A thorough benchmark of density functional methods for general main group thermochemistry, kinetics, and noncovalent interactions

Goerigk, Lars; Grimme, Stefan

doi:10.1039/c0cp02984j

Cited by 1,751 publications

(1,961 citation statements)

References 158 publications

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“…6,17 However, it is also known that it underestimates the strength of hydrogen bonds, 18 as we clearly see for SCS-MP2/CBS for the a-helices (Fig. 2).…”

supporting

confidence: 52%

“…We tested various density functionals that have been shown previously to be accurate for related cases (see ESI †). 6 These DFT calculations were carried out with the VQZ basis set and Grimme's London-dispersion correction DFT-D3. 21 In accordance with previous work, we find the most promising DFT methods to be double-hybrid functionals, 22 which represent a combination of a standard density functional with portions of Hartree-Fock exchange and (SCS-)MP2 correlation.…”

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confidence: 99%

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Accurate quantum chemical energies for tetrapeptide conformations: why MP2 data with an insufficient basis set should be handled with caution

Goerigk

Karton

Martin

et al. 2013

Phys. Chem. Chem. Phys.

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Understanding the structure-function relationship in polypeptides and proteins is a crucial step in the elucidation of biochemical processes. In this regard, constantly improving hardware architectures and program codes have allowed the in silico treatment of proteins to become an important partner in related investigations. Due to the immense size of proteins, their computational study has generally been carried out with molecular mechanics (MM) force-field methods, such as CHARMM or GROMOS. 1 At the other extreme, high-level quantum mechanical (QM) methods, such as coupled-cluster with perturbative triples 2 [CCSD(T)] or composite methods like Gn 3 or Wn, 4 provide results with much higher accuracy. However, due to their computational cost, their applicability has been restricted to smaller systems such as amino acids, and di-and tripeptides. 5,6 Tetrapeptides are the smallest model systems that are able to mimic the typical hydrogen-bond pattern in a-helices. They are therefore of particular biological interest, and QM treatments of them have been reported since the late 1990s. 7 The highest levels of theory used in such studies were often conventional or local second-order Møller-Plesset perturbation theory (MP2) with a triple-z basis set. These levels are still popular in recent similar investigations. 8 Of particular relevance to the present work is the extensive study of 100 tetrapeptides by Jiang et al., 9 who evaluated the performance of a large number of QM and MM methods based on MP2/cc-pVTZ reference values.In the present article, we will demonstrate where potential problems of the MP2 approach combined with finite basis sets might lie when applied to conformers of polypeptides. For this purpose, we selected two systems from the study by Jiang et al. 9 that have the sequence ACE-ALA-X-ALA-NME. ALA is alanine, X is either glycine (GLY) or serine (SER), and ACE and NME stand for acetyl and methylamide groups, respectively (see Fig. 1a). For each peptide, five conformers have been examined, whose backbone dihedral angles (see ESI †) have been fixed such that they resemble those typically found in parallel (b) and antiparallel (b a ) b-sheets, in right-handed (a R ) and left-handed (a L ) a-helices, and in the common polyproline-II (PP-II) helix. We note that while the two a-helical conformers are stabilised by hydrogen bonds, the backbones of the other three conformers are not (see for example Fig. 1).

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“…6,17 However, it is also known that it underestimates the strength of hydrogen bonds, 18 as we clearly see for SCS-MP2/CBS for the a-helices (Fig. 2).…”

supporting

confidence: 52%

mentioning

confidence: 99%

Accurate quantum chemical energies for tetrapeptide conformations: why MP2 data with an insufficient basis set should be handled with caution

Goerigk

Karton

Martin

et al. 2013

Phys. Chem. Chem. Phys.

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“…This issue is known to have particular importance when charged species are involved and/or when a transition from delocalized to localized states is expected to drive the results [114][115][116][117][118][119]. Using the database SIE11, which forms part of the recently launched general benchmark databases called GMTKN30 [120] and its predecessor GMTKN24 [121], comprising a set of reaction energies extremely prone to this generalised drawback, we have recently evaluated the performance of some double-hybrid forms compared to older hybrid expressions. Note that the geometries and the basis set (def2-QZVP) employed readily allows the adequate comparison between the methods in all cases.…”

Section: Self-interaction Errormentioning

confidence: 99%

“…Unless otherwise forced in future developments, neither of these expressions is one-electron SIE-free yet, the essence of selfinteraction, defined for one-electron systems having drρ α = 1 and ρ β = 0, interactions, which is best done through analysing the performance of DH forms for the GMTKN30 database. Herein, a short summary is presented; the interested readers can consult the original work [120]. The values shown in Table 3 3.…”

Section: Self-interaction Errormentioning

confidence: 99%

Double-hybrid density functionals: merging wavefunction and density approaches to get the best of both worlds

Sancho‐García

Adamo

2013

Phys. Chem. Chem. Phys.

109

108

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We review in this Perspective why and how double-hybrid density functionals have become new leading actors in the field of computational chemistry, thanks to the combination of an unprecedented accuracy together with large robustness and reliability. Similarly to their predecessors, the widely employed hybrid density functionals, they are rooted on the Adiabatic Connection Method from which they emerge in a natural way. We present recent achievements concerning applications to chemical systems of the most interest, and current extensions to deal with challenging issues such as non-covalent interactions and excitation energies. These promising methods, despite a slightly higher computational cost than other typical density-based models, are called to play a key role in the near future and can thus pave the way towards new discoveries or advances.2

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“…This was previously recommended after thorough benchmarking for thermochemistry, kinetics, and non-covalent interactions 25 . All such calculations took advantage of the density fitting approximation, and where appropriate included the effect of aqueous solvation via the use of the polarized continuum model (PCM) 26 .…”

Section: Computational Methodsologymentioning

confidence: 99%

Theoretical modelling of epigenetically modified DNA sequences

et al. 2015

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We report herein a set of calculations designed to examine the effects of epigenetic modifications on the structure of DNA. The incorporation of methyl, hydroxymethyl, formyl and carboxy substituents at the 5-position of cytosine is shown to hardly affect the geometry of CG base pairs, but to result in rather larger changes to hydrogen-bond and stacking binding energies, as predicted by dispersion-corrected density functional theory (DFT) methods. The same modifications within double-stranded GCG and ACA trimers exhibit rather larger structural effects, when including the sugar-phosphate backbone as well as sodium counterions and implicit aqueous solvation. In particular, changes are observed in the buckle and propeller angles within base pairs and the slide and roll values of base pair steps, but these leave the overall helical shape of DNA essentially intact. The structures so obtained are useful as a benchmark of faster methods, including molecular mechanics (MM) and hybrid quantum mechanics/molecular mechanics (QM/MM) methods. We show that previously developed MM parameters satisfactorily reproduce the trimer structures, as do QM/MM calculations which treat bases with dispersion-corrected DFT and the sugar-phosphate backbone with AMBER. The latter are improved by inclusion of all six bases in the QM region, since a truncated model including only the central CG base pair in the QM region is considerably further from the DFT structure. This QM/MM method is then applied to a set of double-stranded DNA heptamers derived from a recent X-ray crystallographic study, whose size puts a DFT study beyond our current computational resources. These data show that still larger structural changes are observed than in base pairs or trimers, leading us to conclude that it is important to model epigenetic modifications within realistic molecular contexts.

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A thorough benchmark of density functional methods for general main group thermochemistry, kinetics, and noncovalent interactions

Cited by 1,751 publications

References 158 publications

Accurate quantum chemical energies for tetrapeptide conformations: why MP2 data with an insufficient basis set should be handled with caution

Accurate quantum chemical energies for tetrapeptide conformations: why MP2 data with an insufficient basis set should be handled with caution

Double-hybrid density functionals: merging wavefunction and density approaches to get the best of both worlds

Theoretical modelling of epigenetically modified DNA sequences

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