Effects Of Aqueous Solvation Research Articles

Study of Aqueous Solvent effect and Kinetics in Hydrolysis of Butyle Salicylate in Alkaline Medium of Water and DMF

Study of Aqueous Solvent effect and Kinetics in Hydrolysis of Butyle Salicylate in Alkaline Medium of Water and DMF

Incorporating solvent effects in DFT: insights from cation exchange in faujasites.

Zeolites are versatile materials renowned for their extra-framework cation exchange capabilities, with applications spanning diverse fields, including nuclear waste treatment. While detailed experimental characterization offers valuable insight, density functional theory (DFT) proves particularly adept at investigating ion exchange in zeolites, owing to its atomic and electronic resolution. However, the prevalent occurrence of zeolitic ion exchange in aqueous environments poses a challenge to conventional DFT modeling, traditionally conducted in a vacuum. This study seeks to enhance zeolite modeling by systematically evaluating predictive differences across varying degrees of aqueous solvent inclusion. Specifically focusing on monovalent cation exchange in Na-X zeolites, we explore diverse modeling approaches. These range from simple dehydrated systems (representing bare reference states in vacuum) to more sophisticated models that incorporate aqueous solvent effects through explicit water molecules and/or a dielectric medium. Through comparative analysis of DFT and semi-empirical DFT approaches, along with their validation against experimental results, our findings underscore the necessity to concurrently consider explicit and implicit solvent effects for accurate prediction of zeolitic ionic exchange.

The co-adsorption of sulfate and metal ions on Al-doped graphene: a first principles study.

The co-adsorption of sulfate and metal ions on intrinsic and Al-doped graphene is investigated through first principles calculations. When SO42- ions exist only, both of intrinsic and Al-doped graphene can form stable adsorption configurations with SO42-. However, the presence of Cu2+/Ca2+/Zn2+/Mg2+ ions attenuates the interaction between intrinsic graphene and SO42-, resulting in weak physical adsorption between them, while Al-doped graphene can still constitute co-adsorption chemically with both SO42- and Cu2+/Ca2+/Zn2+/Mg2+ ions simultaneously. The sensitivity of Al-doped graphene towards co-adsorbed ions is in the order of SO42--Cu2+ > SO42--Zn2+ > SO42--Ca2+ > SO42--Mg2+. The research indicates Al-doped graphene could be a promising material for sensing sulfate ions under the presence of various metal ions. All of the calculations were carried out by using a first principles method based on density functional theory (DFT). The generalized gradient approximation (GGA) with the Perdew-Burke-Ernzerhof (PBE) functional was selected to describe electron exchange-correlation energy. The double numerical plus polarization (DNP) was employed as the basis set. The conductor-like screening model (COSMO) was implemented to simulate the aqueous solvent effect.

A high-level quantum chemical study of the thermodynamics associated with chlorine transfer between N-chlorinated nucleobases

The relative free energies of the isomers formed upon N-chlorination of each nitrogen atom within the DNA nucleobases (adenine, guanine, and thymine) have been obtained using the high-level G4(MP2) composite ab initio method (the free energies of the N-chlorinated isomers of cytosine have been reported at the same level of theory previously). Having identified the lowest energy N-chlorinated derivatives for each nucleobase, we have computed the free energies associated with chlorine transfer from N-chlorinated nucleobases to other unsubstituted bases. Our results provide quantitative support pertaining to the results of previous experimental studies, which demonstrated that rapid chlorine transfer occurs from N-chlorothymidine to cytidine or adenosine. The results of our calculations in the gas-phase reveal that chlorine transfer from N-chlorothymine to either cytosine, adenine, or guanine proceed via exergonic processes with ΔG o values of −50.3 (cytosine), −28.0 (guanine), and −6.7 (adenine) kJ mol–1. Additionally, we consider the effect of aqueous solvation by augmenting our gas-phase G4(MP2) energies with solvation corrections obtained using the conductor-like polarizable continuum model. In aqueous solution, we obtain the following G4(MP2) free energies associated with chlorine transfer from N-chlorothymine to the three other nucleobases: −58.4 (cytosine), −26.4 (adenine), and −18.7 (guanine) kJ mol–1. Therefore, our calculations, whether in the gas phase or in aqueous solution, clearly indicate that chlorine transfer from any of the N-chlorinated nucleobases to cytosine provides a thermodynamic sink for the active chlorine. This thermodynamic preference for chlorine transfer to cytidine may be particularly deleterious since previous experimental studies have shown that nitrogen-centered radical formation (via N–Cl bond homolysis) is more easily achieved in N-chlorinated cytidine than in other N-chlorinated nucleosides.

Theoretical Assessment of Carbon Dioxide Reactivity in Methylpiperidines: A Conformational Investigation.

In this work, the possible mechanisms for the reactions of CO2 with various positional isomers of methylpiperidines (MPs) (N-MP, 2-MP, 3-MP, and 4-MP) including the effect of aqueous solvation have been explored using quantum chemical methods. The major pathways investigated for CO2 capture in aqueous amines are carbamate formation, its hydrolysis, and the bicarbonate formation (CO2 + H2O + MP) reaction. The calculations indicate that an axial orientation for the methyl group and an equatorial for the COO- group could be energetically ideal in the carbamate product of MPs. The proton abstraction step in the carbamate pathway is almost barrierless for the zwitterion-amine route, while a much higher energy barrier is observed for the zwitterion-H2O route. During carbamate hydrolysis, the addition of even two explicit water molecules does not exhibit any notable effect on the already high energy barrier associated with this reaction. This indicates that bicarbonate formation is less likely to occur via carbamate hydrolysis. The calculations suggest that, although the carbamate pathway is kinetically favored, the MP carbamate could still be a minor product, especially for sterically hindered conformations, and the bicarbonate pathway should be predominant in aqueous MPs.

Aqueous solvation study of melatonin using ab initio molecular dynamics

Melatonin is an essential human hormone produced mainly by the pineal gland from the amino acid tryptophan; it has several types of bioactivity, such as regulation of circadian rhythm, antioxidant, and DNA protection. Despite the importance of melatonin in the human body, studies on the interaction of melatonin with water molecules, considered explicitly, are quite limited in the literature. Thus, the present work reports a study on the effects of aqueous solvation on the geometric and electronic parameters of melatonin using Car-Parrinello Molecular Dynamics (CPMD). The CPMD results show that the aqueous solvation of melatonin affects mainly C14-O2 (2.176%), N17-C14 (2.169%), and N16-H21 (1.079%) bond lengths as well as O1-C3-C4 (4.37%) and O1-C3-C8 (4.241%) bond angles. These effects are attributed mainly to the H-bond formation between O1, O2, H21, and H30 melatonin sites and water molecules. The topological analysis of the H-bond electron density shows that the H-bond strength varies from weak to intermediate intensities, except for the O2 site – where it varies from weak to strong. The energetic aspect of the H-bonds was investigated using Helmholtz free energy, and the radial distribution function was employed to assess the mean residence time of the water atoms inside the first shell. The supramolecular arrangement of melatonin in the solid-state was investigated using the Hirshfeld surface technique. These findings deepen the knowledge of melatonin chemistry in the human body and help develop explanations for its biological activities.

Dependency of solvation effects on metal identity in surface reactions

Solvent interactions with adsorbed moieties involved in surface reactions are often believed to be similar for different metal surfaces. However, solvents alter the electronic structures of surface atoms, which in turn affects their interaction with adsorbed moieties. To reveal the importance of metal identity on aqueous solvent effects in heterogeneous catalysis, we studied solvent effects on the activation free energies of the O–H and C–H bond cleavages of ethylene glycol over the (111) facet of six transition metals (Ni, Pd, Pt, Cu, Ag, Au) using an explicit solvation approach based on a hybrid quantum mechanical/molecular mechanical (QM/MM) description of the potential energy surface. A significant metal dependence on aqueous solvation effects was observed that suggests solvation effects must be studied in detail for every reaction system. The main reason for this dependence could be traced back to a different amount of charge-transfer between the adsorbed moieties and metals in the reactant and transition states for the different metal surfaces.

Reconciling Work Functions and Adsorption Enthalpies for Implicit Solvent Models: A Pt (111)/Water Interface Case Study.

Implicit solvent models are a computationally efficient method of representing solid/liquid interfaces prevalent in electrocatalysis, energy storage, and materials science. However, electronic structure changes induced at the metallic surface by the dielectric continuum are not fully understood. To address this, we perform DFT calculations for the Pt(111)/water interface, in order to compare Poisson-Boltzmann continuum solvation methods with ab initio molecular dynamics (AIMD) simulations of explicit solvent. We show that the implicit solvent cavity can be parametrized in terms of the electric dipole moment change at the equilibrated explicit Pt/water interface to obtain the potential of zero charge (PZC). We also compare the accuracy of aqueous enthalpies of adsorption of phenol on Pt(111) using geometry and charge density based dielectric cavitation methods. The ability to parametrize the cavity according to individual atoms, as afforded in the geometry based approach, is key to obtaining accurate enthalpy changes of adsorption under aqueous conditions. We also show that the electronic structure changes induced by explicit solvent and our proposed implicit solvent parametrization scheme yield comparable density difference profiles and d-band projected density of states. We therefore demonstrate the capability of implicit solvent approaches to capture both the energetics of adsorption processes and the main electronic effects of aqueous solvent on the metallic surface. This work therefore provides a scheme for computationally efficient simulations of interfacial processes for applications in areas such as heterogeneous catalysis and electrochemistry.

Understanding alkali metal cation affinities of multi-layer guanine quadruplex DNA.

To gain better understanding of the stabilizing interactions between metal ions and DNA quadruplexes, dispersion-corrected density functional theory (DFT-D) based calculations were performed on double-, triple- and four-layer guanine tetrads interacting with alkali metal cations. All computations were performed in aqueous solution that mimics artificial supramolecular conditions where guanine bases assemble into stacked quartets as well as biological environments in which telomeric quadruplexes are formed. To facilitate the computations on these significant larger systems, optimization of the DFT description was performed first by evaluating the performance of partial reduced basis sets. Analysis of the stabilizing interactions between alkali cations and the DNA bases in double and triple-layer guanine quadruplex DNA reproduced the experimental affinity trend of the order Li+< Rb+ < Na+ < K+. The desolvation and the size of alkali metal cations are thought to be responsible for the order of affinity. Nevertheless, for the alkali metal cation species individually, the magnitude of the bond energy stays equal for binding as first, second or third cation in double, triple and four-layer guanine quadruplexes, respectively. This is the result of an interplay between a decreasingly stabilizing interaction energy and increasingly stabilizing solvation effects, along the consecutive binding events. This diminished interaction energy is the result of destabilizing electrostatic repulsion between the hosted alkali metal cations. This work emphasizes the stabilizing effect of aqueous solvent on large highly charged biomolecules.

High temperature aqueous solvent effect on translational and hydrogen bond dynamics of the hydroxyl radical — MD simulation study

MD simulations using flexible models were performed to show how velocity autocorrelation functions, diffusion (DOH) and self-diffusion (Dw) coefficients, continuous and intermittent lifetimes of H-donor and H-acceptor bonds depend on: i) transformations in the hydrogen-bond network (HBN) of water below the critical point, and ii) decreasing density at the supercritical isotherm (∼670 K). Contrary to simulations neglecting short-range hydrogen-oxygen interactions, we show that complexation of OHaq with H2O is enhanced by breakage of the continuous HBN, resulting in the increase of OHaq hydrodynamic radius and the DOH values smaller than Dw by 30%. Difference between DOH and Dw increases to 65% at 670 K below the critical density. It is explained by enhanced aggregation of water molecules around OHaq, earlier recognized as the self-trapping mechanism. Except near-ambient conditions, the intermittent lifetime of H-bonds is longer than the translational time, indicating that OHaq is complexed with water and moves as a molecular aggregate.

Role of hydrogen bonding in the conformations of lidocaine, mepivacaine and bupivacaine under aqueous solvation

We report the lowest energy conformers obtained by a conformational search for protonated lidocaine, mepivacaine and bupivacaine in the gas phase at the B3LYP/cc-pVTZ level of theory, and examine the effect of aqueous solvation on the energetics using the COSMO continuous solvent model. We also look at the effect of microhydration by crystallization water molecules on the relative energies of the conformers. We found that water molecules and chloride ion stabilize conformers by hydrogen bonding. We report a revised structure for the conformer present in solution for lidocaine hydrochloride.

High Temperature Aqueous Solvent Effect on Stretching Vibrations of the Hydroxyl Radical – MD Simulation Study of Spectral Shifts and Hydrogen Bond Statistics

The effect of water temperature and density on stretching vibrations power spectrum of OHaq was studied from ambient to supercritical conditions by molecular dynamics simulation. Decrease in the height, red-shift of the maximum and broadening of the spectrum were found with increasing temperature and decreasing water density. Decomposition of power spectra into Gaussian bands assigned to the radical monomer and hydrogen-bonded complexes OHaq-(H2O)nHB=1,2,3 showed equal spacing of components and the red-shift relative to the monomer band, linearly increasing with the decreasing number of solvent H-bonds. The radical-water H-bond statistics resulting from band-contribution showed the significant increase in the bond number between 373 and 573 K, associated with breakage of the continuous hydrogen-bond network. At 673 K the degree of hydrogen bonding was significantly controlled by density. We found that the most optimized radical-water complexes were formed when fluid density decreased below the critical value.

Experimental and Theoretical Study of Deprotonation of DNA Adenine Cation Radical

Among all the DNA components, extremely redox-active guanine (G) and adenine (A) bases are subject to facile loss of an electron and form cation radicals (G+· and A+·) when exposed to irradiation or radical oxidants. The subsequent deprotonation of G+· and A+· can invoke DNA damage or interrupt hole transfer in DNA. However, compared with intensive reports for G+·, studies on the deprotonation of A+· are still limited at present. Herein, we investigate the deprotonation behavior of A+· by time-resolved laser flash photolysis. The deprotonation product of A(N6-H)· is observed and the deprotonation rate constant, (2.0±0.1) × 107 s−1, is obtained at room temperature. Further, the deprotonation rate constants of A+· are measured at temperatures varying from 280 K to 300 K, from which the activation energy for the N6-H deprotonation is determined to be (17.1±1.0) kJ/mol by Arrhenius equation. In addition, by incorporating the aqueous solvent effect, we perform density functional theory calculations for A+· deprotonation in free base and in duplex DNA. Together with experimental results, the deprotonation mechanisms of A+· in free base and in duplex DNA are revealed, which are of fundamental importance for understanding the oxidative DNA damage and designing DNA-based electrochemical devices.

Relating DNA base-pairing in aqueous media to DNA polymerase fidelity.

Controversy surrounds the perceived absence of a relationship between DNA polymerase fidelity (kinetic discrimination) and free energy changes determined from DNA melting studies (thermodynamic discrimination). Thermodynamic discrimination together with aqueous solvent effects can account for kinetic fidelities on the order of those observed experimentally.

A high-level G4(MP2) thermochemical study of the relative energies of the N -chlorinated isomers formed upon chlorination of cytosine

Abstract Although the relative energies of the various tautomers of cytosine and 5-chlorocytosine have been studied in detail, little is known about the relative energies of the N -chlorinated isomers of cytosine. N -chlorination of cytosine is known to occur when cytosine is exposed to hypochlorous acid, a potent oxidant that is formed during the inflammatory process, and is presumed to have consequences concerning, for example, the structural integrity of DNA and RNA. In this study, the high-level G4(MP2) thermochemical protocol has been employed in studying the relative gas-phase free energies of thirty isomers that may be formed upon N -chlorination of cytosine. Using free energy of solvation corrections obtained by way of continuum models (CPCM and SMD), an approximation of the effect of aqueous solvation on the relative energies of the isomers has also been taken into account. In both the gas- and aqueous-phases, the lowest energy isomer is an exocyclic N -chloroimino derivative.

Chiroptically Active Plasmonic Nanoparticles Having Hidden Helicity and Reversible Aqueous Solvent Effect on Chiroptical Activity.

The geometrical prerequisite for forming a helix is P (helical pitch) > d (wire diameter). Limited by the current development of nanofabrication techniques, it is difficult to minimize d and consequently P to the sub-10 nm molecule-comparable scale, preventing the study of chiral plasmonics at dimensions approaching the physical limit. Herein, glancing angle deposition is operated at substrate temperature of 0 °C and high speed of substrate rotation to generate silver nanoparticles (AgNPs) with nominal P < d. The AgNPs have intrinsic chiroptical activity characterized by circular dichroism (CD), originating from the hidden helicity. With increasing P from 3 to 66 nm, the plasmonic mode barely shifts but shows a logarithmic increase in CD amplitude. Immersing AgNPs in water causes the plasmonic mode to redshift and rise in CD amplitude, i.e., a water effect on chiroptical activity. Hydrophilic AgNP arrays with low array porosity show a reversible water effect, but hydrophobic Ag nanospiral arrays with P > d and high array porosity have an irreversible water effect. This work introduces a cost-effective, facile approach to minimize P to sub-10 nm at a regular substrate temperature, paving the way to study chiral plasmonics approaching the physical limit and exploit chirality-related bioapplications typically operated in aqueous solutions to tackle significant health and environmental problems.

Z-Isomers of (4α→6″, 2α→O→1″)-phenylflavan substituted with R′=R=OH. Conformational properties, electronic structure and aqueous solvent effects

Procyanidins are highly hydroxylated polymers known as antioxidant compounds, thereby exhibiting beneficial effects. These compounds are protective agents against oxidative stress and the damage induced by free radicals in membranes and nucleic acids. This paper describes a study of the conformational space of (4α→6″, 2α→O→1″)-phenylflavan substituted with R'=R=OH as part of a larger study of similar structures with different substitutions. The relationships between aqueous solution-vacuum variations of some properties were studied, as well as the stabilization and reactivity of (4α→6″, 2α→O→1″)-phenylflavan substituted with R'=R=H, R'=H, R=OH, R'=R=OH, and (+)-catechin. The variations in geometric parameters and electronic properties due to conformational changes, as well as the effects of substituents and polar solvents, were evaluated and analyzed. Bader's theory of atoms in molecules was applied to characterize intramolecular interactions, along with a natural bond orbital analysis for each conformer described. The molecular electrostatic potential was rationalized by charge delocalization mechanisms and interatomic intramolecular interactions, relating them to the structural changes and topological properties of the electron charge density. Molecular polarizability and permanent electric dipole moment values were estimated. The results show the importance of a knowledge of the conformational space, and values for each conformer. Based on our previous results, we showed the existence of electron charge delocalization mechanisms acting cooperatively as "delocalization routes", showing interactions between different rings not even sharing the same plane. These "delocalization routes" were more effective for (4α→6″, 2α→O→1″)-phenylflavan substituted with R'=R=OH than for (+)-catechin, and are proposed as adding insight into the structure-antioxidant activity relationship of flavans.

Addition-Elimination or Nucleophilic Substitution? Understanding the Energy Profiles for the Reaction of Chalcogenolates with Dichalcogenides.

We have quantum chemically explored the mechanism of the substitution reaction between CH3X(-) and the homo- and heterodichalcogenides CH3X'X″CH3 (X, X', X″ = S, Se, Te) using relativistic density functional theory at ZORA-OLYP/TZ2P and COSMO for simulating the effect of aqueous solvation. In the gas phase, all substitution reactions proceed via a triple-well addition-elimination mechanism that involves a stable three-center intermediate. Aqueous solvation, in some cases, switches the character of the mechanism to double-well SN2 in which the stable three-center intermediate has become a labile transition state. We rationalize reactivity trends and some puzzling aspects of these elementary reactions, in particular, vanishing activation energies and ghost three-center intermediates, using the activation strain model (ASM).

A polarizable QM/MM approach to the molecular dynamics of amide groups solvated in water.

The infrared (IR) spectra of polypeptides are dominated by the so-called amide bands. Because they originate from the strongly polar and polarizable amide groups (AGs) making up the backbone, their spectral positions sensitively depend on the local electric fields. Aiming at accurate computations of these IR spectra by molecular dynamics (MD) simulations, which derive atomic forces from a hybrid quantum and molecular mechanics (QM/MM) Hamiltonian, here we consider the effects of solvation in bulk liquid water on the amide bands of the AG model compound N-methyl-acetamide (NMA). As QM approach to NMA we choose grid-based density functional theory (DFT). For the surrounding MM water, we develop, largely based on computations, a polarizable molecular mechanics (PMM) model potential called GP6P, which features six Gaussian electrostatic sources (one induced dipole, five static partial charge distributions) and, therefore, avoids spurious distortions of the DFT electron density in hybrid DFT/PMM simulations. Bulk liquid GP6P is shown to have favorable properties at the thermodynamic conditions of the parameterization and beyond. Lennard-Jones (LJ) parameters of the DFT fragment NMA are optimized by comparing radial distribution functions in the surrounding GP6P liquid with reference data obtained from a "first-principles" DFT-MD simulation. Finally, IR spectra of NMA in GP6P water are calculated from extended DFT/PMM-MD trajectories, in which the NMA is treated by three different DFT functionals (BP, BLYP, B3LYP). Method-specific frequency scaling factors are derived from DFT-MD simulations of isolated NMA. The DFT/PMM-MD simulations with GP6P and with the optimized LJ parameters then excellently predict the effects of aqueous solvation and deuteration observed in the IR spectra of NMA. As a result, the methods required to accurately compute such spectra by DFT/PMM-MD also for larger peptides in aqueous solution are now at hand.

How do Water Solvent and Glutathione Ligands Affect the Structure and Electronic Properties of Au25(SR)18(-)?

The effects of aqueous solvent and biological ligands on the structural and electronic properties of thiolate-protected Au25(SR)18(-) clusters have been studied by performing quantum mechanics/molecular mechanics (QM/MM) simulations. Analysis of bond distances and angles show that the solvated nanocluster experiences modest structural changes, which are reflected as flexibility of the Au core. The hydrophilic glutathione ligands shield the metallic core effectively and distort its symmetry via sterical hindrance effects. We show that the previously reported agreement between the calculated HOMO-LUMO gap of the cluster and the optical measurement is due to cancellation of errors, where the typical underestimation of the theoretical band gap compensates the effect of the missing solvent. The use of a hybrid functional results in a HOMO-LUMO gap value of 1.5 eV for the solvated nanocluster with glutathione ligands, in good agreement with optical measurements. Our results demonstrate that ligand/solvent effects should be considered for a proper comparison between theory and experiment.