs. This is explained by the negative charges introduced in the neighboring C atoms by dopant atom. Our results verify that Al-doped CNTs seems to be more suitable materials for Pt adsorption than pure and also B- and N-doped CNTs.

Simulations on the possibility of formation of complexes between fluorouracil drug and cucurbit[n]urils: ab initio van der Waals DFT study

The binding geometry of fluorouracil/cucurbit[n]urils (CB[n]s) complexes with n = 5-8 is investigated using the first-principles van der Waals density functional (vdW-DF) method, involving full geometry optimization. Such host-guest complexes are typically calculated using conventional DFT method, which significantly underestimates non-local dispersion forces (or vdW contributions) and therefore affects interactions between respected entities. We address here the role of vdW forces for the fluorouracil and CB[n]s molecules which can form directional hydrogen bonds with each other. It was found that the inclusion of dispersion interactions significantly affects the host-guest binding properties and the hydrogen bonding between the molecules provides the main binding mechanism, while results in the same geometries for the considered complexes. The 0.84 eV binding energy, for the thermodynamically favorable state, reveals that the interaction of fluorouracil with CB[n]s is an exothermic interaction and typical for strong hydrogen bonding. Furthermore, we have investigated the binding nature of these host-guest systems in aqueous solution with ab initio MD simulations adopting vdW-DF method. These findings afford evidence for the applicability of the vdW-DF approach and provide a realistic benchmark for the investigation of the host-guest complexes.

Adsorption of H2S molecules by cucurbit[7]uril: an ab initio vdW-DF study

Among the cucurbit[n]urils, much attention has been devoted to CB[7] for its intermediary cavity size as well as the significant negative charge density of carbonyl-fringed portals which assists the binding of other species. Adsorption of hydrogen sulfide by CB[7] was studied using ab initio van der Waals density functional (vdW-DF) calculations, involving a full geometry optimization. The encapsulation of up to five H2S molecules inside the cucurbit cavity, with a binding energy of about −0.10 eV per H2S, makes cucurbit[n]urils attractive as a suitable adsorption medium. Furthermore, calculations show that H2S molecules can be adsorbed on the sidewall of the CB[7] with a larger binding energy (−0.31 eV). We also address the role of vdW forces for the system under study and the obtained results revealed that the inclusion of dispersion interactions slightly affects the binding properties of the interacting molecules. In addition, the binding nature of the energetically favorable systems in ambient conditions have been investigated with ab initio MD simulations adopting the vdW-DF method. Our ab initio vdW-DF findings afford evidence for a realistic benchmark for the applicability of these novel nanostructures for H2S adsorption and elimination from various media.

Ab initio and semi-empirical van der Waals study of graphene–boron nitride interaction from a molecular point of view

We have performed a systematic semi-empirical and ab initio van der Waals study to investigate the bonding mechanism of benzene (C6H6), triazine (C3N3H3) and borazine (B3N3H6) adsorbed on graphene and a single boron nitride (BN) sheet. The two semi-empirical approaches used to include the van der Waals (vdW) interactions in our density functional theory (DFT) calculations suggest that the strength of the molecule–surface interaction corresponds to a strong physisorption with no net charge transfer between the molecules and the corresponding substrates. This observation is strengthened by the use of first-principles non-local correlation vdW-DF functionals which provide a sound physical basis to include vdW interactions in DFT calculations. In particular we have employed two flavors of vdW-DF functionals which enabled us to determine the role of the non-local correlation effects in the molecule–surface bonding mechanism which cannot be assessed by using only semi-empirical vdW methods. Our study also reveals that the strength of the molecule–surface interaction can be influenced by the electronegativity of the B, C and N atoms.

Universalities in ultracold reactions of alkali-metal polar molecules

We consider ultracold collisions of ground-state heteronuclear alkali-metal dimers that are susceptible to four-center chemical reactions $2AB\ensuremath{\rightarrow}{A}_{2}+{B}_{2}$ even at submicrokelvin temperatures. These reactions depend strongly on species, temperature, electric field, and confinement in an optical lattice. We calculate ab initio van der Waals coefficients for these interactions and use a quantum formalism to study the scattering properties of such molecules under an external electric field and optical lattice. We also apply a quantum threshold model to explore the dependence of reaction rates on the various parameters. We find that, among the heteronuclear alkali-metal fermionic species, LiNa is the least reactive, whereas LiCs is the most reactive. For the bosonic species, LiK is the most reactive in zero field, but all species considered, LiNa, LiK, LiRb, LiCs, and KRb, share a universal reaction rate once a sufficiently high electric field is applied. For indistinguishable bosons, the inelastic/reactive rate increases as ${d}^{2}$ in the quantum regime, where $d$ is the dipole moment induced by the electric field. This is a weaker power-law dependence than for indistinguishable fermions, for which the rate behaves as ${d}^{6}$.

Ab Initio van der Waals Interactions in Simulations of Water Alter Structure from Mainly Tetrahedral to High-Density-Like

The structure of liquid water at ambient conditions is studied in ab initio molecular dynamics simulations in the NVE ensemble using van der Waals (vdW) density-functional theory, i.e., using the new exchange-correlation functionals optPBE-vdW and vdW-DF2, where the latter has softer nonlocal correlation terms. Inclusion of the more isotropic vdW interactions counteracts highly directional hydrogen bonds, which are enhanced by standard functionals. This brings about a softening of the microscopic structure of water, as seen from the broadening of angular distribution functions and, in particular, from the much lower and broader first peak in the oxygen-oxygen pair-correlation function (PCF) and loss of structure in the outer hydration shells. Inclusion of vdW interactions is shown to shift the balance of resulting structures from open tetrahedral to more close-packed. The resulting O-O PCF shows some resemblance with experiment for high-density water (Soper, A. K. and Ricci, M. A. Phys. Rev. Lett. 2000, 84, 2881), but not directly with experiment for ambient water. Considering the accuracy of the new functionals for interaction energies, we investigate whether the simulation protocol could cause the deviation. An O-O PCF consisting of a linear combination of 70% from vdW-DF2 and 30% from low-density liquid water, as extrapolated from experiments, reproduces near-quantitatively the experimental O-O PCF for ambient water. This suggests the possibility that the new functionals may be reliable and that instead larger-scale simulations in the NPT ensemble, where the density is allowed to fluctuate in accordance with proposals for supercooled water, could resolve the apparent discrepancy with the measured PCF.

Methane adsorption on graphene from first principles including dispersion interaction

The methane–graphene interaction is studied using density functional theory complemented with a semiempirical dispersion correction scheme (DFT-D), an ab initio van der Waals density functional (vdW-DF) ansatz as well as using Møller Plesset perturbation theory (MP2). The adsorption energy of 0.17 eV and the molecular distance of 3.28 Å obtained from the MP2 calculations are close to the experimental data, while the vdW-DF scheme results either in a realistic adsorption energy or a realistic adsorption geometry, depending on the underlying exchange-correlation functional. The present implementation of DFT-D overbinds about as much as bare DFT calculations underbind, but yields a meaningful adsorption height.

Modeling van der Waals interactions between proteins and inorganic surfaces from time-dependent density functional theory calculations

In this work we show how the ab initio determination of van der Waals coefficients within time-dependent density functional theory can be used to build efficient and accurate atomistic models that describe the long-range interactions of proteins with other proteins and of proteins with semi-conducting surfaces. The model parameters are fitted so that they reproduce the ab initio van der Waals coefficients of amino acids and dipeptides. We then assess the quality of our results by comparing ab initio van der Waals coefficients for larger peptides with the coefficients yielded by the models. The different sets of parameters can be easily incorporated in current empirical force field methods, thus providing an essential ingredient for molecular dynamics simulations of proteins close to surfaces.

Stability, Adsorption, and Diffusion ofCH4,CO2, andH2in Clathrate Hydrates

We present a study of the adsorption and diffusion of CH₄, CO₂, and H₂ molecules in clathrate hydrates using ab initio van der Waals density functional formalism [M. Dion, Phys. Rev. Lett. 92, 246401 (2004)10.1103/PhysRevLett.92.246401]. We find that the adsorption energy is dominated by van der Waals interactions and that, without them, gas hydrates would not be stable. We calculate the maximum adsorption capacity as well as the maximum hydrocarbon size that can be adsorbed. The relaxation of the host lattice is essential for a good description of the diffusion activation energies, which are estimated to be of the order of 0.2, 0.4, and 1.0 eV for H₂, CO₂, and CH₄, respectively.

Xe adsorption on aC60monolayer on Ag(111)

Low-energy electron diffraction (LEED) experiments and grand canonical Monte Carlo simulations were carried out to study the adsorption of Xe on a substrate composed of a monolayer of ${\mathrm{C}}_{60}$ molecules on a Ag(111) surface. LEED adsorption isobars indicated that the adsorption occurs in steps, with the Xe initially adopting a structure having the same unit cell as the ${\mathrm{C}}_{60}$. Isosteric heats corresponding to the first two steps were measured to be $234\ifmmode\pm\else\textpm\fi{}8$ and $204\ifmmode\pm\else\textpm\fi{}14\phantom{\rule{0.3em}{0ex}}\mathrm{meV}$, respectively. For the simulations, the interaction potential of Xe with the composite substrate was modeled as the sum of two parts: the Xe-Ag part was computed using an ab initio van der Waals potential that varies as an inverse-distance cubed and the $\mathrm{Xe}\text{\ensuremath{-}}{\mathrm{C}}_{60}$ part was computed using a spherically averaged ${\mathrm{C}}_{60}$ potential [E. S. Hernandez et al., J. Low Temp. Phys. 134, 309 (2004)]. The resulting adsorption potential is highly corrugated, with the most attractive sites located in the threefold hollows between the ${\mathrm{C}}_{60}$ molecules, forming a honeycomb array. The simulations (at temperatures ranging from $55\phantom{\rule{0.3em}{0ex}}\text{to}\phantom{\rule{0.3em}{0ex}}90\phantom{\rule{0.3em}{0ex}}\mathrm{K}$) show that these attractive sites are filled first, followed by adsorption in two types of secondary sites, where a competition exists due to steric hindrance. The thermodynamic properties of film growth obtained in the simulation are in good agreement with the experiment.

Stacking Interactions and the Twist of DNA

The importance of stacking interactions for the Twist and stability of DNA is investigated using the fully ab initio van der Waals density functional (vdW-DF). Our results highlight the role that binary interactions between adjacent sets of base pairs play in defining the sequence-dependent Twists observed in high-resolution experiments. Furthermore, they demonstrate that additional stability gained by the presence of thymine is due to methyl interactions with neighboring bases, thus adding to our understanding of the mechanisms that contribute to the relative stability of DNA and RNA. Our mapping of the energy required to twist each of the 10 unique base pair steps should provide valuable information for future studies of nucleic acid stability and dynamics. The method introduced will enable the nonempirical theoretical study of significantly larger pieces of DNA or DNA/amino acid complexes than previously possible.

Natural steric analysis: Ab initio van der Waals radii of atoms and ions

We employ natural steric analysis (introduced in a previous paper) to evaluate a set of effective ab initio van der Waals radii for free and covalently bonded atoms and ions of H–Ar (Z=1–18) determined using a helium atom probe. We critically examine the degree of anisotropy, dependence on charge state, and other intrinsic limitations of a simple atomic van der Waals hard sphere representation of the accurate steric surface. We also evaluate the ab initio steric force (gradient of steric energy at van der Waals contact) as a measure of “hardness” of the atomic van der Waals spheres. Comparison with empirical van der Waals radii shows reasonable agreement (within the acknowledged uncertainties of the latter values in the most important cases), but suggest a wider range of variability and anisotropy than could be adequately represented by any fixed constant radius. Simple expressions for incorporating the dependence on natural atomic charge or correcting for other types of intermolecular contact are given, extending the accuracy and usefulness of the atomic van der Waals sphere concept.

Mo/ller–Plesset perturbation investigation of the He2 potential and the role of midbond basis functions

The Mo/ller–Plesset perturbation theory up to the complete fourth order is applied to calculate the ab initio van der Waals energy potential of He2. A scheme of constructing a very efficient basis set is proposed based on theoretical considerations. Such a basis set contains a set of Gaussian functions (usually of low angular momentum) centered at the midbond of the van der Waals molecule, which have been proven very efficient to reproduce the intersystem correlation interaction energy normally to be achieved by use of the nucleus-centered high angular momentum polarization functions. A nuclear-centered moderate set [5s4p2d] augmented by a set of midbond functions such as {3s3p2d} produces a value of 10.04 K for the well depth of He2 at the complete fourth-order (MP4) theory. Results from a series of other basis sets suggest that this value is nearly saturated with the further increase of basis, which is in agreement with the estimate of the complete basis-set limit. Calculations of the potential at the minimum and the other distances (3.0–10.0 a0) confirm that the MP4 method, together with the use of midbond functions, is a reliable and convenient choice for the accurate calculations.