Validation of the density-functional based tight-binding approximation method for the calculation of reaction energies and other data

Krüger, Thomas; Elstner, Marcus; Schiffels, Peter; Frauenheim, Thomas

doi:10.1063/1.1871913

Cited by 148 publications

(178 citation statements)

References 19 publications

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“…The applicability of SCC-DFTB method to molecular systems has been tested by several independent benchmark studies [90][91][92], which found that it gives, in general, similar energetics as other NDDO methods, but somewhat better geometries and vibrational frequencies. To determine whether an approximate (QM) method provides a meaningful description for a particular problem, however, it is important to carry out additional benchmark calculations most relevant to the system or problem in hand.…”

Section: Qm/mm Analysis Of Proton Transfersmentioning

confidence: 97%

Toward molecular models of proton pumping: Challenges, methods and relevant applications

et al. 2011

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Motivated by several long-lasting mechanistic questions for biomolecular proton pumps, we have engaged in developing hybrid quantum mechanical/molecular mechanical (QM/MM) methods that allow an efficient and reliable description of long-range proton transport in transmembrane proteins. In this review, we briefly discuss several relevant issues: the need to develop a "multi-scale" generalized solvent boundary potential (GSBP) for the analysis of chemical events in large trans-membrane proteins, approaches to validate such a protocol, and the importance of improving the flexibility of QM/MM Hamiltonian. Several recent studies of model and realistic protein systems are also discussed to help put the discussions into context. Collectively, these studies suggest that the QM/MM-GSBP framework based on an approximate density functional theory (SCC-DFTB) as QM holds the promise to strike the proper balance between computational efficiency, accuracy and generality. With additional improvements in the methodology and recent developments by others, especially powerful sampling techniques, this "multi-scale" framework will be able to help unlock the secrets of proton pumps and other biomolecular machines.proton pumping, QM/MM simulations, SCC-DFTB, microscopic pK a , multi-scale simulations

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Section: Qm/mm Analysis Of Proton Transfersmentioning

confidence: 97%

Toward molecular models of proton pumping: Challenges, methods and relevant applications

et al. 2011

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“…However, multiple interlayer bonding formed over sizeable vacancy sites has a high probability to remain as a localized amorphous domain of several carbon atoms kinetically jammed near the existing defects. To further support this conjecture, we performed growth simulations using self-consistent charge density functional tight binding molecular dynamics 33 , which allows quantum calculations of DFT accuracy in realistic simulations involving a large number of carbon atoms 34 . As fullerene molecules thermally decompose, various carbon structures of different molecular weight are available near the template graphene.…”

Section: Discussionmentioning

confidence: 99%

Observation of the intrinsic bandgap behaviour in as-grown epitaxial twisted graphene

et al. 2015

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Twisted graphene is of particular interest due to several intriguing characteristics, such as its the Fermi velocity, van Hove singularities and electronic localization. Theoretical studies recently suggested the possible bandgap opening and tuning. Here, we report a novel approach to producing epitaxial twisted graphene on SiC (0001) and the observation of its intrinsic bandgap behaviour. The direct deposition of C 60 on pre-grown graphene layers results in few-layer twisted graphene confirmed by angular resolved photoemission spectroscopy and Raman analysis. The strong enhanced G band in Raman and sp 3 bonding characteristic in X-ray photoemission spectroscopy suggests the existence of interlayer interaction between adjacent graphene layers. The interlayer spacing between graphene layers measured by transmission electron microscopy is 0.352 ± 0.012 nm. Thermal activation behaviour and nonlinear current-voltage characteristics conclude that an intrinsic bandgap is opened in twisted graphene. Low sheet resistance (B160 O& À 1 at 10 K) and high mobility (B2,000 cm 2 V À 1 s À 1 at 10 K) are observed.

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“…DFTB2 has been particulariy parametrized for O, N, C, H [9], S [43] and Mg [44], a parameter set called mio. These ONCH parameters have been tested quite intensely with respect to their performance for atomization and reaction energies, molecular geometries, vibrational frequencies, ionization potentials and electron affinities, dipole moments and for non-covalent interactions [45][46][47]. DFTB2 performs very well for reaction energies [45], while for heats of formation other SE methods, in particular the newly developed OMx and PDDG-PM3 methods, turned out to be slightly superior.…”

Section: Performance and Testsmentioning

confidence: 99%

Density functional tight binding

Elstner

Seifert

2014

Phil. Trans. R. Soc. A.

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304

294

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This paper reviews the basic principles of the density-functional tight-binding (DFTB) method, which is based on density-functional theory as formulated by Hohenberg, Kohn and Sham (KS-DFT). DFTB consists of a series of models that are derived from a Taylor series expansion of the KS-DFT total energy. In the lowest order (DFTB1), densities and potentials are written as superpositions of atomic densities and potentials. The Kohn-Sham orbitals are then expanded to a set of localized atom-centred functions, which are obtained for spherical symmetric spin-unpolarized neutral atoms self-consistently. The whole Hamilton and overlap matrices contain one-and two-centre contributions only. Therefore, they can be calculated and tabulated in advance as functions of the distance between atomic pairs. The second contributions to DFTB1, the DFT double counting terms, are summarized together with nuclear repulsion energy terms and can be rewritten as the sum of pairwise repulsive terms. The second-order (DFTB2) and third-order (DFTB3) terms in the energy expansion correspond to a selfconsistent representation, where the deviation of the ground-state density from the reference density is represented by charge monopoles only. This leads to a computationally efficient representation in terms of atomic charges (Mulliken), chemical hardness (Hubbard) parameters and scaled Coulomb laws. Therefore, no additional adjustable parameters enter the DFTB2 and DFTB3 formalism. The handling of parameters, the efficiency, the performance and extensions of DFTB are briefly discussed.

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Validation of the density-functional based tight-binding approximation method for the calculation of reaction energies and other data

Cited by 148 publications

References 19 publications

Toward molecular models of proton pumping: Challenges, methods and relevant applications

Toward molecular models of proton pumping: Challenges, methods and relevant applications

Observation of the intrinsic bandgap behaviour in as-grown epitaxial twisted graphene

Density functional tight binding

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