An Assessment of Theoretical Protocols for Calculation of the pKa Values of the Prototype Imidazolium Cation

2004 ◽  
Vol 57 (12) ◽  
pp. 1205 ◽  
Author(s):  
Alison M. Magill ◽  
Brian F. Yates
Keyword(s):  
Excellent Agreement ◽  
Basis Set ◽  
Hydrogen Atoms ◽  
Imidazolium Cation ◽  
Pka Values ◽  
Experimental Estimate ◽  
Pka Calculation ◽  
Complete Basis Set ◽  
Aqueous Pka ◽  
Experimental Values

The highly accurate complete basis set method CBS-QB3 has been used in conjunction with the conductor-like polarized continuum (CPCM) method to predict the aqueous pKa values for the three different hydrogen atoms in the imidazolium cation. Excellent agreement was obtained with the available experimental values. The pKa for the deprotonation of imidazole was also calculated and found to be quite different from the experimental estimate. The protocol for the pKa calculation was carefully analyzed and some recommendations made about the choice of levels of theory.

scholarly journals Quantum Calculations to Estimate the Heat of Hydrogenation Theoretically

2020 ◽  
Author(s):  
Ali Amir Khairbek
Keyword(s):  
Unsaturated Hydrocarbon ◽  
Experimental Results ◽  
Basis Set ◽  
Good Linear ◽  
Complete Basis ◽  
Complete Basis Set ◽  
Complete Basis Set Limit ◽  
The Mean ◽  
Experimental Values ◽  
Linear Correlations

Standard enthalpies of hydrogenation of 29 unsaturated hydrocarbon compounds were calculated in the gas phase by CCSD(T) theory with complete basis set cc-pVXZ, where X = DZ, TZ, as well as by complete basis set limit extrapolation. Geometries of reactants and products were optimized at the M06-2X/6-31g(d) level. This M06-2X geometries were used in the CCSD(T)/cc-pVXZ//M06-2X/6-31g(d) and cc-pV(DT)Z extrapolation calculations. (MAD) the mean absolute deviations of the enthalpies of hydrogenation between the calculated and experimental results that range from 8.8 to 3.4 kJ mol−1 based on the Comparison between the calculation at CCSD(T) and experimental results. The MAD value has improved and decreased to 1.5 kJ mol−1 after using complete basis set limit extrapolation. The deviations of the experimental values are located inside the “chemical accuracy” (±1 kcal mol−1 ≈ ±4.2 kJ mol−1) as some results showed. A very good linear correlations between experimental and calculated enthalpies of hydro-genation have been obtained at CCSD(T)/cc-pVTZ//M06-2X/6-31g(d) level and CCSD(T)/cc-pV(DT)Z extrapolation levels (SD =2.11 and 2.12 kJ mol−1, respectively).

scholarly journals Calculations of hydrogenation enthalpies of hydrocarbons by M06-2X/CBS extrapolated level in the gas phase

2020 ◽  
Vol 44 (11-12) ◽  
pp. 762-768
Author(s):  
AA Khairbek ◽  
M Abd Al-Hakim Badawi
Keyword(s):  
Standard Deviation ◽  
Gas Phase ◽  
Unsaturated Hydrocarbon ◽  
Basis Set ◽  
Basis Sets ◽  
Good Linear ◽  
Complete Basis Set ◽  
The Mean ◽  
Experimental Values ◽  
Linear Correlations

The standard enthalpies of hydrogenation of 29 unsaturated hydrocarbon compounds were calculated in the gas phase by M06-2X theory with the 6-31g(d) and cc-pVXZ, where X = DZ, TZ, QZ, as well as by complete basis set extrapolated level. Geometries of compounds were optimized at the M06-2X/6-31g(d) level. These M06-2X geometries were used in the M06-2X, and extrapolation calculations with cc-pVXZ basis sets. Comparison of calculation and experimental results shows that the mean absolute deviations between the calculated and experimental enthalpies of hydrogenation range from 25.1 to 5.1 kJ mol−1 at M06-2X calculations, and when using cc-pV(DT)Z extrapolated level, the mean absolute deviations have decreased to 2.7. The results of some calculations showed that the deviations from experimental values are located inside the “chemical accuracy” (±1 kcal mol−1≈±4.2 kJ mol−1). Very good linear correlations between experimental and calculated enthalpies of hydrogenation have been obtained at M06-2X/cc-pVTZ and cc-pV(DT)Z extrapolated levels (standard deviation = 3.2 and 3.4 kJ mol−1, respectively).

Ab-initio Calculations of Electronic, Transport, and Bulk Properties of cubic Boron Nitride (zb-BN)

2015 ◽  
Vol 9 (1) ◽  
pp. 2277-2286 ◽  
Author(s):  
Anthony Duane Stewart
Keyword(s):  
Boron Nitride ◽  
Ab Initio ◽  
Excellent Agreement ◽  
Local Density ◽  
Cubic Boron Nitride ◽  
Basis Set ◽  
Optimal Basis ◽  
Valence Bands ◽  
Indirect Band Gap ◽  
Experimental Values

We present results from ab-initio, self consistent, local density approximation (LDA) calculations of electronic and related properties of cubic boron nitride (zb-BN).  We employed the Ceperley and Alder LDA potential and the linear combination of atomic orbitals (LCAO) formalism in our non-relativistic computations.  We solved the system of LDA equations self-consistently, through the implementation of the LCAO formalism, following the Bagayoko, Zhao, and Williams (BZW) method as enhanced by Ekuma and Franklin (BZW-EF).  The BZW-EF method includes a methodical search for the optimal basis set that yields the absolute minima of the occupied energies.  This search entails increasing the size of the basis set and the related modifications of angular symmetry and of radial orbitals.  Our calculated, indirect band gap of 6.48 eV, from the Γ to the Χ points, and bulk modulus of 375 GPa are in excellent agreement with corresponding experimental values at room temperature (RT).  The calculated widths of the lowest valance band and that of the entire valence bands of 5.65 eV and 20.26 eV are in excellent agreement with the measured values of 5.5 eV and 20 eV, respectively.  We have also calculated electron and hole effective masses for zb-BN, and the total (DOS) and partial (pDOS) densities of states.   

Experiment Stands Corrected: Accurate Prediction of the Aqueous pKa Values of Sulfonamide Drugs Using Equilibrium Bond Lengths

2019 ◽  
Author(s):  
Beth A. Caine ◽  
Maddalena Bronzato ◽  
Paul Popelier
Keyword(s):  
Strongly Correlated ◽  
Pka Values ◽  
Pka Prediction ◽  
Thermodynamic Cycles ◽  
Bond Lengths ◽  
Linear Relationships ◽  
Aqueous Pka ◽  
Experimental Values ◽  
First Time ◽  
Sulfonamide Group

We show here for the first time that strongly correlated linear relationships exist between equilibrium bond lengths of the sulfonamide group and aqueous pKa values. Models are constructed for three variants of the SO2NHR group: primary benzene sulfonamide derivatives (e.g. diuretic drugs furosemide and hydrochlorothiazide), N-phenyl substituted 4-amino-N-phenylbenzenesulfonamide analogues (e.g. the sulfa antibiotic sulfadiazine) and phenylsulfonylureas (e.g. insulin secretogogue, glimepiride). In the context of these compounds, we present solutions to some of the more complex challenges in pKa prediction: (i) prediction for multiprotic compounds, (ii) predicting macroscopic values for compounds that tautomerize, and (iii) quantum chemical pKa prediction for compounds with more than 50 atoms. Using bond lengths as a powerful descriptor of ionization feasibility, we also identify that literature values for drug compounds celecoxib, glimepiride and glipizide are inaccurate. Our newly measured experimental values match our initial predictions to within 0.26 pKa units, whereas previous values were found to deviate by up to 1.68 pKa units. For glimepiride, our corrected value denotes a percentage of ionization at intracellular pH, which is only now in excellent agreement with its known therapeutic efficacy. We propose that linear relationships between bond lengths and pKa should emerge for any set of congeners, thus providing a powerful method of pKa prediction obviating the need for thermodynamic cycles.

Experiment Stands Corrected: Accurate Prediction of the Aqueous pKa Values of Sulfonamide Drugs Using Equilibrium Bond Lengths

2019 ◽  
Author(s):  
Beth A. Caine ◽  
Maddalena Bronzato ◽  
Paul Popelier
Keyword(s):  
Strongly Correlated ◽  
Pka Values ◽  
Pka Prediction ◽  
Thermodynamic Cycles ◽  
Bond Lengths ◽  
Linear Relationships ◽  
Aqueous Pka ◽  
Experimental Values ◽  
First Time ◽  
Sulfonamide Group

We show here for the first time that strongly correlated linear relationships exist between equilibrium bond lengths of the sulfonamide group and aqueous pKa values. Models are constructed for three variants of the SO2NHR group: primary benzene sulfonamide derivatives (e.g. diuretic drugs furosemide and hydrochlorothiazide), N-phenyl substituted 4-amino-N-phenylbenzenesulfonamide analogues (e.g. the sulfa antibiotic sulfadiazine) and phenylsulfonylureas (e.g. insulin secretogogue, glimepiride). In the context of these compounds, we present solutions to some of the more complex challenges in pKa prediction: (i) prediction for multiprotic compounds, (ii) predicting macroscopic values for compounds that tautomerize, and (iii) quantum chemical pKa prediction for compounds with more than 50 atoms. Using bond lengths as a powerful descriptor of ionization feasibility, we also identify that literature values for drug compounds celecoxib, glimepiride and glipizide are inaccurate. Our newly measured experimental values match our initial predictions to within 0.26 pKa units, whereas previous values were found to deviate by up to 1.68 pKa units. For glimepiride, our corrected value denotes a percentage of ionization at intracellular pH, which is only now in excellent agreement with its known therapeutic efficacy. We propose that linear relationships between bond lengths and pKa should emerge for any set of congeners, thus providing a powerful method of pKa prediction obviating the need for thermodynamic cycles.

Measurement and Calculation of Electric Field Gradients in Hg-Mercaptides

1998 ◽  
Vol 53 (6-7) ◽  
pp. 404-410 ◽  
Author(s):  
Torsten Soldner ◽  
Wolfgang Tröger ◽  
Tilman Butz ◽  
Peter Blaha ◽  
Karlheinz Schwarz ◽  
...  
Keyword(s):  
Plane Wave ◽  
Electric Field ◽  
Basis Set ◽  
Full Potential ◽  
Hydrogen Atoms ◽  
Electric Field Gradients ◽  
Field Gradients ◽  
Unit Cells ◽  
Experimental Values ◽  
Linearized Augmented Plane Wave

Abstract Electric field gradients (EFG) at Hg were determined in mercury mercaptides Hg(S(CH2)i CH3)2 experimentally for i ∈ {0, 1, 2} using time differential perturbed angular correlation and theoreti-cally for i ∈ {0, 1} with the full potential linearized augmented plane wave code WIEN95. Due to the large unit cells and small hydrogen atoms not full convergence of the plane wave basis set could be reached. Nevertheless, the calculated EFGs agree with experimental values to better than 20%. Furthermore, isolated molecules for i ∈ {0, 1) were investigated theoretically, and strong differences to the values for the crystalline state, especially for the asymmetry parameters η, were found.

scholarly journals A simple computational approach for pKa calculation of organosulfur compounds

2020 ◽  
pp. 42-42
Author(s):  
Syed Ali ◽  
Aneesa Choudhary ◽  
Majid Khalil ◽  
Arif Zubair
Keyword(s):  
Density Functional ◽  
Dft Method ◽  
Computational Approach ◽  
Basis Set ◽  
Basis Sets ◽  
Organosulfur Compounds ◽  
Pka Values ◽  
Pka Calculation ◽  
Main Emphasis ◽  
Diffuse Function

The present work is related to predicting the pKa values of organosulfur compounds through Density Functional Theory (DFT). In this study 22 organo-sulfur compounds have been considered to calculate theoretical pKa values. Main emphasis has been given on the substitution of different groups on the Sulfur atom. The computations were performed in the presence of Dimethyl sulfoxide (DMSO) as solvent. Experimentally the order of increase of acidity is; Sulfides < < Sulfoxides < Sulfones. Our computed pKa values also follow the same order. The theoretical pKa values are computed using the DFT method B3LYP, with the basis sets 6-31G(d), 6-31+G(d,p) and IEFPCM bulk solvation model. The majority of computed pKa values are in excellent agreement with the experimental ones through the diffuse function basis set. Hence this computational approach, B3LYP/6-31+G(d,p)/IEFPCM, could be utilized to predict the pKa values of these types of organosulfur compounds.

scholarly journals Comparative Study of CBS-Q Calculated and Experimental pKa Values for Fluoro-Acetoxy Derivative

2019 ◽  
pp. 1-12
Author(s):  
Mustafa Lawar ◽  
Safia Elbadwe ◽  
Ismail Yalçin ◽  
Kayhan Bolelli ◽  
Hakan Sezgin Sayiner ◽  
...  
Keyword(s):  
Strong Relationship ◽  
Quantitative Structure Activity Relationship ◽  
Acetoxy Group ◽  
Basis Set ◽  
Quantitative Structure ◽  
Pka Values ◽  
Structure Activity ◽  
Dependent Variables ◽  
Complete Basis Set ◽  
Independent Variable

The pKa values were calculated for some acetoxy group molecules using CBS-Q method which is one of the Complete Basis Set methods to find accurate energies. The acetoxy group molecules were also planned by Quantitative Structure Activity Relationship (QSAR) to study their effect on paraoxonase1 activity. The results of this study showed a strong relationship, (R2=0.99) between the calculated and experimental pka, also showed correlations between the activity of the enzyme and some of the studied descriptors. Moreover, the results of the study revealed that by using the SPSS program, there is a correlation between LUMO, Softness, Nucleofugality and Electrofugality as dependent variables and Cal. pKa as an independent variable.

scholarly journals Evaluation of the IP-EOMCCSD Method for Estimating Experimental Ionization Potentials Using 53 Medium Sized Molecules

2018 ◽  
Author(s):  
Marissa Buzzanca ◽  
Brandon Brummeyer ◽  
Jonathan Gutow
Keyword(s):  
Computational Method ◽  
Ionization Potentials ◽  
Basis Set ◽  
Basis Sets ◽  
Average Deviation ◽  
Complete Basis Set ◽  
Computational Cluster ◽  
Complete Basis Set Limit ◽  
Experimental Values ◽  
Good Agreement

<div> <div> <div>Vertical ionization potentials (IPs) computed using the IP-EOMCCSD method are reported for 53 medium sized molecules (6 – 32 atoms) and compared with average experimental vertical IPs. The calculations are practical on a modest computational cluster and yield good agreement with experimental values using the aug-cc-pVDZ basis set, with an average deviation from the experimental IP of −0.04 eV. The accuracy of IP computations appears to be approaching the point where possible systematic experimental errors can be identified. Although good extrapolations to the complete basis set limit for the IP are achievable using just the aug-cc-pVDZ and aug-cc-pVTZ basis sets, deviations of the extrapolation from experimental values suggest that inclusion of higher order "triples" may make the computational method more broadly applicable. Examination of experimental spectra for ethylene, E-2-butene, 2,5-dihydrofuran and pyrrole reinforces the observations of Davidson and Jarzęcki1 that experimental vertical IPs are usually extracted from experimental data in a manner that does not account for band asymmetries, making direct comparison to computations difficult. Despite the good agreement with experiment when using the aug-cc-pVDZ basis set, for the molecules investigated most of these reported experimental IPs are below the actual value, likely by no more than 0.4 eV. This set of 53 molecules is recommended as a benchmark comparison set for computational and experimental IP results.<br></div> </div> </div>

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

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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