Free Energies of Solvation with Surface, Volume, and Local Electrostatic Effects and Atomic Surface Tensions to Represent the First Solvation Shell

Liu, Junjun; Kelly, Casey P.; Goren, Alan C.; Marenich, Aleksandr V.; Cramer, Christopher J.; Truhlar, Donald G.; Zhan, Chengjun

doi:10.1021/ct100025j

Cited by 54 publications

(87 citation statements)

References 79 publications

(175 reference statements)

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“…Such inconsistencies render many continuum model implementations sensitive to cavity size. 37,38 This hypothesis is in the spirit of newly developed charge-dependent radii models 39,40 and foundations of the model for electrostatic contributions to the free energy of solvation with explicit consideration of both surface and volume polarization effects (SVPE) 38 and other adaptive models. 41,42 Therefore, we have screened all possible models and radii combinations to find some composite solvation models that will be able to predict accurately the difference in Gibbs free solvation energies of neutral and reduced forms.…”

Section: Gibbs Solvation Free Energymentioning

confidence: 99%

Toward robust computational electrochemical predicting the environmental fate of organic pollutants

Sviatenko

Isayev

Gorb³

et al. 2011

J Comput Chem

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A number of density functionals was utilized for the calculation of electron attachment free energy for nitrocompounds, quinones and azacyclic compounds. Different solvation models have been tested on the calculation of difference in free energies of solvation of oxidized and reduced forms of nitrocompounds in aqueous solution, quinones in acetonitrile, and azacyclic compounds in dimethylformamide. Gas-phase free energies evaluated at the mPWB1K/tzvp level and solvation energies obtained using SMD model to compute solvation energies of neutral oxidized forms and PCM(Pauling) to compute solvation energies of anion-radical reduced forms provide reasonable accuracy of the prediction of electron attachment free energy, difference in free solvation energies of oxidized and reduced forms, and as consequence yield reduction potentials in good agreement with experimental data (mean absolute deviation is 0.15 V). It was also found that SMD/M05-2X/tzvp method provides reduction potentials with deviation of 0.12 V from the experimental values but in cases of nitrocompounds and quinones this accuracy is achieved due to the cancelation of errors. To predict reduction ability of naturally occurred iron containing species with respect to organic pollutants we exploited experimental data within the framework of Pourbaix (Eh - pH) diagrams. We conclude that surface-bound Fe(II) as well as certain forms of aqueous Fe(II)aq are capable of reducing a variety of nitroaromatic compounds, quinones and novel high energy materials under basic conditions (pH > 8). At the same time, zero-valent iron is expected to be active under neutral and acidic conditions.

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Section: Gibbs Solvation Free Energymentioning

confidence: 99%

Toward robust computational electrochemical predicting the environmental fate of organic pollutants

Sviatenko

Isayev

Gorb³

et al. 2011

J Comput Chem

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“…For example, the COSMO-RS model 56,57 has been tested for proton exchange and recombination reactions with reasonable accuracy. 58 Other promising approaches are the SMVLE 59 and CMIRS [60][61][62] methods. Essentially, these methods include a term to describe the effect of extremum electric field generated by charged solutes.…”

Section: Resultsmentioning

confidence: 99%

How Accurate is the SMD Model for Predicting Free Energy Barriers for Nucleophilic Substitution Reactions in Polar Protic and Dipolar Aprotic Solvents?

Miguel¹,

Santos²,

Silva³

et al. 2016

Journal of the Brazilian Chemical Society

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In the past seven years, the SMD (Solvent Model Density) method has been widely used by computational chemists. Thus, assessment on the reliability of this model for modeling chemical process in solution is worthwhile. In this report, it was investigated six anion-molecule nucleophilic substitution reactions in methanol and dipolar aprotic solvents. Geometry optimizations have been done at SMD/X3LYP level and single point energy calculations at CCSD(T)/TZVPP + diff level. Our results have indicated that the SMD model is not adequate for dipolar aprotic solvents, with a root of mean squared (RMS) error of 5.6 kcal mol . The classical protic to dipolar aprotic solvent rate acceleration effect was not predicted by the SMD model for the tested systems.Keywords: continuum solvation model, ion solvation, solvent effect, aromatic nucleophilic substitution, M11 functional IntroductionIn the middle of the twentieth century, several experimental studies have led to foundation of empirical rules for qualitative prediction of solvent effects on chemical reactions, authoritatively reviewed by Parker 1 in a classical paper. Nevertheless, a deeper view on solvent effects was only possible with experimental studies of gas phase ion-molecule reactions [2][3][4][5][6] and theoretical modeling of these processes. [7][8][9] It was evident from theoretical studies that solute-solvent interactions can be very strong and produce a profound effect on chemical reactivity. [10][11][12][13][14][15][16][17] On the other hand, gas phase dynamic of chemical reactions can open new mechanistic possibilities. 18,19 Among the different solvents used to conduct ionic chemical reactions, polar protic and dipolar aprotic solvents are paramount due to their property of solubilize ionic species. 20 Methanol is a polar protic solvent and its ability to solvate ions is similar to water. 21,22 In addition, it has the advantage of solubilize many organic molecules not soluble in water. Some usual dipolar aprotic solvents are dimethyl sulfoxide (DMSO), dimethylformamide (DMF) and acetonitrile. Because anions are less solvated in these solvents, anion-molecule reactions are accelerated when transferred from protic to dipolar aprotic solvents. Our ability to describe theoretically this effect is an important goal and a challenge for continuum solvation models once requires these models be able to describe specific solutesolvent interactions. 23 Considering that the Born formula for solvation of a spherical ion of charge q and radius R into a solvent with dielectric constant ε is given by:(1) it could be noted that the use of the same "molecular cavity" for an ionic solute into a protic and dipolar aprotic solvent with high dielectric constant would lead to very similar solvation free energy of ions. A possibility to overcome this problem would be to use different molecular cavity for protic and dipolar aprotic solvents. This approach has reached some successful ten years ago using the polarizable continuum model (PCM) in the study of anion-molecule reaction...

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“…Recent studies have demonstrated reasonable accuracy and excellent agreement with experimentation in many cases. 36,37 ■ ASSOCIATED CONTENT * S Supporting Information Additional information regarding simulation parameters and results are contained in Supplemental Tables 1−7. Table S1 contains standard free energy changes and equilibrium constants of reactions for each of the three TCA cycles.…”

Section: ■ Conclusionmentioning

confidence: 99%

Comparison of Optimal Thermodynamic Models of the Tricarboxylic Acid Cycle from Heterotrophs, Cyanobacteria, and Green Sulfur Bacteria

et al. 2014

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We have applied a new stochastic simulation approach to predict the metabolite levels, material flux, and thermodynamic profiles of the oxidative TCA cycles found in E. coli and Synechococcus sp. PCC 7002, and in the reductive TCA cycle typical of chemolithoautotrophs and phototrophic green sulfur bacteria such as Chlorobaculum tepidum. The simulation approach is based on modeling states using statistical thermodynamics and employs an assumption similar to that used in transition state theory. The ability to evaluate the thermodynamics of metabolic pathways allows one to understand the relationship between coupling of energy and material gradients in the environment and the self-organization of stable biological systems, and it is shown that each cycle operates in the direction expected due to its environmental niche. The simulations predict changes in metabolite levels and flux in response to changes in cofactor concentrations that would be hard to predict without an elaborate model based on the law of mass action. In fact, we show that a thermodynamically unfavorable reaction can still have flux in the forward direction when it is part of a reaction network. The ability to predict metabolite levels, energy flow, and material flux should be significant for understanding the dynamics of natural systems and for understanding principles for engineering organisms for production of specialty chemicals.

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Free Energies of Solvation with Surface, Volume, and Local Electrostatic Effects and Atomic Surface Tensions to Represent the First Solvation Shell

Cited by 54 publications

References 79 publications

Toward robust computational electrochemical predicting the environmental fate of organic pollutants

Toward robust computational electrochemical predicting the environmental fate of organic pollutants

How Accurate is the SMD Model for Predicting Free Energy Barriers for Nucleophilic Substitution Reactions in Polar Protic and Dipolar Aprotic Solvents?

Comparison of Optimal Thermodynamic Models of the Tricarboxylic Acid Cycle from Heterotrophs, Cyanobacteria, and Green Sulfur Bacteria

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