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Benchmarking density functional tight binding models for barrier heights and reaction energetics of organic molecules.

ABSTRACT: Density Functional Tight Binding (DFTB) models are two to three orders of magnitude faster than ab initio and Density Functional Theory (DFT) methods and therefore are particularly attractive in applications to large molecules and condensed phase systems. To establish the applicability of DFTB models to general chemical reactions, we conduct benchmark calculations for barrier heights and reaction energetics of organic molecules using existing databases and several new ones compiled in this study. Structures for the transition states and stable species have been fully optimized at the DFTB level, making it possible to characterize the reliability of DFTB models in a more thorough fashion compared to conducting single point energy calculations as done in previous benchmark studies. The encouraging results for the diverse sets of reactions studied here suggest that DFTB models, especially the most recent third-order version (DFTB3/3OB augmented with dispersion correction), in most cases provide satisfactory description of organic chemical reactions with accuracy almost comparable to popular DFT methods with large basis sets, although larger errors are also seen for certain cases. Therefore, DFTB models can be effective for mechanistic analysis (e.g., transition state search) of large (bio)molecules, especially when coupled with single point energy calculations at higher levels of theory. © 2017 Wiley Periodicals, Inc.

SUBMITTER: Gruden M

PROVIDER: S-EPMC5554453 | biostudies-literature | 2017 Sep

REPOSITORIES: biostudies-literature

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Benchmarking density functional tight binding models for barrier heights and reaction energetics of organic molecules.

Gruden Maja M Andjeklović Ljubica L Jissy Akkarapattiakal Kuriappan AK Stepanović Stepan S Zlatar Matija M Cui Qiang Q Elstner Marcus M

Journal of computational chemistry 20170724 25

Density Functional Tight Binding (DFTB) models are two to three orders of magnitude faster than ab initio and Density Functional Theory (DFT) methods and therefore are particularly attractive in applications to large molecules and condensed phase systems. To establish the applicability of DFTB models to general chemical reactions, we conduct benchmark calculations for barrier heights and reaction energetics of organic molecules using existing databases and several new ones compiled in this study ...[more]

PMID: 28736893

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Project description:We have revisited the MOBH35 (Metal-Organic Barrier Heights, 35 reactions) benchmark [Iron; , Janes, J. Phys. Chem. A, 2019, 123 (17), 3761-3781; ibid. 2019, 123, 6379-6380] for realistic organometallic catalytic reactions, using both canonical CCSD(T) and localized orbital approximations to it. For low levels of static correlation, all of DLPNO-CCSD(T), PNO-LCCSD(T), and LNO-CCSD(T) perform well; for moderately strong levels of static correlation, DLPNO-CCSD(T) and (T1) may break down catastrophically, and PNO-LCCSD(T) is vulnerable as well. In contrast, LNO-CCSD(T) converges smoothly to the canonical CCSD(T) answer with increasingly tight convergence settings. The only two reactions for which our revised MOBH35 reference values differ substantially from the original ones are reaction 9 and to a lesser extent 8, both involving iron. For the purpose of evaluating density functional theory (DFT) methods for MOBH35, it would be best to remove reaction 9 entirely as its severe level of static correlation makes it just too demanding for a test. The magnitude of the difference between DLPNO-CCSD(T) and DLPNO-CCSD(T1) is a reasonably good predictor for errors in DLPNO-CCSD(T1) compared to canonical CCSD(T); otherwise, monitoring all of T1, D1, max|tiA|, and 1/(εLUMO - εHOMO) should provide adequate warning for potential problems. Our conclusions are not specific to the def2-SVP basis set but are largely conserved for the larger def2-TZVPP, as they are for the smaller def2-SV(P): the latter may be an economical choice for calibrating against canonical CCSD(T). Finally, diagnostics for static correlation are statistically clustered into groups corresponding to (1) importance of single excitations in the wavefunction; (2a) the small band gap, weakly separated from (2b) correlation entropy; and (3) thermochemical importance of correlation energy, as well as the slope of the DFT reaction energy with respect to the percentage of HF exchange. Finally, a variable reduction analysis reveals that much information on the multireference character is provided by T1, IND/Itot, and the exchange-based diagnostic A100[TPSS].

Project description:We selected 145 reference organic molecules that include model fragments used in computer-aided drug design. We calculated 158 conformational energies and barriers using force fields, with wide applicability in commercial and free softwares and extensive application on the calculation of conformational energies of organic molecules, e.g. the UFF and DREIDING force fields, the Allinger's force fields MM3-96, MM3-00, MM4-8, the MM2-91 clones MMX and MM+, the MMFF94 force field, MM4, ab initio Hartree-Fock (HF) theory with different basis sets, the standard density functional theory B3LYP, the second-order post-HF MP2 theory and the Domain-based Local Pair Natural Orbital Coupled Cluster DLPNO-CCSD(T) theory, with the latter used for accurate reference values. The data set of the organic molecules includes hydrocarbons, haloalkanes, conjugated compounds, and oxygen-, nitrogen-, phosphorus- and sulphur-containing compounds. We reviewed in detail the conformational aspects of these model organic molecules providing the current understanding of the steric and electronic factors that determine the stability of low energy conformers and the literature including previous experimental observations and calculated findings. While progress on the computer hardware allows the calculations of thousands of conformations for later use in drug design projects, this study is an update from previous classical studies that used, as reference values, experimental ones using a variety of methods and different environments. The lowest mean error against the DLPNO-CCSD(T) reference was calculated for MP2 (0.35 kcal mol-1), followed by B3LYP (0.69 kcal mol-1) and the HF theories (0.81-1.0 kcal mol-1). As regards the force fields, the lowest errors were observed for the Allinger's force fields MM3-00 (1.28 kcal mol-1), ΜΜ3-96 (1.40 kcal mol-1) and the Halgren's MMFF94 force field (1.30 kcal mol-1) and then for the MM2-91 clones MMX (1.77 kcal mol-1) and MM+ (2.01 kcal mol-1) and MM4 (2.05 kcal mol-1). The DREIDING (3.63 kcal mol-1) and UFF (3.77 kcal mol-1) force fields have the lowest performance. These model organic molecules we used are often present as fragments in drug-like molecules. The values calculated using DLPNO-CCSD(T) make up a valuable data set for further comparisons and for improved force field parameterization.

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Benchmarking density functional tight binding models for barrier heights and reaction energetics of organic molecules.

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Benchmarking density functional tight binding models for barrier heights and reaction energetics of organic molecules.

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