vdW-DF Method Research Articles

Understanding adsorption of divalent metals ions (Mg, Ca) on Nitrogen-, Boron- doped, and defective graphene in nanofiltration process using van der Waals density functional method

Removal of divalent metal ions (Mg and Ca) by graphene membrane has a great implication for manufacturing chitin and chitosan in filtration process. Despite its importance, influences of the doping and vacancy in graphene on the adsorption of those metal ions remain unclear. Here, we study the adsorption of those metal ions on several graphene surfaces, namely pristine graphene (Gra), graphitic N- and B- doped graphene (N- and B-Gra), monovacancy graphene (MV-Gra), monovacancy graphene functionalized by an epoxy (O-MV-Gra), and monovacancy graphene functionalized by an hydroxyl group (OH-MV-Gra) by van der Waals density functional (vdW-DF) method. It was found all considered graphene surfaces have strong interactions with Ca, whereas Mg only chemisorbs on MV-Gra and B-Gra. Energetically, comparing with Ca adosprtion on pristine graphene, both B doping and vacancy creation strengthen the Ca adsorption, while N doping slight decreases it. The electronic structure analysis uncovers enhancement of the Cagraphene interaction by B doping and vacancy formation. Because of the results that have been observed, the removal of Ca ions from aqueous solution can be enhanced by the creation of nanopore or B doping in graphene, in which Ca atom are strongly captured by graphene.

Accurate Nonempirical Range-Separated Hybrid van der Waals Density Functional for Complex Molecular Problems, Solids, and Surfaces

We introduce a new, general-purpose, range-separated hybrid van der Waals density \ph{functional, termed vdW-DF-ahbr,} within the non-empirical vdW-DF method [JPCM 32, 393001 (2020)]. It combines correlation from vdW-DF2 with a screened Fock exchange that is fixed by \ph{a new model of exchange effects} in the density-explicit vdW-DF2-b86r functional [PRB 89, 121103(R) (2014)]. The new vdW-DF2-ahbr prevents spurious exchange binding and has a small-density-gradient form set from many-body perturbation analysis. It is accurate for \ph{bulk as well as layered materials} and it systematically and significantly improves the performance of present vdW-DFs for molecular problems. Importantly, vdW-DF2-ahbr also outperforms present-standard (dispersion-corrected) range-separated hybrids on a broad collection of noncovalent-interaction benchmark sets, while at the same time successfully mitigating the density-driven errors that often affect the description of molecular transition states and isomerization calculations. vdW-DF2-ahbr furthermore improves on state of the art density functional theory approaches by 1) correctly predicting both the substrate structure and the site preference for CO adsorption on Pt(111), 2) outperforming existing non-empirical vdW-DFs for the description of CO$_2$ adsorption in both a functionalized and in a simple metal-organic framework, and 3) being highly accurate \ph{for the} set of base-pair interactions in a model of DNA assembly.

Hard and soft materials: putting consistent van der Waals density functionals to work

We present the idea and illustrate potential benefits of having a tool chain of closely related regular, unscreened and screened hybrid exchange–correlation (XC) functionals, all within the consistent formulation of the van der Waals density functional (vdW-DF) method (Hyldgaard et al (2020 J. Phys.: Condens. Matter 32 393001)). Use of this chain of nonempirical XC functionals allows us to map when the inclusion of truly nonlocal exchange and of truly nonlocal correlation is important. Here we begin the mapping by addressing hard and soft material challenges: magnetic elements, perovskites, and biomolecular problems. We also predict the structure and polarization for a ferroelectric polymer. To facilitate this work and future broader explorations, we present a stress formulation for spin vdW-DF and illustrate the use of a simple stability-modeling scheme. The modeling supplements density functional theory (DFT) (with a specific XC functional) by asserting whether the finding of a soft mode (an imaginary-frequency vibrational mode, ubiquitous in perovskites and soft matter) implies an actual DFT-based prediction of a low-temperature transformation.

VdW-DF-ahcx: a range-separated van der Waals density functional hybrid

Hybrid density functionals replace a fraction of an underlying generalized-gradient approximation (GGA) exchange description with a Fock-exchange component. Range-separated hybrids (RSHs) also effectively screen the Fock-exchange component and thus open the door for characterizations of metals and adsorption at metal surfaces. The RSHs are traditionally based on a robust GGA, such as PBE (Perdew J P et al 1996 Phys. Rev. Lett. 77 3865), for example, as implemented in the HSE design (Heyd J et al 2003 J. Chem. Phys. 118 8207). Here we define an analytical-hole (Henderson T M et al 2008 J. Chem. Phys. 128 194105) consistent-exchange RSH extension to the van der Waals density functional (vdW-DF) method (Berland K et al 2015 Rep. Prog. Phys. 78 066501), launching vdW-DF-ahcx. We characterize the GGA-type exchange in the vdW-DF-cx version (Berland K and Hyldgaard P 2014 Phys. Rev. B 89 035412), isolate the short-ranged exchange component, and define the new vdW-DF hybrid. We find that the performance vdW-DF-ahcx compares favorably to (dispersion-corrected) HSE for descriptions of bulk (broad molecular) properties. We also find that it provides accurate descriptions of noble-metal surface properties, including CO adsorption.

First-Principles Study of the Adsorption of Carboxylic Acid on Cu(111)

The geometric structure and electronic properties of the adsorption of organic carboxylic acids on the closed-packed Cu(111) surface have been addressed by periodic density functional theory (DFT) calculations. We also have taken into account van der Waals (vdW) interaction by the VdW-DF method. The optimized structures show that formic and acetic acids have stable structures of molecular adsorption in clean copper surfaces. We find that the adsorption energies at 1/16 ML coverage are -0.27, -0.30 and -0.10 eV for formic, acetic, and propionic acid, respectively. On the other hand, in the case of vdW-DF, their adsorption energies increased to -0.63, -0.70 and -0.73 eV.

Sensing Behavior of Hexagonal-Aluminum Nitride to Phosgene Molecule Based on Van der Waals–Density Functional Theory and Molecular Dynamic Simulation

In this paper, we evaluated adsorption of phosgene gas molecule (COCl2), on the hexagonal-aluminum nitride (h-AlN) nanosheet by using first-principles van der Waals density functional theory calculations (vdW-DF) method. The nature of interaction between the phosgene molecule and h-AlN is discovered by geometries, adsorption energies, Mulliken, Hirshfeld as well as Voronoi charges analyses. The density of states (DOS) was calculated and the results show that HOMO/LUMO energy gap of h-AlN is significantly reduced upon the COCl2 adsorption. The projected density of states (PDOS) of the adsorption systems suggested that the enhancement of adsorption was owing to the hybridization between Al atom of h-AlN sheet and the O atom of phosgene molecule. Interestingly, the results reveal that the Eg of h-AlN is very sensitive to the presence of COCl2 molecule as its value reduces from 3.337 eV in pure h-AlN to 1.966 eV (41.08% change) after the COCl2 adsorption which would result in electrical conductance increment. Global reactivity descriptor values such as electronegativity (χ), global hardness (η), global softness (S), electronic chemical potential (μ), electrophilicity index (ω), and electro accepting power (ω+) were calculated. Additionally, the stability of the most stable phosgene/h-AlN complex was evaluated by means of DFT molecular dynamics (MD) simulation at room temperature under constant volume and temperature conditions with PBE method. Based on the DFT calculation results, the h-AlN nano sheet is expected to be potential novel sensor for detecting the presence of COCl2 gas.

Unraveling the electromagnetic structure of the epitaxial graphene buffer layer

We have employed density functional theory to study the structural, electronic and magnetic properties of the first all-carbon layer grown epitaxially on 6H-SiC(0 0 0 1). Using VDW-DF, M06-L, LSDA, LSDA+U, PBE and PBE-D2 methods we have performed a comparative study of the preferable magnetic configuration of the system. In this work, for the first time, we report a stable antiferromagnetic (AF) ordering in the buffer layer caused by the presence of silicon dangling bonds in the SiC top layer. This state is nearly degenerated with the ferromagnetic state with a magnetic moment equal to the number of silicon dangling bonds. A net magnetic moment of 0.55 µb per Si dangling bond was found for both states. However, only for the ferromagnetic state the carbon atoms of the buffer layer exhibited a magnetic moment. The magnetic configuration is much more stable than the non-polarized one and might explain SQUID results and spin transport experiments with epitaxial graphene. Furthermore, we found that, as previously observed experimentally, the buffer layer is a true semiconductor.

Adsorption of water on fluorinated graphene

In this paper, we investigate the adsorption of water monomer on fluorinated graphene using state-of-the-art first-principles methods within the framework of density functional theory (DFT). Four different types of methods are employed to describe the van der Waals (vdW) interactions between water molecule and the carbon surface: The traditional DFT calculations within the generalized gradient approximation (GGA), and three additional types of calculations using respectively the semi-empirical DFT-D2 method, the original van der Waals density functional (vdW-DF) method, and one of its variants. Two situations and totally four adsorption configurations are considered. Compared with the adsorption on pristine graphene, the adsorption energies of water on fluorinated graphene are significantly increased, and the orientations of water diploe moment are notably changed. The most stable configuration is found to stay right above the top site of the C atom which is bonded with F, and the dipole moment of water molecule aligns spontaneously along the surface normal.

Signatures of van der Waals binding: A coupling-constant scaling analysis

The van der Waals (vdW) density functional (vdW-DF) method [Rep. Prog. Phys. 78, 066501 (2015)] describes dispersion or vdW binding by tracking the effects of an electrodynamic coupling among pairs of electrons and their associated exchange-correlation holes. This is done in a nonlocal-correlation energy term ${E}_{\mathrm{c}}^{\mathrm{nl}}$, which permits density functional theory calculation in the Kohn-Sham scheme. However, to map the nature of vdW forces in a fully interacting materials system, it is necessary to also account for associated kinetic-correlation energy effects. Here, we present a coupling-constant scaling analysis, which permits us to compute the kinetic-correlation energy ${T}_{\mathrm{c}}^{\mathrm{nl}}$ that is specific to the vdW-DF account of nonlocal correlations. We thus provide a more complete spatially resolved analysis of the electrodynamical-coupling nature of nonlocal-correlation binding, including vdW attraction, in both covalently and noncovalently bonded systems. We find that kinetic-correlation energy effects play a significant role in the account of vdW or dispersion interactions among molecules. Furthermore, our mapping shows that the total nonlocal-correlation binding is concentrated to pockets in the sparse electron distribution located between the material fragments.

Libvdwxc: a library for exchange–correlation functionals in the vdW-DF family

We present libvdwxc, a general library for evaluating the energy and potential for the family of vdW-DF exchange–correlation functionals. libvdwxc is written in C and provides an efficient implementation of the vdW-DF method and can be interfaced with various general-purpose DFT codes. Currently, the Gpaw and Octopus codes implement interfaces to libvdwxc. The present implementation emphasizes scalability and parallel performance, and thereby enables ab initio calculations of nanometer-scale complexes. The numerical accuracy is benchmarked on the S22 test set whereas parallel performance is benchmarked on ligand-protected gold nanoparticles () up to 9696 atoms.

Adsorption of CO2on Graphene: A Combined TPD, XPS, and vdW-DF Study

The adsorption of CO2 molecules on monolayer epitaxial graphene on a SiC(0001) surface at 30 K was investigated by temperature-programmed desorption and X-ray photoelectron spectroscopy. The desorption energy of CO2 on graphene was determined to be (30.1–25.1) ± 1.5 kJ/mol at low coverages and approached the sublimation energy of dry ice (27–25 kJ/mol) with increasing the coverage. The adsorption of CO2 on graphene was thus categorized into physisorption, which was further supported by the binding energies of CO2 in core-level spectra. The adsorption states of CO2 on graphene were theoretically examined by means of the van der Waals density functional (vdW-DF) method that includes nonlocal correlation. The experimental desorption energy was successfully reproduced with high accuracy using vdW-DF calculations; the optB86b-vdW functional was found to be most appropriate to reproduce the desorption energy in the present system.

Adsorption of CO on the rutile TiO2(110) surface: a dispersion-corrected density functional theory study.

The geometry, energy and stretching frequency of carbon monoxide on the rutile TiO2(110) surface for coverages between 0.125 and 1.5 ML are investigated by means of density functional theory calculations. Four different approaches were considered, namely, the PBE exchange-correlation functional and the PBE-D2, vdW-DF and vdW-DF2 methods incorporating van der Waals dispersion interactions of different theoretical complexity and empiricism. It is found that upon the increase of the surface coverage, the adsorption becomes less favorable due to lateral destabilizing interactions between adsorbed molecules. The preferred geometry for CO changes from an upright configuration at 0.125 ML to tilted configurations at 1.5 ML and the tilting of the C-O axis from the surface normal increases with the increase of the surface coverage. At 1 ML, all computational approaches predict alternate tilted configurations which contradict the interpretation of recent experimental infrared reflection-absorption spectroscopic findings suggesting upright CO geometries. Encouragingly, a very good agreement between calculated and experimental shifts of the C-O stretching frequency of adsorbed CO at different coverages with respect to gaseous CO species was reached.

Theoretical study of disorder-order transition of sodium borohydride

The disorder-order phase transition of NaBH4 from the cubic to tetragonal structures has been studied based on density functional theory. The disordered high temperature phase is expressed as a statistical average of three substructures with a hypothesis that each BH4− tetrahedron has a fixed orientation. Our calculations show that the phase transition is mainly induced by synergic rotation of BH4− ion and the energy barrier is sensitive to volume change. We also investigated the role of van der Waals corrections in describing phase transition with DFT-D2 and vdW-DF methods.

Self-consistent van der Waals density functional study of benzene adsorption on Si(100)

The adsorption of benzene on the Si(100) surface is studied theoretically using the self-consistent van der Waals density functional (vdW-DF) method. The adsorption energies of two competing adsorption structures, butterfly (BF) and tight-bridge (TB) structures, are calculated with several vdW-DFs at saturation coverage. Our results show that recently proposed vdW-DFs with high accuracy all prefer TB to BF, in accord with more accurate calculations based on exact exchange and correlation within the random phase approximation. Detailed analyses reveal the important roles played by the molecule-surface interaction and molecular deformation upon adsorption, and we suggest that their precise description is prerequisite for accurate prediction of the most stable adsorption structure of organic molecules on semiconductor surfaces.

A comparative study of structural and electronic properties of formaldehyde molecule on monolayer honeycomb structures based on vdW-DF prospective

In order to develop the potential applications of monolayer sheets as gas sensors, the adsorption of formaldehyde (H2CO) molecule on graphene, hexagonal silicon carbide (h-SiC) as well as hexagonal aluminum nitride (h-AlN) monolayer sheets have been investigated. In this work we have used the so-called van der Waals density functional (vdW-DF) method. It was found that H2CO molecule adsorption on h-AlN nanosheet had relatively higher adsorption energy and shorter binding distance and finally much more reactive in the adsorption of H2CO compared with the h-SiC and graphene sheets. The density of states (DOS) was calculated and the results show that the highest occupied molecular orbital (HOMO)-lowest unoccupied molecular orbital (LUMO) energy gap of h-AlN and h-SiC sheets is significantly reduced upon the H2CO adsorption compared to the graphene which leads to an enhancement in the electrical conductivity of respective systems. We have evaluated these findings by well-known Mulliken as well as Hirshfeld and Voronoi charges analyses for aforementioned systems. The purpose of this work is to achieve deep insights into the influence of H2CO molecule on the electronic properties of h-AlN and h-SiC monolayer sheets, and how these effects could be used to design more sensitive gas sensing devices. Based on the DFT calculation results, the h-AlN and also h-h-SiC sheets are anticipated to be potential novel sensor for detecting the presence of H2CO toxic gas.

Adsorption of TCNQ and F4-TCNQ molecules on hydrogen-terminated Si(1 1 1) surface: van der Waals interactions included DFT study of the molecular orientations

A study of the molecules TCNQ and F4-TCNQ surface doped on hydrogen-terminated Si(111) surface [H–Si(111)], with emphasis on the role of van der Waals interactions in stabilizing the molecular adsorption orientations and the binding energy, has been carried out using density functional theory (DFT). The dispersion energy in the adsorption process is estimated using the DFT-D2/D3 and vdW-DF methods. The most stable spatial configuration of the adsorbed molecules predicted with and without including the dispersion energy in a low concentration dopant system is same though the magnitude of the binding energy is much larger in the former case. On the other hand in the case of increased dopant concentration (doubling the number of molecules on the same surface) the adsorption orientations predicted with and without the inclusion of dispersion energy are different and so is the magnitude of the binding energy. We conclude that inclusion of dispersion energy term is important for correct prediction of the spatial configurations of the adsorbed molecules in surface transfer doping of semiconductors.

Thickness dependence of surface energy and contact angle of water droplets on ultrathin MoS2 films.

We have performed a systematic density functional study of surface energy of MoS2 films as a function of thickness from one to twelve layers with the consideration of van der Waals (vdW) interactions using the vdW-DF and DFT-D2 methods. Both vdW schemes show that the surface energy will increase with the increase of the number of atomic layers and converge to a constant value at about six layers. Based on the calculated surface energies, we further analyze the surface contact angle of water droplets on the MoS2 film surface using Young's equation as a function of thickness in comparison with experiments, from which the water-MoS2 interfacial energy is derived to be independent of MoS2 thickness. Our calculations indicate that the vdW interactions between the MoS2 layers play an important role in determining surface energy, and results in the thickness dependence of the contact angle of water droplets on the MoS2 film surface. Our results explain well the recent wetting experiment [Nano Lett., 2014, 14(8), 4314], and will be useful for future studies of physical and chemical properties of ultrathin MoS2 films.

Acetone Adsorption on Pristine and Pt-doped Graphene: A First-Principles vdW-DF Study

Using van der Waals corrected density functional theory (vdW-DF) method we have investigated the adsorption of acetone molecule on pristine and Pt-doped graphene. Several active sites for both the interacting systems have been considered in the adsorption process including full geometry optimization. We have analyzed the structural and electrical properties of energetically favorable configurations. The results show that adsorption of acetone molecule on the Pt-doped graphene is energetically preferable. The binding energy and bonding distance are determined to be −5.277 eV and 2.206 Å, respectively, accompanying with charge transfer of 1.11 e. Furthermore, the Pt-O bond is rather significantly elongated when acetone is adsorbed on Pt-doped graphene. Compared to pristine graphene, the Pt-doped graphene has stronger interaction with the acetone and may provide more sensitive signal for a single acetone molecule. Meanwhile, practically, the band gap of Pt-doped graphene would become reduced after acetone adsorption. Consequently, our first-principles study presents evidence for a coherent benchmark for the applicability of Pt-doped graphene for acetone adsorption and detection.

Spin Signature of Nonlocal Correlation Binding in Metal-Organic Frameworks

We develop a proper nonempirical spin-density formalism for the van der Waals density functional (vdW-DF) method. We show that this generalization, termed svdW-DF, is firmly rooted in the single-particle nature of exchange and we test it on a range of spin systems. We investigate in detail the role of spin in the nonlocal correlation driven adsorption of H_{2} and CO_{2} in the linear magnets Mn-MOF74, Fe-MOF74, Co-MOF74, and Ni-MOF74. In all cases, we find that spin plays a significant role during the adsorption process despite the general weakness of the molecular-magnetic responses. The case of CO_{2} adsorption in Ni-MOF74 is particularly interesting, as the inclusion of spin effects results in an increased attraction, opposite to what the diamagnetic nature of CO_{2} would suggest. We explain this counterintuitive result, tracking the behavior to a coincidental hybridization of the O p states with the Ni d states in the down-spin channel. More generally, by providing insight on nonlocal correlation in concert with spin effects, our nonempirical svdW-DF method opens the door for a deeper understanding of weak nonlocal magnetic interactions.

Gold and Silver Clusters on TiO2 and ZrO2 (101) Surfaces: Role of Dispersion Forces

The adsorption of Ag and Au atoms and Ag4 and Au4 clusters on the stoichiometric TiO2 (anatase) and ZrO2 (tetragonal) (101) surfaces has been investigated using DFT+U calculations with and without the inclusion of van der Waals (vdW) forces. We considered the effects of vdW interactions on the physical properties of the adsorbed species using three different approaches: two variants of the pairwise force field method proposed by Grimme (DFT+D2 and DFT+D2′), and the vdW-DF method in which the vdW contribution is expressed directly as a function of the electron density. The results show that, already at the level of metal atoms and small clusters, the inclusion of vdW interactions can change the order of stability of various isomers and, more importantly, can result in major corrections to the adsorption energies. These effects can, in turn, affect other properties such as the structure and chemical reactivity of supported metal particles on oxides or their diffusion properties.