scholarly journals Quantification of σ–Holes and Their Use as a Descriptor for the Theoretical Calculation of pKa Values for Carboxylic Acids

2018 ◽  
Author(s):  
Guillermo Caballero-García ◽  
Gustavo Mondragón-Solórzano ◽  
Raúl Torres-Cadena ◽  
Marco Díaz-García ◽  
Jacinto Sandoval-Lira ◽  
...  
Keyword(s):  
Basis Sets ◽  
Implicit Solvent ◽  
Density Functionals ◽  
Hydrogen Atoms ◽  
Acidity Constants ◽  
Pka Values ◽  
Theoretical Approaches ◽  
Solvent Model ◽  
Acidic Hydrogen ◽  
Model Water

Theoretical approaches to calculate pKa values for Brønsted acids is a challenging task that, most of the time, involves sophisticated and time-consuming methods. Therefore, heuristic approaches are efficient and appealing methodologies to approximate these values. Herein, by considering the electrostatic potential on acidic hydrogen atoms in a similar fashion that a σ–hole is defined, we calculated the maximum surface potential, VS,max, and used it as a descriptor to correlate it with experimental acidity constants. These values were calculated using the CPCM implicit solvent model (water) with six different methods: five density functionals and the Møller–Plesset second order perturbation theory. Six different basis sets were combined with each method in order to benchmark a total of thirty-six levels of theory. Overall, 1080 calculations were performed and found to correlate with experimental data. The ωB97X-D/6-31+G(d,p) level of theory stands as the best one for consistently reproduce the reported pKa values.

scholarly journals Calculation of VS,max and Its Use as a Descriptor for the Theoretical Calculation of pKa Values for Carboxylic Acids

Molecules ◽  
2018 ◽  
Vol 24 (1) ◽  
pp. 79 ◽  
Author(s):  
Guillermo Caballero-García ◽  
Gustavo Mondragón-Solórzano ◽  
Raúl Torres-Cadena ◽  
Marco Díaz-García ◽  
Jacinto Sandoval-Lira ◽  
...  
Keyword(s):  
Theoretical Calculation ◽  
Carboxylic Acids ◽  
Predictive Power ◽  
Basis Sets ◽  
Hydrogen Atoms ◽  
Pka Values ◽  
Implicit Solvation Model ◽  
Moller Plesset ◽  
Surface Electrostatic Potential ◽  
Acidic Hydrogen

The theoretical calculation of pKa values for Brønsted acids is a challenging task that involves sophisticated and time-consuming methods. Therefore, heuristic approaches are efficient and appealing methodologies to approximate these values. Herein, we used the maximum surface electrostatic potential (VS,max) on the acidic hydrogen atoms of carboxylic acids to describe the H-bond interaction with water (the same descriptor that is used to characterize σ-bonded complexes) and correlate the results with experimental pKa values to obtain a predictive model for other carboxylic acids. We benchmarked six different methods, all including an implicit solvation model (water): Five density functionals and the Møller–Plesset second order perturbation theory in combination with six different basis sets for a total of thirty-six levels of theory. The ωB97X-D/cc-pVDZ level of theory stood out as the best one for consistently reproducing the reported pKa values, with a predictive power of 98% correlation in a test set of ten other carboxylic acids.

Benchmarking Density Functionals, Basis Sets, and Solvent Models in Predicting Thermodynamic Hydricities of Organic Hydrides

2021 ◽  
Author(s):  
Christina Yeo ◽  
Minh Nguyen ◽  
Lee-Ping Wang
Keyword(s):  
Density Functional ◽  
Mean Squared Error ◽  
Theoretical Calculations ◽  
Computational Cost ◽  
Hydrogen Gas ◽  
Basis Set ◽  
Basis Sets ◽  
Density Functionals ◽  
Solvent Models ◽  
Solvent Model

Many renewable energy technologies, such as hydrogen gas synthesis and carbon dioxide reduction, rely on chemical reactions involving hydride anions. When selecting molecules to be used in such applications, an important quantity to consider is the thermodynamic hydricity, which is the free energy required for a species to donate a hydride anion. Theoretical calculations of thermodynamic hydricity depend on several parameters, mainly the density functional, basis set, and solvent model. In order to assess the effects of the above three parameters, we carry out hydricity calculations for a set of molecules with known experimental hydricity values, generate linear �fits, and compare the R-squared, root-mean-squared error, and Akaike Information Criterion across different combinations of density functionals, basis sets, and solvent models. Based on these results we are able to quantify the accuracy of theoretical predictions of hydricity and recommend the parameters with the best compromise between accuracy and computational cost.

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.

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.

scholarly journals A Density Functional Theory-Based Scheme to Compute the Redox Potential of a Transition Metal Complex: Applications to Heme Compound

Molecules ◽  
2019 ◽  
Vol 24 (4) ◽  
pp. 819
Author(s):  
Toru Matsui ◽  
Jong-Won Song
Keyword(s):  
Dielectric Constant ◽  
Redox Potential ◽  
Density Functional ◽  
Absolute Error ◽  
Low Dielectric Constant ◽  
Density Functionals ◽  
Protonation State ◽  
Functional Theory ◽  
Low Dielectric ◽  
Solvent Model

We estimated the redox potential of a model heme compound by using the combination of our density functionals with a computational scheme, which corrects the solvation energy to the normal solvent model. Among many density functionals, the LC-BOP12 functional gave the smallest mean absolute error of 0.16 V in the test molecular sets. The application of these methods revealed that the redox potential of a model heme can be controlled within 200 mV by changing the protonation state and even within 20 mV by the flipping of the ligand histidine. In addition, the redox potential depends on the inverse of the dielectric constant, which controls the surroundings. The computational results also imply that a system with a low dielectric constant avoids the charged molecule by controlling either the redox potential or the protonation system.

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