Literature DB >> 28564543

Improved pKa Prediction of Substituted Alcohols, Phenols, and Hydroperoxides in Aqueous Medium Using Density Functional Theory and a Cluster-Continuum Solvation Model.

Bishnu Thapa1, H Bernhard Schlegel1.   

Abstract

Acid dissociation constants (pKa's) are key physicochemical properties that are needed to understand the structure and reactivity of molecules in solution. Theoretical pKa's have been calculated for a set of 72 organic compounds with -OH and -OOH groups (48 with known experimental pKa's). This test set includes 17 aliphatic alcohols, 25 substituted phenols, and 30 hydroperoxides. Calculations in aqueous medium have been carried out with SMD implicit solvation and three hybrid DFT functionals (B3LYP, ωB97XD, and M06-2X) with two basis sets (6-31+G(d,p) and 6-311++G(d,p)). The effect of explicit water molecules on calculated pKa's was assessed by including up to three water molecules. pKa's calculated with only SMD implicit solvation are found to have average errors greater than 6 pKa units. Including one explicit water reduces the error by about 3 pKa units, but the error is still far from chemical accuracy. With B3LYP/6-311++G(d,p) and three explicit water molecules in SMD solvation, the mean signed error and standard deviation are only -0.02 ± 0.55; a linear fit with zero intercept has a slope of 1.005 and R2 = 0.97. Thus, this level of theory can be used to calculate pKa's directly without the need for linear correlations or thermodynamic cycles. Estimated pKa values are reported for 24 hydroperoxides that have not yet been determined experimentally.

Entities:  

Year:  2017        PMID: 28564543     DOI: 10.1021/acs.jpca.7b03907

Source DB:  PubMed          Journal:  J Phys Chem A        ISSN: 1089-5639            Impact factor:   2.781


  8 in total

1.  Correlations between the 1H NMR chemical shieldings and the pKa values of organic acids and amines.

Authors:  Juanfeng Lu; Tingting Lu; Xinyun Zhao; Xi Chen; Chang-Guo Zhan
Journal:  J Mol Model       Date:  2018-06-01       Impact factor: 1.810

2.  Absolute and relative pKa predictions via a DFT approach applied to the SAMPL6 blind challenge.

Authors:  Qiao Zeng; Michael R Jones; Bernard R Brooks
Journal:  J Comput Aided Mol Des       Date:  2018-08-20       Impact factor: 3.686

3.  O-Acetyl Migration within the Sialic Acid Side Chain: A Mechanistic Study Using the Ab Initio Nanoreactor.

Authors:  Lisa Oh; Yang Ji; Wanqing Li; Ajit Varki; Xi Chen; Lee-Ping Wang
Journal:  Biochemistry       Date:  2022-09-02       Impact factor: 3.321

4.  An explicit-solvent hybrid QM and MM approach for predicting pKa of small molecules in SAMPL6 challenge.

Authors:  Samarjeet Prasad; Jing Huang; Qiao Zeng; Bernard R Brooks
Journal:  J Comput Aided Mol Des       Date:  2018-10-01       Impact factor: 3.686

5.  Determination of the Bridging Ligand in the Active Site of Tyrosinase.

Authors:  Congming Zou; Wei Huang; Gaokun Zhao; Xiao Wan; Xiaodong Hu; Yan Jin; Junying Li; Junjun Liu
Journal:  Molecules       Date:  2017-10-28       Impact factor: 4.411

6.  Ionization Energies and Redox Potentials of Hydrated Transition Metal Ions: Evaluation of Domain-Based Local Pair Natural Orbital Coupled Cluster Approaches.

Authors:  Sinjini Bhattacharjee; Miho Isegawa; Miquel Garcia-Ratés; Frank Neese; Dimitrios A Pantazis
Journal:  J Chem Theory Comput       Date:  2022-02-22       Impact factor: 6.006

7.  Molecular docking assisted exploration on solubilization of poorly soluble drug remdesivir in sulfobutyl ether-tycyclodextrin.

Authors:  Yumeng Zhang; Zhouming Zhao; Kai Wang; Kangjie Lyu; Cai Yao; Lin Li; Xia Shen; Tengfei Liu; Xiaodi Guo; Haiyan Li; Wenshou Wang; Tsai-Ta Lai
Journal:  AAPS Open       Date:  2022-04-25

8.  A ratiometric near-infrared fluorescent probe based on a novel reactive cyanine platform for mitochondrial pH detection.

Authors:  Shulin Wan; Shuai Xia; Jerry Medford; Emma Durocher; Tessa E Steenwinkel; Lexi Rule; Yibin Zhang; Rudy L Luck; Thomas Werner; Haiying Liu
Journal:  J Mater Chem B       Date:  2021-06-16       Impact factor: 7.571

  8 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.