Parametrization and Benchmark of DFTB3 for Organic Molecules

Gaus, Michael; Goez, Albrecht; Elstner, Marcus

doi:10.1021/ct300849w

Cited by 896 publications

(1,118 citation statements)

References 72 publications

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“…Here, 3rd order as well as dispersion corrections have been used together with the 3-ob Slater-Koster parameter set [26,27,28,29]. A 25 ps NVT trajectory has been simulated (time step 0.5 fs), which was used to sample starting points for NVE trajectories every 5 ps.…”

Section: Molecular Dynamicsmentioning

confidence: 99%

Hydrogen bonding in protic ionic liquids: structural correlations, vibrational spectroscopy, and rotational dynamics of liquid ethylammonium nitrate

Zentel

Overbeck

Michalik

et al. 2018

J. Phys. B: At. Mol. Opt. Phys.

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Abstract. The properties of the hydrogen bonds in ethylammonium nitrate are analyzed by using molecular dynamics simulations and infrared as well as nuclear magnetic resonance experiments. Ethylammonium nitrate features a flexible three-dimensional network of hydrogen bonds with moderate strengths, which makes it distinct from related triethylammonium-based ionic liquids. First, the network's flexibility is manifested in a not very pronounced correlation of the hydrogen bond geometries, which is caused by rapid interchanges of bonding partners. The large flexibility of the network leads to a substantial broadening of the mid-IR absorption band, with the contributions due to N-H stretching motions ranging from 2800 to 3250 cm −1 . Finally, the different dynamics are also seen in the rotational correlation of the N-H bond vector, where a correlation time as short as 16.1 ps is observed.

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Section: Molecular Dynamicsmentioning

confidence: 99%

Hydrogen bonding in protic ionic liquids: structural correlations, vibrational spectroscopy, and rotational dynamics of liquid ethylammonium nitrate

Zentel

Overbeck

Michalik

et al. 2018

J. Phys. B: At. Mol. Opt. Phys.

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“…Alternatives to overcome these limitation are semi-empirical QM methods [13][14][15][16] , as well as linear scaling QM codes 17,18 . In contrast, the Hirshfeld-I (HI) atoms-in-molecules partitioning scheme 19 is purely electron density based, similar to Baders' Quantum Theory of Atoms In Molecules (QTAIM) 20 , and as such can be performed as a grid-based, basis set independent charge scheme.…”

Section: Introductionmentioning

confidence: 99%

Convergence of Atomic Charges with the Size of the Enzymatic Environment

Vanpoucke

Oláh

Proft

et al. 2015

J. Chem. Inf. Model.

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Atomic charges are a key concept to give more insight into the electronic structure and chemical reactivity. The Hirshfeld-I partitioning scheme applied to the model protein human 2-cysteine peroxiredoxin thioredoxin peroxidase B is used to investigate how large a protein fragment needs to be in order to achieve convergence of the atomic charge of both, neutral and negatively charged residues. Convergence in atomic charges is rapidly reached for neutral residues, but not for negatively charged ones. This study pinpoints difficulties on the road towards accurate modeling of negatively charged residues of large biomolecular systems in a multiscale approach.3

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“…The parameter set (Slater-Koster files) 3ob-2-1 which has been benchmarked for organic systems including non-covalent bonds is used in this study. 16,17 Dispersion corrections based on the UFF force field were used 18,19 with the parameters taken from the study of Zhechkov et al 20 Large periodic simulation cells were used with 1368 atoms for both α and γ phases. The large cells are required to model defected systems and justify the use of the tight-binding approach.…”

Section: Methodsmentioning

confidence: 99%

Defects in alpha and gamma crystalline nylon6: A computational study

Arabnejad

Manzhos

2015

AIP Advances

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We present a comparative Density Functional Tight Binding study of structures, energetics, and vibrational properties of α and γ crystalline phases of nylon6 with different types of defects: single and double chain vacancies and interstitials. The defect formation energies are: for a single vacancy 0.66 and 0.64 kcal/mol per monomer, and for an interstitial strand 1.35 and 2.45 kcal/mol per monomer in the α and γ phases, respectively. The presence of defects does not materially influence the relative stability of the two phases, within the accuracy of the method. The inclusion of phononic contributions has a negligible effect. The calculations show that even if it were possible to synthesize the pure phases of nylon6, the defects will be easily induced at room temperature, because vacancy formation energies in both phases are of the order of kT at room temperature. The formation of interstitial defects, on the contrary, requires the energy equivalent to multiple kT values and is much less likely; it is also much less probable in the γ phase than in α. The vibration spectra do not show significant sensitivity to the presence of these defects.

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Parametrization and Benchmark of DFTB3 for Organic Molecules

Cited by 896 publications

References 72 publications

Hydrogen bonding in protic ionic liquids: structural correlations, vibrational spectroscopy, and rotational dynamics of liquid ethylammonium nitrate

Hydrogen bonding in protic ionic liquids: structural correlations, vibrational spectroscopy, and rotational dynamics of liquid ethylammonium nitrate

Convergence of Atomic Charges with the Size of the Enzymatic Environment

Defects in alpha and gamma crystalline nylon6: A computational study

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