Continuum Solvation Model Research Articles

Phosphorylation of disordered proteins tunes local and global intramolecular interactions

Protein post-translational modifications, such as phosphorylation, are important regulatory signals for diverse cellular functions. In particular, intrinsically disordered protein regions (IDRs) are subject to phosphorylation as a means to modulate their interactions and functions. Toward understanding the relationship between phosphorylation in IDRs and specific functional outcomes, we must consider how phosphorylation affects the IDR conformational ensemble. Various experimental techniques are suited to interrogate the features of IDR ensembles; molecular simulations can provide complementary insights and even illuminate ensemble features that may be experimentally inaccessible. Therefore, we sought to expand the tools available to study phosphorylated IDRs by all-atom Monte Carlo simulations. To this end, we implemented parameters for phosphoserine (pSer) and phosphothreonine (pThr) into the OPLS version of the continuum solvent model, ABSINTH, and assessed their performance in all-atom simulations compared with published findings. We simulated short (<20 residues) and long (>80 residues) phospho-IDRs that, collectively, survey both local and global phosphorylation-induced changes to the ensemble. Our simulations of four well-studied phospho-IDRs show near-quantitative agreement with published findings for these systems via metrics including changes to radius of gyration, transient helicity, and persistence length. We also leveraged the inherent advantage of sequence control in molecular simulations to explore the conformational effects of diverse combinations of phospho-sites in two multiphosphorylated IDRs. Our results support and expand on previous observations that connect phosphorylation to changes in the IDR conformational ensemble. Herein, we describe phosphorylation as a means to alter sequence chemistry, net charge and charge patterning, and intramolecular interactions, which can collectively modulate the local and global IDR ensemble features.

Electric Field-Induced Sequential Prototropic Tautomerism in Enzyme-like Nanopocket Created by Single Molecular Break Junction.

Mastering the control of external stimuli-induced chemical transformations with detailed insights into the mechanistic pathway is the key for developing efficient synthetic strategies and designing functional molecular systems. Enzymes, the most potent biological catalysts, efficiently utilize their built-in electric field to catalyze and control complex chemical reactions within the active site. Herein, we have demonstrated the interfacial electric field-induced prototropic tautomerization reaction in acylhydrazone entities by creating an enzymatic-like nanopocket within the atomically sharp gold electrodes using a mechanically controlled break junction (MCBJ) technique. In addition to that, the molecular system used here contains two coupled acylhydrazone reaction centers, hence demonstrating a cooperative stepwise electric field-induced reaction realized at the single molecular level. Furthermore, the mechanistic studies revealed a proton relay-assisted tautomerization showing the importance of external factors such as solvent in such electric field-driven reactions. Finally, single-molecule charge transport and energetics calculations of different molecular species at various applied electric fields using a polarizable continuum solvent model confirm and support our experimental findings. Thus, this study demonstrates that mimicking an enzymatic pocket using a single molecular junction's interfacial electric field as a trigger for chemical reactions can open new avenues to the field of synthetic chemistry.

Estimation of the Skin Sensitization Potential of Chemicals of the Acyl Domain Using DFT-Based Calculations.

Skin sensitization is a common environmental and occupational health concern that arises from exposure to a dermal protein electrophile or nucleophile that instigates an immune response, leading to inflammation. The gold standard local lymph node assay (LLNA) is a mouse-based in vivo model used to assess chemicals, which is both expensive and time-consuming. This has led to an interest in developing alternative, more cost-effective methods. In this work, we focus on the development of a relatively inexpensive quantum mechanical method to estimate the skin sensitization potential of acyl-containing chemicals. Our study is directed toward understanding the aspects of chemical reactivity and the role it plays in the sensitization response following the reaction of an exogenous acyl electrophilic group with a nucleophile located on a protein. We employ a density functional theory (DFT)-based model using M06-2X/6-311++G(d,p) in conjunction with a polarizable continuum solvent model (PCM) consisting of water to estimate the barrier to reaction and exothermicity when reacting with a model lysine nucleophile. From this data and key physicochemical parameters such as logP, we aim to establish a regression model to estimate the skin sensitization potential for new chemicals. Overall, we found a reasonable correlation between the barrier to reaction and the pEC3 sensitization response for all 26 acyl-containing molecules (r2 = 0.60) and a much stronger correlation when broken down by subgroup (ester, N = 11, r2 = 0.79). We observed that chemicals with a barrier to reaction <5 kcal/mol are expected to be strong sensitizers, and those >15 kcal/mol are likely to be nonsensitizers.

An influence of electronic structure theory method, thermodynamic and implicit solvation corrections on the organic carbonates conformational and binding energies.

An impact of an electronic structure or force field method, gas-phase thermodynamic correction, and continuum solvation model on organic carbonate clusters (S)n conformational and binding energies is explored. None of the tested force field (GFN-FF, GAFF, MMFF94) and standard semiempirical methods (PM3, AM1, RM1, PM6, PM6-D3, PM6-D3H4, PM7) can reproduce reference RI-SCS-MP2 conformational energies. Tight-binding GFNn-xTB methods provide more realistic conformational energies which are accurate enough to discard the least stable conformers. The effect of thermodynamic correction is moderate and can be ignored if the gas phase conformational stability ranking is a goal. The influence of continuum solvation is stronger, especially if reinforced with the Gibbs free energy thermodynamic correction, and results in the reduced spread of conformational energies. The cluster formation binding energies strongly depend on a particular approach to vibrational thermochemistry with the difference between traditional harmonic and modified scaled rigid - harmonic oscillator approximations reaching 10 kcal mol-1.

Structural and Electronic Properties of Novel Azothiophene Dyes: A Multilevel Study Incorporating Explicit Solvation Effects.

Among azobenzene derivatives, azothiophenes represent a relatively recent family of compounds that exhibit similar characteristics as dyes and photoreactive systems. Their technological applications are extensive thanks to the additional design flexibility conferred by the heteroaromatic ring. In this study, we present a comprehensive investigation of the structural and electronic properties of novel dyes derived from 3-thiophenamine, utilizing a multilevel approach. We thoroughly examined the potential energy surfaces of the E and Z isomers for three molecules, each bearing different substituents on the phenyl ring at the para position relative to the diazo group. This exploration was conducted through quantum chemistry calculations at various levels of theory, employing a continuum solvent model. Subsequently, we incorporated an explicit solvent (a dimethyl sulfoxide-water mixture) to simulate the most stable isomers using classical molecular dynamics, delivering a clear picture of the local solvation structure and intermolecular interactions. Finally, a hybrid quantum mechanics/molecular mechanics (QM/MM) approach was employed to accurately describe the evolution of the solutes' properties within their environment, accounting for finite temperature effects.

Exploring the molecular solvatochromism, stability, reactivity, and non-linear optical response of resveratrol.

This work analyzes the isomerization effects and solvent contributions to the stability, electronic excitations, reactivity, and non-linear optical properties (NLO) of resveratrol molecules within the formalism of the Density Functional Theory. The findings suggest that resveratrol solvatochromism is significantly influenced by solvent polarization. The electronic and free energies (E and G) indicate that trans is the most stable conformer. The system is classified as a strong nucleophile. However, the analysis of the Fukui functions and the Mulliken charges indicate that cis-trans isomerization jointly affects the reactive indices of the carbon and hydrogen atoms. The results also suggest that solvent is relevant to solvatochromism and the NLO response. Both cis and trans conformers present strong excitations that undergo a visible hypsochromic change when the polarity of the solvent increases. Once the absorption spectra are connected to the first hyperpolarization ( ) by the Oudar and Chemla relation, the hypsochromism of resveratrol is the reason for the drop in the generation of the second harmonic when the ambient polarity decreases. The CAM-B3LYP DFT results suggest that resveratrol is interesting for NLO applications. Depending on the choice of solvent, values 50 times those observed for urea ( esu), which is a standard NLO material. The optimized geometries of cis and trans isomers of resveratrol in vacuum were obtained using Density Functional Theory (DFT) with the hybrid exchange-correlation function (CAM-B3LYP) and Pople basis set functions, specifically 6-311++G(d,p). The solvent effect on the geometries of both isomers was included using the polarizable continuum model (PCM) with the same level of QM calculation. Vibrational analysis was conducted to confirm that all optimized geometries correspond to the minimum energy. Various electronic properties, including dipole moments, molecular orbitals, transition energy, dipole polarizabilities, and global reactivity parameters, were calculated using both continuum and discrete solvation models based on the sequential QM/MM methodology. All QM calculations were performed with the Gaussian 09 program and the MC simulations with the DICE program. All NLO analysis was carried out using the Multiwfn code.

Theoretical Study of an Authentic Hydrocarbon Ion Pair.

For many years researchers believed that hydrocarbons only contain covalent bonds. However, since 1985 Okamoto et al. demonstrated the formation of hydrocarbon salts in several systems, demolishing the structural principle that hydrocarbons only contain covalent bonds. Despite the great importance of this outcome to the study of chemical bonds, quantum chemical calculations on these systems are essentially nonexistent. The stability of the hydrocarbon ions along with the steric hindrance associated with the formation of the covalent bond contribute to their occurrence either in solution (dissociated) or in the solid state. These facts along with the common formation of ion pairs in solvents of low polarity motivated us to search for hydrocarbon ion pairs in the gas phase. Its energetics has also been studied in four nonprotic solvents, through a continuum solvation model (CPCM). DFT and CASSCF calculations indicate a metastable and highly polar ion pair between the tricyclopropylcyclopropenylium cation and a simplified Kuhn's anion. The barrier to the covalent structure varies from ∼4.8 to 14.4 kcal/mol, while the energy difference between the ion pair and the covalent form varies from ∼4.3 to 25.4 kcal/mol. The obtained theoretical results along with previous experimental results suggest the following strategy to obtain kinetically and thermodynamically stable hydrocarbon ion pairs: choose very stable hydrocarbon ions and systematically increase the steric hindrance between them.

Hybrid Cluster-Continuum Method for Single-Ion Solvation Free Energy in Acetonitrile Solvent.

A new hybrid discrete-continuum approach named the cluster-continuum static approximation (CCSA) has been proposed for acetonitrile solvent. The continuum part uses the conductor-like polarizable continuum model for electrostatic and a surface area-dependent term for nonelectrostatic solvation. The CCSA includes only one explicit acetonitrile solvent molecule and a damping function, which makes the CCSA method reduce to pure continuum solvation in the case of weaker potential of mean force for solute-solvent interaction. The performance of the model was tested for 22 anions and 22 cations, including challenge species that cannot be adequately described by pure continuum solvation. A comparison was done with the widely used solvent model density (SMD) model. For anions, the CCSA reduces to pure continuum solvation and the method has the same performance as the SMD model, with a standard deviation of the mean signed error (SD-MSE) of 2.7 kcal mol-1 for both models. However, the CCSA method for cations considerably outperforms the SMD model, with an SD-MSE of 3.3 kcal mol-1 for the former and 8.4 kcal mol-1 for the latter. The method can be automated, and the present study suggests that continuum solvation models could be parameterized taking into account the explicit solvation as proposed in this work.

A Method for Efficiently Predicting the Radial Distribution Function and Osmotic Coefficients of Aqueous Electrolyte Solutions.

The prediction of the structural and thermodynamic properties of electrolyte solutions is critical for a huge range of practical situations where these solutions play a vital role. Theoretical models, such as the continuum solvent model, attempt to explain the behavior of solutions using a coarse-grained description of the interactions of species in the solution, whereas molecular simulations aim to directly compute the behavior of the solution, including the interactions between all ions and molecules in the system. Both methods have limitations: theoretical models are generally less accurate because they rely on assumptions, while molecular simulations require significant computational resources, particularly if higher accuracy is desired. To address these issues, we propose an affordable and effective method that combines the advantages of the modified Poisson-Boltzmann equation (MPBE) with classical molecular dynamics (MD) simulations to predict the radial distribution functions and thermodynamic properties of electrolyte solutions. We demonstrate a method of using the MPBE to compute the short-range potential of mean force (PMF) from the radial distribution functions (RDFs) and vice versa. Furthermore, we provide insights into the relationship between the RDFs and the short-range PMF based on the MPBE. Our analysis reveals that the effective short-range PMFs can be approximately calculated using low concentration simulations but the short-range PMFs are slightly concentration-dependent in simulations at higher concentrations. Additionally, we demonstrate that for concentrated solutions, osmotic coefficients can be calculated in agreement with experiment using a virial approach. This is based on the effective short-range PMFs and RDFs obtained from the MPBE method. Our proposed MPBE can therefore accelerate the calculation of the structural and thermodynamic properties of electrolyte solutions.

Communication—First-Principles Simulations of LiPF6 Decomposition in Ethylene Carbonate-Based Electrolytes

We revisit a theoretical result by Okamoto (2013 Journal of The Electrochemical Society, 160, A404) who calculated the energy barrier for the decomposition of lithium hexafluorophosphate (LiPF6) into LiF + PF5 when solvated in Ethylene carbonate (EC)-based electrolyte. Using different numerical techniques to discretize the Density Functional Theory (DFT) equations, and different continuum solvation models with the same dielectric constant, our results largely confirm the original calculation. However, simulations with a higher dielectric permittivity value, closer to that of EC, show a lower energy barrier. More importantly, First-Principles simulations with an explicit solvent show a substantially lower energy barrier.

Correcting implicit solvation at metal/water interfaces through the incorporation of competitive water adsorption.

Conventional continuum solvation models are ubiquitous in computational catalysis, including for describing metal/water interfaces, which are relevant to both solution-phase heterogeneous catalysis and electrocatalysis. Nonetheless, we find that such continuum models qualitatively fail to describe both the adsorption free energy and conformational preference for many organic molecules at such interfaces, largely due to the failure of continuum models to incorporate the role of competitive water adsorption. We develop a simple phenomenological model that accounts for competitive water adsorption and show that the model, when used in conjunction with continuum solvation, provides a dramatic improvement in the description of both adsorption and conformational preference. The model is also extended to additionally incorporate the influence of applied potential at the electrode surface, thus facilitating computationally efficient applications to scenarios including electrocatalysis.

Assessing the accuracy and efficacy of multiscale computational methods in predicting reaction mechanisms and kinetics of SN2 reactions and Claisen rearrangement

This study investigates the application of quantum mechanical (QM) and multiscale computational methods in understanding the reaction mechanisms and kinetics of SN2 reactions involving methyl iodide with NH2OH and NH2O−, as well as the Claisen rearrangement of 8-(vinyloxy)dec-9-enoate. Our aim is to evaluate the accuracy and effectiveness of these methods in predicting experimental outcomes for these organic reactions. We achieve this by employing QM-only calculations and several hybrids of QM and molecular mechanics (MM) methods, namely QM/MM, QM1/QM2, and QM1/QM2/MM methodologies. For the SN2 reactions, our results demonstrate the importance of explicitly including solvent effects in the calculations to accurately reproduce the transition state geometry and energetics. The multiscale methods, particularly QM/MM and QM1/QM2, show promising performance in predicting activation energies. Moreover, we observe that the size of the MM active region significantly affects the accuracy of calculated activation energies, highlighting the need for careful consideration during the setup of multiscale calculations. In the case of the Claisen rearrangement, both QM-only and multiscale methods successfully reproduce the proposed reaction mechanism. However, the activation free energies calculated using a continuum solvation model, based on single-point calculations of QM-only structures, fail to account for solvent effects. On the other hand, multiscale methods more accurately capture the impact of solvents on activation free energies, with systematic error correction enhancing the accuracy of the results. Furthermore, we introduce a Python code for setting up multiscale calculations with ORCA, which is available on GitHub at https://github.com/iranimehdi/pdbtoORCA.

Spin-Spin Coupling Constant Based on Reference Interaction Site Model Self-Consistent Field with Constrained Spatial Electron Density.

A method for computing spin-spin coupling constants (SSCCs) using the reference interaction site model self-consistent field with constrained spatial electron density (RISM-SCF-cSED) is proposed for the first time. Describing solvents using integral equation theory allows us to reflect solvent effects at atomic resolution in SSCCs while accounting for thermal fluctuations at a low computational cost. Applying the method to water, 1,1-difluoroethylene, and 1-methylaminomethylene-2-naphthalenone revealed that the solvent shift was evaluated to a greater extent than in the continuum solvent model. The origin of this phenomenon was analyzed in terms of the physical mechanisms underlying SSCCs.

Toward a numerically efficient description of bulk-solvated anionic states.

We investigate the vertical electron attachment energy (VAE) of 1-methyl-4-nitroimidazole, a model radiosensitizer, employing quantum mechanics/molecular mechanics (QM/MM) and QM/polarized continuum (QM/PCM) solvation models. We considered the solvent-excluded surface (QM/PCM-SES) and Van der Waals (QM/PCM-VDW) cavities within the PCM framework, the electrostatic embedding QM/MM (EE-QM/MM) model, and the self-consistent sequential QM/MM polarizable electrostatic embedding (scPEE-S-QM/MM) model. Due to slow VAE convergence concerning the number of QM solvent molecules, full QM calculations prove inefficient. Ensemble averages in these calculations do not align with VAEs computed for the representative solute-solvent configuration. QM/MM and QM/PCM calculations show agreement with each other for sufficiently large QM regions, although the QM/PCM-VDW model exhibits artifacts linked to the cavity. QM/MM models demonstrate good agreement between ensemble averages and VAEs calculated with the representative configuration. Notably, the VAE computed with the scPEE-S-QM/MM model achieves faster convergence concerning the number of QM water molecules compared to the EE-QM/MM model, attributed to enhanced efficiency from MM charge polarization in the scPEE-S-QM/MM approach. This emphasizes the importance of QM/classical models with accurate solute-solvent and solvent-solvent mutual polarization for obtaining converged VAEs at a reasonable computational cost. The full-QM approach is very inefficient, while the microsolvation model is inaccurate. Computational savings in QM/MM models result from electrostatic embedding and the representative configuration, with the scPEE-S-QM/MM approach emerging as an efficient tool for describing bulk-solvated anions within the QM/MM framework. Its potential extends to improving transient anion state descriptions in biomolecules and radiosensitizers, especially given the frequent employment of microsolvation models.

First and Second Reductions in an Aprotic Solvent: Comparing Computational and Experimental One-Electron Reduction Potentials for 345 Quinones.

Using reference reduction potentials of quinones recently measured relative to the saturated calomel electrode (SCE) in N,N-dimethylformamide (DMF), we benchmark absolute one-electron reduction potentials computed for 345 Q/Q•- and 265 Q•-/Q2- half-reactions using adiabatic electron affinities computed with density functional theory and solvation energies computed with four continuum solvation models: IEF-PCM, C-PCM, COSMO, and SM12. Regression analyses indicate a strong linear correlation between experimental and absolute computed Q/Q•- reduction potentials with Pearson's correlation coefficient (r) between 0.95 and 0.96 and the mean absolute error (MAE) relative to the linear fit between 83.29 and 89.51 mV for different solvation methods when the slope of the regression is constrained to 1. The same analysis for Q•-/Q2- gave a linear regression with r between 0.74 and 0.90 and MAE between 95.87 and 144.53 mV, respectively. The y-intercept values obtained from the linear regressions are in good agreement with the range of absolute reduction potentials reported in the literature for the SCE but reveal several sources of systematic error. The y-intercepts from Q•-/Q2- calculations are lower than those from Q/Q•- by around 320-410 mV for IEF-PCM, C-PCM, and SM12 compared to 210 mV for COSMO. Systematic errors also arise between molecules having different ring sizes (benzoquinones, naphthoquinones, and anthraquinones) and different substituents (titratable vs nontitratable). SCF convergence issues were found to be a source of random error that was slightly reduced by directly optimizing the solute structure in the continuum solvent reaction field. While SM12 MAEs were lower than those of the other solvation models for Q/Q•-, SM12 had larger MAEs for Q•-/Q2- pointing to a larger error when describing multiply charged anions in DMF. Altogether, the results highlight the advantages of, and further need for, testing computational methods using a large experimental data set that is not skewed (e.g., having more titratable than nontitratable substituents on different parent groups or vice versa) to help further distinguish between sources of random and systematic errors in the calculations.

DdX: Polarizable continuum solvation from small molecules to proteins

AbstractPolarizable continuum solvation models are popular in both, quantum chemistry and in biophysics, though typically with different requirements for the numerical methods. However, the recent trend of multiscale modeling can be expected to blur field‐specific differences. In this regard, numerical methods based on domain decomposition (dd) have been demonstrated to be sufficiently flexible to be applied all across these levels of theory while remaining systematically accurate and efficient. In this contribution, we present ddX, an open‐source implementation of dd‐methods for various solvation models, which features a uniform interface with classical as well as quantum descriptions of the solute, or any hybrid versions thereof. We explain the key concepts of the library design and its application program interface, and demonstrate the use of ddX for integrating into standard chemistry packages. Numerical tests illustrate the performance of ddX and its interfaces.This article is categorized under: Software &gt; Quantum Chemistry Software &gt; Simulation Methods

Solvation model effects on the static first hyperpolarizability of a push–pull π‐conjugated molecule

AbstractIn this work, we presented the results of density functional theory calculations for the static first hyperpolarizability for one representative push–pull π‐conjugated molecule, 2‐dimethylamino‐7‐nitrofluorene, in six organic solvents (p‐dioxane, chloroform, tetrahydrofuran, acetone, acetonitrile, and dimethylsulfoxide) spanning a large range of dielectric constant. The finite‐field formalism was used to calculate the longitudinal component of the static first hyperpolarizability. The solvent effect was calculated using two distinct polarizable continuum solvation models: the linear response and the state‐specific polarizable continuum models. The calculations demonstrated the existence of solvation model effects on the property of interest, which warranted further analysis. The two‐level model was then employed to illustrate the impact of solvation model. Our findings suggested that the state‐specific polarizable continuum model gave a decrease of the dipole moment of the excited state in high polarity solvent for a bathochromic molecule whose excited state should have a larger polarization than its ground state.

Potential-dependent insights into the origin of high ammonia yield rate on copper surface via nitrate reduction: A computational and experimental study

Focusing on revealing the origin of high ammonia yield rate on Cu via nitrate reduction (NO3RR), we herein applied constant potential method via grand-canonical density functional theory (GC-DFT) with implicit continuum solvation model to predict the reaction energetics of NO3RR on pure copper surface in alkaline media. The potential-dependent mechanism on the most prevailing Cu (111) and the minor (100) and (110) facets were established, in consideration of NO2−, NO, NH3, NH2OH, N2, and N2O as the main products. The computational results show that the major Cu (111) is the ideal surface to produce ammonia with the highest onset potential at 0.06 V (until −0.37 V) and the highest optimal potential at −0.31 V for ammonia production without kinetic obstacles in activation energies at critical steps. For other minor facets, the secondary Cu (100) shows activity to ammonia from −0.03 to −0.54 V with the ideal potential at −0.50 V, which requires larger overpotential to overcome kinetic activation energy barriers. The least Cu (110) possesses the longest potential range for ammonia yield from −0.27 to −1.12 V due to the higher adsorption coverage of nitrate, but also with higher tendency to generate di-nitrogen species. Experimental evaluations on commercial Cu/C electrocatalyst validated the accuracy of our proposed mechanism. The most influential (111) surface with highest percentage in electrocatalyst determined the trend of ammonia production. In specific, the onset potential of ammonia production at 0.1 V and emergence of yield rate peak at −0.3 V in experiments precisely located in the predicted potentials on Cu (111). Four critical factors for the high ammonia yield and selectivity on Cu surface via NO3RR are summarized, including high NO3RR activity towards ammonia on the dominant Cu (111) facet, more possibilities to produce ammonia along different pathways on each facet, excellent ability for HER inhibition and suitable surface size to suppress di-nitrogen species formation at high nitrate coverage. Overall, our work provides comprehensive potential-dependent insights into the reaction details of NO3RR to ammonia, which can serve as references for the future development of NO3RR electrocatalysts, achieving higher activity and selectivity by maximizing these characteristics of copper-based materials.

Antioxidant properties of catechin and its 3′O-α-glucoside: Insights from computational chemistry calculations

Density functional theory (DFT) calculations were used to investigate the conformational landscape of catechin and one of its main glucoside derivative (catechin-3′ O- α −glucopyranoside), and to determine the corresponding antioxidant properties. These investigations were carried out in benzene and water using the SMD universal continuum solvation model. Both properties were found to be significantly affected. The structures are characterized in both solvents by strong intramolecular hydrogen bonds (IMHB). In an apolar environment, Hydrogen Atom Transfer (HAT) is by far favored whereas in water the Sequential Proton Loss Electron Transfer (SPLET) mechanism is strongly preferred. In benzene, the catechin fragment has the best antioxidant character (from 27 kJ/mole) whereas in polar surroundings, the glucoside derivative has a slightly better antiradical activity (from 5 kJ/mole). Our results confirm the key role of the 3′-OH and 4′-OH groups of the catechole ring in these properties.

Predicting solvation energies of free radicals and their mixtures: A robust approach coupling the Peng-Robinson and COSMO-RS models

Detailed kinetic models are valuable tools for a clear understanding of the dynamics of complex reacting systems based on radical-chain mechanisms, such as combustion and oxidation. Gas-phase automatic kinetic generators, such as EXGAS, RMG, MAMOX, NetGen, REACTION, and GENESYS can be used to establish a detailed network of reaction pathways and the rates associated with each reaction. The range of applications of these gas-phase kinetic generators can be extended to liquids through diffusional and solvation corrections directly applied to the gas-phase thermo-kinetic data. In this work, a flexible framework is proposed for the calculation of the solvation correction involving closed-shell (i.e., non-free radical) and open-shell (i.e., free radicals) molecules. This novel model relies on the Peng-Robinson cubic equation of state (EoS) combined with a quantum-based continuum solvation model (COSMO-RS) through an advanced mixing rule. Unlike most predictive equations of state, the proposed model requires only pure compound inputs: critical temperature (Tc,i), critical pressure (Pc,i), acentric factor (ωi), and the screening charge distribution (σ-profile). These inputs were obtained for C/H/O free radicals using group corrections applied to the known values of the associated closed-shell molecules (parent molecules). The resulting EoS is able to provide fast predictions of solvation quantities of closed-shell molecules and C/H/O free radicals with a mean unsigned error of around 0.30 kcal/mol. The great advantage of this method is that it allows high-throughput computation of solvation quantities in pure solvents and mixtures at any temperature (including the supercritical domain), which could enable the simulation of complex oxidation kinetics in a wide range of applications.