Van der Waals interactions at the molecule-metal interface: PTCDA on Ag (111) (original) (raw)
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Van der Waals density functional calculations of binding in molecular crystals
Computer Physics Communications, 2011
A recent paper [J. Chem. Phys. 132 134705 (2010)] illustrated the potential of the van der Waals density functional (vdW-DF) method [Phys. Rev. Lett. 92, 246401 (2004)] for efficient first-principle accounts of structure and cohesion in molecular crystals. Since then, modifications of the original vdW-DF version (identified as vdW-DF1) has been proposed, and there is also a new version called vdW-DF2 [ArXiv 1003.5255], within the vdW-DF framework. Here we investigate the performance and nature of the modifications and the new version for the binding of a set of simple molecular crystals: hexamine, dodecahedrane, C60, and graphite. These extended systems provide benchmarks for computational methods dealing with sparse matter. We show that a previously documented enhancement of non-local correlations of vdW-DF1 over an asymptotic atom-based account close to and a few Å beyond binding separation persists in vdW-DF2. The calculation and analysis of the binding in molecular crystals requires appropriate computational tools. In this paper, we also present details on our real-space parallel implementation of the vdW-DF correlation and on the method used to generate asymptotic atom-based pair potentials based on vdW-DF.
Physical Review Materials
Semi-local density functional approximations are widely used. None of them can capture the longrange van der Waals (vdW) attraction between separated subsystems, but they differ remarkably in the extent to which they capture intermediate-range vdW effects responsible for equilibrium bonds between neighboring small closed-shell subsystems. The local density approximation (LDA) often overestimates this effect, while the Perdew-Burke-Ernzerhof (PBE) generalized gradient approximation (GGA) underestimates it. The strongly-constrained and appropriately normed (SCAN) meta-GGA often estimates it well. All of these semi-local functionals require an additive nonlocal correction such as the revised Vydrov-Van Voorhis 2010 (rVV10) to capture the long-range part. This work reports adsorption energies and the corresponding geometry of aromatic thiophene (C4H4S) bound to transition metal surfaces. The adsorption process requires a genuine interplay of covalent and weak binding and requires a simultaneously accurate description of surface and adsorption energies with the correct prediction of the adsorption site. All these quantities must come from well balanced short and long-range correlation effects for a universally applicable method for weak interactions with chemical accuracy. Our methods indicate that the correct interplay is not present in any combination of recent meta-GGA's and rVV10. The simple short-range damping of the vdW correction scheme that is practically successful in the combination of GGA's and vdW approximations is less transferable in SCAN+rVV10 or in the revised version, revSCAN+rVV10. In addition, we present accurate random-phase-approximation-quality adsorption energies from a model based on the one of Zaremba and Kohn.
Theoretical study of PTCDA adsorbed on the coinage metal surfaces, Ag(111), Au(111) and Cu(111)
New Journal of Physics, 2009
A thorough understanding of the adsorption of molecules on metallic surfaces is a crucial prerequisite for the development and improvement of functionalized materials. A prominent representative within the class of π-conjugated molecules is 3,4,9,10-perylene-tetracarboxylic acid dianhydride (PTCDA) which, adsorbed on the Ag(111), Au(111) or Cu(111) surfaces, shows characteristic trends for work-function modification, alignment of molecular levels with the substrate Fermi energy and binding distances. We carried out density functional theory (DFT) calculations to investigate to what extent these trends can be rationalized on a theoretical basis. We used different density functionals (DF) including a fully non-local van der Waals (vdW) DF capable of describing dispersion interactions. We show that, rather independent of the DF, the calculations yield level alignments and work-function modifications consistent with ultra-violet photoelectron spectroscopy when the monolayer is placed onto the surfaces at the experimental distances (as determined from xray standing wave experiments). The lowest unoccupied molecular orbital is occupied on the Ag and Cu surfaces, whereas it remains unoccupied on the Au surface. Simultaneously, the work function increases for Ag but decreases for Cu and Au. Adsorption distances and energies, on the other hand, depend very sensitively on the choice of the DF. While calculations in the local density approximation bind the monolayer consistently with the experimental trends, the generalized gradient approximation in several flavors fails to reproduce 2 realistic distances and energies. Calculations employing the vdW-DF reveal that substantial bonding contributions arise from dispersive interactions. They yield reasonable binding energies but larger binding distances than the experiments.
van der Waals forces in density functional theory: a review of the vdW-DF method
Reports on Progress in Physics, 2015
A density functional theory (DFT) that accounts for van der Waals (vdW) interactions in condensed matter, materials physics, chemistry, and biology is reviewed. The insights that led to the construction of the Rutgers-Chalmers van der Waals Density Functional (vdW-DF) are presented with the aim of giving a historical perspective, while also emphasising more recent efforts which have sought to improve its accuracy. In addition to technical details, we discuss a range of recent applications that illustrate the necessity of including dispersion interactions in DFT. This review highlights the value of the vdW-DF method as a general-purpose method, not only for dispersion bound systems, but also in densely packed systems where these types of interactions are traditionally thought to be negligible.
The Journal of Chemical Physics, 2008
Density functional theory ͑DFT͒ in the commonly used local density or generalized gradient approximation fails to describe van der Waals ͑vdW͒ interactions that are vital to organic, biological, and other molecular systems. Here, we propose a simple, efficient, yet accurate local atomic potential ͑LAP͒ approach, named DFT+ LAP, for including vdW interactions in the framework of DFT. The LAPs for H, C, N, and O are generated by fitting the DFT+ LAP potential energy curves of small molecule dimers to those obtained from coupled cluster calculations with single, double, and perturbatively treated triple excitations, CCSD͑T͒. Excellent transferability of the LAPs is demonstrated by remarkable agreement with the JSCH-2005 benchmark database ͓P. Jurečka et al. Phys. Chem. Chem. Phys. 8, 1985 ͑2006͔͒, which provides the interaction energies of CCSD͑T͒ quality for 165 vdW and hydrogen-bonded complexes. For over 100 vdW dominant complexes in this database, our DFT+ LAP calculations give a mean absolute deviation from the benchmark results less than 0.5 kcal/ mol. The DFT+ LAP approach involves no extra computational cost other than standard DFT calculations and no modification of existing DFT codes, which enables straightforward quantum simulations, such as ab initio molecular dynamics, on biomolecular systems, as well as on other organic systems.
Two- and three-body interatomic dispersion energy contributions to binding in molecules and solids
The Journal of Chemical Physics, 2010
We present numerical estimates of the leading two-and three-body dispersion energy terms in van der Waals interactions for a broad variety of molecules and solids. The calculations are based on London and Axilrod-Teller-Muto expressions where the required interatomic dispersion energy coefficients, C 6 and C 9 , are computed "on the fly" from the electron density. Inter-and intramolecular energy contributions are obtained using the Tang-Toennies ͑TT͒ damping function for short interatomic distances. The TT range parameters are equally extracted on the fly from the electron density using their linear relationship to van der Waals radii. This relationship is empiricially determined for all the combinations of He-Xe rare gas dimers, as well as for the He and Ar trimers. The investigated systems include the S22 database of noncovalent interactions, Ar, benzene and ice crystals, bilayer graphene, C 60 dimer, a peptide ͑Ala 10 ͒, an intercalated drug-DNA model ͓ellipticine-d͑CG͒ 2 ͔, 42 DNA base pairs, a protein ͑DHFR, 2616 atoms͒, double stranded DNA ͑1905 atoms͒, and 12 molecular crystal polymorphs from crystal structure prediction blind test studies. The two-and three-body interatomic dispersion energies are found to contribute significantly to binding and cohesive energies, for bilayer graphene the latter reaches 50% of experimentally derived binding energy. These results suggest that interatomic three-body dispersion potentials should be accounted for in atomistic simulations when modeling bulky molecules or condensed phase systems.
The adsorption of benzene on metal surfaces is an important benchmark system for hybrid inorganic/organic interfaces. The reliable determination of the interface geometry and binding energy presents a significant challenge for both theory and experiment. Using the Perdew-Burke-Ernzerhof (PBE), PBE+vdW (van der Waals) and the recently developed PBE+vdW surf (densityfunctional theory with vdW interactions that include the collective electronic response of the substrate) methods, we calculated the structures and energetics for benzene on transition-metal surfaces: Cu, Ag, Au, Pd, Pt, Rh and Ir. Our calculations demonstrate that vdW interactions increase the binding energy by more than 0.70 eV for physisorbed systems (Cu, Ag and Au) and by an even larger amount for strongly bound systems (Pd, Pt, Rh and Ir). The collective response of the substrate electrons captured via the vdW surf method plays a significant role for most substrates, shortening the equilibrium distance by 0.25 Å for Cu and decreasing the binding energy by 0.27 eV for Rh. The reliability of our results is assessed by comparison with calculations using the random-phase approximation including renormalized single excitations, often hard to interpret, or even lacking. For example, due to the relative difficulty of controlling and measuring weakly bound systems, no experimental adsorption height has been reported so far for Bz physisorbed on noble metals. The only experimentally deduced adsorption height, to the best of our knowledge, was determined for the disordered Bz chemisorbed on the Pt(111) surface at a coverage close to or less than one .
Chemistry Central Journal, 2007
Background: The prediction of ligand binding or protein structure requires very accurate force field potentials-even small errors in force field potentials can make a 'wrong' structure (from the billions possible) more stable than the single, 'correct' one. However, despite huge efforts to optimize them, currently-used all-atom force fields are still not able, in a vast majority of cases, even to keep a protein molecule in its native conformation in the course of molecular dynamics simulations or to bring an approximate, homology-based model of protein structure closer to its native conformation. Results: A strict analysis shows that a specific coupling of multi-atom Van der Waals interactions with covalent bonding can, in extreme cases, increase (or decrease) the interaction energy by about 20-40% at certain angles between the direction of interaction and the covalent bond. It is also shown that on average multi-body effects decrease the total Van der Waals energy in proportion to the square root of the electronic component of dielectric permittivity corresponding to dipoledipole interactions at small distances, where Van der Waals interactions take place. Conclusion: The study shows that currently-ignored multi-atom Van der Waals interactions can, in certain instances, lead to significant energy effects, comparable to those caused by the replacement of atoms (for instance, C by N) in conventional pairwise Van der Waals interactions.
van der Waals forces in density functional theory: The vdW-DF method
2014
A density functional theory (DFT) that accounts for van der Waals (vdW) interactions in condensed matter, materials physics, chemistry, and biology is reviewed. The insights that led to the construction of the Rutgers-Chalmers van der Waals Density Functional (vdW-DF) are presented with the aim of giving a historical perspective, while also emphasising more recent efforts which have sought to improve its accuracy. In addition to technical details, we discuss a range of recent applications that illustrate the necessity of including dispersion interactions in DFT. This review highlights the value of the vdW-DF method as a general-purpose method, not only for dispersion bound systems, but also in densely packed systems where these types of interactions are traditionally thought to be negligible.