Theoretical representation of solvent effects in the study of biochemical systems

Orozco, Modesto; Roca, Ramón; Alemán, Carlos; Busquets, Montserrat; López, José María Botana; Luque, F. Javier

doi:10.1016/s0166-1280(96)04529-0

Cited by 17 publications

(10 citation statements)

References 49 publications

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“…The translation of eq. (12) to the classical framework is straightforward,61, 62 as shown in eq. (13), where {Q

_{i}^{0}

} stands for the point charges (typically located at the N ′ nuclei) representing the solute charge distribution in the gas phase and {q

_{j}^{sol}

} denotes the point charges located at surface elements (j=1,… M ) representing the final solvent reaction field.…”

Section: Theoretical Frameworkmentioning

confidence: 99%

“…(13), where {Q

_{i}^{0}

} stands for the point charges (typically located at the N ′ nuclei) representing the solute charge distribution in the gas phase and {q

_{j}^{sol}

} denotes the point charges located at surface elements (j=1,… M ) representing the final solvent reaction field. We previously showed that the best results are obtained when the set {Q

_{i}^{0}

} is determined by fitting to the QM electrostatic potential and field at the solute cavity surface (ESPF charges61–64). However, reasonable results are also obtained by using electrostatic fitted charges (ESP or RESP) identical to those used in force‐field calculations (see below).…”

Section: Theoretical Frameworkmentioning

confidence: 99%

“…The electrostatic contribution to the free energy of hydration was determined using four levels of theory: linear response approach from discrete samplings obtained from MD simulations using nonpolarizable force‐fields (LRT/MD); MST calculations at the QM level using the HF/6‐31G(d)‐optimized model (MST/6‐31G(d)40, 51–54); MST calculations at the QM level using the semiempirical AM1 version of the method (AM1/MST40, 51–54); and classical MST calculations using eq. (14) and RESP charges determined from 6‐31G(d) calculations (MM/MST61, 62, 73). The AM1 gas phase optimized geometries of the drugs were used without further refinement for QM and MM versions of the MST method.…”

Section: Theoretical Frameworkmentioning

confidence: 99%

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Continuum and discrete calculation of fractional contributions to solvation free energy

et al. 2003

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Approaches to compute fractional contributions to the solvation free energy are developed in the context of continuum self consistent reaction field calculations (both classical and quantum mechanical), as well as in the framework of discrete molecular dynamics simulations. It is found that for a series of typical pharmacological drugs there is a good agreement between the different fractional descriptions. Algorithms reported here can be easily applied as molecular descriptors in the context of quantitative structure-activity relationships.

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“…The translation of eq. (12) to the classical framework is straightforward,61, 62 as shown in eq. (13), where {Q

_{i}^{0}

} stands for the point charges (typically located at the N ′ nuclei) representing the solute charge distribution in the gas phase and {q

_{j}^{sol}

} denotes the point charges located at surface elements (j=1,… M ) representing the final solvent reaction field.…”

Section: Theoretical Frameworkmentioning

confidence: 99%

“…(13), where {Q

_{i}^{0}

} stands for the point charges (typically located at the N ′ nuclei) representing the solute charge distribution in the gas phase and {q

_{j}^{sol}

} denotes the point charges located at surface elements (j=1,… M ) representing the final solvent reaction field. We previously showed that the best results are obtained when the set {Q

_{i}^{0}

Section: Theoretical Frameworkmentioning

confidence: 99%

Section: Theoretical Frameworkmentioning

confidence: 99%

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Continuum and discrete calculation of fractional contributions to solvation free energy

et al. 2003

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“…Calculations in aqueous solution were performed by using the parametrization for the united-atom model recently developed in our laboratory. 56 The gas-phase geometries were used in solvation calculations. This is necessary, at least partially, to maintain the restriction of the backbone dihedral angles in order to analyze the helical propensities of the residues and the relative stability between helices.…”

Section: Calculations In Solutionmentioning

confidence: 99%

Helical preferences of alanine, glycine, and aminoisobutyric homopeptides

et al. 1997

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The stability between helical conformations of homopeptides of alanine, glycine, and aminoisobutyric acid has been studied by means of quantum-mechanical methods. The influence of peptide length on the relative stability between helical conformations has also been analyzed by means of systematic studies for peptides of size up to 11 residues. Finally, the influence of the solvent has been examined by using self-consistent reaction field methods. The results provide a detailed picture of the modulation exerted by these factors on the helical preferences of these peptides.

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“…Calculations in aqueous solution were performed by using the parametrization for the united-atom model recently developed by Luque and coworkers. 34 The gas-phase geometries were used in solvation calculations. This is necessary, at least partially, to maintain the restriction of the backbone dihedral angles in order to analyze the relative stability between helices.…”

Section: Solution-phase Calculationsmentioning

confidence: 99%

Chain conformation in polyretropeptides III: Design of a 310 helix using α,α-dialkylated amino acids and retropeptide bonds

Alemán

1997

Proteins

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Computer simulations have been used to design a polypeptide with a 3(10) helix conformation. The study has been been performed taking advantage of the intrinsic helix forming tendency of alpha-Aminoisobutyric acid. In order to avoid the formation of the alpha helix, which is the other common helical conformation adopted by alpha-Aminoisobutyric acid-based peptides, retropeptide bonds have been included in the sequence. Thus, retropeptides are not able to form the intramolecular hydrogen bonding interactions characteristic of the alpha helix. The influences of both the peptide length and the solvent have been examined and compared with those of the polypeptide without retropeptide bonds.

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Theoretical representation of solvent effects in the study of biochemical systems

Cited by 17 publications

References 49 publications

Continuum and discrete calculation of fractional contributions to solvation free energy

Continuum and discrete calculation of fractional contributions to solvation free energy

Helical preferences of alanine, glycine, and aminoisobutyric homopeptides

Chain conformation in polyretropeptides III: Design of a 310 helix using α,α-dialkylated amino acids and retropeptide bonds

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