Implicit Solvation Models:  Equilibria, Structure, Spectra, and Dynamics

Cramer, Christopher J.; Truhlar, Donald G.

doi:10.1021/cr960149m

Cited by 2,226 publications

(2,127 citation statements)

References 882 publications

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“…As the temperature increased from 273 to 313 K, the k total increased from 2.61 × 10 9 to 7.31 × 10 9 M −1 s −1 . These data are close to the estimated diffusion limit (4 × 10 9 M −1 s −1 ) [39], indicating that MPB could be rapidly degraded by • OH by a diffusion-controlled process within the entire temperature range investigated. In addition, the rate constant of each route also increased with increasing temperature, e.g., the rate constant of R add 1 route increased from 1.97 × 10 9 to 2.51 × 10 9 M −1 s −1 as temperature increased from 273 to 313 K, indicating that increasing temperature can promote • OH-initiated degradation of MPB during AOPs.…”

Section: Initial Reaction Of Mpb With • Ohsupporting

confidence: 84%

Computational consideration on advanced oxidation degradation of phenolic preservative, methylparaben, in water: mechanisms, kinetics, and toxicity assessments

Gao

Fang

et al. 2014

Journal of Hazardous Materials

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Section: Initial Reaction Of Mpb With • Ohsupporting

confidence: 84%

Computational consideration on advanced oxidation degradation of phenolic preservative, methylparaben, in water: mechanisms, kinetics, and toxicity assessments

Gao

Fang

et al. 2014

Journal of Hazardous Materials

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“…The interaction of a molecule with a more complex environment, in particular a solvent, is easily incorporated into the Toy Model using an implicit solvation model [58] such as Kirkwood's equation…”

Section: Discussionmentioning

confidence: 99%

A Graph-Based Toy Model of Chemistry

Benkö

Flamm

Stadler

2003

J. Chem. Inf. Comput. Sci.

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Large scale chemical reaction networks are a ubiquitous phenomenon, from the metabolism of living cells to processes in planetary atmospheres and chemical technology. At least some of these networks exhibit distinctive global features such as the "small world" behavior. The systematic study of such properties, however, suffers from substantial sampling biases in the few networks that are known in detail. A computational model for generating them is therefore required. Here we present a Toy Model that provides a consistent framework in which generic properties of extensive chemical reaction networks can be explored in detail and that at the same time preserves the "look-and-feel" of chemistry: Molecules are represented as labeled graphs, i.e., by their structural formulae; their basic properties are derived by a caricature version of the Extended Hückel MO theory that operates directly on the graphs; chemical reaction mechanisms are implemented as graph rewriting rules acting on the structural formulae; reactivities and selectivities are modeled by a variant of the Frontier Molecular Orbital Theory based on the Extended Hückel scheme. The approach is illustrated for two types of reaction networks: Diels-Alder reactions and the formose reaction implicated in prebiotic sugar synthesis.

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“…For this purpose we have used the selfconsistent reaction field (SCRF) technique [27][28][29][30] in which the statistically averaged effect of the solvent is simulated by representing the medium with appropriate physical properties, such as the dielectric permittivity (ε) and the coefficient of thermal expansion. Dielectric continuum theories [31][32][33][34] are widely used to describe hydration because accurate results are produced at a relatively low computational cost; we have used the Conductor-like Polarizable Continuum…”

Section: Methodsmentioning

confidence: 99%

A Density Functional Theory- and Atoms in Molecules-based Study of NiNTA and NiNTPA Complexes toward Physical Properties Controlling their Stability. A New Method of Computing a Formation Constant

Cukrowski

Govender

2010

Inorg. Chem.

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The log K 1 value of analytical quality was obtained for the NiNTPA complex using the DFTcomputed (at the B3LYP/6-311++G(d,p) level of theory in solvent, CPCM/UAKS) G (aq) values of the lowest energy conformers of the ligands, NTA (nitrilotriacetic acid) and NTPA (nitrilotri-3-propanoic acid), and Ni(II) complexes (NiNTA and NiNTPA). The described mathematical protocol is of general nature. The topological analysis, based on the Quantum Theory of Atoms in Molecules (QTAIM) of Bader, was used to characterize coordination bonds, chelating rings and additional intramolecular interactions in the complexes. The topological data, but not the structural analysis, explained the observed difference in stability of the NiNTA and NiNTPA complexes. It was found that the structural H···H contacts (classically regarded H-clashes, a steric hindrance destabilizing the complex) are in fact the H-H bonds contributing to the overall stability of NiNTPA. Also a CH-O bond was found in NiNTPA. The absence of intramolecular bonds between the atoms that fulfill a distance criterion in NiNTPA is explained by the formation of adjacent intramolecular rings that have larger electron density at the ring critical points when compared with the rings containing these atoms. It is postulated that the strength of a chelating ring (a chelating effect) can be measured by the electron density at the ring critical point. It was found that the strain energy, E s , in the as-in-complex NTPA ligand (E s is significantly lowered by the presence of the intramolecular bonded interactions found by QTAIM) is responsible for the decrease in strength of NiNTPA; the E s ratio (NTPA/NTA) of 1.9 correlates well with the experimental log K 1 ratio (NTA/NTPA) of 1.98.2

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Implicit Solvation Models: Equilibria, Structure, Spectra, and Dynamics

Cited by 2,226 publications

References 882 publications

Computational consideration on advanced oxidation degradation of phenolic preservative, methylparaben, in water: mechanisms, kinetics, and toxicity assessments

Computational consideration on advanced oxidation degradation of phenolic preservative, methylparaben, in water: mechanisms, kinetics, and toxicity assessments

A Graph-Based Toy Model of Chemistry

A Density Functional Theory- and Atoms in Molecules-based Study of NiNTA and NiNTPA Complexes toward Physical Properties Controlling their Stability. A New Method of Computing a Formation Constant

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