Empirical Van Der Waals Research Articles

"Noncovalent Interaction": A Chemical Misnomer That Inhibits Proper Understanding of Hydrogen Bonding, Rotation Barriers, and Other Topics.

We discuss the problematic terminology of "noncovalent interactions" as commonly applied to hydrogen bonds, rotation barriers, steric repulsions, and other stereoelectronic phenomena. Although categorization as "noncovalent" seems to justify classical-type pedagogical rationalizations, we show that these phenomena are irreducible corollaries of the same orbital-level conceptions of electronic covalency and resonance that govern all chemical bonding phenomena. Retention of such nomenclature is pedagogically misleading in supporting superficial dipole-dipole and related "simple, neat, and wrong" conceptions as well as perpetuating inappropriate bifurcation of the introductory chemistry curriculum into distinct "covalent" vs. "noncovalent" modules. If retained at all, the line of dichotomization between "covalent" and "noncovalent" interaction should be re-drawn beyond the range of quantal exchange effects (roughly, at the contact boundary of empirical van der Waals radii) to better unify the pedagogy of molecular and supramolecular bonding phenomena.

Thermodynamic analysis of the difference in adsorption characteristics of CH4 and CO2 on continental shale

In order to explain the difference in adsorption characteristics of CH4 and CO2 on continental shale from the perspective of thermodynamics, the isothermal adsorption experiments of CH4 and CO2 adsorbed by shale in Yanchang Formation in Ordos Basin were carried out, and the excess adsorption capacity was corrected to absolute adsorption capacity. Then the Clausius-Clapeyron equation was used to analyze the isosteric heat of adsorption of CH4 and CO2 on shale. The results show that, for calculating the absolute adsorption capacity, Ozawa empirical formula or Van der Waals approximation method should be used to calculate the adsorption phase density. The absolute adsorption capacity should be selected as the basic data for calculating the isosteric heat of adsorption. The reason is that the excess isosteric heat of adsorption has a negative value in the low adsorption capacity stage, which is contradictory to the fact that the adsorption process is exothermic, and is significantly higher than the absolute isosteric heat of adsorption. There is a good linear positive correlation between the isosteric heat of adsorption and the adsorption amount of CH4 and CO2 adsorbed by continental shale, and the isosteric heat of adsorption of CH4 is greater than that of CO2. The absolute initial isosteric heat of adsorption of CH4 and CO2 adsorbed by shale is 52.04 kJ/mol and 27.71 kJ/mol, indicating that the adsorption force of CH4 on Yanchang Formation shale is stronger than that of CO2.

Assessment of the van der Waals, Hubbard U parameter and spin-orbit coupling corrections on the 2D/3D structures from metal gold congeners clusters.

The coinage-metal clusters possess a natural complexity in their theoretical treatment that may be accompanied by inherent shortcomings in the methodological approach. Herein, we performed a scalar-relativistic density functional theory study, considering Perdew, Burke, and Ernzerhof (PBE) with (empirical and semi empirical) van der Waals (vdW), spin-orbit coupling (SOC), +U (Hubbard term), and their combinations, to treat the , , and clusters in different structural motifs. The energetic scenario is given by the confirmation of the 3D lowest energy configurations for and within all approaches, while for there is a 2D/3D competition, depending on the applied correction. The 2D geometry is 0.43 eV more stable with plain PBE than the 3D one, the SOC, +U, and/or vdW inclusion decreases the overestimated stability of the planar configurations, where the most surprising result is found by the D3 and D3BJ vdW corrections, for which the 3D configuration is 0.29 and 0.11 eV, respectively, more stable than the 2D geometry (with even higher values when SOC and/or +U are added). The D3 dispersion correction represents 7.9% (4.4%) of the total binding energy for the 3D (2D) configuration, (not) being enough to change the hybridization and the position of the occupied -states. Our predictions are in agreement with experimental results and in line with the best results obtained for bulk systems, as well as with hybrid functionals within D3 corrections. The properties description undergoes small corrections with the different approaches, where general trends are maintained, that is, the average bond length is smaller (larger) for lower (higher)-coordinated structures, since a same number of electrons are shared by a smaller (larger) number of bonds, consequently, the bonds are stronger (weaker) and shorter (longer) and the hybridization index is larger (smaller). Thus, Au has a distinct behavior in relation to its lighter congeners, with a complex potential energy surface, where in addition to the relevant relativistic effects, correlation and dispersion effects must also be considered.

Wannier-function-based constrained DFT with nonorthogonality-correcting Pulay forces in application to the reorganization effects in graphene-adsorbed pentacene

Pulay terms arise in the Hellman-Feynman forces in electronic structure calculations when one employs a basis set made of localized orbitals that move with their host atoms. If the total energy of the system depends on a subspace population defined in terms of the localized orbitals across multiple atoms, then unconventional Pulay terms will emerge due to the variation of the orbital nonorthogonality with ionic translation. Here, we derive the required exact expressions for such terms, which cannot be eliminated by orbital orthonormalization. We have implemented these corrected ionic forces within the linear-scaling density functional theory (DFT) package ONETEP, and have used constrained DFT to calculate the reorganization energy of a pentacene molecule adsorbed on a graphene flake. The calculations are performed by including ensemble DFT, corrections for periodic boundary conditions, and empirical Van der Waals interactions. For this system we find that tensorially invariant population analysis yields an adsorbate subspace population that is very close to integer-valued when based upon nonorthogonal Wannier functions, and also but less precisely when using pseudoatomic functions. Thus, orbitals can provide a very effective population analysis for constrained DFT. Our calculations show that the reorganization energy of the adsorbed pentacene is typically lower than that of pentacene in the gas phase. We attribute this effect to steric hindrance.

Thermodynamics of the Flexible Metal-Organic Framework Material MIL-53(Cr) From First Principles.

We use first-principles density functional theory total energy and linear response phonon calculations to compute the Helmholtz and Gibbs free energy as a function of temperature, pressure, and cell volume in the flexible metal-organic framework material MIL-53(Cr) within the quasiharmonic approximation. GGA and metaGGA calculations were performed, each including empirical van der Waals (vdW) forces under the D2, D3, or D3(BJ) parameterizations. At all temperatures up to 500 K and pressures from -30 MPa to 30 MPa, two minima in the free energy versus volume are found, corresponding to the narrow pore (np) and large pore (lp) structures. Critical positive and negative pressures are identified, beyond which there is only one free energy minimum. While all results overestimated the stability of the np phase relative to the lp phase, the best overall agreement with experiment is found for the metaGGA PBEsol+RTPSS+U+J approach with D3 or D3(BJ) vdW forces. For these parameterizations, the calculated free energy barrier for the np-lp transition is only 3 to 6 kJ per mole of Cr4(OH)4(C8H4O4)4.

Electronic Structures and Li-Diffusion Properties of Group IV–V Layered Materials: Hexagonal Germanium Phosphide and Germanium Arsenide

Based on density functional theory (DFT) calculations that include an empirical van der Waals interaction, we propose a layered hexagonal phase of bulk GeP and GeAs that is marginally less stable than the monoclinic phase experimentally observed. Both types of monolayers are dynamically stable semiconductors. Application of 2% isotropic stretching along two in-plane directions practically transforms the GeAs monolayer into a direct-gap (= 1.60 eV) material, rendering it useful in optoelectronics. In addition, comparison of effective masses shows that the GeAs monolayer can function better as n-type materials, especially when it is subject to the in-plane strain. Furthermore, a detailed comparison of the activation barriers for the rate-determining steps along the different paths on the GeP surface indicates that the Li atom can diffuse on the surface ∼1000 times faster than on graphene. Another comparison of the barriers allows us to identify a preferred diffusion path in the interlayer region of bulk hex...

Understanding the thermodynamic pathways of SnO-to-SnOx phase transition

SnO decomposes into SnO2 and Sn above a certain temperature either directly or through intermediate phases. This phase transition, although has been known for a century, is not well understood yet. Further, to date, a consensus on the correct stoichiometry and crystal structures of intermediate SnOx phases formed during that phase transition is absent. Our work attempts to elucidate SnO-to-SnOx phase transition at thermodynamic growth conditions for the first time. The results presented here show that oxygen-poor and tin-rich growth conditions promote SnO-to-SnOx phase transition to happen. At these growth conditions, indirect phase transition is the most probable, and in such transition, the formation of any (Sn2O3 or Sn3O4) intermediate phases is equally probable depending on initial growth conditions. All these findings are consistent with experimental results. Further, it was demonstrated that empirical van der Waals (vdW) correction of SnO is required to reproduce the pathways of this phase transition correctly. At the end, the opto-electronic properties of Sn2O3 have been investigated.

Beyond Energies: Geometries of Nonbonded Molecular Complexes as Metrics for Assessing Electronic Structure Approaches.

Electronic structure approaches for calculating intermolecular interactions have traditionally been benchmarked almost exclusively on the basis of energy-centric metrics. Herein, we explore the idea of utilizing a metric related to geometry. On a diverse series of noncovalently interacting systems of different sizes, from the water dimer to the coronene dimer, we evaluate a variety of electronic structure approximations with respect to their abilities to reproduce coupled-cluster-level geometries. Specifically, we examine Hartree-Fock, second-order Møller-Plesset perturbation theory (MP2), attenuated MP2, scaled MP2, and a number of density functionals, many of which include empirical or nonempirical van der Waals dispersion corrections. We find a number of trends that transcend system size and interaction type. For instance, functionals incorporating VV10 nonlocal correlation tend to yield highly accurate geometries; ωB97X-V and B97M-V, in particular, stand out. We establish that intermolecular distance, as measured by, e.g., the center-of-mass separation of two molecules, is the geometric parameter that deviates most profoundly among the various methods. This property of the equilibrium intermolecular separation, coupled with its accessibility via a small series of well-defined single-point calculations, makes it an ideal metric for the development and evaluation of electronic structure methods.

Structure, Dynamics, and Spectral Diffusion of Water from First-Principles Molecular Dynamics

We have carried out first-principles Born–Oppenheimer molecular dynamics (BOMD) simulations of heavy water using density functional theory in conjunction with either empirical van der Waals (vdW) corrections or semilocal (van der Waals) exchange and correlation functionals. Specifically, gradient-corrected density functionals (BLYP), semiempirical vdW methods (BLYP-D2, BLYP-D3, PBE-D3, revPBE-D3), and vdW density functionals (DRSLL-PBE, DRSLL-optB88) are applied to evaluate their accuracy in describing the hydrogen-bonded network of heavy water. Ab initio trajectories are used to calculate structural and dynamical properties, with special emphasis on vibrational spectral diffusion and hydrogen bond dynamics. Our results show that inclusion of vdW interactions in DFT-GGA significantly affects the structure of liquid water and results in a faster diffusion. The combination of BLYP and revPBE functionals with the semiempirical vdW method of Grimme et al. [J. Chem. Phys. 2010, 132, 154104] and modified B88 fu...

A six-dimensional potential energy surface for Ru(0001)(2×2):CO.

We present a new global ground state potential energy surface (PES) for carbon monoxide at a coverage of 1/4, on a rigid Ru(0001) surface [Ru(0001)(2×2):CO]. All six adsorbate degrees of freedom are considered. For constructing the PES, we make use of more than 90,000 points calculated with periodic density functional theory using the RPBE exchange-correlation functional and an empirical van der Waals correction. These points are used for interpolation, utilizing a symmetry-adapted corrugation reducing procedure (CRP). Three different interpolation schemes with increasing accuracy have been realized, giving rise to three flavours of the CRP PES. The CRP PES yields in agreement with the DFT reference and experiments, the atop position of CO to be the most stable adsorption geometry, for the most accurate interpolation with an adsorption energy of 1.69 eV. The CRP PES shows that diffusion parallel to the surface is hindered by a barrier of 430 meV, and that dissociation is facilitated but still activated. As a first "real" application and further test of the new potential, the six-dimensional vibrational Schrödinger equation is solved variationally to arrive at fully coupled, anharmonic frequencies and vibrational wavefunctions for the vibrating, adsorbed CO molecule. Good agreement with experiment is found also here. Being analytical, the new PES opens an efficient way towards multidimensional dynamics.

Assessing electronic structure approaches for gas-ligand interactions in metal-organic frameworks: The CO2-benzene complex

Adsorption of gas molecules in metal-organic frameworks is governed by many factors, the most dominant of which are the interaction of the gas with open metal sites, and the interaction of the gas with the ligands. Herein, we examine the latter class of interaction in the context of CO2 binding to benzene. We begin by clarifying the geometry of the CO2-benzene complex. We then generate a benchmark binding curve using a coupled-cluster approach with single, double, and perturbative triple excitations [CCSD(T)] at the complete basis set (CBS) limit. Against this ΔCCSD(T)/CBS standard, we evaluate a plethora of electronic structure approximations: Hartree-Fock, second-order Møller-Plesset perturbation theory (MP2) with the resolution-of-the-identity approximation, attenuated MP2, and a number of density functionals with and without different empirical and nonempirical van der Waals corrections. We find that finite-basis MP2 significantly overbinds the complex. On the other hand, even the simplest empirical correction to standard density functionals is sufficient to bring the binding energies to well within 1 kJ/mol of the benchmark, corresponding to an error of less than 10%; PBE-D in particular performs well. Methods that explicitly include nonlocal correlation kernels, such as VV10, vdW-DF2, and ωB97X-V, perform with similar accuracy for this system, as do ωB97X and M06-L.

Magnetic properties of graphene/BN/Co(111) and potential spintronics

Using the Vienna ab initio simulation package (VASP) we have explored structural, adsorption, and magnetic properties of graphene/BN/Co(111) with the help of semi empirical and non-local van der Waals functional methods such as DFT-D2, vdW-DF2, optPBE-vdW, and optB88-vdW. In the most stable optimized structure, one carbon is on top of B atom and the other carbon is on top of hollow site of BN layer. No buckling geometry is found in both graphene and BN layers with vdW-DF2 method. In contrast, all three other approaches show that a buckling feature takes place in BN layer adjacent to Co substrate and due to this buckling an adsorption energy of graphene is significantly enhanced. Very interestingly, the graphene has an energy gap only in one spin band due to the influence of Co and an insulating state in BN layer adjacent to graphene is observed. In addition, the Co layer displays half metallic states as well. This feature suggests that the graphene/BN/Co(111) can be utilized for ideal tunneling magnetoresistance (TMR) structure because a high TMR ratio is expected.

Electronic-structure modification of graphene on Ni(111) surface by the intercalation of a noble metal

First-principles calculations based on the density functional theory supplemented with an empirical van der Waals interaction are used to explore the effect of Ag-atom intercalation on the electronic structure of graphene on Ni(111) surface. We first confirm that in the most stable configuration graphene is chemisorbed on Ni(111) with binding distance in good agreement with experiments. We also clarify the conflicting interplay of symmetry breaking of the graphene sublattice and hybridization of graphene \ensuremath{\pi} orbitals with Ni $d$ states in the bandgap opening of graphene. Upon intercalation of Ag atoms in the interface of graphene/Ni(111), the characteristic energy bands of graphene recover with or without a bandgap depending on Ag coverage. The bandgap is largest for fractional Ag coverage of \ensuremath{\sim}1.3 monolayer (ML) and is appreciable for fractional Ag coverage. These bandgap openings are consistent with the recent experiments [Varykhalov, Scholz, Kim, and Rader, Phys. Rev. B 82, 121101(R) (2010)], which, however, have been claimed to be the results for 1 ML Ag coverage. Our calculations also demonstrate that an appreciable bandgap does not open when intercalated Ag atoms of high concentration form a flat layer, which mimics the situation of graphene/Ag(111). These results imply that the actual Ag coverage achieved in the experiments was different from 1 ML. A key role may be assigned to such a fractional Ag coverage, for which graphene--Ag distances are intermediate between those of chemisorption and physisorption, and a bandgap is induced by rather strong interactions with Ag atoms. The Ni(111) substrate plays only a role of supporting such a sparse Ag-atom distribution. Similar arguments also apply to the recent experiments on graphene/Au/Ru(0001) [Enderlein, Kim, Bostwick, Rotenberg, and Horn, New J. Phys. 12, 033014 (2010)] in which a substantial bandgap also opened in graphene for the claimed 1 ML Au coverage.

Potential energy surface of 4-hexyl-4′-cyanobiphenyl (6CB) on graphite surface: a DFT study with van der Waals corrections

The potential energy surface (PES) between a 4-hexyl-4′-cyanobiphenyl (6CB) molecule and a graphite surface was calculated by the first-principles method based on the density functional theory with empirical van der Waals (vdW) corrections. The parameters of the empirical vdW corrections were derived by fitting the PESs for the benzene–methane, benzene dimer and benzene–benzonitrile molecules to high-level ab initio calculations. The obtained potential energy minimum between 6CB and graphite surface for a configuration was ca. − 27.8 kcal/mol. Based on this PES, we determined the force-field parameters between 6CB and graphite surface to be used in classical molecular simulations in the future work.

Cooperativity in the stacking of benzene-1,3,5-tricarboxamide: The role of dispersion

Quantum chemical calculations have been carried out to study the stacking and cooperativity in oligomers of benzene-1,3,5-tricarboxamide (BTA). Comparison between density functional theory (DFT) and SCS-MP2/cc-PVTZ level calculations for a dimer indicates the significant contribution of dispersive interactions in this system. Oligomers up to a decamer have thus been studied with DFT augmented by empirical van der Waals corrections. The stabilisation energy of the stack improves with oligomer size and a converged value of −27.1 kcal/mol is estimated. The presence of cooperativity in the system is reflected in a variety of structural parameters of the stack.

Vibrational and thermodynamic properties of β-HMX: A first-principles investigation

Thermodynamic properties of β-HMX crystal are investigated using the quasi-harmonic approximation and density functional theory within the local density approximation (LDA), generalized gradient approximation (GGA), and GGA + empirical van der Waals (vdW) correction. It is found that GGA well describes the thermal expansion coefficient and heat capacity but fails to produce correct bulk modulus and equilibrium volume. The vdW correction improves the bulk modulus and volume, but worsens the thermal expansion coefficient and heat capacity. In contrast, LDA describes all thermodynamic properties with reasonable accuracy, and overall is a good exchange-correlation functional for β-HMX molecular crystal. The results also demonstrate significant contributions of phonons to the equation of state. The static calculation of equilibrium volume for β-HMX differs from the room-temperature value incorporating lattice vibrations by over 5%. Therefore, for molecular crystals, it is essential to include phonon contributions when calculated equation of state is compared with experimental data at ambient condition.

Equations of state for energetic materials from density functional theory with van der Waals, thermal, and zero-point energy corrections

It is shown that the introduction of zero-point energy and thermal effects to density functional theory with an empirical van der Waals correction results in a significant improvement in the prediction of equilibrium volumes and isothermal equations of state for hydrostatic compressions of energetic materials at nonzero temperatures. This method can be used to predict the thermophysical properties of these materials for a wide range of pressures and temperatures.

Hydrostatic and uniaxial compression studies of 1,3,5-triamino- 2,4,6-trinitrobenzene using density functional theory with van der Waals correction

Hydrostatic and uniaxial compressions of 1,3,5-triamino-2,4,6-trinitrobenzene were investigated using first-principles density functional theory with an empirical van der Waals correction. The equilibrium structural and elastic properties and the hydrostatic equation of state are in good agreement with available experimental data. Physical properties such as the principal stresses, shear stresses, band gap, and the change in energy per atom as a function of compression ratio V/V0 in the directions normal to the (100), (010), (001),(110), (101), (011), and (111) crystallographic planes were calculated, showing highly anisotropic behavior under uniaxial compressions.

Theoretical Study of the Hydrolysis of Pentameric Aluminum Complexes

Static quantum chemical calculations and Car−Parrinello molecular dynamics (CPMD) simulations were used to investigate the structural characteristics and the stability of pentameric aluminum clusters in both gas phase and aquatic environments. The accuracy of several generalized gradient approximation (GGA) and hybrid exchange-correlation functionals were tested with and without empirical van der Waals corrections to ensure the accuracy of the selected methods. Conformational analysis was performed for experimentally detected (electrospray ionization mass spectrometry, ESI MS) structural isomers of cationic [Al5O6H2Cl4]+, [Al5O7H4Cl4]+, [Al5O8H6Cl4]+, and [Al5O9H8Cl4]+ complexes. Conductor-like screening model (COSMO) was used to investigate the stability of the gas phase optimized structures in aquatic environments. Four of the main pentameric aluminum complexes were then selected for the CPMD investigation. The effect of the long-range empirical vdW corrections (-D) was also tested employing two identic...

Prediction of Isothermal Equation of State of an Explosive Nitrate Ester by van der Waals Density Functional Theory

A new energetic material, nitrate ester 1 (NEST-1), has shown promise as a powerful, technologically attractive explosive. Its physical properties under compression, however, are currently unknown. Accurate density functional calculations together with a reliable empirical van der Waals correction are employed to predict the isothermal hydrostatic equation of state for this material prior to any known experimental results. The accuracy of results obtained from this approach was tested against experimentally known NEST-1 equilibrium properties and found to be excellent.