Van Der Waals Corrections Research Articles

Influence of spin-phonon coupling on antiferromagnetic spin fluctuations in FeSe under pressure: First-principles calculations with van der Waals corrections

The electronic structures, lattice dynamics, and magnetic properties of crystal $\ensuremath{\beta}$-FeSe under hydrostatic pressure have been studied by using the first-principles electronic structure calculations with van der Waals corrections. With applied pressure, the energy bands around the Fermi energy level consisting mainly of Fe-$3d$ orbitals show obvious energy shifts and occupation variations, and meanwhile the frequencies of all optical phonon modes increase. Among these phonon modes, the ${A}_{1g}$ mode, which relates to the Se height from the Fe-Fe plane, shows a clear frequency jump in a pressure range between 5 and 6 GPa. This is also the pressure range within which the highest superconducting transition temperature ${T}_{c}$ of FeSe is reached in experiments. In comparison with other phonon modes, the atomic displacement due to the zero-point vibration of the ${A}_{1g}$ mode induces the strongest fluctuation of local magnetic moment on Fe under pressures from 0 to 9 GPa, and the induced fluctuation reaches a maximum around 5 GPa. These results suggest that the effect of phonon via spin-phonon coupling could not be completely omitted when exploring the superconducting mechanism in iron-based superconductors.

Three-dimensional diffusion of molecular hydrogen in graphdiyne: a first-principles study

First-principles calculations with van der Waals correction included are carried out to investigate the intercalation and diffusion of molecular hydrogen in single-layer and bulk graphdiyne, which is crucial for understanding and improving the hydrogen storage capacity of graphdiyne. Different intercalation sites and hydrogen molecular orientations have been considered and compared. It is found that configurations with the axis of the hydrogen molecule parallel to graphdiyne layers are favoured. In contrast to graphite where hydrogen diffusion is restricted within the interlayer space, the unique porous structure of graphdiyne enables three-dimensional diffusion of hydrogen (in-plane diffusion and out-plane diffusion) with moderate energy barriers, thus ensuring easy hydrogen loading and unloading. The in-plane diffusion barriers largely depend on the interlayer distance, whereas the interlayer spacing has little effect on the out-plane diffusion barriers. This experimentally available novel carbon allotrope is expected to find applications in hydrogen storage.

Refined phase coexistence line between graphite and diamond from density-functional theory and van der Waals correction

In the present paper, we provide the refined pressure–temperature phase coexistence line between graphite and diamond with van der Waals (vdW) energy corrected density-functional theory and quasiharmonic approximation. A systematic comparison of the generalized gradient approximation (GGA) results for the lattice-related properties, phonon dispersion curves, and thermodynamic properties of graphite and diamond with and without vdW correction is presented. It is shown that adding the vdW interactions over the GGA exchange-correlation energy is positively necessary to obtain the reliable phase coexistence line between graphite and diamond, as compared with the experimental data. The 0K phase transition pressure calculated with the GGA+vdW formalism is 1.6GPa, which is sufficiently close to the value of 1.4GPa extrapolated from the experimental values. We find the flattening of the coexistence line at low temperatures below ~300K with GGA+vdW as well as GGA. The slope of the coexistence line calculated by the GGA+vdW approach is 2.5×10−3GPaK−1 placed within the experimental value range.

Identifying the nature of interaction between LiBH4 and two-dimensional substrates: DFT study with van der Waals correction

Abstract Addressing the nature of interaction at the LiBH 4 −carbon interface is the key to unveiling mechanism for the carbon-facilitated desorption of lithium borohydride (LiBH 4 ). Density functional theory calculations, taking into account the long range dispersion forces, have been performed to explore the interaction between LiBH 4 , in the form of either a monomer unit or a crystalline bulk, and two-dimensional (2D) substrate, represented by graphene and hexagonal boron nitride. At the monomer−2D contact, the permanent dipole of LiBH 4 induces polarization of the π electrons of the 2D, and the resultant permanent dipole–induced dipole attraction becomes the main source of binding. At the bulk−2D interface, van der Waals attraction dominates the interfacial binding rather than the dipole–dipole attraction. The absolute values of the calculated interface energy match closely with the surface energy of pristine (0 0 1) LiBH 4 , hinting that the energy released by the formation of the interface has enough magnitude to overcome the surface energy of LiBH 4 .

First-principles investigations of electronic and mechanical properties for stable Ge2Sb2Te5 with van der Waals corrections

The Te–Te weak van der Waals-type bonding plays an important role in Ge2Sb2Te5, a widely investigated phase-change material and a potential topological insulator. In this work, we have studied the electronic and mechanical properties of stable Ge2Sb2Te5 using ab initio calculations with the van der Waals corrections. The results show that the van der Waals corrections combined with hybrid functions improve the descriptions of the electronic structure of stable Ge2Sb2Te5. The band gap of ∼0.5eV in very good agreement with the experimental value for stable Ge2Sb2Te5 has been successfully reproduced. Furthermore, we have predicted the elastic constants and mechanical properties of stable trigonal Ge2Sb2Te5.

Volume shrinkage of a metal–organic framework host induced by the dispersive attraction of guest gas molecules

Using a density functional theory calculation including van der Waals (vdW) corrections, we report that H2 adsorption in a cubic-crystalline microporous metal-organic framework (MOF-5) leads to volume shrinkage, which is in contrast to the intuition that gas adsorption in a confined system (e.g., pores in a material) increases the internal pressure and then leads to volumetric expansion. This extraordinary phenomenon is closely related to the vdW interactions between MOF and H2 along with the H2-H2 interaction, rather than the Madelung-type electrostatic interaction. At low temperatures, H2 molecules adsorbed in the MOF-5 form highly symmetrical interlinked nanocages that change from a cube-like shape to a sphere-like shape with H2 loading, helping to exert centrosymmetric forces and hydrostatic (volumetric) stresses from the collection of dispersive interactions. The generated internal negative stress is sufficient to overcome the stiffness of the MOF-5 which is a soft material with a low bulk modulus (15.54 GPa).

Molecular modeling of adsorbed NDMA and water in MFI zeolites

N-nitrosodimethylamine (NDMA), which is a carcinogenic and toxic N-nitrosamine, can be found in water resources associated with a multitude of processes in various industrial facilities or merely as a by-product of water or wastewater treatment. Therefore, the removal of NDMA from drinking water represents an important human safety and public health concern. The present paper presents a density functional theory study of NDMA adsorption in all-silica MFI, Na-ZSM-5 and H-ZSM-5 zeolites. The stability of NDMA inside the zeolite pores was investigated by calculating the amount of energy released during adsorption. Various configurations of adsorbed NDMA to the zeolites were investigated, predominantly at the intersection of straight and sinusoidal channels. The strength of the adsorption energies followed the order H-ZSM-5>Na-ZSM-5>all-silica MFI. NDMA has a dipole moment and the strongest binding of NDMA occurred through the interactions of the negatively charged O atom of the molecule to positive atoms of the zeolite. For comparison, similar calculations were performed for water adsorption in these three zeolites. The adsorption energy of water in these three structures followed the order Na-ZSM-5>H-ZSM-5>all-silica MFI. We also incorporated van der Waals corrections in the simulations, which had the effect of stabilizing NDMA within the zeolite channels, but did not significantly change the relative stability of the different adsorption geometries. It was concluded that H-ZSM-5 is a good candidate to remove NDMA. Finally, it should be pointed out that H-ZSM-5 has the largest difference in binding energy between NDMA and water of the studied zeolites, suggesting that separation of the two molecules is indeed feasible due to preferential interactions between zeolite and adsorbate molecule.

First-Principles Studies of Photoinduced Charge Transfer in Noncovalently Functionalized Carbon Nanotubes

We have studied the energetics, electronic structure, optical excitation, and electron relaxation of dinitromethane molecules (CH2N2O4) adsorbed on semiconducting carbon nanotubes (CNTs) of chiral index (n,0) (n = 7, 10, 13, 16, 19). Using first-principles density functional theory (DFT) with generalized gradient approximations and van der Waals corrections, we have calculated adsorption energies of dinitropentylpyrene, in which the dinitromethane is linked to the pyrene via an aliphatic chain, on a CNT. A 780 meV (18.0 kcal/mol) binding energy has been found, which explains why such aliphatic chain–pyrene units can be and have been used in experiments to bind functional molecules to CNTs. The calculated electronic structures show that the dinitromethane introduces a localized state inside the band gap of CNT systems of n = 10, 13, 16. and 19; such a state can trap an electron when the CNT is photoexcited. We have therefore investigated the dynamics of intraband relaxations using the reduced density matrix formalism in conjunction with DFT. For pristine CNTs, we have found that the calculated charge relaxation constants agree well with the experimental time scales. Upon adsorption, these constants are modified, but there is not a clear trend for the direction and magnitude of the change. Nevertheless, our calculations predict that electron relaxation in the conduction band is faster than hole relaxation in the valence band for CNTs with and without molecular adsorbates.

Role of van der Waals corrections for the PtX2(X=O, S, Se) compounds

Dispersion (van der Waals) forces play an important role in determining the structural properties of the systems where dispersion is crucial, for example, layerlike crystals (CdI${}_{2}$ type). Thus, to contribute to the understanding of the role of van der Waals (vdW) corrections for the Pt${X}_{2}$ ($X=\text{O}$, S, Se) compounds, we report a density functional theory (DFT) investigation within nonlocal vdW corrections for the atomic structure and electronic properties of bulk Pt${X}_{2}$. From our calculations, we identified the lowest energy structures, CaCl${}_{2}$ type for PtO${}_{2}$ and CdI${}_{2}$ type for both PtS${}_{2}$ and PtSe${}_{2}$, i.e., CdI${}_{2}$ type is not the lowest energy structure for PtO${}_{2}$. We reported the structural changes for higher energy Pt${X}_{2}$ systems and the changes in the stability order compared with plain DFT-PBE calculations. The structural changes induced by vdW corrections affects the electronic structure of the layered CdI${}_{2}$-type structures (PtS${}_{2}$ and PtSe${}_{2}$), where a metallic behavior is obtained in contrast to PBE calculations, which yields an energy separation between the unoccupied and occupied states.

Density Functional Investigation of the Adsorption of Ethanol–Water Mixture on the Pt(111) Surface

Steam reforming of ethanol–water mixture is a promising renewable route to obtain hydrogen; however, our atomistic understanding of the interaction of ethanol–water mixture with transition-metal surfaces is far from satisfactory. In this work, we report a density functional theory investigation of the adsorption properties of the ethanol–water mixture on the Pt(111) surface employing semilocal exchange-correlation functional within nonlocal van der Waals corrections. From our calculations and analysis, we found that water molecules are located near the surface instead of ethanol, which is in contrast with our initial expectation based on the large magnitude of the adsorption energy of ethanol on Pt(111) compared with water/Pt(111). We found that the formation of hydrogen bonds among ethanol–ethanol, water–water, and ethanol–water molecules plays an important role in the adsorbate structure of the ethanol–water mixture on Pt(111), in particular, due to the enhancement of the binding energy of the hydrogen ...

Properties of Weakly Bound Molecular Oxygen on the Rutile TiO2(110) Surface from Density Functional Theory

We have used density functional theory with van der Waals (vdW) corrections to study the energetics, structure, and vibrational modes of physisorbed O2 on the rutile TiO2(110) surface. We find that vdW interactions dominate the adsorption energy of physisorbed O2 molecules. We have identified the ground state geometry for physisorbed O2 on the TiO2(110) surface from the vdW corrected potential energy surface. We have computed the vibrational frequencies of O2 molecules in various physisorbed conformations from the partial dynamical matrix of O2 and have identified conformations that have frequencies close to the gas phase Raman displacement of O2, in agreement with recent experimental infrared (IR) measurements of physisorbed O2 on TiO2 [J. Phys. Chem. C 2010, 114, 11924]. The intensities of the modes were calculated through dipole moment displacements and were found to be in qualitative agreement with experimental findings. Our calculations show that the appearance of IR modes for physisorbed O2 on the T...

Nonlocal van der Waals Approach Merged with Double-Hybrid Density Functionals: Toward the Accurate Treatment of Noncovalent Interactions.

Noncovalent interactions drive the self-assembly of weakly interacting molecular systems to form supramolecular aggregates, which play a major role in nanotechnology and biochemistry. In this work, we present a thorough assessment of the performance of different double-hybrid density functionals (PBE0-DH-NL, revPBE0-DH-NL, B2PLYP-NL, and TPSS0-DH-NL), as well as their parent hybrid and (meta)GGA functionals, in combination with the most modern version of the nonlocal (NL) van der Waals correction. It is shown that this nonlocal correction can be successfully coupled with double-hybrid density functionals thanks to the short-range attenuation parameter b, which has been optimized against reference interaction energies of benchmarking molecular complexes (S22 and S66 databases). Among all the double-hybrid functionals evaluated, revPBE0-DH-NL and B2PLYP-NL behave remarkably accurate with mean unsigned errors (MUE) as small as 0.20 kcal/mol for the training sets and in the 0.25-0.42 kcal/mol range for an independent database (NCCE31). They can be thus seen as appropriate functionals to use in a broad number of applications where noncovalent interactions play an important role. Overall, the nonlocal van der Waals approach combined with last-generation density functionals is confirmed as an accurate and affordable computational tool for the modeling of weakly bonded molecular systems.

Characterization of graphene–fullerene interactions: Insights from density functional theory

Using density functional theory (DFT) based approaches that utilize appropriate semi-empirical and nonlocal van der Waals corrections, we rigorously examine the interactions between fullerene (C60) molecules and pristine single layer graphene (SLG) sheets as well as SLG containing isolated mono-vacancy, divacancy and Stone–Wales defect-sites respectively. Our results show that chemical bonding between the C60 molecule and SLG at mono-vacancy defect-sites demonstrate predominantly sp3-like hybridization, in contrast to weaker π–π interactions that characterize C60–SLG systems containing divacancies and Stone–Wales defects.

Ability of analytical and artificial approaches for prediction of the volumetric properties of some polymer blends

In this research the statistical–mechanical equation of state and artificial neural network approaches are developed for volumetric properties of polymer blends. The Ihm–Song–Mason (ISM) and Tao–Mason (TM) equations of state based on density and surface tension at melting point (ρm and γm), as scaling constants, were developed. The calculation of second virial coefficients (B2), effective van der Waals co-volume (b) and correction factor (α) are required for judgment about applicability of these models. Also another model such as an artificial neural network (ANN) based on back propagation training with 15 neurons was used. A collection of 5397 data points for five polymer blends in the temperature range of 298.15–605.05K and pressures to 200MPa was used. The obtained results by ISM, TM and ANN models had good agreement with the experimental data with absolute average deviations of 0.72%, 0.84% and 0.34%, respectively. Among the applied methods, higher efficiency and better accuracy was achieved using ANN.

Density functional study of acrolein adsorption on Pt (111)

The electronic structure and bonding of acrolein (propenal) adsorption on Pt (111) were studied by density functional calculations (DFT). We optimized different adsorption configurations on the surface using the VASP code. The energetic study indicates that acrolein trans isomers are less stable on the Pt surface than cis configurations, which have a similar stability in all cases. We found that the inclusion of Van der Waals (vdW) corrections does not change the obtained adsorption geometries or preferential sites relative energies. We also analyzed the evolution of the chemical bonding changes in the adsorbate and the metal surface by crystal orbital overlap population (COOP) and overlap population (OP) analysis of selected bonds. Except for the η1 configuration, the adsorption of acrolein on the surface is mainly due to the formation of C–Pt bonds. We also found that the acrolein C pz orbital, perpendicular to the surface, play an important role in the adsorption, as well as Pt pz and dz2 orbitals, whose lobes are well oriented to overlap with the adsorbate orbitals.

Substrate-induced changes in the magnetic and electronic properties of hexagonal boron nitride

Using ab initio density functional theory we study the structure and electronic properties of hexagonal BN (h-BN) on Ni(111) and Co(0001) surfaces. Our calculations show that while dispersion interactions play an important role in stabilizing h-BN on the Ni(111) surface, on the Co(0001) surface it is primarily the covalent interactions. For h-BN on Ni(111) we show that semiempirical van der Waals correction proposed by Grimme to total energies obtained from density functional theory can correctly capture both the strong chemisorption minima closer to the surface and the weak physisorption minima further away from the surface. On both surfaces, the h-BN sheet becomes weakly ferrimagnetic. Additionally, on Ni(111) the h-BN sheet becomes half metallic and on Co(0001) it becomes metallic.

Mobile metal adatoms on single layer, bilayer, and trilayer graphene: Anab initioDFT study with van der Waals corrections correlated with electron microscopy data

The plane-wave density functional theory code CASTEP was used with the Tkatchenko-Scheffler van der Waals correction scheme and the generalized gradient approximation of Perdew, Burke, and Ernzerhof (GGA PBE) to calculate the binding energy of Au, Cr, and Al atoms on the armchair and zigzag edge binding sites of monolayer graphene, and at the high-symmetry adsorption sites of single layer, bilayer, and trilayer graphene. All edge site binding energies were found to be substantially higher than the adsorption energies for all metals. The adatom migration activation barriers for the lowest energy migration paths on pristine monolayer, bilayer, and trilayer graphene were then calculated and found to be smaller than or within an order of magnitude of ${k}_{B}T$ at room temperature, implying very high mobility for all adatoms studied. This suggests that metal atoms evaporated onto graphene samples quickly migrate across the lattice and bind to the energetically favorable edge sites before being characterized in the microscope. We then prove this notion for Al and Au on graphene with scanning transmission electron microscopy (STEM) images showing that these atoms are observed exclusively at edge sites, and also hydrocarbon-contaminated regions, where the pristine regions of the lattice are completely devoid of adatoms. Additionally, we review the issue of fixing selected atomic positions during geometry optimization calculations for graphene/adatom systems and suggest a guiding principle for future studies.

Magnetic coupling of Fe-porphyrin molecules adsorbed on clean andc(2×2) oxygen-reconstructed Co(100) investigated by spin-polarized photoemission spectroscopy

The spin-polarized electronic structure of iron octaethylporphyrin (FeOEP) molecules adsorbed on a pristine and on a $c$($2\ifmmode\times\else\texttimes\fi{}2$) oxygen-reconstructed Co(100) surface has been analyzed by means of spin-polarized photoemission spectroscopy (SPPES) and first-principles density functional theory with the on-site Coulomb repulsion $U$ term ($\mathrm{DFT}+U$) calculations with and without Van der Waals corrections. The aim is to examine the magnetic exchange mechanism between the FeOEP molecules and the Co(100) substrate in the presence or absence of the oxygen mediator. The results demonstrate that the magnetic coupling from the ferromagnetic substrate to the adsorbed FeOEP molecules is ferromagnetic, whereas, the coupling is antiferromagnetic for the FeOEP on the $c$($2\ifmmode\times\else\texttimes\fi{}2$)O/Co(100) system. Spin-resolved partial densities of states extracted from ab initio $\mathrm{DFT}+U$ modeling are in fairly good comparison with the electronic spectral densities seen in angle-integrated SPPES energy dispersion curves for submonolayer coverages of FeOEP. Through combined analysis of these spectra and theoretical results, we determine that hybridization of 2$p$ orbitals of N and O with Co 3$d$ orbitals facilitates indirect magnetic exchange interactions between Fe and Co, whereas, a direct Fe-Co interaction involving the Fe ${d}_{{z}^{2}}$ orbital is also found for FeOEP on Co. It is observed through SPPES that the spin polarization of the photoemission-visible molecular overlayers decreases to zero as coverage is increased beyond the submonolayer regime, indicating that only interfacial magnetic coupling is at work. Microspot low-energy electron diffraction and low-energy electron microscopy were performed to characterize the physical order of the molecular coverage, revealing that FeOEP structural domains are orders of magnitude greater in size on $c$($2\ifmmode\times\else\texttimes\fi{}2$)O/Co(100) than on clean Co(100), which coincides with reduced scattering from the disorder and sharper features seen in SPPES.

The scaling of contact rates with population density for the infectious disease models

Contact rates and patterns among individuals in a geographic area drive transmission of directly-transmitted pathogens, making it essential to understand and estimate contacts for simulation of disease dynamics. Under the uniform mixing assumption, one of two mechanisms is typically used to describe the relation between contact rate and population density: density-dependent or frequency-dependent. Based on existing evidence of population threshold and human mobility patterns, we formulated a spatial contact model to describe the appropriate form of transmission with initial growth at low density and saturation at higher density. We show that the two mechanisms are extreme cases that do not capture real population movement across all scales. Empirical data of human and wildlife diseases indicate that a nonlinear function may work better when looking at the full spectrum of densities. This estimation can be applied to large areas with population mixing in general activities. For crowds with unusually large densities (e.g., transportation terminals, stadiums, or mass gatherings), the lack of organized social contact structure deviates the physical contacts towards a special case of the spatial contact model – the dynamics of kinetic gas molecule collision. In this case, an ideal gas model with van der Waals correction fits well; existing movement observation data and the contact rate between individuals is estimated using kinetic theory. A complete picture of contact rate scaling with population density may help clarify the definition of transmission rates in heterogeneous, large-scale spatial systems.

A Density-Functional Theory-Based Neural Network Potential for Water Clusters Including van der Waals Corrections

The fundamental importance of water for many chemical processes has motivated the development of countless efficient but approximate water potentials for large-scale molecular dynamics simulations, from simple empirical force fields to very sophisticated flexible water models. Accurate and generally applicable water potentials should fulfill a number of requirements. They should have a quality close to quantum chemical methods, they should explicitly depend on all degrees of freedom including all relevant many-body interactions, and they should be able to describe molecular dissociation and recombination. In this work, we present a high-dimensional neural network (NN) potential for water clusters based on density-functional theory (DFT) calculations, which is constructed using clusters containing up to 10 monomers and is in principle able to meet all these requirements. We investigate the reliability of specific parametrizations employing two frequently used generalized gradient approximation (GGA) exchange-correlation functionals, PBE and RPBE, as reference methods. We find that the binding energy errors of the NN potentials with respect to DFT are significantly lower than the typical uncertainties of DFT calculations arising from the choice of the exchange-correlation functional. Further, we examine the role of van der Waals interactions, which are not properly described by GGA functionals. Specifically, we incorporate the D3 scheme suggested by Grimme (J. Chem. Phys. 2010, 132, 154104) in our potentials and demonstrate that it can be applied to GGA-based NN potentials in the same way as to DFT calculations without modification. Our results show that the description of small water clusters provided by the RPBE functional is significantly improved if van der Waals interactions are included, while in case of the PBE functional, which is well-known to yield stronger binding than RPBE, van der Waals corrections lead to overestimated binding energies.