Calculation of Absolute and Relative Acidities of Substituted Imidazoles in Aqueous Solvent

Topol, Igor A.; Tawa, Gregory J.; Burt, Stanley K.; Rashin, A. A.

doi:10.1021/jp9723168

Cited by 168 publications

(201 citation statements)

References 63 publications

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“…1 Examples 1-24 include carboxylic acids, [7][8][9]11,14,[17][18][19] alcohols, 11 thiols, 11 phenols, 21 pyrone derivatives, 12 amines, 3 imidazoles, 5,24 hydrated transition metal cations, 2 transition metal complexes, 16 phosphoranes, 22 and DNA (RNA) bases. 6,15,23 Recent applications are extended to the evaluation of pK a values of 1) intermediate species that are not easily measured experimentally, 22 2) weak organic acids with high pK a values, 13 which cannot be measured experimentally in aqueous phase, and 3) molecules having multiple protonation sites.…”

Section: Introductionmentioning

confidence: 99%

Calculation of the Solvation Free Energy of the Proton in Methanol

Hwang¹,

Chung²

2005

Bulletin of the Korean Chemical Society

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The solvation free energy of proton in methanol was calculated by B3LYP flavor of density functional calculations in combination with the Poisson-Boltzmann continuum solvation model. In order to check the adequacy of the computation level, the free energies of clustering in the gas phase were compared with the experimental data. The solvents were taken into account in a hybrid manner, i.e. one to five molecules of methanol were explicitly considered while other solvent molecules were represented with an implicit solvation model.

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Section: Introductionmentioning

confidence: 99%

Calculation of the Solvation Free Energy of the Proton in Methanol

Hwang¹,

Chung²

2005

Bulletin of the Korean Chemical Society

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“…We used ∆Gg 7.76 = -6.28 kcal/mol from the literature. 11,12 All QM calculations used the Jaguar v 5.5 quantum chemistry software. 13 To calculate the geometries and energies of the various molecules, we used the B3LYP flavor of density functional theory (DFT), which includes the generalized gradient approximation and a component of the exact Hartree-Fock (HF) exchange.…”

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confidence: 99%

Study of 7-Methylguanine on pK_aValues by Using Density Functional Theoretical Method

Hwang¹,

Jang²,

Cho³

et al. 2010

Bulletin of the Korean Chemical Society

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Methylation of DNA by endogenous methylating agents generates a variety of genotoxic adducts.1 The N7 position of guanine is known as the most nucleophilic site within the heterocyclic bases of DNA.2 Accordingly, N7-methylguanine (7MeG) is the one of the most prevailing forms of the methylated guanine. 7MeG is also generated by methylation in order to be used as a probe of protein-DNA interactions and DNA sequencing. Recently, a DNA double helical structure of a 25-mer containing a 7MeG was reported, which revealed the base pairing characteristics of 7MeG.1 Information on the acid dissociation constants and the relative populations of various tautomers would provide valuable clues toward optimizing analysis of 7MeG and to understand the biological consequences of the modified base.We have developed a scheme based on density-functional theoretical calculations in combination with the Poisson-Boltzmann continuum solvation model for water to predict pKa values and the major tautomeric forms of a number of nucleobases, their oxidative damage products, 3-5 and heteronuclear aromatic compounds. 6,7 As well as macroscopic pKa values, we reproduced the micro pKa values of individual protonation sites of purine nucleobases.8 Hydrogen transfer between paired nucleobases was also investigated using the same computational model. Among methylated guanine species, we have already reported computations on the tautomerism and pK a values of 9-methylguanine (9MeG) and 7,9-dimethylguanine.8 Gas-phase vibrational experiments and computation results on 1,7-dimethylguanine, 7MeG, and 9MeG were also reported. 10In the current work, we report calculated relative stabilities of the tautomers of 7MeG at each ionization stage and the pKa values of 7MeG in aqueous solution.pKa calculations on the nucleobases and their derivatives are complicated due to the presence of multiple tautomers with different site-specific microscopic pKa values. A way to estimate the overall macroscopic pKa from the site-specific pKa's of the tautomers devised in our previous studies and the details of the computation scheme have been presented elsewhere. 3,4For a deprotonation process leading the i-th tautomer of an acid HA into the j-th tautomer of the conjugate base A -, the Gibbs energy of deprotonation reaction is calculated as (1) and the corresponding micro pKa ij values is given bywhere R is the gas constant and T is 298.15 K. From this micro pK a ij value, the partial population of the i-th tautomer out of all of the acid species ( fi), and the partial population of the j-th tautomer out of all of the conjugate base species ( fj ' ), the macro pKa value is estimated as 4 pKa = pKa ij -log fi + log fj ' .The standard free energy of each species (HA, A -, and H + ) in water, ∆Ga 0 q, can be written as the sum of the gas-phase standard Gibbs energy ∆Gg 0 and the standard Gibbs energy of solvation in water ∆Gs 0 olv:The standard Gibbs energy of each species in the gas phase, ∆Gg 0 , is obtained byThe total energy of the molecule at 0 K (E0 K) is calculated ...

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“…[34][35][36][37][38] Here, we will focus on the solvation contribution to the protonation equilibrium and reserve quantum mechanical intramolecular effects for subsequent treatment.…”

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Molecular Theories and Simulation of Ions and Polar Molecules in Water

1998

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Recent developments in molecular theories and simulation of ions and polar molecules in water are reviewed. The hydration of imidazole and imidazolium solutes is used to exemplify the theoretical issues. The treatment of long-ranged electrostatic interactions in simulations is discussed extensively. It is argued that the Ewald approach is an easy way to get correct hydration free energies in the thermodynamic limit from molecular calculations; and that molecular simulations with Ewald interactions and periodic boundary conditions can also be more efficient than many common alternatives. The Ewald treatment permits a conclusive extrapolation to infinite system size. Accurate results for well-defined models have permitted careful testing of simple theories of electrostatic hydration free energies, such as dielectric continuum models. The picture that emerges from such testing is that the most prominent failings of the simplest theories are associated with solvent proton conformations that lead to non-gaussian fluctuations of electrostatic potentials. Thus, the most favorable cases for second-order perturbation theories are monoatomic positive ions. For polar and anionic solutes, continuum or gaussian theories are less accurate. The appreciation of the specific deficiencies of those simple models have led to new concepts, multistate gaussian and quasi-chemical theories, that address the cases for which the simpler theories fail. It is argued that, relative to direct dielectric continuum treatments, the quasi-chemical theories provide a better theoretical organization for the computational study of the electronic structure of solution species.2

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Calculation of Absolute and Relative Acidities of Substituted Imidazoles in Aqueous Solvent

Cited by 168 publications

References 63 publications

Calculation of the Solvation Free Energy of the Proton in Methanol

Calculation of the Solvation Free Energy of the Proton in Methanol

Study of 7-Methylguanine on pK_aValues by Using Density Functional Theoretical Method

Molecular Theories and Simulation of Ions and Polar Molecules in Water

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Calculation of Absolute and Relative Acidities of Substituted Imidazoles in Aqueous Solvent

Cited by 168 publications

References 63 publications

Calculation of the Solvation Free Energy of the Proton in Methanol

Calculation of the Solvation Free Energy of the Proton in Methanol

Study of 7-Methylguanine on pKaValues by Using Density Functional Theoretical Method

Molecular Theories and Simulation of Ions and Polar Molecules in Water

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Study of 7-Methylguanine on pK_aValues by Using Density Functional Theoretical Method