Literature DB >> 15535550

Accurate pKa determination for a heterogeneous group of organic molecules.

Marcel Schmidt am Busch1, Ernst-Walter Knapp.   

Abstract

Single-molecule studies that allow to compute pKa values, proton affinities (gas-phase acidity/basicity) and the electrostatic energy of solvation have been performed for a heterogeneous set of 26 organic compounds. Quantum mechanical density functional theory (DFT) using the Becke-half&half and B3LYP functionals on optimized molecular geometries have been carried out to investigate the energetics of gas-phase protonation. The electrostatic contribution to the solvation energies of protonated and deprotonated compounds were calculated by solving the Poisson equation using atomic charges generated by fitting the electrostatic potential derived from the molecular wave functions in vacuum. The combination of gas-phase and electrostatic solvation energies by means of the thermodynamic cycle enabled us to compute pKa values for the 26 compounds, which cover six distinct chemical groups (carboxylic acids, benzoic acids, phenols, imides, pyridines and imidazoles). The computational procedure for determining pKa values is accurate and transferable with a root-mean-square deviation of 0.53 and 0.57 pKa units and a maximum error of 1.0 pKa and 1.3 pKa units for Becke-half&half and B3LYP DFT functionals, respectively.

Entities:  

Year:  2004        PMID: 15535550     DOI: 10.1002/cphc.200400171

Source DB:  PubMed          Journal:  Chemphyschem        ISSN: 1439-4235            Impact factor:   3.102


  13 in total

1.  First-principles calculation of pKa for cocaine, nicotine, neurotransmitters, and anilines in aqueous solution.

Authors:  Haiting Lu; Xi Chen; Chang-Guo Zhan
Journal:  J Phys Chem B       Date:  2007-08-11       Impact factor: 2.991

Review 2.  Proton transfer reactions and hydrogen-bond networks in protein environments.

Authors:  Hiroshi Ishikita; Keisuke Saito
Journal:  J R Soc Interface       Date:  2013-11-27       Impact factor: 4.118

3.  Proton transfer in the K-channel analog of B-type Cytochrome c oxidase from Thermus thermophilus.

Authors:  Anna Lena Woelke; Anke Wagner; Gegham Galstyan; Tim Meyer; Ernst-Walter Knapp
Journal:  Biophys J       Date:  2014-11-04       Impact factor: 4.033

4.  Correlation between molecular acidity (pKa) and vibrational spectroscopy.

Authors:  Niraj Verma; Yunwen Tao; Bruna Luana Marcial; Elfi Kraka
Journal:  J Mol Model       Date:  2019-01-30       Impact factor: 1.810

5.  Calculating pKa values for substituted phenols and hydration energies for other compounds with the first-order Fuzzy-Border continuum solvation model.

Authors:  Ity Sharma; George A Kaminski
Journal:  J Comput Chem       Date:  2012-07-19       Impact factor: 3.376

6.  Single-ion solvation free energies and the normal hydrogen electrode potential in methanol, acetonitrile, and dimethyl sulfoxide.

Authors:  Casey P Kelly; Christopher J Cramer; Donald G Truhlar
Journal:  J Phys Chem B       Date:  2007-01-18       Impact factor: 2.991

7.  Computational studies on imidazole heme conformations.

Authors:  Artur S Galstyan; Snezana D Zarić; Ernst-Walter Knapp
Journal:  J Biol Inorg Chem       Date:  2005-04-21       Impact factor: 3.358

8.  Using polarizable POSSIM force field and fuzzy-border continuum solvent model to calculate pK(a) shifts of protein residues.

Authors:  Ity Sharma; George A Kaminski
Journal:  J Comput Chem       Date:  2016-10-27       Impact factor: 3.376

9.  Synthesis and enzymatic evaluation of 2- and 4-aminothiazole-based inhibitors of neuronal nitric oxide synthase.

Authors:  Graham R Lawton; Haitao Ji; Pavel Martásek; Linda J Roman; Richard B Silverman
Journal:  Beilstein J Org Chem       Date:  2009-06-04       Impact factor: 2.883

10.  Adding explicit solvent molecules to continuum solvent calculations for the calculation of aqueous acid dissociation constants.

Authors:  Casey P Kelly; Christopher J Cramer; Donald G Truhlar
Journal:  J Phys Chem A       Date:  2006-02-23       Impact factor: 2.781

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