Calculated Solvation Energies Research Articles

An Unfitted Finite Element Poisson-Boltzmann Solver with Automatic Resolving of Curved Molecular Surface.

So far, the existing Poisson-Boltzmann (PB) solvers that accurately take into account the interface jump conditions need a pregenerated body-fitted mesh (molecular surface mesh). However, qualified biomolecular surface meshing and its implementation into numerical methods remains a challenging and laborious issue, which practically hinders the progress of further developments and applications of a bunch of numerical methods in this field. In addition, even with a molecular surface mesh, it is only a low-order approximation of the original curved surface. In this article, an interface-penalty finite element method (IPFEM), which is a typical unfitted finite element method, is proposed to solve the Poisson-Boltzmann equation (PBE) without requiring the user to generate a molecular surface mesh. The Gaussian molecular surface is used to represent the molecular surface and can be automatically resolved with a high-order approximation within our method. Theoretical convergence rates of the IPFEM for the linear PB equation have been provided and are well validated on a benchmark problem with an analytical solution (we also noticed from numerical examples that the IPFEM has similar convergence rates for the nonlinear PBE). Numerical results on a set of different-sized biomolecules demonstrate that the IPFEM is numerically stable and accurate in the calculation of biomolecular electrostatic solvation energy.

Low pH Titanium Electrochemistry in the Presence of Sulfuric Acid and its Implications for Redox Flow Battery Applications

Titanium (Ti) is a promising elemental redox active species for redox flow batteries (RFBs) due to its 100x availability in the Earth crust, and 10x lower cost (compared to elemental vanadium). Furthermore, Ti salts are highly soluble in water and concentrations >5 M can be easily obtained. Seeking to harness the higher solubility (and hence energy density) of the Ti electrolyte for flow battery applications, the Ti4+/Ti3+ redox couple was investigated at high concentrations (up to 5 M) relevant to RFB applications. The behavior of Ti ions in H2SO4 supported electrolytes was investigated by varying the ratio of Ti redox active species to counterion. The electrochemical characteristics, transport properties, and redox kinetics of the Ti4+/Ti3+ redox couple were measured and the impact of the Tix+ to solvating ligand ratio was examined. The coordination structures around solvated Tix+ ions were spectroscopically determined and the effect of solvation structure on the Ti3+/Ti4+ redox rate constants were examined and correlated to the calculated solvation energy (hence distinguishing between inner- and outer-sphere processes) and the role of catalysts was addressed. The Ti electrolyte development guidelines presented herein will advance the development of Ti-based RFBs as a promising pathway towards cost effective, grid-scale energy storage.

Parameterization of the IEF PCM model for calculating solvation energies in N-methylpyrrolidone solution

ABSTRACT Theoretical modelling of N-methylpyrrolidone (NMP) solutions, using a polarisable continuum model (IEFPCM), has been carried out with the aim to find the optimal value of a model parameter, a so-called scaling factor (α) for NMP, which should afford an improved modelling of various N-methylpyrrolidone solutions. Our working protocol comprised evaluations of the Gibbs free energy for the dissociation reaction of a set of 22 acids, employing the B2PLYP-D2/6–311+G**//B3LYP/6–31+G* approach, which were then used to calculate the acidity indices by considering the solvation energy at various values of α within the IEFPCM model. The optimal value of α for the N-methylpyrrolidone solvent has been found to amount to 1.40.

A $p$-Laplacian approach and its analysis for the calculation of ensemble average solvation energy

A $p$-Laplacian approach and its analysis for the calculation of ensemble average solvation energy

Electrochemical and Spectroscopic Investigation of Solvation and Complexation Effects on Titanium Redox Flow Battery Electrolytes

Titanium (Ti) is a promising elemental redox active species for redox flow batteries (RFBs) as an alternative to the commercially advanced vanadium RFB (V-RFB) due to its 100x availability in the Earth crust1, and 10x lower cost1 (both compared to elemental vanadium). The half-cell potential of the Ti4+/Ti3+ (0.1 V vs SHE) redox couple is closer to the H+/H2 (0V vs SHE) redox couple compared to V3+/V2+ (-0.26V vs SHE)2 thereby mitigating parasitic hydrogen evolution reactions. Thus, the development of Ti-based RFBs (by coupling it with another economical and abundant elemental active) is a promising pathway towards cost effective, grid-scale energy storage and the present work aims to optimize the Ti electrolyte to enable this integration.Ti electrolytes (typically as the anolyte) have been coupled withFe3, 4, Mn5 and Ce6 based catholytes to yield a number of relatively (compared to other aqueous systems) high-potential and high energy density RFBs7. The Ti-Fe, Ti-Mn, and Ti-Ce RFBs have theoretical energy densities of 9 Wh.L-1, 18.9 Wh.L-1, and 19.4 Wh.L-1 respectively7. Electrolyte design with an eye towards improving actives solubility (thereby increasing energy density) and decreasing side-reactions has proven crucial to realizing these systems. For example, deleterious Cl2 evolution reduced the coulombic efficiency of the earliest Ti-Fe RFBs3 and has been overcome by the use of H2SO4 as an alternate supporting electrolyte4. In Ti-Mn RFBs, Mn3+ is highly unstable and inclined to form MnO2. A highly acidic environment or increasing the amount of Mn2+ reduces the disproportionation of Mn3+. Alternatively, the addition of an equal concentration of TiOSO4 with MnSO4 at the catholyte and reducing the maximum operational state of charge to 50%5 reduces MnO2 precipitation. In Ti-Ce RFBs, Ce is the limiting element in terms of solubility as the solubility of Ce is lower (0.5M in H2SO4 and 0.9M in CH3SO3H)6, 8, 9 whereas Ti is highly soluble (up to 5M TiOSO4 in 4M H2SO4). On the other hand, kinetically, Ti is the limiting element with 3x lower rate constant than the Ce redox couple6.Seeking to harness the higher solubility (and hence energy density) of the Ti electrolyte while overcoming the kinetic limitations, we investigated the solubility and the electrochemical reversibility of Ti4+/Ti3+. We characterized the behavior of Ti ions in various supporting electrolytes namely, H2SO4, HCl, HNO3, CH3SO3H by varying the ratio of Ti redox active species to counterion. The diffusion coefficients of the Ti3+ and Ti4+ ions were measured and the impact of the Tix+ to solvating ligand ratio was examined (see example in Fig.1(a)). Spectroscopically determining the coordination structures around solvated Tix+ ions10, we identified electrolyte compositions that result in increasing ionic conductivity (Fig.1(b)). The effect (or lack thereof) of solvation structure on the Ti3+/Ti4+ redox rate constants were examined and correlated to the calculated solvation energy (hence distinguishing between inner- and outer-sphere processes) and the role of catalysts was addressed. Finally, utilizing the electrochemical Thiele modulus framework11, 12, the best (highest energy density coupled with optimal transport and kinetic properties) Ti electrolyte compositions for Ti-Fe, Ti-Mn and Ti-Ce RFBs has been identified.

Polarization consistent dielectric screening in polarizable continuum model calculations of solvation energies.

A polarization consistent framework, where dielectric screening is affected consistently in polarizable continuum model (PCM) calculations, is employed for the study of solvation energies. The computational framework combines a screened range-separated-hybrid functional (SRSH) with PCM calculations, SRSH-PCM, where dielectric screening is imposed in both PCM self-consistent reaction field (SCRF) iterations and the electronic structure Hamiltonian. We begin by demonstrating the impact of modifying the Hamiltonian to include such dielectric screening in SCRF iterations by considering the solutions of electrostatically embedded Hartree-Fock (HF) exact exchange equations. Long-range screened HF-PCM calculations are shown to capture properly the linear dependence of gap energy of frontier orbitals on the inverse of the dielectric constant, whereas unscreened HF-PCM orbital energies are fallaciously semi-constant with respect to the dielectric constant and, therefore, inconsistent with the ionization energy gaps. Similar trends affect density functional theory (DFT) calculations that aim to achieve predictive quality. Importantly, the dielectric screened calculations are shown to significantly affect DFT- and HF PCM-based solvation energies, where screened solvation energies are smaller compared to the unscreened values. Importantly, SRSH-PCM, therefore, appears to reduce the tendency of DFT-PCM to overestimate solvation energies, where we find the effect to increase with the dielectric constant and the polarity of the molecular solute, trends that enhance the quality of DFT-PCM calculations of solvation energy. Understanding the relationship of dielectric screening in the Hamiltonian and DFT-PCM calculations can ultimately benefit on-going efforts for the design of predictive and parameter free descriptions of solvation energies.

Accurate Boundary Integral Formulations for the Calculation of Electrostatic Forces with an Implicit-Solvent Model

An accurate force calculation with the Poisson-Boltzmann equation is challenging, as it requires the electric field on the molecular surface. Here we present a calculation of the electric field on the solute-solvent interface that is exact for piecewise linear variations of the potential and analyze four different alternatives to compute the force using a boundary element method. We performed a verification exercise for two cases: the isolated and two interacting molecules. Our results suggest that the boundary element method outperforms the finite difference method, as the latter needs a much finer mesh than in solvation energy calculations to get acceptable accuracy in the force, whereas the same surface mesh as in a standard energy calculation is appropriate for the boundary element method. Among the four evaluated alternatives of force calculation, we saw that the most accurate one is based on the Maxwell stress tensor. However, for a realistic application, like the barnase-barstar complex, the approach based on variations of the energy functional, which is less accurate, gives equivalent results. This analysis is useful toward using the Poisson-Boltzmann equation for force calculations in applications where high accuracy is key, for example, to feed molecular dynamics models or to enable the study of the interaction between large molecular structures, like viruses adsorbed onto substrates.

Quantitative Solvation Energies from Gas-Phase Calculations: First-Principles Charge Transfer and Perturbation Approaches.

We present a first-principles approach for the calculation of solvation energies and enthalpies with respect to different ion pair combinations in various solvents. The method relies on the conceptual density functional theory (DFT) of solvation, from which detailed expressions for the solvation energies can be derived. In addition to fast and straightforward gas phase calculations, we also study the influence of modified chemical reactivity descriptors in terms of electronic perturbations. The corresponding phenomenological changes in molecular energy levels can be interpreted as the influence of continuum solvents. Our approach shows that the introduction of these modified expressions is essential for a quantitative agreement between the calculated and the experimental results.

Molecular Modelling of Ionic Liquids: Situations When Charge Scaling Seems Insufficient.

Charge scaling as an effective solution to the experiment-computation disagreement in molecular modelling of ionic liquids (ILs) could bring the computational results close to the experimental reference for various thermodynamic properties. According to the large-scale benchmark calculations of mass density, solvation, and water-ILs transfer-free energies in our series of papers, the charge-scaling factor of 0.8 serves as a near-optimal option generally applicable to most ILs, although a system-dependent parameter adjustment could be attempted for further improved performance. However, there are situations in which such a charge-scaling treatment would fail. Namely, charge scaling cannot really affect the simulation outcome, or minimally perturbs the results that are still far from the experimental value. In such situations, the vdW radius as an additional adjustable parameter is commonly tuned to minimize the experiment-calculation deviation. In the current work, considering two ILs from the quinuclidinium family, we investigate the impacts of this vdW-scaling treatment on the mass density and the solvation/partition thermodynamics in a fashion similar to our previous charge-scaling works, i.e., scanning the vdW-scaling factor and computing physical properties under these parameter sets. It is observed that the mass density exhibits a linear response to the vdW-scaling factor with slopes close to -1.8 g/mL. By further investigating a set of physiochemically relevant temperatures between 288 K and 348 K, we confirm the robustness of the vdW-scaling treatment in the estimation of bulk properties. The best vdW-scaling parameter for mass density would worsen the computation of solvation/partition thermodynamics, and a marginal decrease in the vdW-scaling factor is considered as an intermediate option balancing the reproductions of bulk properties and solvation thermodynamics. These observations could be understood in a way similar to the charge-scaling situation. i.e., overfitting some properties (e.g., mass density) would degrade the accuracy of the other properties (e.g., solvation free energies). Following this principle, the general guideline for applying this vdW-tuning protocol is by using values between the density-derived choice and the solvation/partition-derived solution. The charge and current vdW scaling treatments cover commonly encountered ILs, completing the protocol for accurate modelling of ILs with fixed-charge force fields.

The structure, stability, thermochemistry, and bonding in SO3-(H2O)n (n = 1–7) clusters: a computational analysis

The structure, stability, and intermolecular interactions in SO3-(H2O)n (n = 1–7) clusters were investigated using density functional and wave functional methods. The putative global minimum shows the SO3 molecule tends to be on the surface water clusters. The increase in the number of water molecules chalcogen bond distance between water molecules and SO3 decreases, while the maximum number of water molecules coordinated to the SO3 molecule remains at three. The calculated solvation energy increases with the increase in the number of water molecules, and it does not saturate, which indicates that the addition of water molecules can add up to the existing water cluster network. The interaction energy between water molecules and SO3 was less than the solvation energy conforming to the cluster forming of water molecules. The Gibbs free energy and entropy values decrease with the increase in cluster size, signifying the amount of water molecule decide the sequential hydration process. Thermochemistry data at various temperatures show that low-temperature regions found in the upper part of the troposphere favor hydration formation. Molecular electrostatic potentials (MESP) show reduced Vs,max value of π-hole on sulfur atom and increased value on hydrogens of water molecules which results in the addition of water which leads to the sequential addition of water molecules to the water network. The quantum theory of atoms in molecules (QTAIM) shows the presence of S···O, O···H interactions between SO3 and water molecules. Between water molecules O···H, H-bonding interactions were observed, and in larger clusters, O···O interaction was also noticed. QTAIM analysis shows that the water–water HBs in these clusters are weak H-bond, while the SO3-water interaction can be classified as medium H-bonds which was further supported by the NCI and 2D RDG plots.

Coarse-Graining ddCOSMO through an Interface between Tinker and the ddX Library.

The domain decomposition conductor-like screening model is an efficient way to compute the solvation energy of solutes within a polarizable continuum medium in a linear scaling computational time. Despite its efficiency, the application to very large systems is still challenging. A possibility to further accelerate the algorithm is resorting to coarse-graining strategies. In this paper we present a preliminary interface between the molecular dynamics package Tinker and the ddX library. The interface was used to test a united atom coarse-graining strategy that allowed us to push ddCOSMO to its limits by computing solvation energies on systems with up to 7 million atoms. We first present benchmarks to find an optimal discretization, and then, we discuss the performance and results obtained with fine- and coarse-grained solvation energy calculations.

Quantum-Chemical Evaluation of the Energies of Solvation of Humic Substances in Various Solvents

The results of the DFT (b3lyp/sto-3g*) quantum-chemical calculations of solvation energies of humic substances in organic solvents and water based on a structural model of humic acids are presented. It was shown that the solvation of humic substances depends on their quantitative functional composition. It was proposed to use the results obtained for the fractionation of these natural compounds and for target-oriented changes in their properties.

Potential of aluminum nitride nanocone as a chemical sensor for anticancer drug detection

The adsorption of temozolomide (TMZ) onto an aluminum nitride nanocone (AlNNC) was inspected via density functional theory (DFT) computations. The energy of adsorption for TMZ on the surface of the AlNNC was estimated to be approximately −17.88 kcal/mol. Owing to steric hindrance, an increase in the number of TMZ molecules resulted in less negative adsorption energy values per molecule. In this study, we proposed an electrostatic interaction as the mechanism between TMZ and the AlNNC. After the adsorption of TMZ onto the surface of the AlNNC, the electrical conductivity of this nanocone increased dramatically by approximately 41.98 %, showing that it can be used as a drug detector. Moreover, the AlNNC-TMZ complex has higher stability in water according to solvation energy calculations. Finally, based on our results, the AlNNC could selectively detect TMZ moieties among environmental contaminants.

Comprehensive modelling of pharmaceutical solvation energy in different solvents

Crystallization is an important processing step in production of active pharmaceutical ingredients (API). This process is used to recover/separate the synthesized APIs for further processing to final solid dosage oral formulations. Control and understanding of crystallization are of great importance for development of high-efficient processing step in pharmaceutical manufacturing. Different types of models have been developed so far for prediction of crystallization, however development of a comprehensive hybrid model is lacking. In this work, a comprehensive hybrid model is developed based on quantum chemical calculations and artificial intelligence model. The quantum chemical calculation was used to compute the solvation energy of several solutes in various organic solvents. 42 data set was collected from literature, and the solvation energy was computed using Material Studios software. The calculated solvation energy was used to build a predictive model based on artificial intelligence (AI). Artificial neural network (ANN) was employed for prediction of API solvation energy in various solvents. KFold technique was used for validation of the model in which 1/3 of the data was used for validation of the trained neural network. It was indicated that the developed ANN is capable of predicting solvation energy versus solute and solvent, with high accuracy. R2 more than 0.999 was obtained for both training and validation stages, revealing the robustness of the developed ANN in predicting solvation energy of APIs. The results can be used as predictive tool for understanding and optimization of crystallization process.

DFT exploration of sensor performances of pristine and metal-doped graphdiyne monolayer to acetaminophen drug in terms of charge transfer and bandgap changes

In order to study the electronic identity of pristine graphdiyne (GDY) as well as Zinc-doped graphdiyne (ZnGDY), first-principles calculations were done. Main parameters were investigated to analyze the adsorption behavior of acetaminophen (ACE) on the GDY and Zn GDY substrates, including the energy of adsorption, charge transfer along with the shift in the energy gap. The pristine DY sheet showed a weak attraction toward the ACE adsorbate. Additionally, the ACE adsorption onto GDY resulted in a negligible band gap energy shift of about 5.65%. On the contrary, in the gas phase, ZnGDY is mainly affected by the ACE adsorption with the adsorption energy of about 13.65. In addition, the ACE adsorption energy over the Zn-doped sheet was obtained to be 26.76 kcal/mol in the aqueous medium. A mild water solubility of ACE was reported regarding the moderate value of the calculated solvation energy. Noticeable charge transfer occurred during the ACE adsorption onto the ZnGDY substrate compared to the pristine GDY. Finally, the Zn addition resulted in an enhanced tendency toward ACE and the electrical conductivity was shifted by 13.92%, which is required for the sensory role of an adsorbent toward the ACE drug species.

Modeling the effect of surfactant (linoleic acid/oleic acid/stearic acid) on the stability of kerosene-based magnetic fluid with Fe3O4

The poor stability of magnetic fluid is a key problem which limits its application. To understand the impact of surfactants on stability, we prepare kerosene-based magnetic fluid with Fe3O4 magnetic nanoparticles (MNPs) using different surfactants i.e. linoleic acid, oleic acid and stearic acid. The distribution of nanoparticles in magnetic fluid is obtained by transmission electron microscope (TEM) and granularity analyzer. We find that MNPs coated with stearic acid agglomerate and the size is the largest. In contrast, the MNPs coated with linoleic acid or oleic acid are well dispersed with smaller size, which reveals that the type of surfactant will affect the stability of the magnetic fluid. To understand this, the adhesion energy of surfactant on particles and the solvation energy of surfactant in carrier fluid are calculated by ab initio and molecular dynamics. Based on the calculation results, we propose a formula for estimating the stability of magnetic fluid by combining the repulsive energy between Fe3O4 nanoparticles covered by surfactant and the calculated solvation energy of surfactants and carrier fluid, which can well interpret our experimental results. Our study reveals the mechanism of magnetic fluid stability and provides theoretical guidance for the preparation of stable magnetic fluid.

Using Quantum Density Functional Theory Methods to Study the Adsorption of Fluorouracil Drug on Pristine and Al, Ga, P and As Doped Boron Nitride Nanosheets

AbstractFluorouracil (5‐FU) is one of the most essential drugs, and widely used to treat different types of cancers. However, direct injection of 5‐FU causes many inevitable side effects, and therefore, the design of new and targeted drug delivery methods can reduce such undesirable effects. In the present work, density functional theory methods at B3LYP‐D3(BJ)/6‐31 g* level of theory were used to study the pristine and Al, Ga, P and As doped monolayer boron nitride (BN) nanosheets, as possible adsorption substrates for modern and targeted nanotechnology based drug delivery methods. Natural bond orbitals and quantum theory of atoms in molecules analyses were further used to reveal the physicochemical nature of the adsorption process. It was found that, adsorption process is endothermic in all studied cases, and the interactions energies are in the range of physisorption for pristine, P and As doped BN nanosheets, whereas, the chemical absorption of the 5‐FU on Al and Ga doped nanosheets was obtained with adsorption energies of −45.7 and −46.3 kcal/mol, respectively. The calculated solvation energies also show that, the dissolution of the 5‐FU/nanosheet complexes in water is more than the pristine nanosheets. The overall results confirm the great potential of the studied nanosheets and specially Al and Ga doped BNNSs as promising drug delivery substances in modern targeted drug delivery methods for 5‐FU drug.

Solvation of Potassium 5-Hydroxy Pentanoyl Trifluoroborate Salt in Aqueous Environment by Using FT-Raman and UV-Visible Spectra

The hydration process of potassium 5-hydroxypentanoyltrifluoroborate salt, K[C5H9BF3O2] and its 5-hydroxypentanoyltrifluoroborate [C5H9BF3O2]- anion have been studied by combining the experimental FT-Raman and ultraviolet-visible spectra in aqueous solution with hybrid B3LYP/6-311++G** calculations. Solvent effects have been considered with the self-consistent reaction field (SCRF) and solvation (SM) models. Here, the structures of [C5H9BF3O2].[H2O]n clusters of anion, with n from 1 to 5 implicit water molecules, were proposed in order to study the number of water molecules that could hydrate the anion. Calculations were performed in the gas phase and an aqueous solution to observe the effect of the medium on the dipole moment and volume values. Calculated solvation energies for all clusters were corrected by zero-point vibrational energy (ZPVE), non-electrostatic terms and by basis set superposition energy (BSSE). The dipole moment of salt in solution (10.19 D) suggests that the number of water molecules that could hydrate the anion vary between 3 and 4, in total agreement with the observed and predicted bands in the UV-Vis spectra for the salt and these two clusters in water between 180 and 400 nm. Comparisons among experimental and predicted Raman spectra show clearly the hydration effect because the bands attributed to OH, BF3 and C=O groups are shifted in solution, while, the predicted Raman spectra for all clusters in solution show strong changes in the intensities of many bands, in accordance with the corresponding experimental one. Evidently, the hydration occurs on the OH, BF3 and C=O groups.

Biomolecular Simulations with the Three-Dimensional Reference Interaction Site Model with the Kovalenko-Hirata Closure Molecular Solvation Theory.

The statistical mechanics-based 3-dimensional reference interaction site model with the Kovalenko-Hirata closure (3D-RISM-KH) molecular solvation theory has proven to be an essential part of a multiscale modeling framework, covering a vast region of molecular simulation techniques. The successful application ranges from the small molecule solvation energy to the bulk phase behavior of polymers, macromolecules, etc. The 3D-RISM-KH successfully predicts and explains the molecular mechanisms of self-assembly and aggregation of proteins and peptides related to neurodegeneration, protein-ligand binding, and structure-function related solvation properties. Upon coupling the 3D-RISM-KH theory with a novel multiple time-step molecular dynamic (MD) of the solute biomolecule stabilized by the optimized isokinetic Nosé–Hoover chain thermostat driven by effective solvation forces obtained from 3D-RISM-KH and extrapolated forward by generalized solvation force extrapolation (GSFE), gigantic outer time-steps up to picoseconds to accurately calculate equilibrium properties were obtained in this new quasidynamics protocol. The multiscale OIN/GSFE/3D-RISM-KH algorithm was implemented in the Amber package and well documented for fully flexible model of alanine dipeptide, miniprotein 1L2Y, and protein G in aqueous solution, with a solvent sampling rate ~150 times faster than a standard MD simulation in explicit water. Further acceleration in computation can be achieved by modifying the extent of solvation layers considered in the calculation, as well as by modifying existing closure relations. This enhanced simulation technique has proven applications in protein-ligand binding energy calculations, ligand/solvent binding site prediction, molecular solvation energy calculations, etc. Applications of the RISM-KH theory in molecular simulation are discussed in this work.

Fast non-iterative calculation of solvation energies for water and non-aqueous solvents.

We propose an efficient and accurate non-iterative method, dubbed uESE, for calculating solvation free energies. Apart from a COSMO-like electrostatic term, the model takes into account non-electrostatic contributions, which depend on atomic surfaces, induced surface charge densities, and the molecular volume. uESE is tested on 35 polar and 57 non-polar solvents. The calculated and experimental solvation free energies are compared for 2892 systems. The method exhibits an excellent performance, which is superior to major solvation methods. The mean absolute error of predicted solvation energies is found below 1 kcal/mol for neutral solutes and below 3 kcal/mol for ions. The calculated data are almost independent of the quantum-chemical method or/and basis sets employed.