scholarly journals Hydrophobic association and solvation of neopentane in Urea, TMAO and Urea-TMAO solution

2021 ◽  
Author(s):  
Timir Hajari ◽  
Mayank Dixit ◽  
Hari O. S. Yadav
Keyword(s):  
Interaction Energy ◽  
Force Fields ◽  
Water Solution ◽  
Pure Water ◽  
Hydrophobic Association ◽  
Urea Solution ◽  
Detailed Knowledge ◽  
Cavity Formation ◽  
Neat Water ◽  
Dynamics Simulations

A detailed knowledge on hydrophobic association and solvation is crucial in understanding the con-formational stability of proteins and polymers in osmolyte solutions. Using Molecular Dynamics simulations, we found the hydrophobic association using neopentane molecules is greater in mixed urea-TMAO-water solution in comparison to that in 8 M urea solution, in 4 M TMAO solution and in neat water. The neopentane association in urea solution is greater than that in TMAO solution or neat water. We find the association is even less in TMAO solution than pure water. From free ener-gy calculations, it is revealed that the neopentane sized cavity creation in mixed urea-TMAO-water is most unfavorable and that causes the highest hydrophobic association. The cavity formation in urea solution is either more unfavorable or comparable to that in TMAO solution. Importantly, it is found that the population of neopentane-neopentane contact pair and the free energy contribution for cavity formation step in TMAO solution are very sensitive towards the choice of TMAO force-fields. A careful construction of TMAO force-fields is important for studying hydrophobic associa-tion. Interestingly it is observed that the total solute-solvent dispersion interaction energy contribu-tion is always most favorable in mixed urea-TMAO-water. The magnitude of this interaction energy is greater in urea solution relative to TMAO solution for two different force-fields of TMAO, whereas the lowest value is obtained in pure water. It is revealed that the extent of the overall hy-drophobic association in osmolyte solutions is mainly governed by the cavity creation step and it nullifies the contribution comes from the solute-solvent interaction contribution.

scholarly journals Role of the Counterions in the Surface Tension of Aqueous Surfactant Solutions. A Computer Simulation Study of Alkali Dodecyl Sulfate Systems

2020 ◽  
Vol 4 (2) ◽  
pp. 15 ◽  
Author(s):  
György Hantal ◽  
Marcello Sega ◽  
George Horvai ◽  
Pál Jedlovszky
Keyword(s):  
Surface Tension ◽  
Force Fields ◽  
Surface Concentration ◽  
Pressure Profile ◽  
Water Model ◽  
Model Combination ◽  
Neat Water ◽  
Surfactant Solutions ◽  
Dodecyl Sulfate ◽  
Dynamics Simulations

We have investigated the surface tension contributions of the counterions, surfactant headgroups and tails, and water molecules in aqueous alkali dodecyl sulfate (DS) solutions close to the saturated surface concentration by analyzing the lateral pressure profile contribution of these components using molecular dynamics simulations. For this purpose, we have used the combination of two popular force fields, namely KBFF for the counterions and GROMOS96 for the surfactant, which are both parameterized for the SPC/E water model. Except for the system containing Na+ counterions, the surface tension of the surfactant solutions has turned out to be larger rather than smaller than that of neat water, showing a severe shortcoming of the combination of the two force fields. We have traced back this failure of the potential model combination to the unphysically strong attraction of the KBFF counterions, except for Na+, to the anionic head of the surfactants. Despite this failure of the model, we have observed a clear relation between the soft/hard character (in the sense of the Hofmeister series) and the surface tension contribution of the counterions, which, given the above limitations of the model, can only be regarded as an indicative result. We emphasize that the obtained results, although in a twisted way, clearly stress the crucial role the counterions of ionic surfactants play in determining the surface tension of the aqueous surfactant solutions.

Association of Graft Copolymers of Alkyl Methacrylates with α-Methyl-ω-hydroxy-poly(oxyethylene) ethacrylates

1995 ◽  
Vol 60 (11) ◽  
pp. 1971-1985 ◽  
Author(s):  
Čestmír Koňák ◽  
Zdeněk Tuzar ◽  
Pavla Kopečková ◽  
Joseph D. Andrade ◽  
Jindřich Kopeček
Keyword(s):  
Light Scattering ◽  
Graft Copolymers ◽  
Water Solution ◽  
Pure Water ◽  
Solution Properties ◽  
Monomer Composition ◽  
Special Procedure ◽  
Methyl Cellosolve ◽  
Hexyl Methacrylate ◽  
Alkyl Methacrylates

Solution properties of the statistical copolymers of alkyl methacrylates (AMA) with α-methyl-ω-hydroxy-poly(oxyethylene) methacrylates (MPOEMA) (nonionic polysoaps) were studied using static and dynamic ligh scattering as a function of monomer composition and concentration in aqueous and methyl cellosolve solutions. The solubility of the copolymers in water was found to be dependent on molar contant of AMA. While copolymers with low content of hexyl methacrylate (HMA) (0 and 20 mole %) were directly soluble in water, forming true solutions with a low content of large swollen aggregates, copolymers with a higher content of HMA or lauryl methacrylate (LMA) were not directly dispersable in water. A special procedure, the stepwise dialysis from methyl cellosolve solutions against water, had to be used to prepare them in the pseudomicellar form. The copolymers were directly soluble in methyl cellosolve and its water solution containing up to 60 vol.% of water. Nevertheless, the light scattering experiments were dominated by light scattering of swollen particles of aggregated copolymer molecules. The copolymers were not soluble in the mixtures containing 70-100 vol.% of water. Paramaters of aggregates in the mixture with 60 vol.% of water and in pure water were found to be very similar.

scholarly journals Behavior and properties of water in silicate melts under deep mantle conditions

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Bijaya B. Karki ◽  
Dipta B. Ghosh ◽  
Shun-ichiro Karato
Keyword(s):  
Electrical Conductivity ◽  
Molar Volume ◽  
Water Solution ◽  
Pure Water ◽  
Electrical Conductance ◽  
Water Structure ◽  
Bulk Water ◽  
Silicate Melts ◽  
Pressure Regime ◽  
Low Pressures

AbstractWater (H2O) as one of the most abundant fluids present in Earth plays crucial role in the generation and transport of magmas in the interior. Though hydrous silicate melts have been studied extensively, the experimental data are confined to relatively low pressures and the computational results are still rare. Moreover, these studies imply large differences in the way water influences the physical properties of silicate magmas, such as density and electrical conductivity. Here, we investigate the equation of state, speciation, and transport properties of water dissolved in Mg1−xFexSiO3 and Mg2(1−x)Fe2xSiO4 melts (for x = 0 and 0.25) as well as in its bulk (pure) fluid state over the entire mantle pressure regime at 2000–4000 K using first-principles molecular dynamics. The simulation results allow us to constrain the partial molar volume of the water component in melts along with the molar volume of pure water. The predicted volume of silicate melt + water solution is negative at low pressures and becomes almost zero above 15 GPa. Consequently, the hydrous component tends to lower the melt density to similar extent over much of the mantle pressure regime irrespective of composition. Our results also show that hydrogen diffuses fast in silicate melts and enhances the melt electrical conductivity in a way that differs from electrical conduction in the bulk water. The speciation of the water component varies considerably from the bulk water structure as well. Water is dissolved in melts mostly as hydroxyls at low pressure and as –O–H–O–, –O–H–O–H– and other extended species with increasing pressure. On the other hand, the pure water behaves as a molecular fluid below 15 GPa, gradually becoming a dissociated fluid with further compression. On the basis of modeled density and conductivity results, we suggest that partial melts containing a few percent of water may be gravitationally trapped both above and below the upper mantle-transition region. Moreover, such hydrous melts can give rise to detectable electrical conductance by means of electromagnetic sounding observations.

scholarly journals Testing for ion-mediated enhancement of the hydraulic conductance of the leaf xylem in diverse angiosperms

2017 ◽  
Vol 4 ◽  
pp. e004 ◽  
Author(s):  
Christine Scoffoni ◽  
Grace John ◽  
Herve Cochard ◽  
Lawren Sack
Keyword(s):  
Water Solution ◽  
Pure Water ◽  
Xylem Sap ◽  
Hydraulic Conductance ◽  
Membrane Pores ◽  
Whole Plant ◽  
Pit Membrane ◽  
Major Bottleneck ◽  
The Difference ◽  
Xylem Conduits

Replacing ultra-pure water solution with ion solution closer to the composition of natural xylem sap increases stem hydraulic conductance by up to 58%, likely due to changes in electroviscosity in the pit membrane pores. This effect has been proposed to contribute to the control of plant hydraulic and stomatal conductance and potentially to influence on carbon balance during dehydration. However, this effect has never been directly tested for leaf xylem, which constitutes a major bottleneck in the whole plant. We tested for an ion-mediated increase in the hydraulic conductance of the leaf xylem (Kx) for seven species diverse in phylogeny and drought tolerance. Across species, no significant changes in Kx were observed between 0 and 15 mM KCl. We further tested for an effect of ion solution during measurements of Kx vulnerability to dehydration in Quercus agrifolia and found no significant impact. These results for leaf xylem contrast with the often strong ion effect reported for stems, and we suggest several hypotheses to account for the difference, relating to the structure of xylem conduits across vein orders, and the ultrastructure of leaf xylem pores. A negligible ion response in leaves would weaken xylem sap ion-mediated control of plant hydraulic conductance, facilitating modeling of whole plant hydraulic behavior and its influence on productivity.

scholarly journals A universal framework for featurization of atomistic systems

2021 ◽  
Author(s):  
Xiangyun Lei ◽  
Andrew Medford
Keyword(s):  
Machine Learning ◽  
Molecular Dynamics ◽  
Force Fields ◽  
Reactive Systems ◽  
Quantum Molecular Dynamics ◽  
Learning Models ◽  
Fixed Dimension ◽  
Comparable Performance ◽  
Invaluable Tool ◽  
Dynamics Simulations

Abstract Molecular dynamics simulations are an invaluable tool in numerous scientific fields. However, the ubiquitous classical force fields cannot describe reactive systems, and quantum molecular dynamics are too computationally demanding to treat large systems or long timescales. Reactive force fields based on physics or machine learning can be used to bridge the gap in time and length scales, but these force fields require substantial effort to construct and are highly specific to a given chemical composition and application. A significant limitation of machine learning models is the use of element-specific features, leading to models that scale poorly with the number of elements. This work introduces the Gaussian multipole (GMP) featurization scheme that utilizes physically-relevant multipole expansions of the electron density around atoms to yield feature vectors that interpolate between element types and have a fixed dimension regardless of the number of elements present. We combine GMP with neural networks to directly compare it to the widely used Behler-Parinello symmetry functions for the MD17 dataset, revealing that it exhibits improved accuracy and computational efficiency. Further, we demonstrate that GMP-based models can achieve chemical accuracy for the QM9 dataset, and their accuracy remains reasonable even when extrapolating to new elements. Finally, we test GMP-based models for the Open Catalysis Project (OCP) dataset, revealing comparable performance to graph convolutional deep learning models. The results indicate that this featurization scheme fills a critical gap in the construction of efficient and transferable machine-learned force fields.

scholarly journals The Role of Electrostatics in Enzymes: Do Biomolecular Force Fields Reflect Protein Electric Fields?

2020 ◽  
Author(s):  
Richard T Bradshaw ◽  
Jacek Dziedzic ◽  
Chris-Kriton Skylaris ◽  
Jonathan W. Essex
Keyword(s):  
Electric Fields ◽  
Active Sites ◽  
Catalytic Mechanism ◽  
Force Fields ◽  
Prolyl Isomerase ◽  
Peptidyl Prolyl Isomerase ◽  
Polarizable Force Field ◽  
Polarizable Force Fields ◽  
Protein Active Sites ◽  
Dynamics Simulations

<div><div><div><p>Preorganization of large, directionally oriented, electric fields inside protein active sites has been proposed as a crucial contributor to catalytic mechanism in many enzymes, and may be efficiently investigated at the atomistic level with molecular dynamics simulations. Here we evaluate the ability of the AMOEBA polarizable force field, as well as the additive Amber ff14SB and Charmm C36m models, to describe the electric fields present inside the active site of the peptidyl-prolyl isomerase cyclophilin A. We compare the molecular mechanical electric fields to those calculated with a fully first principles quantum mechanical (QM) representation of the protein, solvent, and ions, and find that AMOEBA consistently shows far greater correlation with the QM electric fields than either of the additive force fields tested. Catalytically-relevant fields calculated with AMOEBA were typically smaller than those observed with additive potentials, but were generally consistent with an electrostatically-driven mechanism for catalysis. Our results highlight the accuracy and the potential advantages of using polarizable force fields in systems where accurate electrostatics may be crucial for providing mechanistic insights.</p></div></div></div>

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