Perdew, Burke, and Ernzerhof Reply:

Perdew, John P.; Burke, Kieron; Ernzerhof, Matthias

doi:10.1103/physrevlett.80.891

Cited by 6,265 publications

(6,342 citation statements)

References 16 publications

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“…In the SCCDFTB structure, this water formed two H-bonds with an edge of the cuboid, which again led to an unusual triangular structure of water cluster, similar to the Hbonded triangle in the structure of (H 2 O) 10 cluster. (Figure 3b) For the (H 2 O) 14 cluster, the lowest-energy structures from two methods are shown in Fig 6. The overall structures are surprisingly similar to each other, except that the size of the SCCDFTB structure is slightly smaller than the HF/6-31G(d,p) structure. The most important difference is the H-bonding pattern of the four/five-member rings at the top: in the SCCDFTB structure, there are two OH bonds at the top free of H-bond; in the HF/6-31G(d,p) structure, the OH bonds of the top level are all saturated by H-bonds.…”

Section: Resultsmentioning

confidence: 99%

Simulating Water with the Self-Consistent-Charge Density Functional Tight Binding Method: From Molecular Clusters to the Liquid State

Elstner

et al. 2007

J. Phys. Chem. A

100

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The recently developed self-consistent-charge density functional tight binding (SCCDFTB) method provides an accurate and inexpensive quantum mechanical solution to many molecular systems of interests. To examine the performance of the SCCDFTB method on (liquid) water, the most fundamental yet indispensable molecule in biological systems, we have reported here the simulation results of water in sizes ranging from molecular clusters to the liquid state. The latter simulation was achieved through the use of the linear scaling divide-and-conquer approach. The results of liquid water simulation indicated that the SCCDFTB method can describe the structural and energetics of liquid water in qualitative agreement with experiments, while the results of water clusters suggested potential future improvements that may apply to the SCCDFTB method.

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Section: Resultsmentioning

confidence: 99%

Simulating Water with the Self-Consistent-Charge Density Functional Tight Binding Method: From Molecular Clusters to the Liquid State

Elstner

et al. 2007

J. Phys. Chem. A

100

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“…68 Overall, atomic displacements within the molecules are not larger than 0.01 Å . Note that because the revPBE exchange tends to give longer bond lengths, 71 we may expect that our molecule-to-surface distances are slightly overestimated. The calculated electron densities differences, shown in Fig.…”

Section: Molecules and Dimers On Surfacesmentioning

confidence: 94%

Role of van der Waals interaction in forming molecule-metal junctions: flat organic molecules on the Au(111) surface

Mura

Guļāns

Thonhauser

et al. 2010

Phys. Chem. Chem. Phys.

115

147

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The self-assembly of flat organic molecules on metal surfaces is controlled, apart from the kinetic factors, by the interplay between the molecule-molecule and molecule-surface interactions. These are typically calculated using standard density functional theory within the generalized gradient approximation, which significantly underestimates nonlocal correlations, i.e. van der Waals (vdW) contributions, and thus affects interactions between molecules and the metal surface in the junction. In this paper we address this question systematically for the Au(111) surface and a number of popular flat organic molecules which form directional hydrogen bonds with each other. This is done using the recently developed first-principles vdW-DF method which takes into account the nonlocal nature of electron correlation [M. Dion et al., Phys. Rev. Lett. 2004, 92, 246401]. We report here a systematic study of such systems involving completely self-consistent vdW-DF calculations with full geometry relaxation. We find that the hydrogen bonding between the molecules is only insignificantly affected by the vdW contribution, both in the gas phase and on the gold surface. However, the adsorption energies of these molecules on the surface increase dramatically as compared with the ordinary density functional (within the generalized gradient approximation, GGA) calculations, in agreement with available experimental data and previous calculations performed within approximate or semiempirical models, and this is entirely due to the vdW contribution which provides the main binding mechanism. We also stress the importance of self-consistency in calculating the binding energy by the vdW-DF method since the results of non-self-consistent calculations in some cases may be off by up to 20%. Our calculations still support the usually made assumption of the molecule-surface interaction changing little laterally suggesting that single molecules and their small clusters should be quite mobile at room temperature on the surface. These findings support a gas-phase modeling for some flat metal surfaces, such as Au(111), and flat molecules, at least as a first approximation.

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“…Computational Details: Density functional theory (DFT) calculations were performed with the Quickstep code [33] within the CP2K package [34], using a mixed Gaussian and plane waves basis set, the Goedecker, Teter and Hutter (GTH) pseudo-potentials [35] and a GGA-PBE [36] + rVV10 [37] exchange-correlation functional including self-consistently the van der Waals (vdW) interaction.…”

Section: Methodsmentioning

confidence: 99%

Driving Forces for Covalent Assembly of Porphyrins by Selective C–H Bond Activation and Intermolecular Coupling on a Copper Surface

et al. 2016

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Recent synthesis of covalent organic assemblies at surfaces has opened up the promise of producing robust nanostructures for functional interfaces. To uncover how this new chemistry works at surfaces and understand the underlying mechanism(s) that control bond-breaking and bond-making processes at specific positions of the participating molecules, we study here the coupling reaction of tetra(mesityl)porphyrin molecules, which creates covalently connected networks on the Cu(110) surface by utilising the 4-methyl groups as unique connection points. Using scanning tunneling microscopy (STM), state-of-the-art density functional theory (DFT) andNudged Elastic Band (NEB) calculations, we show that the unique directionality of the covalent bonding is found to stem from a chain of highly selective C-H activation and dehydrogenation processes, followed by specific intermolecular C-C coupling reactions that are facilitated by the surface, by steric constraints and by anisotropic molecular diffusion. These insights provide the first steps towards developing synthetic rules for complex two-dimensional covalent organic chemistry that can be enacted directly at a surface to deliver specific macromolecular structures designed for specific functions.

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Perdew, Burke, and Ernzerhof Reply:

Cited by 6,265 publications

References 16 publications

Simulating Water with the Self-Consistent-Charge Density Functional Tight Binding Method: From Molecular Clusters to the Liquid State

Simulating Water with the Self-Consistent-Charge Density Functional Tight Binding Method: From Molecular Clusters to the Liquid State

Role of van der Waals interaction in forming molecule-metal junctions: flat organic molecules on the Au(111) surface

Driving Forces for Covalent Assembly of Porphyrins by Selective C–H Bond Activation and Intermolecular Coupling on a Copper Surface

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