The electrostatic response of water to neutral polar solutes: implications for continuum solvent modeling.
Ontology highlight
ABSTRACT:
SUBMITTER: Muddana HS
PROVIDER: S-EPMC3695974 | biostudies-other | 2013 Jun
REPOSITORIES: biostudies-other
Similar Datasets
Project description:The solvent-composition dependence of quenching triplet states of benzophenone (3BP) by anisole in acetonitrile-water (ACN-H2O) mixtures was investigated by laser flash photolysis over the water mole fraction (xw) increasing from 0 to 0.92. Single exponential decay of 3BP was observed over the whole composition range. The quenching rate constant consistently increased with the water content but increased far more rapidly with xw > 0.7. The water-triggered electron-transfer (ET) mechanism was confirmed by a steeply growing quantum yield of the benzophenone ketyl radical anion, escaping back-ET when the partial water volume exceeded the acetonitrile one. The water-content influence on the 3BP quenching rate was described by a kinetic model accounting for the microheterogeneous structure of the ACN-H2O mixtures and the very different solubility of the reactants in the solvent components. According to the model, the ET mechanism occurs at a rate constant of 1.46 × 109 M-1 s-1 and is presumably assisted by the ACN-H2O hydrogen-bonding interaction.
| S-EPMC7590979 | biostudies-literature
Project description:In this work, a simple two-parameters correlation based on the Rice and Gray, Lennard-Jones, and Stockmayer theories was devised for the calculation of binary diffusion coefficients (D12) of any type of solutes at infinite dilution in polar and non-polar solvents. This equation can be relevant for systems with polar solvents, since most models in the literature fail when strong intermolecular forces predominate in solution. The new correlation embodies the Stockmayer potential without requiring the dipole moments of any component, which significantly enlarges its application. It was validated with the largest D12 database of polar and non-polar dense systems, with 8812 data points (NDP) spanning 553 systems, of which 133 have water as solvent (NDP = 1266), 89 contain polar solvents excluding water (NDP = 1405), 177 have supercritical carbon dioxide (SC-CO2) as solvent (NDP = 5028), and 154 have non-polar or weakly polar solvents excluding SC-CO2 (NDP = 1113). Overall, the model achieved an average deviation of only 3.43%, with accurate and unbiased behavior even for polar systems.
| S-EPMC9502877 | biostudies-literature
Project description:In this study, the anion-binding bis(cyclopeptide) 2 is introduced, which dissolves freely in water, affording up to 10 mM concentrations, thanks to triethylene glycol-derived substituents in the cyclopeptide subunits and the linker connecting them. Binding studies provided evidence that the anion affinity previously demonstrated for less-soluble analogs of this compound is retained under highly competitive aqueous conditions. The highest affinity in water was observed for iodide, closely followed by sulfate anions, whereas binding of soft and weakly coordinating anions could not be observed. The anion selectivity of 2 thus differs from that of other recently described receptors, which also do not require electrostatic or coordinative interactions for anion binding in water but typically fail to bind strongly coordinating sulfate anions. The ability of 2 to overcome sulfate hydration is attributed to the special mode of binding, combining direct N-H···A- interactions with the release of water molecules from the receptor cavity. The characterization of the anion binding of 2 and a related bis(cyclopeptide) in a variety of different solvents and aqueous solvent mixtures furthermore allowed the correlation of the binding properties with solvent parameters. These analyses provided qualitative and even quantitative insights into the solvent properties and solvation phenomena that mainly affect anion complexation.
| S-EPMC6641638 | biostudies-literature
Project description:Due to the importance of water in chemical and biological systems, a coarse-grained representation of the solvent can greatly simplify the description of the system while retaining key thermodynamic properties of the medium. A multiscale solvation model that couples all-atom solutes and polarizable Martini coarse-grained water (AAX/CGS) is developed to reproduce free energies of hydration of organic solutes. Using Monte Carlo/free energy perturbation (MC/FEP) calculations, results from multiscale and all-atom simulations are compared. Improved accuracy is obtained with the AAX/CGS approach for hydrophobic and sulfur- or halogen-containing solutes, but larger deviations are found for polar solute molecules where hydrogen bonding is featured. Furthermore, solvent effects on conformational and tautomeric equilibria of AA solutes were investigated using AA, CG, and GB/SA solvent models. It is found that the CG solvent model can reproduce well the medium effects from experiment and AA simulations; however, the GB/SA solvent model fails in some cases. A 7-30-fold reduction in computational cost is found for the present AAX/CGS multiscale simulations compared to the AA alternative.
| S-EPMC5816953 | biostudies-other
Project description:Modeling the change in the electrostatics of organic molecules upon moving from vacuum into solvent, due to polarization, has long been an interesting problem. In vacuum, experimental values for the dipole moments and polarizabilities of small, rigid molecules are known to high accuracy; however, it has generally been difficult to determine these quantities for a polar molecule in water. A theoretical approach introduced by Onsager [J. Am. Chem. Soc. 58, 1486 (1936)] used vacuum properties of small molecules, including polarizability, dipole moment, and size, to predict experimentally known permittivities of neat liquids via the Poisson equation. Since this important advance in understanding the condensed phase, a large number of computational methods have been developed to study solutes embedded in a continuum via numerical solutions to the Poisson-Boltzmann equation. Only recently have the classical force fields used for studying biomolecules begun to include explicit polarization in their functional forms. Here the authors describe the theory underlying a newly developed polarizable multipole Poisson-Boltzmann (PMPB) continuum electrostatics model, which builds on the atomic multipole optimized energetics for biomolecular applications (AMOEBA) force field. As an application of the PMPB methodology, results are presented for several small folded proteins studied by molecular dynamics in explicit water as well as embedded in the PMPB continuum. The dipole moment of each protein increased on average by a factor of 1.27 in explicit AMOEBA water and 1.26 in continuum solvent. The essentially identical electrostatic response in both models suggests that PMPB electrostatics offers an efficient alternative to sampling explicit solvent molecules for a variety of interesting applications, including binding energies, conformational analysis, and pK(a) prediction. Introduction of 150 mM salt lowered the electrostatic solvation energy between 2 and 13 kcalmole, depending on the formal charge of the protein, but had only a small influence on dipole moments.
| S-EPMC2430168 | biostudies-literature
Project description:The generalized Born (GB) model of continuum electrostatics is an analytic approximation to the Poisson equation useful for predicting the electrostatic component of the solvation free energy for solutes ranging in size from small organic molecules to large macromolecular complexes. This work presents a new continuum electrostatics model based on Kirkwood's analytic result for the electrostatic component of the solvation free energy for a solute with arbitrary charge distribution. Unlike GB, which is limited to monopoles, our generalized Kirkwood (GK) model can treat solute electrostatics represented by any combination of permanent and induced atomic multipole moments of arbitrary degree. Here we apply the GK model to the newly developed Atomic Multipole Optimized Energetics for Biomolecular Applications (AMOEBA) force field, which includes permanent atomic multipoles through the quadrupole and treats polarization via induced dipoles. A derivation of the GK gradient is presented, which enables energy minimization or molecular dynamics of an AMOEBA solute within a GK continuum. For a series of 55 proteins, GK electrostatic solvation free energies are compared to the Polarizable Multipole Poisson-Boltzmann (PMPB) model and yield a mean unsigned relative difference of 0.9%. Additionally, the reaction field of GK compares well to that of the PMPB model, as shown by a mean unsigned relative difference of 2.7% in predicting the total solvated dipole moment for each protein in this test set. The CPU time needed for GK relative to vacuum AMOEBA calculations is approximately a factor of 3, making it suitable for applications that require significant sampling of configuration space.
| S-EPMC4767294 | biostudies-literature
Project description:Previous work describes a computational solvation model called semi-explicit assembly (SEA). The SEA water model computes the free energies of solvation of nonpolar and polar solutes in water with good efficiency and accuracy. However, SEA gives systematic errors in the solvation free energies of ions and charged solutes. Here, we describe field-SEA, an improved treatment that gives accurate solvation free energies of charged solutes, including monatomic and polyatomic ions and model dipeptides, as well as nonpolar and polar molecules. Field-SEA is computationally inexpensive for a given solute because explicit-solvent model simulations are relegated to a precomputation step and because it represents solvating waters in terms of a solute's free-energy field. In essence, field-SEA approximates the physics of explicit-model simulations within a computationally efficient framework. A key finding is that an atom's solvation shell inherits characteristics of a neighboring atom, especially strongly charged neighbors. Field-SEA may be useful where there is a need for solvation free-energy computations that are faster than explicit-solvent simulations and more accurate than traditional implicit-solvent simulations for a wide range of solutes.
| S-EPMC4065164 | biostudies-literature
Project description:We study the solvation of polar molecules in water. The center of water's dipole moment is offset from its steric center. In common water models, the Lennard-Jones center is closer to the negatively charged oxygen than to the positively charged hydrogens. This asymmetry of water's charge sites leads to different hydration free energies of positive versus negative ions of the same size. Here, we explore these hydration effects for some hypothetical neutral solutes, and two real solutes, with molecular dynamics simulations using several different water models. We find that, like ions, polar solutes are solvated differently in water depending on the sign of the partial charges. Solutes having a large negative charge balancing diffuse positive charges are preferentially solvated relative to those having a large positive charge balancing diffuse negative charges. Asymmetries in hydration free energies can be as large as 10 kcal/mol for neutral benzene-sized solutes. These asymmetries are mainly enthalpic, arising primarily from the first solvation shell water structure. Such effects are not readily captured by implicit solvent models, which respond symmetrically with respect to charge.
| S-EPMC2745216 | biostudies-other
Project description:The use of oxidoreductases (EC1) in non-conventional reaction media has been increasingly explored. In particular, deep eutectic solvents (DESs) have emerged as a novel class of solvents. Herein, an in-depth study of bioreduction with an alcohol dehydrogenase (ADH) in the DES glyceline is presented. The activity and stability of ADH in mixtures of glyceline/water with varying water contents were measured. Furthermore, the thermodynamic water activity and viscosity of mixtures of glyceline/water have been determined. For a better understanding of the observations, molecular dynamics simulations were performed to quantify the molecular flexibility, hydration layer, and intraprotein hydrogen bonds of ADH. The behavior of the enzyme in DESs follows the classic dependence of water activity (aW ) in non-conventional media. At low aW values (<0.2), ADH does not show any activity; at higher aW values, the activity was still lower than that in pure water due to the high viscosities of the DES. These findings could be further explained by increased enzyme flexibility with increasing water content.
| S-EPMC7154551 | biostudies-literature
Project description:Despite considerable advances in computing power, atomistic simulations under nonperiodic boundary conditions, with Coulombic electrostatic interactions and in systems large enough to reduce finite-size associated errors in thermodynamic quantities to within the thermal energy, are still not affordable. As a result, periodic boundary conditions, systems of microscopic size and effective electrostatic interaction functions are frequently resorted to. Ensuing artifacts in thermodynamic quantities are nowadays routinely corrected a posteriori, but the underlying configurational sampling still descends from spurious forces. The present study addresses this problem through the introduction of on-the-fly corrections to the physical forces during an atomistic molecular dynamics simulation. Two different approaches are suggested, where the force corrections are derived from special potential energy terms. In the first approach, the solvent-generated electrostatic potential sampled at a given atom site is restrained to a target value involving corrections for electrostatic artifacts. In the second approach, the long-range regime of the solvent polarization around a given atom site is restrained to the Born polarization, i.e., the solvent polarization corresponding to the ideal situation of a macroscopic system under nonperiodic boundary conditions and governed by Coulombic electrostatic interactions. The restraints are applied to the explicit-water simulation of a hydrated sodium ion, and the effect of the restraints on the structural and energetic properties of the solvent is illustrated. Furthermore, by means of the calculation of the charging free energy of a hydrated sodium ion, it is shown how the electrostatic potential restraint translates into the on-the-fly consideration of the corresponding free-energy correction terms. It is discussed how the restraints can be generalized to situations involving several solute particles. Although the present study considers a very simple system only, it is an important step toward the on-the-fly elimination of finite-size and approximate-electrostatic artifacts during atomistic molecular dynamics simulations.
| S-EPMC4470580 | biostudies-literature