Solvent effects in polyelectrolyte adsorption: Computer simulations with explicit and implicit solvent

2010 ◽  
Vol 132 (7) ◽  
pp. 074903 ◽  
Author(s):  
Govardhan Reddy ◽  
Arun Yethiraj
Keyword(s):  
Computer Simulations ◽  
Solvent Effects ◽  
Implicit Solvent ◽  
Polyelectrolyte Adsorption

scholarly journals Conformational study of L-methionine and L-cysteine derivatives through quantum chemical calculations and 3 J HH coupling constant analyses

2017 ◽  
Vol 13 ◽  
pp. 925-937 ◽  
Author(s):  
Weslley G D P Silva ◽  
Carolyne B Braga ◽  
Roberto Rittner
Keyword(s):  
Solvent Effects ◽  
Noncovalent Interactions ◽  
Conformational Stability ◽  
Intramolecular Hydrogen Bonding ◽  
Polarizable Continuum Model ◽  
Coupling Constants ◽  
Implicit Solvent ◽  
Conformational Preferences ◽  
Joint Contribution ◽  
Intramolecular Hydrogen

The understanding of the conformational behavior of amino acids and their derivatives is a challenging task. Here, the conformational analysis of esterified and N-acetylated derivatives of L-methionine and L-cysteine using a combination of 1H NMR and electronic structure calculations is reported. The geometries and energies of the most stable conformers in isolated phase and taking into account the implicit solvent effects, according to the integral equation formalism polarizable continuum model (IEF−PCM), were obtained at the ωB97X-D/aug-cc-pVTZ level. The conformational preferences of the compounds in solution were also determined from experimental and theoretical 3 J HH coupling constants analysis in different aprotic solvents. The results showed that the conformational stability of the esterified derivatives is not very sensitive to solvent effects, whereas the conformational equilibrium of the N-acetylated derivatives changes in the presence of solvent. According to the natural bond orbital (NBO), quantum theory of atoms in molecules (QTAIM) and noncovalent interactions (NCI) methodologies, the conformational preferences for the compounds are not dictated by intramolecular hydrogen bonding, but by a joint contribution of hyperconjugative and steric effects.

scholarly journals Implicit solvent effects in the determination of Brønsted–Evans–Polanyi relationships for heterogeneously catalyzed reactions

2019 ◽  
Vol 21 (32) ◽  
pp. 17687-17695 ◽  
Author(s):  
José R. B. Gomes ◽  
Francesc Viñes ◽  
Francesc Illas ◽  
José L. C. Fajín
Keyword(s):  
Solvent Effects ◽  
Water Dissociation ◽  
Implicit Solvent ◽  
Dissociation Reaction ◽  
Catalyzed Reactions

The Brønsted–Evans–Polanyi relationship derived for the water dissociation reaction within an implicit solvent approach is similar to that without such effects.

scholarly journals Short solvent model for ion correlations and hydrophobic association

2020 ◽  
Vol 117 (3) ◽  
pp. 1293-1302 ◽  
Author(s):  
Ang Gao ◽  
Richard C. Remsing ◽  
John D. Weeks
Keyword(s):  
Computer Simulations ◽  
Potential Of Mean Force ◽  
Implicit Solvent ◽  
Coulomb Interactions ◽  
Solvent Models ◽  
Solvent Model ◽  
Dilute Aqueous Solutions ◽  
Hydrophobic Solutes ◽  
Local Molecular Field Theory ◽  
Implicit Solvent Models

Coulomb interactions play a major role in determining the thermodynamics, structure, and dynamics of condensed-phase systems, but often present significant challenges. Computer simulations usually use periodic boundary conditions to minimize corrections from finite cell boundaries but the long range of the Coulomb interactions generates significant contributions from distant periodic images of the simulation cell, usually calculated by Ewald sum techniques. This can add significant overhead to computer simulations and hampers the development of intuitive local pictures and simple analytic theory. In this paper, we present a general framework based on local molecular field theory to accurately determine the contributions from long-ranged Coulomb interactions to the potential of mean force between ionic or apolar hydrophobic solutes in dilute aqueous solutions described by standard classical point charge water models. The simplest approximation leads to a short solvent (SS) model, with truncated solvent–solvent and solute–solvent Coulomb interactions and long-ranged but screened Coulomb interactions only between charged solutes. The SS model accurately describes the interplay between strong short-ranged solute core interactions, local hydrogen-bond configurations, and long-ranged dielectric screening of distant charges, competing effects that are difficult to capture in standard implicit solvent models.

scholarly journals Comparing state-of-the-art approaches to back-calculate SAXS spectra from atomistic molecular dynamics simulations

2021 ◽  
Vol 94 (9) ◽  
Author(s):  
Mattia Bernetti ◽  
Giovanni Bussi
Keyword(s):  
Molecular Dynamics ◽  
Solvent Effects ◽  
Conformational Dynamics ◽  
Md Simulations ◽  
Implicit Solvent ◽  
Remarkable Effect ◽  
Rna Molecules ◽  
Reaction Coordinates ◽  
Effective Instrument ◽  
Dynamics Simulations

Abstract Small-angle X-ray scattering (SAXS) experiments are arising as an effective instrument in the structural characterization of biomolecules in solution. However, they suffer from limited resolution, and complementing them with molecular dynamics (MD) simulations can be a successful strategy to obtain information at a finer scale. To this end, tools that allow computing SAXS spectra from MD-sampled structures have been designed over the years, mainly differing in how the solvent contribution is accounted for. In this context, RNA molecules represent a particularly challenging case, as they can have a remarkable effect on the surrounding solvent. Herein, we provide a comparison of SAXS spectra computed through different available software packages for a prototypical RNA system. RNA conformational dynamics is intentionally neglected so as to focus on solvent effects. The results highlight that solvent effects are important also at relatively low scattering vector, suggesting that approaches explicitly modeling solvent contribution are advisable when comparing with experimental data, while more efficient implicit-solvent methods can be a better choice as reaction coordinates to improve MD sampling on-the-fly. Graphic abstract

Novel keto–enol tautomerism in 1,3,5-trihydroxybenzene systems

2020 ◽  
Vol 56 (85) ◽  
pp. 12985-12988
Author(s):  
Makabodee Ruaysap ◽  
Stuart R. Kennedy ◽  
Collin M. Mayhan ◽  
Steven P. Kelley ◽  
Harshita Kumari ◽  
...  
Keyword(s):  
Solvent Effects ◽  
Lanthanide Complexes ◽  
Water Soluble ◽  
Implicit Solvent ◽  
Tautomeric Forms ◽  
New Synthesis ◽  
Water Soluble Compound ◽  
Soluble Compound

We report a new synthesis of the water-soluble compound 1,3,5-trihydroxy-2,4,6-trimethylsulfonic acid (1), which exists in two tautomeric forms (60 : 40::enol%:keto%), and its lanthanide complexes. Relative tautomer stability is influenced by intramolecular H-bonding and competing implicit solvent effects.

Investigation of solvent effects on pericyclic reactions by computer simulations

1994 ◽  
Vol 90 (12) ◽  
pp. 1727 ◽  
Author(s):  
William L. Jorgensen ◽  
James F. Blake ◽  
Dongchul Lim ◽  
Daniel L. Severance
Keyword(s):  
Computer Simulations ◽  
Solvent Effects ◽  
Pericyclic Reactions
Sign in / Sign up

Export Citation Format

Share Document