Changes In Solvation Energy Research Articles

Influence of surfactants in improving degradation of polluting dyes photocatalyzed by TiO2 in aqueous dispersion

The role of tetraalkylammonium bromide surfactants on the TiO2 photocatalyzed degradation of Alizarin, Purpurin and Bromothymol Blue has been studied in air-equilibrated aqueous medium under UV light irradiation. Alizarin has also been investigated by carrying out the photodegradation in TiO2/surfactant dispersions irradiated by natural solar light. Absorption spectral analysis showed that the photodegradation efficiency of the dyes was significantly enhanced by the addition of the cationic surfactants. The effect of pre-micellar, micellar and post-micellar concentrations of the surfactants was analyzed to gain insight into the mechanism of the surfactant-assisted TiO2-photocatalytic degradation of the three dyes. The findings revealed that various parameters, such as initial pH, dye pK’s, type of water and light source exerted their influence on the photocatalytic degradation. The results were explained on the basis of hydrophobic and electrostatic interactions between dye and surfactant/TiO2 in the various forms of aggregation. Density functional theory (DFT) calculations of charge distribution and Gibbs free energy changes of solvation of the species involved were used as a support in rationalizing the surfactant effect on the photodegradation process.

Outer-sphere effects on ligand-field excited-state dynamics: solvent dependence of high-spin to low-spin conversion in [Fe(bpy)3]2.

In condensed phase chemistry, the solvent can have a significant impact on everything from yield to product distribution to mechanism. With regard to photo-induced processes, solvent effects have been well-documented for charge-transfer states wherein the redistribution of charge subsequent to light absorption couples intramolecular dynamics to the local environment of the chromophore. Ligand-field excited states are expected to be largely insensitive to such perturbations given that their electronic rearrangements are localized on the metal center and are therefore insulated from so-called outer-sphere effects by the ligands themselves. In contrast to this expectation, we document herein a nearly two-fold variation in the time constant associated with the 5T2 → 1A1 high-spin to low-spin relaxation process of tris(2,2′-bipyridine)iron(ii) ([Fe(bpy)3]2+) across a range of different solvents. Likely origins for this solvent dependence, including relevant solvent properties, ion pairing, and changes in solvation energy, were considered and assessed by studying [Fe(bpy)3]2+ and related derivatives via ultrafast time-resolved absorption spectroscopy and computational analyses. It was concluded that the effect is most likely associated with the volume change of the chromophore arising from the interconfigurational nature of the 5T2 → 1A1 relaxation process, resulting in changes to the solvent–solvent and/or solvent–solute interactions of the primary solvation shell sufficient to alter the overall reorganization energy of the system and influencing the kinetics of ground-state recovery.

PerMM: A Web Tool and Database for Analysis of Passive Membrane Permeability and Translocation Pathways of Bioactive Molecules.

The PerMM web server and database were developed for quantitative analysis and visualization of passive translocation of bioactive molecules across lipid membranes. The server is the first physics-based web tool that calculates membrane binding energies and permeability coefficients of diverse molecules through artificial and natural membranes (phospholipid bilayers, PAMPA-DS, blood-brain barrier, and Caco-2/MDCK cell membranes). It also visualizes the transmembrane translocation pathway as a sequence of translational and rotational positions of a permeant as it moves across the lipid bilayer, along with the corresponding changes in solvation energy. The server can be applied for prediction of permeability coefficients of compounds with diverse chemical scaffolds to facilitate selection and optimization of potential drug leads. The complementary PerMM database allows comparison of computationally and experimentally determined permeability coefficients for more than 500 compounds in different membrane systems. The website and database are freely accessible at https://permm.phar.umich.edu/ .

Synthesis and experimental/theoretical evaluations on redox potentials and electronic absorption spectra for copper symmetric bis(thiosemicarbazone) complexes

Two new bis(thiosemicarbazone) ligands 2-[1-(2-{3-[2-({2[(methyl)carbothioyl]hydrazono}-methyl)phenoxy]propoxy}phenyl)methylidene]-N1-(methyl)-1-hydrazinecarbothiamide (H2L5), 2-[1-(2-{3-[2-({2-[(methyl)carbothioyl]hydrazono}methyl)phenoxy]-2-hydroxypropoxy}-phenyl)methylidene]-N1-(methyl)-1-hydrazinecarbothiamide (H3L6), and their Cu(II) complexes were synthesized and characterized by physico-chemical and spectroscopic methods. Among eight DFT calculation methods PBE0/6-311+G(d,p)//B3LYP/6-31+G(d) method was the best method to predict one-electron reduction potentials (Ecalc) of these two new and four previously prepared copper complexes in DMF. The effects of solvation in DMF is incorporated as a self-consistent reaction field (SCRF) using the PCM solvent model. This model was capable to predict the experimental results with an error in the range of −0.200 to −0.002 V in comparison with experimental values (Eexp) derived from CV. The changes in solvation energy, ΔΔsolvG°, play important role and without considering the effects of solvation in the calculations, the results are more different from the experimental ones. The calculated one-electron reduction potentials correlated with the energies of both the LUMO of the CuII and the HOMO of the CuI complexes.

Phase transition of carbonate solvent mixture solutions at low temperatures

The phase transition of carbonate solvent mixture solutions consisting of ethylene carbonate (EC), dimethyl carbonate (DMC), ethyl methyl carbonate (EMC), and LiPF6 salt have been studied for improving the low temperature performance of lithium-ion batteries.The Li ion conductivity at 25 °C was maximum at x = 0.3 in a series of 1 M LiPF6 mixed carbonate solvents compositions consisting of ECxDMC0.5−0.5xEMC0.5−0.5x (x = 0 to 0.6), while the maximum tended to shift to x = 0.2 as the temperature lowered. The differential scanning calorimetry results showed that the freezing temperature depressions of EC in the 1 M LiPF6 solution were larger than those of the DMC or EMC. The chemical shift of 7Li nuclear magnetic resonance changed from a constant to increasing at around x = 0.3, which could be reasonably understood by focusing on the change in solvation energy calculated using Born equation. However, in the region of a high EC concentration of over x = 0.3 (EC/LiPF6 > 4) in the 1 M LiPF6 solution, the free EC from the solvation to the lithium ions seems to reduce the freezing temperature depression of the EC, and thus, decreases the ionic conductivity of the solution at low temperatures, due to the EC freezing.

Ion effects at electrode/solid polymer electrolyte membrane interfaces

The differential capacity and the potential distribution at electrode/solid polymer electrolyte membrane/solution interfaces are calculated through an analytical approach. The model considers coions' and counterions' permeation through the membrane from the solvent phase and the ions' partitioning equilibrium at the SPEM/solution interface. The latter effects are included by incorporating the Donnan equilibrium, the steric hindrance, the solvation energy change when ions move from water to membrane pores and ion electrostatic interactions. It is shown that capacitance maxima in capacitance-potential curves may appear because of the acid-base dissociation process inside the membrane and the change in the ions' total interaction energy with the applied potential. For low dielectric constants inside membrane pores, εp, sharp peaks can be obtained. These peaks broaden, decrease in magnitude and shift to positive potentials once εp is increased. Finally, model predictions are discussed in light of recent experimental data obtained on Nafion® covered Pt(111) electrodes, providing a theoretical framework for the qualitative electroanalysis of these systems.

Phenomenological theory of a charged polymer molecule in a nanosized gap between two fluidic reservoirs

We use a simple Born ion continuum model to analyse the effect of solvation energy change on the translocation of a charged linear polymer molecule through a nanosized vapor gap between two fluid reservoirs. As the effective radius of the discretely spaced charges increases, our model predicts a transition from trapping to diffusion of the molecule in the vapor gap. We discuss the applicability of our model to single-stranded DNA translocations in gaps, suggest experiments to validate our prediction and propose immediate applications of this new trapping mechanism for slowing down DNA motion for electronic DNA sequencing.

Semimicroscopic investigation of active site pK a values in peptidylarginine deiminase 4

Peptidylarginine deiminase 4 (PAD4), also known as protein arginine deiminase 4, performs a post-translational deimination that converts arginine to citrulline. The dysregulation of PAD4 has been implicated in a number of diseases, including rheumatoid arthritis (RA) and cancer. This makes PAD4 an important therapeutic target. To develop small-molecule inhibitors as potential treatments, it is advantageous if the catalytic mechanism is well understood. The protonation states of the active site residues, which have long been under controversy, have a direct impact on the catalytic mechanism. Two competing mechanisms are under investigation in the current literature. The first is a reverse protonation mechanism that depends on the active site histidine and cysteine existing as an ion pair. The second is a substrate-assisted mechanism that depends on the active site histidine and cysteine being neutral. This study uses the semimicroscopic protein dipoles Langevin dipoles (PDLD/S) linear response approximation method in the MOLARIS software package to calculate the change in solvation energy of moving the residue from water to the protein interior, and then using that information to assess the protonation states of the active site residues of PAD4. Results from these calculations suggest that in the enzyme–substrate complex of PAD4, the cysteine and histidine are protonated and deprotonated, respectively, and are therefore both neutral, analogous to the proposed protonation states of the active site residues in the Michaelis complex in the substrate-assisted mechanism.

Molecular Simulations of Carbon Dioxide and Water: Cation Solvation

Proposed carbon dioxide sequestration scenarios in sedimentary reservoirs require investigation into the interactions between supercritical carbon dioxide, brines, and the mineral phases found in the basin and overlying caprock. Molecular simulations can help to understand the partitioning of metal cations between aqueous solutions and supercritical carbon dioxide where limited experimental data exist. In this effort, we used classical molecular dynamics simulations to compare the solvation of alkali and alkaline-earth metal cations in water and liquid CO(2) at 300 K by combining a flexible simple point charge model for water and an accurate flexible force field for CO(2). Solvation energies for these cations are larger in water than in carbon dioxide, suggesting that they will partition preferentially into water. In both aqueous and CO(2) solutions, the solvation energies decrease with cation size and increase with cation charge. However, changes in solvation energy with ionic radii are smaller in CO(2) than in water suggesting that the partitioning of cations into CO(2) will increase with ion size. Simulations of the interface between aqueous solution and supercritical CO(2) support this suggestion in that some large cations (e.g., Cs(+) and K(+)) partition into the CO(2) phase, often with a partial solvation sphere of water molecules.

Dissociation constants of 2-azidoethanamines in aqueous solution

Aqueous-phase dissociation constants (Ka) for the conjugate acids of a series of 2-azidoethanamine bases: R1N(R2)CH2CH2N3 (1, R1 = CH3, R2 = H; 2, R1 = CH3, R2 = CH3; 3, R1 = CH2CH3, R2 = CH2CH3; 4, R1/R2 = CH2CH2CH2CH2; 5, R1/R2 = CH2CH2OCH2CH2; 6, R1 = CH2CH3, R2 = CH2CH2N3) were measured and found to fall between those for analogous unfunctionalized and cyano-functionalized ethanamines. To explore the possibility of a relationship existing between the constants and molecular geometry, a theoretically based study was conducted. In it, the Gibbs free energies of aqueous-phase (equilibrium) conformers of the bases and their conjugate acids were determined via a density functional theory/polarizable continuum model method. The results indicate that an attractive interaction between the amine and azide groups that underlies the lowest-energy gas-phase conformer of 2 is negated in an aqueous environment by solvent–solute interactions. The magnitudes of the free energy changes of solvation and −TS (entropic) energies of the conformers of the 2-azidoethanamines and their conjugate acids are observed to correlate with the magnitude of the separation between the conformers' amine and azide groups. However, those correlations are not by themselves sufficient to predict the relative free energies of a molecule's conformers in an aqueous environment. That insufficiency is due to the influence of the correlations being mitigated by three other parameters that arise within the thermodynamic framework employed to compute the observable. The nature of those parameters is discussed. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010

Continuum Solvation Models in the Linear Interaction Energy Method

The linear interaction energy (LIE) method in combination with two different continuum solvent models has been applied to calculate protein-ligand binding free energies for a set of inhibitors against the malarial aspartic protease plasmepsin II. Ligand-water interaction energies are calculated from both Poisson-Boltzmann (PB) and Generalized Born (GB) continuum models using snapshots from explicit solvent simulations of the ligand and protein-ligand complex. These are compared to explicit solvent calculations, and we find close agreement between the explicit water and PB solvation models. The GB model overestimates the change in solvation energy, and this is caused by consistent underestimation of the effective Born radii in the protein-ligand complex. The explicit solvent LIE calculations and LIE-PB, with our standard parametrization, reproduce absolute experimental binding free energies with an average unsigned error of 0.5 and 0.7 kcal/mol, respectively. The LIE-GB method, however, requires a constant offset to approach the same level of accuracy.

Solvation Dynamics of C153 in Supercritical Fluoroform: A Simulation Study Based on Two-Site and Five-Site Models of the Solvent

Molecular dynamics (MD) simulations of a probe solute (coumarin C153) in supercritical fluoroform are used to study time-dependent solute-solvent interactions. We study the dynamics of solvent reorganization in response to electronic excitation of C153 at a temperature of 1.03 T(c) (the critical temperature) and a series of densities above and below the critical density. Simulations of a two-site and five-site models of fluoroform are presented and compared. The time-dependent solvation response after solute electronic excitation is studied in the two cases, and the five-site results present an earlier onset of exponential decay that is closer to what is expected to be the experimental response. This is confirmed by comparison to experiment. In addition to obtaining the solvation response from nonequilibrium MD trajectories, approximate solvation responses were obtained from equilibrium time correlations of the fluctuations in the solvation energy change in the presence of ground- and excited-state solutes. For the five-site model, the equilibrium excited-state response shows stronger density dependence than the ground-state one. The nonequilibrium response appears to have an intermediate decay rate between the two equilibrium functions. The solute-partial-charge-solvent-induced-dipole interaction was also taken into account by means of a perturbative approach, which improved the agreement with experimental measurements available at densities corresponding to 1.4-1.6 rho(c) (where rho(c) the critical density). From the comparison between the two models, it is possible to conclude that an atomistic description is necessary for correctly representing the portion of solvation dynamics that is related to reorientation. This consideration is supported by providing results for orientational time correlation functions and by comparing the correlation times with the experimental ones.

Flexible docking of DNA fragments and actinocin derivatives

We have applied molecular docking methods to systems containing nucleic acids as targets and biologically active substances as ligands. The complexes of DNA fragments and actinocin derivatives with different lengths of aminoalkyl side chains were obtained by molecular docking. It was observed that actinocin derivatives could form energetically favourable complexes with DNA both as intercalators and minor groove binders. It was shown that small changes in the binding energy (∼1 kcal/mol) could result in complexes with substantially different structure. The complexes of actinocin derivatives and DNA fragments were stabilized by hydrogen bonding upon intercalation and minor groove binding. It was found that the change of solvent-accessible surface area upon binding of the actinocin derivative to DNA linear increased with the growth of methylene groups' number in ligand side chains. The solvation energy change upon binding of actinocin derivatives to DNA calculated by the WSAS method was favourable in the case of small uncharged ligands and unfavourable for positively charged ligands.

Realistic Simulations of Proton Transport along the Gramicidin Channel: Demonstrating the Importance of Solvation Effects

The nature of proton transduction (PTR) through a file of water molecules, along the gramicidin A (gA) channel, has long been considered as being highly relevant to PTR in biological systems. Previous attempts to model this process implied that the so-called Grotthuss mechanism and the corresponding orientation of the water file plays a major role. The present work reexamines the PTR in gA by combining a fully microscopic empirical valence bond (EVB) model and a recently developed simplified EVB-based model with Langevin dynamics (LD) simulations. The full model is used first to evaluate the free energy profile for a stepwise PTR process. The corresponding results are then used to construct the effective potential of the simplified EVB. This later model is then used in Langevin dynamics simulations, taking into account the correct physics of possible concerted motions and the effect of the solvent reorganization. The simulations reproduce the observed experimental trend and lead to a picture that is quite different from that assumed previously. It is found that the PTR in gA is controlled by the change in solvation energy of the transferred proton along the channel axis. Although the time dependent electrostatic fluctuations of the channel and water dipoles play their usual role in modulating the proton-transfer process (Proc. Natl. Acad. Sci. U.S.A. 1984, 81, 444), the PTR rate is mainly determined by the free energy profile. Furthermore, the energetics of the reorientation of the unprotonated water file do not appear to provide a consistent way of assessing the activation barrier for the PTR process. It seems to us that in the case of gA, and probably other systems with significant electrostatic barriers for the transfer of the proton charge, the PTR rate is controlled by the electrostatic barrier. This finding has clear consequences with regards to PTR processes in biological systems.

Monte Carlo Simulation Study of a System with a Dielectric Boundary: Application to Calcium Channel Selectivity

Equilibrium Monte Carlo simulations are reported for a model of a biological calcium channel in which the region that includes the channel and the selectivity filter has a different dielectric coefficient than that of the bath. These regions are separated by a sharp dielectric boundary. This simple geometry makes it possible to use the image charge method to incorporate polarization effects. We also include a description of changes in solvation energy that arise when ions move between different dielectrics; we use the Born description of hydration with empirical ionic radii that yield experimental hydration energies. In calculations of Ca2+vs. Na+ selectivity analogous to those of earlier work (Boda et al., Molec. Phys., 100, 2361 (2002)), we find that reducing the dielectric coefficient in the channel to values as low as 10 renders the channel model less calcium selective. Thus, this continuum description of polarization effects does not capture a delicate balance that seems to exist in biological channels between the energy that ions require for dehydration and the energy that ions gain by interaction with the charged groups in the pore.

Is Silica Really an Anomalous Oxide? Surface Acidity and Aqueous Hydrolysis Revisited

The single-site Solvation, Bond Strength, and Electrostatic (SBE) model accounts for the anomalous position of silica onthe surface acidity versus aqueous acidity correlation developed for metal oxides, by considering the solvation energy change in the protonation reaction implemented through the dielectric constant (1/epsilon(k)) and the electrostatic energy change through the Pauling bond strength to bond length ratio (s/r) of the oxide. I address here why inclusion of the solid's dielectric constant brings silica into the same correlation as other oxides like TiO2, Al2O3, and Fe2O3. The solvation and electrostatic contributions are interpreted in terms of classical concepts such as chemical hardness, polarizability, ionicity, electronegativity, and local charge densities. Silica is acidic (PZC < 7), not because of its small dielectric constant, its tetrahedral coordination, or its high bond strength alone. Surface acidity depends largely on high values of the s/r ratio. The dielectric constant of the solid affects acidity mainly by reflecting the nature of water-surface interactions. Solids with large values of epsilon(k) are interpreted as being less polarizable and more ionic so that water, a hard polar solvent, interacts favorably with such surfaces and scales similar to water-water interactions regardless of whether the metal-oxide bond is in the solid or in the aqueous state. For these oxides, pKa(s) = pKa(aq) +/- 1. Silica, with a small dielectric constant, is interpreted as being more polarizable and more covalent so that water-SiO2 interactions scale differently than for the more ionic oxides. Such an interpretation when combined with the Partial Charge Model for metal hydrolysis suggests that the surfaces of RuO2, W03, Sb2O5, and Ta2O5 should be acidic similar to silica. But, unlike silica, they would lie on the pKa correlation defined by the other oxides because of their larger dielectric constants. The mixed oxide, AlPO4, is predicted to behave like silica.

Microscopic formulation of Marcus’ theory of electron transfer

A microscopic theory for the rate of nonadiabatic electron transfer is developed and its relation to classical Marcus theory is analyzed. The focus is on how the nonlinear response of a molecular solvent to a change in the charge distribution of the donor–acceptor pair influences the rate; quantum mechanical and solvent dynamical effects are ignored. Under these restrictions, the rate is determined by the probability density of the energy gap, which is defined as the instantaneous change in solvation energy upon moving an electron from the donor to the acceptor. It is shown how this probability density can be obtained from the free energies of transferring varying amounts of charge between the donor and acceptor (as specified by a charging parameter). A simple algorithm is proposed for calculating these free-energy changes (and hence the energy gap probability density) from computer simulations on just three states: the reactant, the product, and an ‘‘anti’’-product formed by transferring a positive unit charge from the donor to the acceptor. Microscopic generalizations of the Marcus nonequilibrium free-energy surfaces for the reactant and the product, constructed as functions of the charging parameter, are presented. Their relation to surfaces constructed as functions of the energy gap is also established. The Marcus relation (i.e., the activation energy as a parabolic function of the free-energy change of reaction) is derived in a way that clearly shows that it is a good approximation in the normal region even when the solvent response is significantly nonlinear. A simple generalization of this relation, in which the activation energy is given by parabolic functions with different curvatures in the normal and inverted regions, is proposed. These curvatures are inversely proportional to the reorganization energies of the product and the antiproduct, respectively. Computer simulations of a simple model system are performed to illustrate and test these results and procedures.

Characterization of Calcium Lanthanum Oxalate Powders Coprecipitated from Different Binary Solvent Mixtures

White amorphous powders of well-mixed calcium and lanthanum oxalates were prepared by coprecipitation of calcium and lanthanum nitrates with 1M oxalic acid. SEM observation showed particle shapes of cubes, flakes, and agglomerates when water-organic solvent mixtures were employed as the precipitation media. The measured specific surface area and the median particle diameter (D50) ranged between 1.5–76 m2/g and 0.9–14 μm, respectively, as a result of the divergent particle morphology. The morphology changes were attributed to a change of precipitation rate in different solvent mixtures. An attempt was made to explain the rate changes by the solvation energy change of ions which resulted in interfacial energy change within the depositing surface region.

Nonequilibrium computer simulation of a salt solution

A nonequilibrium computer simulation is performed to investigate the relaxation of a realistic polar solvent near a rapidly dissociating ion pair. The time evolution of the reaction coordinate, the ultrashort time scale changes in solvation energy and solvent forces, the local density response, the heating of certain librational degrees of freedom, and the time-dependent polarization are studied during the first 125 fs of the reaction. It is found that the relaxation behaviors in the anionic and cationic shells are very different. On average, the solvation process under study takes about 30-40 fs to break the original cage. After another 50 fs, the solvated ion pair reforms a new metastable structure, which feeds energy back into the reacting system to break the cage further. This procedure is apparently repeated many times until dissociation is complete. The results obtained in this work provide a graphic picture of some of the features of ultrashort dynamics of ionic photodissociation reactions in a polar medium.

A profound solvent effect on the diketopiperazine formation of the new dipeptide angiotensin-converting enzyme inhibitor, Moexipril

The effect of organic solvents on the degradation kinetics, products and mechanisms of Moexipril (1) was investigated at 25°C. Like those observed in aqueous solution, the degradation kinetics leading to the diketopiperazine (2) and hydrolysis product (3) in mixed solvents were found to be pseudo-first-order. Added organic solvent, however, produced a dramatic effect on the rate and product ratio of the degradation. Thus, the hydrolysis process ( k 3) was suppressed in solvents with high organic content. The two water or neutral catalyzed cyclizaation processes ( k 1 and k 2) responsible for the diketopiperazine formation, on the other hand, were enhanced by the addition of organic solvent; a maximum increase of 5.5 and 29-fold for k 1 and k 2, respectively, was observed in 75–90% ethanol solutions. Attempts were made to rationalize such rate enhancement through changes in solvation energy, p K a values of 1 and equilibrium constants of the intermediates with added organics. The application of the results to some of the formulation problems is discussed.