Benchmarking Density Functional Methods against the S66 and S66x8 Datasets for Non‐Covalent Interactions

Goerigk, Lars; Kruse, Holger; Grimme, Stefan

doi:10.1002/cphc.201100826

Cited by 308 publications

(400 citation statements)

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“…18 Because the S22 set is part of the fit set, the performance of B97-D for the S66 and S66 × 8 sets 19 was tested, leading to MADs of 0.29 and 0.27 kcal mol −1 (def2-QZVP basis set), respectively. 20 Noteworthy are the balanced descriptions of both equilibrium and nonequilibrium structures as represented by the S66 and S66 × 8 sets and between the different interaction types in the three subsets of S66 with B97-D reported in ref 20. In another benchmark on noncovalent interactions in smaller complexes, B97-D was the best-performing GGA density functional.…”

Section: ■ Computational Methodsmentioning

confidence: 99%

Theoretical Study of the Stacking Behavior of Selected Polycondensed Aromatic Hydrocarbons with Various Symmetries

2013

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Stacked dimers of four polycondensed aromatic hydrocarbons, with structures varying from high to reduced symmetries, have been calculated with dispersion-corrected density functional theory. The configurations of the stacked dimers are readily classified by two in-plane displacements and a relative rotation. The potential energy surface in these three coordinates was calculated with rigid monomers and appears to be slightly flat. Full geometry optimization was performed for selected low-energy structures, resulting in an energy ranking of a series of conformations whose geometries were characterized in considerable detail. The dissociation energy values reveal a clear preference for the symmetrical disk-shaped and triangular structures to dimerize into two in-plane-displaced arrangements, whereas the less symmetrical trapezoidal structures show a tendency to stack in displaced antiparallel over parallel arrangements. According to methodical checks, the key computational results, namely, the shape of the potential energy surface and the geometrical structures and energy ranking of dimer conformations, are essentially insensitive to computational assumptions such as the atomic orbital basis set and density functional chosen. This is shown in particular for the basis set superposition error, which, for the selected level of theory [B97-D3(BJ)/ TZV(d,p)] was estimated by the counterpoise correction procedure to be in the narrow range between 7% and 8% of the uncorrected dissociation energies. ■ INTRODUCTIONThe significant stability and unrivaled noncovalent π−π stacking 1 bonding that confer self-assembled polycondensed aromatic hydrocarbons (PAHs) with superior physicochemical 2a−g and optoelectronic 3a−k properties have drawn considerable attention in the past two decades. To simplify their synthesis, experimental efforts have focused on making highly symmetrical PAHs with structures ranging from linear to diskshaped. 4a−i Nevertheless, the high symmetry of these structures complicates their uneven decoration with lateral groups (i.e., solubilizing aliphatic chains). A more convenient approach is to synthesize multisubstituted PAHs with analogous lateral groups, which hinders the stacking of the aromatic core by reducing the desired π−π noncovalent bonding. 5a,b We are interested in exploring the π−π stacking of PAH structures whose reduced symmetry allows a disproportionate decoration with lateral groups. Among others, the half-lunar tribenzo[fg,ij,rst]pentaphene (1, TBP; Figure 1 with R = H) is believed to be a potential candidate. Derivatives of this compound substituted by a wide variety of pending groups have been explored as materials for optoelectronic devices. 6a,b Furthermore, a TBP derivative substituted in all six positions by alkyl chains has also been reported but was not further investigated. 7 To minimize steric hindrance that reduces π−π stacking, we recently reported a versatile synthesis of TBP derivatives bearing pairs of alkyl side chains at the specific positions R 1 , R 2 , and R ...

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Section: ■ Computational Methodsmentioning

confidence: 99%

Theoretical Study of the Stacking Behavior of Selected Polycondensed Aromatic Hydrocarbons with Various Symmetries

2013

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“…They have been thoroughly studied by a variety of experimental and theoretical methods [2,3,4,5,6,7,8,9,10,11,12,13,14,15] so that the strengths of the common hydrogen bonds in biological systems are accurately known.…”

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confidence: 99%

How are hydrogen bonds modified by metal binding?

Husberg

Ryde

2013

J Biol Inorg Chem

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How are hydrogen bonds modified by metal binding?Husberg, Charlotte; Ryde, Ulf General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights.• Users may download and print one copy of any publication from the public portal for the purpose of private study or research.• You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying the publication in the public portal Take down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. AbstractWe have used density-functional theory calculations to investigate how the hydrogenbond strength is modified when a ligand is bound to a metal, using over 60 model systems involving six metals and eight ligands frequently encountered in metalloproteins. We study how the hydrogen-bond geometry and energy vary with the nature of metal, the oxidation state, the coordination number, the ligand involved in the hydrogen bond, other first-sphere ligands, and different hydrogen-bond probe molecules. The results show that in general, the hydrogen-bond strength is increased for neutral ligands and decreased for negatively charged ligands. The size of the effect is mainly determined by the net charge of the metal complex and all effects are typically decreased when the model is solvated. In water solution, the hydrogen-bond strength can increase by up to 37 kJ/mol for neutral ligands, and that of negatively charged ligands can both increase (for complexes with a negative net charge) or decrease (for positively charged complexes). If the net charge of the complex does not change, there is normally little difference between different metals or different types of complexes. The only exception is observed for sulphur-containing ligands (Met and Cys) and if the ligand is redox active (e.g. high-valent Fe-O complexes).Key Words: hydrogen bonds, metalloproteins, quantum-mechanical calculations, densityfunctional theory, dispersion correction, solvation. 2 IntroductionHydrogen bonds play an important role in all types of biochemical systems, strongly affecting catalysis, ligand binding, and enzyme function, for example [1]. They have been thoroughly studied by a variety of experimental and theoretical methods [2,3,4,5,6,7,8,9,10,11,12,13,14,15] so that the strengths of the common hydrogen bonds in biological systems are accurately known.However, it is well-known that metal sites affect the properties of bound ligands. For example, the pK a value of water in aqueous metal complexes is reduced from 15.7 for bulk water, to 12.8 for Ca 2+ and to 2.2 for Fe 3+ [16]. Therefore, it is also likely that metal ions also change the strength and structure of hydrogen bonds inv...

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“…A wide range of methods is available for treating dispersion interactions in electronic structure calculations (21,23,53) and we consider four alternatives. Three present different flavors of dispersion-corrected DFT; these are labeled PBE (Perdew, Burke, and Ernzerhof)-D3/PAW, PBE-DRSLL (Dion, Rydberg, Schröder, Langreth, and Lundqvist)/DZP, and PW91-D3/USPP.…”

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A priori calculations of the free energy of formation from solution of polymorphic self-assembled monolayers

Reimers

Panduwinata

Visser

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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Modern quantum chemical electronic structure methods typically applied to localized chemical bonding are developed to predict atomic structures and free energies for meso-tetraalkylporphyrin self-assembled monolayer (SAM) polymorph formation from organic solution on highly ordered pyrolytic graphite surfaces. Large polymorphdependent dispersion-induced substrate−molecule interactions (e.g., −100 kcal mol −1 to −150 kcal mol −1 for tetratrisdecylporphyrin) are found to drive SAM formation, opposed nearly completely by large polymorph-dependent dispersion-induced solvent interactions (70-110 kcal mol −1 ) and entropy effects (25-40 kcal mol −1 at 298 K) favoring dissolution. Dielectric continuum models of the solvent are used, facilitating consideration of many possible SAM polymorphs, along with quantum mechanical/molecular mechanical and dispersion-corrected density functional theory calculations. These predict and interpret newly measured and existing high-resolution scanning tunnelling microscopy images of SAM structure, rationalizing polymorph formation conditions. A wide range of molecular condensed matter properties at room temperature now appear suitable for prediction and analysis using electronic structure calculations.self-assembled monolayers | density functional theory | dispersion | free energy | polymorphism A priori calculations of the free energies of chemical reactions using density functional theory (DFT) and/or ab initio methods are now well established for gas-phase processes (1, 2), gas surface reactions (3), and, using continuum self-consistent reaction field (SCRF) methods, for condensed phase processes also (4). Over the last few years, a major advance in computational methods has occurred, however, allowing for rapid and accurate evaluation of intermolecular dispersion interactions. This makes feasible similar SCRF calculations for physisorption, macromolecule structuring, and other self-assembly processes in condensed phases. We present the first application of this type, to our knowledge, considering the free energy of formation of various polymorphs of tetraalkylporphyrin self-assembled monolayers (SAMs) at solid/liquid interfaces on highly ordered pyrolytic graphite (HOPG) surfaces. Calculated structures and free energies are used to interpret new and existing high-resolution scanning tunneling microscopy (STM) images, focusing on the critical roles played by the dispersion interaction in driving SAM formation and by entropy and dispersion-based desolvation effects that oppose it.Calculating a priori free energies for SAM formation from solution is a significant challenge. Accurate representations of the substrate−molecule energies, the intermolecular energies, the solvent interaction energies, and the effects of solvent structure are required, a set of tasks that, with a few exceptions (see e.g., refs. 5 and 6), has remained prohibitive a priori. Alternatively, model calculations have been useful for identifying key qualitative features (7-11), whereas some full molecular dynamics si...

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Benchmarking Density Functional Methods against the S66 and S66x8 Datasets for Non‐Covalent Interactions

Cited by 308 publications

References 104 publications

Theoretical Study of the Stacking Behavior of Selected Polycondensed Aromatic Hydrocarbons with Various Symmetries

Theoretical Study of the Stacking Behavior of Selected Polycondensed Aromatic Hydrocarbons with Various Symmetries

How are hydrogen bonds modified by metal binding?

A priori calculations of the free energy of formation from solution of polymorphic self-assembled monolayers

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