Benchmarking on H2S and SO2 molecules using the software ORCA

The Fenton reaction plays a central role in many chemical and biological processes and has various applications as e.g. water remediation. The reaction consists of the iron-catalyzed homolytic cleavage of the oxygen-oxygen bond in the hydrogen peroxide molecule and the reduction of the hydroxyl radical. Here, we study these two elementary steps with high-level ab-initio calculations at the complete basis set limit and address the performance of different DFT methods following a specific classification based on the Jacob´s ladder in combination with various Pople's basis sets. Ab-initio calculations at the complete basis set limit are in agreement to experimental reference data and identified a significant contribution of the electron correlation energy to the bond dissociation energy (BDE) of the oxygen-oxygen bond in hydrogen peroxide and the electron affinity (EA) of the hydroxyl radical. The studied DFT methods were able to reproduce the ab-initio reference values, although no functional was particularly better for both reactions. The inclusion of HF exchange in the DFT functionals lead in most cases to larger deviations, which might be related to the poor description of the two reactions by the HF method. Considering the computational cost, DFT methods provide better BDE and EA values than HF and post--HF methods with an almost MP2 or CCSD level of accuracy. However, no systematic general prediction of the error based on the employed functional could be established and no systematic improvement with increasing the size in the Pople's basis set was found, although for BDE values certain systematic basis set dependence was observed. Moreover, the quality of the hydrogen peroxide, hydroxyl radical and hydroxyl anion structures obtained from these functionals was compared to experimental reference data. In general, bond lengths were well reproduced and the error in the angles were between one and two degrees with some systematic trend with the basis sets. From our results we conclude that DFT methods present a computationally less expensive alternative to describe the two elementary steps of the Fenton reaction. However, choice of approximated functionals and basis sets must be carefully done and the provided benchmark allows a systematic validation of the electronic structure method to be employed

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Selecting DFT methods for use in optimizations of enzyme active sites: applications to ONIOM treatments of DNA glycosylases

Canadian Journal of Chemistry ◽

10.1139/cjc-2012-0506 ◽

2013 ◽

Vol 91 (7) ◽

pp. 559-572 ◽

Cited By ~ 14

Author(s):

Jennifer L. Kellie ◽

Stacey D. Wetmore

Keyword(s):

Active Sites ◽

Noncovalent Interactions ◽

Single Point ◽

Enzymatic Reaction ◽

Basis Set ◽

Basis Sets ◽

Dna Glycosylases ◽

Dft Methods ◽

Primary Focus ◽

High Level

When using a hybrid methodology to treat an enzymatic reaction, many factors contribute to selecting the method for the high-level region, which can be complicated by the presence of dispersion-driven interactions such as π–π stacking. In addition, the proper treatment of the reaction center often requires a large number of heavy atoms to be included in the high-level region, precluding the use of ab initio methods such as MP2 as well as large basis sets, in the optimization step. In the present work, popular DFT methods were tested to identify an appropriate functional for treating the high-level region in ONIOM optimizations of reactions catalyzed by nonmetalloenzymes. Eight different DFT methods (B3LYP, B97-2, MPW1K, MPWB1K, BB1K, B1B95, M06-2X, and ωB97X-D) in combination with four double-ζ quality Pople basis sets were tested for their ability to optimize noncovalent interactions (hydrogen bonding and π–π) and characterize reactions (proton transfer, SN2 hydrolysis, and unimolecular cleavage). Although the primary focus of this study is accurate structure determination, energetics were also examined at both the optimization level of theory, and with triple-ζ quality basis set and select (M06-2X or ωB97X-D) methods. If dispersion-driven interactions exist within the active site, then MPWB1K/6-31G(d,p) or M06-2X/6-31+G(d,p) are recommended for the optimization step with subsequent triple-ζ quality single-point energies. However, since dispersion-corrected functionals (M06-2X and ωB97X-D) generally require diffuse functions to yield appropriate geometries, the possible size of the high-level region is greatly limited with these methods. In contrast, if the model is large enough to recover steric constraints on π–π interactions, then B3LYP with a small basis set performs comparatively well for the optimization step and is significantly less computationally expensive. Interestingly, the functionals that afford the best geometries often do not yield the best energetics, which emphasizes the importance of structural benchmark studies.

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Basis Set Effects in the Description of the Cl-O Bond in ClO and XClO/ClOX Isomers (X = H, O, and Cl) Using DFT and CCSD(T) Methods

Journal of Chemistry ◽

10.1155/2019/4057848 ◽

2019 ◽

Vol 2019 ◽

pp. 1-23 ◽

Cited By ~ 2

Author(s):

Kenneth Irving ◽

Martina Kieninger ◽

Oscar N. Ventura

Keyword(s):

Density Functional ◽

Basis Set ◽

Basis Sets ◽

Enthalpies Of Formation ◽

Isodesmic Reactions ◽

Dft Methods ◽

Functional Methods ◽

The One ◽

Isomeric Structures ◽

Different Sources

The performance of a group of density functional methods of progressive complexity for the description of the ClO bond in a series of chlorine oxides was investigated. The simplest ClO radical species and the two isomeric structures XClO/ClOX for each X = H, Cl, and O were studied using the PW91, TPSS, B3LYP, PBE0, M06, M06-2X, BMK, and B2PLYP functionals. Geometry optimizations and reaction enthalpies and enthalpies of formation for each species were calculated using Pople basis sets and the (aug)-cc-pVnZ Dunning sets, with n = D, T, Q, 5, and 6. For the calculation of enthalpies of formation, atomization and isodesmic reactions were employed. Both the precision of the methods with respect to the increase of the basis sets, as well as their accuracy, were gauged by comparing the results with the more accurate CCSD(T) calculations, performed using the same basis sets as for the DFT methods. The results obtained employing composite chemical methods (G4, CBS-QB3, and W1BD) were also used for the comparisons, as well as the experimental results when they are available. The results obtained show that error compensation is the key for successful description of molecular properties (geometries and energies) by carefully selecting the method and basis sets. In general, expansion of the one-electron basis set to the limit of completeness does not improve results at the DFT level, but just the opposite. The enthalpies of formation calculated at the CCSD(T)/aug-cc-pV6Z for the species considered are generally in agreement with experimental determinations and the most accurate theoretical values. Different sources of error in the calculations are discussed in detail.

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DFT calculation of the Renner Teller Effect in NCO: Preliminary assessment of Exact Exchange Energy on the accuracy of the X2Π Renner Coefficient

10.22541/au.162141413.36924342/v1 ◽

2021 ◽

Author(s):

David Kashinski ◽

Tyler Radziewicz ◽

Matthew Suarez ◽

Constantine Stephens ◽

Edward Byrd

Keyword(s):

Teller Effect ◽

Basis Set ◽

Basis Sets ◽

Preliminary Assessment ◽

Molecular Physics ◽

Dft Methods ◽

Exact Exchange ◽

Correlation Consistent ◽

Bending Modes ◽

Split Valence

Assessment of DFT methods through analysis of the Renner-Teller Effect (RTE) in the XΠ state of the NCO radical was completed. Our results suggest that the amount of exact exchange at long range is important for an accurate description of the RTE in NCO. DFT functionals from the B3LYP, PBE, TPSS, M06, and M11 families with standard Correlation Consistent, 6-311G split valence family, as well as Sadlej, and Sapporo polarized triple-ζ basis sets were assessed. Our Renner coefficients are compared with previously published theoretical and experimental results to characterize the overall accuracy of various functional/basis set combinations in determining the RTE splitting in the Π (bending) modes of NCO(XΠ). We suggest that this method of analysis can be extended to other systems, serve as an accuracy metric when selecting a functional, and provide a means to create training sets for machine learning in computational molecular physics applications.

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A Systematic DFT Study of Two Elementary Steps Involving Hydrogen Peroxide and the Hydroxyl Radical in the Fenton Reaction

10.26434/chemrxiv.6160142.v1 ◽

2018 ◽

Author(s):

Danilo Carmona ◽

David Contreras ◽

Oscar A. Douglas-Gallardo ◽

Stefan Vogt-Geisse ◽

Pablo Jaque ◽

...

Keyword(s):

Hydrogen Peroxide ◽

Hydroxyl Radical ◽

Ab Initio ◽

Fenton Reaction ◽

Basis Set ◽

Basis Sets ◽

Dft Methods ◽

Elementary Steps ◽

Oxygen Oxygen ◽

Complete Basis Set

The Fenton reaction plays a central role in many chemical and biological processes and has various applications as e.g. water remediation. The reaction consists of the iron-catalyzed homolytic cleavage of the oxygen-oxygen bond in the hydrogen peroxide molecule and the reduction of the hydroxyl radical. Here, we study these two elementary steps with high-level ab-initio calculations at the complete basis set limit and address the performance of different DFT methods following a specific classification based on the Jacob´s ladder in combination with various Pople's basis sets. Ab-initio calculations at the complete basis set limit are in agreement to experimental reference data and identified a significant contribution of the electron correlation energy to the bond dissociation energy (BDE) of the oxygen-oxygen bond in hydrogen peroxide and the electron affinity (EA) of the hydroxyl radical. The studied DFT methods were able to reproduce the ab-initio reference values, although no functional was particularly better for both reactions. The inclusion of HF exchange in the DFT functionals lead in most cases to larger deviations, which might be related to the poor description of the two reactions by the HF method. Considering the computational cost, DFT methods provide better BDE and EA values than HF and post--HF methods with an almost MP2 or CCSD level of accuracy. However, no systematic general prediction of the error based on the employed functional could be established and no systematic improvement with increasing the size in the Pople's basis set was found, although for BDE values certain systematic basis set dependence was observed. Moreover, the quality of the hydrogen peroxide, hydroxyl radical and hydroxyl anion structures obtained from these functionals was compared to experimental reference data. In general, bond lengths were well reproduced and the error in the angles were between one and two degrees with some systematic trend with the basis sets. From our results we conclude that DFT methods present a computationally less expensive alternative to describe the two elementary steps of the Fenton reaction. However, choice of approximated functionals and basis sets must be carefully done and the provided benchmark allows a systematic validation of the electronic structure method to be employed

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Basis Set Effects in the Description of the Cl-O Bond in ClO and XClO Isomers (X=H,O,Cl) Using DFT and CCSD(T) Methods

10.26434/chemrxiv.6135389 ◽

2018 ◽

Author(s):

Oscar Ventura ◽

Kenneth Irving ◽

Martina Kieninger

Keyword(s):

Density Functional ◽

Basis Set ◽

Basis Sets ◽

Enthalpies Of Formation ◽

Isodesmic Reactions ◽

Dft Methods ◽

Functional Methods ◽

The One ◽

Isomeric Structures ◽

Different Sources

<p>The performance of a group of density functional methods of progressive complexity for the description of the ClO bond in a series of chlorine oxides was investigated. The simplest ClO radical species as well as the two isomeric structures XClO/ClOX for each X=H, Cl and O were studied using the PW91, TPSS, B3LYP, PBE0, M06, M06-2X, BMK and B2PLYP functionals. Geometry optimizations as well as reaction enthalpies and enthalpies of formation for each species were calculated using Pople basis sets and the (aug)-cc-pVnZ Dunning sets, with n=2-6. For the calculation of enthalpies of formation, atomization as well as isodesmic reactions were employed. Both the precision of the methods with respect to the increase of the basis sets, as well as their accuracy, were gauged by comparing the results with the more accurate CCSD(T) calculations, performed using the same basis sets as for the DFT methods. The results obtained employing composite chemical methods (G4, CBS-QB3 and W1BD) were also used for the comparisons, as well as the experimental results when they are available. The results obtained show that error compensation is the key for successful description of molecular properties (geometries and energies) by carefully selecting method and basis sets. In general, expansion of the one-electron basis set to the limit of completeness does not improve results at the DFT level, but just the opposite. The enthalpies of formation calculated at the CCSD(T)/aug-cc-pV6Z for the species considered are generally in agreement with experimental determinations, and the most accurate derived theoretically up to present. Different sources of error in the calculations are discussed in detail.</p>

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Application of numerical basis sets with a family of DFT methods to predict the transition states of Diels-Alder reactions: Assessing the accuracy through synchronous transit method

10.26434/chemrxiv.5696410 ◽

2017 ◽

Author(s):

Saurav Dutta ◽

Bhabani S. Mallik

Keyword(s):

Transition State ◽

Alder Reaction ◽

Diels Alder ◽

Computational Method ◽

Basis Set ◽

Basis Sets ◽

Gaussian Basis Sets ◽

Dft Methods ◽

Diels Alder Reaction ◽

Transition State Search

<div> <table> <tr> <td> <p>Knowledge of the transition state is crucial in determining the mechanism in order to diversify the applicability of the reaction. The computational method is the most convenient way to locate the transition state in the absence any efficient experimental technique. We have applied the method of the transition state search on the Diels-Alder reaction computationally by means of combined linear synchronous transit and quadratic synchronous transit methods. Here we have shown that, of various methods adopted, BOP functional with numerical basis set provides a computationally economical alternative to the widely used B3LYP functional with higher Gaussian basis sets in the transition state search. It can reproduce the experimental parameters like activation energy of the Diels-Alder reaction, and the calculations are much faster than the corresponding other functional based calculations.</p> </td> </tr> </table> </div>

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DFT-ONIOM study of the dopamine–β-CD complex: NBO and AIM analysis

Canadian Journal of Chemistry ◽

10.1139/cjc-2014-0481 ◽

2015 ◽

Vol 93 (10) ◽

pp. 1115-1121 ◽

Cited By ~ 8

Author(s):

Rayenne Djemil ◽

Ouassila Attoui-Yahia ◽

Djameleddine Khatmi

Keyword(s):

Intermolecular Hydrogen Bond ◽

Minimum Energy ◽

Reference Method ◽

Dft Method ◽

Relative Performance ◽

Basis Set ◽

Basis Sets ◽

Density Functionals ◽

Cyclodextrin Complex ◽

Aim Analysis

In this work, we conducted a systematic search of the minimum energy of a dopamine–β-cyclodextrin complex via different ONIOM approaches using both mixed (DFT-HF) and nonmixed (DFT-DFT) combinations. Different density functionals were employed: B3LYP, MPW1PW91, M05-2X, M06-2X, and ωB97X-D. Two different basis sets were used on the dopamine–β-cyclodextrin complex; a lower basis set (3-21G*) is used on β-cyclodextrin and a higher basis set (6-31G(d)) is used on dopamine. To fulfill this task, complexation and deformation energies were determined. The relative performance of these functionals was compared with that obtained with the DFT method at the M06-2X/6-31G(d) level that is chosen as a reference method. Although we did not clearly establish an assessment of the relative performance of these density functionals, the efficacy of the ONIOM combination (DFT-HF) is shown compared with a nonmixed ONIOM combination (DFT-DFT). The intermolecular hydrogen bond interactions of the complex obtained with the full M06-2X/6-31G(d) have been analyzed with the atoms-in-molecules and natural bond rrbital methodologies.

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Application of numerical basis sets with a family of DFT methods to predict the transition states of Diels-Alder reactions: Assessing the accuracy through synchronous transit method

10.26434/chemrxiv.5696410.v1 ◽

2017 ◽

Author(s):

Saurav Dutta ◽

Bhabani S. Mallik

Keyword(s):

Transition State ◽

Alder Reaction ◽

Diels Alder ◽

Computational Method ◽

Basis Set ◽

Basis Sets ◽

Gaussian Basis Sets ◽

Dft Methods ◽

Diels Alder Reaction ◽

Transition State Search

<div> <table> <tr> <td> <p>Knowledge of the transition state is crucial in determining the mechanism in order to diversify the applicability of the reaction. The computational method is the most convenient way to locate the transition state in the absence any efficient experimental technique. We have applied the method of the transition state search on the Diels-Alder reaction computationally by means of combined linear synchronous transit and quadratic synchronous transit methods. Here we have shown that, of various methods adopted, BOP functional with numerical basis set provides a computationally economical alternative to the widely used B3LYP functional with higher Gaussian basis sets in the transition state search. It can reproduce the experimental parameters like activation energy of the Diels-Alder reaction, and the calculations are much faster than the corresponding other functional based calculations.</p> </td> </tr> </table> </div>

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COMPARATIVE QUANTUM STUDY ON TERT-BUTYL RADICAL AND CATION

Journal of Theoretical and Computational Chemistry ◽

10.1142/s0219633611006487 ◽

2011 ◽

Vol 10 (03) ◽

pp. 325-348 ◽

Cited By ~ 4

Author(s):

ANNA IGNACZAK

Keyword(s):

Density Functional ◽

Structural Parameters ◽

Coupling Constants ◽

Basis Set ◽

Basis Sets ◽

Inversion Barrier ◽

Gaussian Basis Sets ◽

Dft Methods ◽

Tert Butyl ◽

Butyl Radical

Detailed comparative analysis of properties of the tert-butyl radical and cation is performed using 14 density functional (DFT) methods combined with double-zeta and triple-zeta quality Gaussian basis sets with polarization and diffuse functions. Stability of different conformers is discussed. Structural parameters, dipole moment, adiabatic ionization potential (IP), inversion barrier and isotropic hyperfine coupling constants are examined and compared to values obtained at the standard MP2 level and to experimental data available. All methods indicate that that the CC bond in the radical is longer than in the cation by about 0.033 Å. The IP values are found to be very sensitive to the method used and range from 612 to 709 kJ/mol, but majority oscillate around 646÷656 kJ/mol. Calculated inversion barrier for the radical is higher than the experimental estimate of 2.68 kJ/mol; with the 6-311++G** basis set and most DFT methods it is predicted in the range 3.86÷4.82 kJ/mol. All DFT methods predict for the out-of-plane CC3 bending mode of the radical the frequency around 260 cm-1, while in the cation the corresponding frequency is higher by about 180 cm-1.

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