scholarly journals Benchmarking of Density Functionals for Z-Azoarene Half-Lives via Automated Transition State Search

2021 ◽  
Author(s):  
Daniel Adrion ◽  
Danil Kaliakin ◽  
Patrick Neal ◽  
Steven Lopez
Keyword(s):  
Rate Constants ◽  
Photochemical Reactions ◽  
Basis Sets ◽  
Local Spin Density Approximation ◽  
Density Functionals ◽  
Stable Isomer ◽  
Generalized Gradient ◽  
Functional Classes ◽  
Transition State Search ◽  
The Mean

Molecular photoswitches use light to interconvert from a thermodynamically stable isomer into a meta-stable isomer. Chemists and materials scientists have applied photoswitches in photopharmacology, catalysis, and molecular solar thermal (MOST) materials. Visible-light-absorbing photoswitches are attractive because the relatively low-energy light minimizes undesired photochemical reactions and enables biological applications. Designing ideal photoswitches requires long-lived metastable states; predicting their half-lives with theory is difficult because it requires locating transition structures. We now report the EZ-TS code, which automates the prediction of rate constants for the thermal Z → E isomerization. We leverage EZ-TS to automate the location of the favored transition structure and to comprehensively benchmark the performance of 140 model chemistries against the experimental rate constants of 11 azoarenes. We used 28 density functionals [local spin density approximation, generalized gradient approximation, meta-GGA, hybrid GGA, hybrid meta-GGA], and five basis sets [6-31G(d), 6-31+G(d,p), 6-311+G(d,p), cc-pvdz, and aug-cc-pvdz]. The hybrid GGA functionals performed the best of all tested functional classes. We demonstrate that the mean absolute errors of 14 model chemistries approach chemical accuracy, and mPWPW91/6-31+G(d,p) achieves chemical accuracy and should be used with EZ-TS.<br>

scholarly journals Benchmarking of Density Functionals for Z-Azoarene Half-Lives via Automated Transition State Search

2021 ◽  
Author(s):  
Daniel Adrion ◽  
Danil Kaliakin ◽  
Patrick Neal ◽  
Steven Lopez
Keyword(s):  
Rate Constants ◽  
Photochemical Reactions ◽  
Basis Sets ◽  
Local Spin Density Approximation ◽  
Density Functionals ◽  
Stable Isomer ◽  
Generalized Gradient ◽  
Functional Classes ◽  
Transition State Search ◽  
The Mean

Molecular photoswitches use light to interconvert from a thermodynamically stable isomer into a meta-stable isomer. Chemists and materials scientists have applied photoswitches in photopharmacology, catalysis, and molecular solar thermal (MOST) materials. Visible-light-absorbing photoswitches are attractive because the relatively low-energy light minimizes undesired photochemical reactions and enables biological applications. Designing ideal photoswitches requires long-lived metastable states; predicting their half-lives with theory is difficult because it requires locating transition structures. We now report the EZ-TS code, which automates the prediction of rate constants for the thermal Z → E isomerization. We leverage EZ-TS to automate the location of the favored transition structure and to comprehensively benchmark the performance of 140 model chemistries against the experimental rate constants of 11 azoarenes. We used 28 density functionals [local spin density approximation, generalized gradient approximation, meta-GGA, hybrid GGA, hybrid meta-GGA], and five basis sets [6-31G(d), 6-31+G(d,p), 6-311+G(d,p), cc-pvdz, and aug-cc-pvdz]. The hybrid GGA functionals performed the best of all tested functional classes. We demonstrate that the mean absolute errors of 14 model chemistries approach chemical accuracy, and mPWPW91/6-31+G(d,p) achieves chemical accuracy and should be used with EZ-TS.<br>

DFT Benchmark Study of the O--O Bond Dissociation Energy in Peroxides Validated with High-Level Ab-Initio Calculations

2019 ◽  
Author(s):  
Danilo Carmona ◽  
Pablo Jaque ◽  
Esteban Vöhringer-Martinez
Keyword(s):  
Reference Value ◽  
Basis Set ◽  
Basis Sets ◽  
Mean Deviation ◽  
Bond Dissociation ◽  
Dissociation Energies ◽  
The Mean ◽  
Experimental Values ◽  
High Level ◽  
Almost All

<div><div><div><p>Peroxides play a central role in many chemical and biological pro- cesses such as the Fenton reaction. The relevance of these compounds lies in the low stability of the O–O bond which upon dissociation results in radical species able to initiate various chemical or biological processes. In this work, a set of 64 DFT functional-basis set combinations has been validated in terms of their capability to describe bond dissociation energies (BDE) for the O–O bond in a database of 14 ROOH peroxides for which experimental values ofBDE are available. Moreover, the electronic contributions to the BDE were obtained for four of the peroxides and the anion H2O2− at the CBS limit at CCSD(T) level with Dunning’s basis sets up to triple–ζ quality provid- ing a reference value for the hydrogen peroxide anion as a model. Almost all the functionals considered here yielded mean absolute deviations around 5.0 kcal mol−1. The smallest values were observed for the ωB97 family and the Minnesota M11 functional with a marked basis set dependence. Despite the mean deviation, order relations among BDE experimental values of peroxides were also considered. The ωB97 family was able to reproduce the relations correctly whereas other functionals presented a marked dependence on the chemical nature of the R group. Interestingly, M11 functional did not show a very good agreement with the established order despite its good performance in the mean error. The obtained results support the use of similar validation strategies for proper prediction of BDE or other molecular properties by DF Tmethods in subsequent related studies.</p></div></div></div>

The assessment of density functionals for DNA–protein stacked and T-shaped complexes

2010 ◽  
Vol 88 (8) ◽  
pp. 815-830 ◽  
Author(s):  
Lesley R. Rutledge ◽  
Stacey D. Wetmore
Keyword(s):  
Amino Acid ◽  
Potential Energy ◽  
Large Scale ◽  
Enzymatic Reaction ◽  
Basis Sets ◽  
Density Functionals ◽  
Interaction Energies ◽  
Π Interactions ◽  
Hybrid Techniques ◽  
Semi Empirical

The present work uses 129 nucleobase – amino acid CCSD(T)/CBS stacking and T-shaped interaction energies as reference data to test the ability of various density functionals with double-zeta quality basis sets, as well as some semi-empirical and molecular mechanics methods, to accurately describe noncovalent DNA–protein π–π and π+–π interactions. The goal of this work is to identify methods that can be used in hybrid approaches (QM/MM, ONIOM) for large-scale modeling of enzymatic systems involving active-site (substrate) π–π contacts. Our results indicate that AMBER is a more appropriate choice for the lower-level method in hybrid techniques than popular semi-empirical methods (AM1, PM3), and suggest that AMBER accurately describes the π–π interactions found throughout DNA–protein complexes. The M06–2X and PBE-D density functionals were found to provide very promising descriptions of the 129 nucleobase – amino acid interaction energies, which suggests that these may be the most suitable methods for describing high-level regions. Therefore, M06–2X and PBE-D with both the 6–31G(d) and 6–31+G(d,p) basis sets were further examined through potential-energy surface scans to better understand how these techniques describe DNA–protein π–π interactions in both minimum and nonminimum regions of the potential-energy surfaces, which is critical information when modeling enzymatic reaction pathways. Our results suggest that studies of stacked nucleobase – amino acid systems should implement the PBE-D/6–31+G(d,p) method. However, if T-shaped contacts are involved and (or) smaller basis sets must be considered due to limitations in computational resources, then M06–2X/6–31G(d) provides an overall excellent description of both nucleobase – amino acid stacking and T-shaped interactions for a range of DNA–protein π–π and π+–π interactions.

Application of generalized gradient-corrected density functionals to iron

1992 ◽  
Vol 46 (3) ◽  
pp. 1870-1873 ◽  
Author(s):  
Carlos Amador ◽  
Walter R. L. Lambrecht ◽  
Benjamin Segall
Keyword(s):  
Density Functionals ◽  
Generalized Gradient

scholarly journals The crystalline structure of SrRuO3: Application of hybrid scheme to the density functionals revised for solids

2017 ◽  
Vol 57 (2) ◽  
Author(s):  
Šarūnas Masys ◽  
Valdas Jonauskas
Keyword(s):  
Crystalline Structure ◽  
Density Functional ◽  
Theoretical Modelling ◽  
Density Functionals ◽  
Hybrid Scheme ◽  
Generalized Gradient ◽  
Functional Theory ◽  
Hartree Fock ◽  
Hybrid Density Functional ◽  
Theory Scheme

The crystalline structure of ground-state orthorhombic SrRuO3 is reproduced by applying the hybrid density functional theory scheme to the functionals based on the revised generalized-gradient approximations for solidstate calculations. The amount of Hartree–Fock (HF) exchange energy is varied in the range of 5–20% in order to systematically ascertain the optimum value of HF mixing which in turn ensures the best correspondence to the experimental measurements. Such investigation allows one to expand the set of tools that could be used for the efficient theoretical modelling of, for example, only recently stabilized phases of SrRuO3, helping to resolve issues emerging for the experimentalists.

scholarly journals Performances of different DFT functionals to calculate the anodic limit of fluorinated sulphonyl-imide anions for lithium cells

2021 ◽  
Vol 2090 (1) ◽  
pp. 012078
Author(s):  
A Paolone ◽  
S Brutti
Keyword(s):  
Ionic Liquids ◽  
Lithium Batteries ◽  
Basis Set ◽  
Basis Sets ◽  
Computational Time ◽  
Generalized Gradient ◽  
Neutral Species ◽  
Generalized Gradient Approximation ◽  
Model Based ◽  
Computationally Expensive

Abstract In this paper we investigated the calculation of the anodic limit of two anions of ionic liquids, largely used as electrolyte of lithium batteries. Starting from a model based on calculations performed on single ions at the MP2 level of theory, we showed that the matching between calculation and experiments decreases while using more expanded basis set with respect to 6-31G**, possibly because of the destabilization of the neutral species when larger basis sets are considered. Additionally, in order to decrease the computational time, the performances for the calculation of the anodic limit obtained by means of a series of DFT functionals with increasing level of complexity (from the Generalized Gradient Approximation to the Range Separated Hybrid meta-Generalized Gradient Approximation) were compared. Overall, the best performing functionals are BMK, ωB97M-V and MN12-SX, while acceptable results can be obtained by M06-2X, M11, M08-HX and M11-L. Some less computationally expensive functionals, like CAM-B3LYP and ωB97X-D, also provide reasonable values of the anodic limit.

scholarly journals Probing Protein Shelf Lives from Inverse Mean First Passage Times

2019 ◽  
Author(s):  
Vishal Singh ◽  
Parbati Biswas
Keyword(s):  
Protein Aggregation ◽  
Rate Constants ◽  
Survival Probability ◽  
First Passage Time ◽  
Passage Time ◽  
First Passage ◽  
First Order Kinetics ◽  
The Mean ◽  
Passage Times ◽  
Good Agreement

Protein aggregation is investigated theoretically via protein turnover, misfolding, aggregation and degradation. The Mean First Passage Time (MFPT) of aggregation is evaluated within the framework of Chemical Master Equation (CME) and pseudo first order kinetics with appropriate boundary conditions. The rate constants of aggregation of different proteins are calculated from the inverse MFPT, which show an excellent match with the experimentally reported rate constants and those extracted from the ThT/ThS fluorescence data. Protein aggregation is found to be practically independent of the number of contacts and the critical number of misfolded contacts. The age of appearance of aggregation-related diseases is obtained from the survival probability and the MFPT results, which matches with those reported in the literature. The calculated survival probability is in good agreement with the only available clinical data for Parkinson’s disease.<br>

scholarly journals Double-Hybrid DFT Functionals for the Condensed Phase: Gaussian and Plane Waves Implementation and Evaluation

Molecules ◽  
2020 ◽  
Vol 25 (21) ◽  
pp. 5174
Author(s):  
Frederick Stein ◽  
Jürg Hutter ◽  
Vladimir V. Rybkin
Keyword(s):  
Condensed Phase ◽  
Density Functional ◽  
Plane Waves ◽  
Basis Set ◽  
Basis Sets ◽  
Density Functionals ◽  
Basis Set Superposition Error ◽  
Super Cell ◽  
Long Range Interactions ◽  
Function Correlation

Intermolecular interactions play an important role for the understanding of catalysis, biochemistry and pharmacy. Double-hybrid density functionals (DHDFs) combine the proper treatment of short-range interactions of common density functionals with the correct description of long-range interactions of wave-function correlation methods. Up to now, there are only a few benchmark studies available examining the performance of DHDFs in condensed phase. We studied the performance of a small but diverse selection of DHDFs implemented within Gaussian and plane waves formalism on cohesive energies of four representative dispersion interaction dominated crystal structures. We found that the PWRB95 and ωB97X-2 functionals provide an excellent description of long-ranged interactions in solids. In addition, we identified numerical issues due to the extreme grid dependence of the underlying density functional for PWRB95. The basis set superposition error (BSSE) and convergence with respect to the super cell size are discussed for two different large basis sets.

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