Continuum and discrete calculation of fractional contributions to solvation free energy

Morreale, Antonio; Gelpí, Josep Lluís; Luque, F. Javier; Orozco, Modesto

doi:10.1002/jcc.10323

Cited by 9 publications

(10 citation statements)

References 70 publications

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“…The picrate anion is larger than the other ions studied here and one might expect for larger ions that steric terms represent an important contribution to the total solvation energy [69][70][71]. Results obtained from the inclusion of the steric terms by our Methodology II (see below) support this possibility.…”

Section: Resultssupporting

confidence: 73%

Solvation of monovalent anions in acetonitrile and N,N-dimethylformamide: Parameterization of the IEF-PCM model

2006

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Section: Resultssupporting

confidence: 73%

Solvation of monovalent anions in acetonitrile and N,N-dimethylformamide: Parameterization of the IEF-PCM model

2006

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“…Thus, the largest differences amount to around 0.7 and 0.5 kcal/mol for the fragmental contributions to the solvation in water and in octanol, and to around 0.3 logP units for the partition coefficient. This agreement strongly supports the qualitative value of the fractional contributions derived here, since they do not appear to be very dependent on the arbitrary selection of a given partitioning scheme [30].…”

Section: Compoundsupporting

confidence: 85%

“…Accordinhly, the fractional contribution of a given atom i is determined from the interaction energy between the ele-ments µν associated to the atom i with the whole set of apparent charges spread over the cavity. This approach, which has already been examined by treating the solute charge distribution at the classical level [30], is denoted atom-based partitioning scheme.…”

Section: Partitioning Of the Free Energy Of Solvationmentioning

confidence: 99%

Group contributions to the solvation free energy from MST continuum calculations

Soteras¹,

Morreale²,

López³

et al. 2004

Braz. J. Phys.

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Group contributions to the free energy of solvation in water and octanol as well as to the octanol/water partition coefficient have been determined from Miertus-Scrocco-Tomasi continuum calculations. Particular attention is paid to the influence exerted by the procedure used to carry out the charge normalization in the MST model, as well as to the formalism of the partitioning scheme. A good agreement is found between the group contributions calculated by using different charge normalization and partitioning schemes in a series of structurally related drug-like molecule. Finally, the transferability of the group contributions determined for common chemical fragments along the series of molecules is discussed.

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“…The MD/LRT approach avoids the uncertainties implicit to the partition of the system into solvent and solute regions. Furthermore, Δ G solv can be easily decomposed into group contributions (Morreale et al 2003), which in turn might be used to identify residues that are crucial for the physical properties of proteins or that display unusual solvation, thus unraveling their potential role in molecular recognition and signaling.…”

mentioning

confidence: 99%

“…Recently we have developed an intuitive fractional solvation scheme where is determined from the magnitude of the protein–solvent interaction in the vicinities of residue i . The method can be applied within the continuum SCRF formalism (Luque et al 1995, 2003; Muñoz et al 2002; Morreale et al 2003), and also within discrete MD/LRT calculations (Morreale et al 2005). In this latter case, is computed using a simple expression over the ensemble of structures collected along an equilibrated trajectory of the solvated protein (Equation 4)…”

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confidence: 99%

A fast method for the determination of fractional contributions to solvation in proteins

et al. 2006

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A fast method for the calculation of residue contributions to protein solvation is presented. The approach uses the exposed polar and apolar surface of protein residues and has been parametrized from the fractional contributions to solvation determined from linear response theory coupled to molecular dynamics simulations. Application of the method to a large subset of proteins taken from the Protein Data Bank allowed us to compute the expected fractional solvation of residues. This information is used to discuss when a residue or a group of residues presents an uncommon solvation profile.Keywords: protein solvation; protein structure; molecular dynamics; protein stability Supplemental material: see www.proteinscience.orgThe solvation free energy is the reversible work needed to transfer the solute from the gas phase to solution at constant pressure, temperature, and concentration (Böttcher 1952;Tomasi and Persico 1994;Rivail and Rinaldi 1995;Cramer and Truhlar 1999;Orozco and Luque 2000). From a computational point of view, it is convenient to partition such process into three steps: (1) creation of a solute-shaped cavity in the solvent, (2) switching on the steric properties of the solute inside the cavity, and (3) building up of the charge distribution of the solute. According to this partitioning scheme, the solvation free energy (DG solv ) is determined as the addition of electrostatic (DG ele ), cavitation (DG cav ), and van der Waals (DG vw ) terms (Equation 1), though these two latter contributions are often grouped into the ''steric'' contribution (DG ster ).The experimental determination of DG solv is difficult even for small molecules and impossible for large macromolecules. This has fueled the development of accurate theoretical approaches to calculate DG solv of small and medium molecules in water with an error <1 kcal/mol (see discussion in Tomasi and Persico 1994; Rivail and 9 These authors contributed equally to this work. Reprint requests to: Modesto Orozco, Molecular Modeling and Bioinformatics Unit, Institut de Rercerca Biomèdica, Parc Científic de Barcelona, Josep Samitier 1-5, Barcelona 08028, Spain; e-mail: modesto@mmb.pcb.ub.es; fax: +34-93-4037158.Article published online ahead of print. Article and publication date are at http://www.proteinscience.org/cgi

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Continuum and discrete calculation of fractional contributions to solvation free energy

Cited by 9 publications

References 70 publications

Solvation of monovalent anions in acetonitrile and N,N-dimethylformamide: Parameterization of the IEF-PCM model

Solvation of monovalent anions in acetonitrile and N,N-dimethylformamide: Parameterization of the IEF-PCM model

Group contributions to the solvation free energy from MST continuum calculations

A fast method for the determination of fractional contributions to solvation in proteins

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