SM6: A Density Functional Theory Continuum Solvation Model for Calculating Aqueous Solvation Free Energies of Neutrals, Ions, and Solute-Water Clusters

The radical scavenging activity of muriolide in physiological environments: mechanistic and kinetic insights into double processes

Muriolide, which is a natural lactone that was isolated from Ranunculus muricatus, is a promising natural radical scavenger in the physiological environment.

Rhodium(III)-Catalyzed C-H/N-H Alkyne Annulation of Nonsymmetric 2-Aryl (Benz)imidazole Derivatives: Photophysical and Mechanistic Insights

Rhodium(III) catalysis enabled C-H/N-H alkyne annulation of nonsymmetric imidazole derivatives. This study encompasses the synthesis of imidazoles from a naturally occurring quinoidal compound and their use for the preparation of rigid π-extended imidazole derivatives with outstanding fluorescence. Our study also brings to light the photophysical aspects and the mechanism of the reaction studied via computational calculations. This method provided an efficient and versatile tool for the synthesis of fluorescent compounds with a wide range of chemical and biological applications.

How Alcoholic Disinfectants Affect Coronavirus Model Membranes: Membrane Fluidity, Permeability, and Disintegration

Atomistic molecular dynamics simulations have been carried out with a view to investigating the stability of the SARS-CoV-2 exterior membrane with respect to two common disinfectants, namely, aqueous solutions of ethanol and n-propanol. We used dipalmitoylphosphatidylcholine (DPPC) as a model membrane material and did simulations on both gel and liquid crystalline phases of membrane surrounded by aqueous solutions of varying alcohol concentrations (up to 17.5 mol %). While a moderate effect of alcohol on the gel phase of membrane is observed, its liquid crystalline phase is shown to be influenced dramatically by either alcohol. Our results show that aqueous solutions of only 5 and 10 mol % alcohol already have significant weakening effects on the membrane. The effects of n-propanol are always stronger than those of ethanol. The membrane changes its structure, when exposed to disinfectant solutions; uptake of alcohol causes it to swell laterally but to shrink vertically. At the same time, the orientational order of lipid tails decreases significantly. Metadynamics and grand-canonical ensemble simulations were done to calculate the free-energy profiles for permeation of alcohol and alcohol/water solubility in the DPPC. We found that the free-energy barrier to permeation of the DPPC liquid crystalline phase by all permeants is significantly lowered by alcohol uptake. At a disinfectant concentration of 10 mol %, it becomes insignificant enough to allow almost free passage of the disinfectant to the inside of the virus to cause damage there. It should be noted that the disinfectant also causes the barrier for water permeation to drop. Furthermore, the shrinking of the membrane thickness shortens the gap needed to be crossed by penetrants from outside the virus into its core. The lateral swelling also increases the average distance between head groups, which is a secondary barrier to membrane penetration, and hence further increases the penetration by disinfectants. At alcohol concentrations in the disinfectant solution above 15 mol %, we reliably observe disintegration of the DPPC membrane in its liquid crystalline phase.

Semicontinuum (Cluster-Continuum) Modeling of Acid-Catalyzed Aqueous Reactions: Alkene Hydration

An effort is made to reduce the errors of continuum solvation models (CSMs) with semicontinuum modeling to achieve 3 kcal mol^-1 agreement with experiment for acid-catalysis activation Gibbs energies. First, two underappreciated CSM issues are reviewed: errors in the CSM solvation Gibbs energies grow beyond 5 kcal mol^-1 (i) as ions are made smaller and (ii) as water clusters grow larger. Second, the computational reproduction of the known Gibbs energies (Δ_rG and Δ^‡G) of the paradigmatic reaction ethene + H₂O + H₃O⁺ → TS⁺ → ethanol + H₃O⁺ is attempted. It is argued that, despite the >5 kcal mol^-1 solvation errors for ions, it is possible to employ error cancellation strategies to reduce the errors in the reaction and activation Gibbs energies to 3 kcal mol^-1 accuracy. A new 3 kcal mol^-1 effect due to solvent-molecule "placement" (confinement from 1 M bulk concentration) was isolated and proved useful. Third, computational reproduction of the known entropies (Δ_rS and Δ^‡S) of the paradigmatic reaction is attempted using Trouton's constant and neglect of solvent structure reorganization effects (which must cancel well for this reaction); this worked well for Δ_rS but needs empirical correction of ∼11 cal mol^-1 K^-1 for Δ^‡S due to solvent disorientation when H₃O⁺ is consumed. These entropy estimates allow for enthalpy (Δ_rH and Δ^‡H) estimation from the Gibbs energy values. Fourth, two recommended options, including A + H₃O⁺·2W → [AHOH₂⁺·2W]^‡, are shown to also work well for the activations of propene and isobutene.

Solvation Free Energies and Adsorption Energies at the Metal/Water Interface from Hybrid Quantum-Mechanical/Molecular Mechanics Simulations

Modeling adsorption at metal/water interfaces is a cornerstone toward an improved understanding in a variety of fields from heterogeneous catalysis to corrosion. We propose and validate a hybrid scheme that combines the adsorption free energies obtained in the gas phase at the density functional theory level with the variation in solvation from the bulk phase to the interface evaluated using a MM-based alchemical transformation, denoted MMsolv. Using the GAL17 force field for the platinum/water interaction, we retrieve a qualitatively correct interaction energy of the water solvent at the interface. This interaction is of near chemisorption character and thus challenging, both for the alchemical transformation and also for the fixed point-charge electrostatics. Our scheme passes through a state characterized by a well-behaved physisorption potential for the Pt(111)/H₂O interaction to converge the free energy difference. The workflow is implemented in the freely available SolvHybrid package. We first assess the adsorption of a water molecule at the Pt/water interface, which turns out to be a stringent test. The intrinsic error of our quantum-mechanical/molecular mechanics (QM/MM) hybrid scheme is limited to 6 kcal mol^-1 through the introduction of a correction term to attenuate the electrostatic interaction between near-chemisorbed water molecules and the underlying Pt atoms. Next, we show that the MMsolv solvation free energy of Pt (-0.46 J m^-2) is in good agreement with the experimental estimate (-0.32 J m^-2). Furthermore, we show that the entropy contribution at room temperature is roughly of equal magnitude as the free energy but with an opposite sign. Finally, we compute the adsorption energy of benzene and phenol at the Pt(111)/water interface, one of the rare systems for which experimental data are available. In qualitative agreement with the experiment, but in stark contrast with a standard implicit solvent model, the adsorption of these aromatic molecules is strongly reduced (i.e., less exothermic by ∼30 and 40 kcal mol^-1 for our QM/MM hybrid scheme and experiment, respectively, but ∼0 with the implicit solvent) at the solid/liquid interface compared to the solid/gas interface. This reduction occurs mainly because of the competition between the organic adsorbate and the solvent for adsorption on the metallic surface. The semiquantitative agreement with experimental estimates for the adsorption energy of aromatic molecules thus validates the soundness of our hybrid QM/MM scheme.

Ab initio valence bond theory: A brief history, recent developments, and near future

This Perspective presents a survey of several issues in ab initio valence bond (VB) theory with a primary focus on recent advances made by the Xiamen VB group, including a brief review of the earlier history of the ab initio VB methods, in-depth discussion of algorithms for nonorthogonal orbital optimization in the VB self-consistent field method and VB methods incorporating dynamic electron correlation, along with a concise overview of VB methods for complex systems and VB models for chemical bonding and reactivity, and an outlook of opportunities and challenges for the near future of the VB theory.

Balanced polarizable Drude force field parameters for molecular anions: phosphates, sulfates, sulfamates, and oxides

Polarizable force fields are emerging as a more accurate alternative to additive force fields in terms of modeling and simulations of a variety of chemicals including biomolecules. Explicit treatment of induced polarization in charged species such as phosphates and sulfates offers the potential for achieving an improved atomistic understanding of the physical forces driving their interactions with their environments. To help achieve this, in this study we present balanced Drude polarizable force field parameters for molecular ions including phosphates, sulfates, sulfamates, and oxides. Better balance was primarily achieved in the relative values of minimum interaction energies and distances of the anionic model compounds with water at the Drude and quantum mechanical (QM) model chemistries. Parametrization involved reoptimizing available parameters as well as extending the force field to new molecules with the goal of achieving self-consistency with respect to the Lennard-Jones and electrostatic parameters targeting QM and experimental hydration free energies. The resulting force field parameters achieve consistent treatment across the studied anions, facilitating more balanced simulations of biomolecules and small organic molecules in the context of the classical Drude polarizable force field. Graphical abstract.

Prediction of Solvation Free Energies of Ionic Solutes in Neutral Solvents

The prediction of solvation free energies is essential for a variety of applications. Solvation free energies of neutral systems can be predicted quite accurately. The accuracy of predictions for solvation free energies of ionic solutes dissolved in neutral solvents, however, has been reported to be worse by at least 1 order of magnitude. In this study, the performance of three approaches for solvation free energy prediction of several hundred ions dissolved in neutral solvents is evaluated. The applied methods are COSMO-RS, cluster continuum model (CCM) together with COSMO-RS, and COSMO-RS-ES. It is emphasized that the reference data for model evaluation are subject to large uncertainties stemming from the impossibility to measure the so-called elusive absolute free energies of solvation of a single ion. Consequently, such uncertainty must be considered during the evaluation of prediction methods. Therefore, a straightforward approach to account for the underlying uncertainty is applied here. Hereby, it is revealed that the true performance of the method is better than what is often reported. The average absolute deviation (AAD) of COSMO-RS is calculated to be 2.3 kcal mol^-1, while applying the CCM and COSMO-RS-ES each results in AADs of 2.0 kcal mol^-1. This accuracy allows for qualitative assessment of solvation free energy-dependent quantities, such as reaction rate constants.

Tuning Supramolecular Selectivity for Hydrosulfide: Linear Free Energy Relationships Reveal Preferential C-H Hydrogen Bond Interactions

Supramolecular anion receptors can be used to study the molecular recognition properties of the reactive yet biologically critical hydrochalcogenide anions (HCh^-). Achieving selectivity for HCh^- over the halides is challenging but necessary for not only developing future supramolecular probes for HCh^- binding and detection, but also for understanding the fundamental properties that govern these binding and recognition events. Here we demonstrate that linear free energy relationships (LFERs)-including Hammett and Swain-Lupton plots-reveal a clear difference in sensitivity to the polarity of an aryl C-H hydrogen bond (HB) donor for HS^- over other HCh^- and halides. Analysis using electrostatic potential maps highlights that this difference in sensitivity results from a preference of the aryl C-H HB donor for HS^- in this host scaffold. From this study, we demonstrate that LFERs are a powerful tool to gain interpretative insight into motif design for future anion-selective supramolecular receptors and highlight the importance of C-H HB donors for HS^- recognition. From our results, we suggest that aryl C-H HB donors should be investigated in the next generation of HS^- selective receptors based on the enhanced HS^- selectivity over other competing anions in this system.

Chemical Equilibrium of Zinc Acetate Complexes in Ethanol Solution. A Theoretical Description through Thermodynamic Cycles

The Gibbs free energy of complexation between the Zn(II) species and acetate ligands, forming the [Zn(OAc)_n]^2-n complexes with n = 1, 2 in an ethanol solution, was assessed by two different theoretical protocols based on thermodynamic cycles. In both approaches, the solution phase Gibbs free energy of each reaction is computed by summing up contributions from gas phase thermochemistry calculations to solvation Gibbs free energies obtained in a hybrid fashion, i.e., each (neutral or electrically charged) solute was first solvated by explicit solvent molecules in order to capture relevant (micro) solute-solvent and/or solvent-solvent interactions and then, a continuum model calculation is performed in order to get the corresponding bulky solute-solvent contributions. For our first thermodynamic protocol, here denominated as variant 1, a set of x independent solvent molecules are used to screen each of the involved solutes, while the variant 2 strategy uses the fact that a set of solvent molecules may exist as aggregates (or molecular clusters) in the solvent macroscopic media, before the solvation process of solutes. Our selected quantum theoretical protocol was the M05-2X/6-31+G(d)/SMD level. We made a systematic exploration about the influence of several sources of errors, such as the solvent conformation, the number of solvent molecules used to screen each of the involved solutes, the coordination geometry of the metallic center before and after the complexation process, and the pertinence of using molecular geometries optimized in gas phase and in ethanol solution, for the computation of the Gibbs free energy variation regarding the two chemical reactions under study. We set an accuracy threshold equal or less than 4.0 kcal·mol^-1, with respect to the corresponding experimental records. The robustness of our thermodynamic strategies was then tested by computing the gas phase free energy contributions to the (solution phase) reaction free energies here assessed, using different density functional approximations, namely the M05-2X, BH&HLYP, PBE0, ωb97X-D and M06-2X functionals in conjunction with the larger 6-311+G(d,p) basis set.

Hybrid Solvation Model with First Solvation Shell for Calculation of Solvation Free Energy

We present a hybrid solvation model with first solvation shell to calculate solvation free energies. This hybrid model combines the quantum mechanics and molecular mechanics methods with the analytical expression based on the Born solvation model to calculate solvation free energies. Based on calculated free energies of solvation and reaction profiles in gas phase, we set up a unified scheme to predict reaction profiles in solution. The predicted solvation free energies and reaction barriers are compared with experimental results for twenty bimolecular nucleophilic substitution reactions. These comparisons show that our hybrid solvation model can predict reliable solvation free energies and reaction barriers for chemical reactions of small molecules in aqueous solution.

The SAMPL6 challenge on predicting octanol-water partition coefficients from EC-RISM theory

Results are reported for octanol–water partition coefficients (log P) of the neutral states of drug-like molecules provided during the SAMPL6 (Statistical Assessment of Modeling of Proteins and Ligands) blind prediction challenge from applying the “embedded cluster reference interaction site model” (EC-RISM) as a solvation model for quantum-chemical calculations. Following the strategy outlined during earlier SAMPL challenges we first train 1- and 2-parameter water-free (“dry”) and water-saturated (“wet”) models for n-octanol solvation Gibbs energies with respect to experimental values from the “Minnesota Solvation Database” (MNSOL), yielding a root mean square error (RMSE) of 1.5 kcal mol⁻¹ for the best-performing 2-parameter wet model, while the optimal water model developed for the pK_a part of the SAMPL6 challenge is kept unchanged (RMSE 1.6 kcal mol⁻¹ for neutral compounds from a model trained on both neutral and ionic species). Applying these models to the blind prediction set yields a log P RMSE of less than 0.5 for our best model (2-parameters, wet). Further analysis of our results reveals that a single compound is responsible for most of the error, SM15, without which the RMSE drops to 0.2. Since this is the only compound in the challenge dataset with a hydroxyl group we investigate other alcohols for which Gibbs energy of solvation data for both water and n-octanol are available in the MNSOL database to demonstrate a systematic cause of error and to discuss strategies for improvement.

Selective Oxidation of H2 and CO by NiIr Catalyst in Aqueous Solution: A DFT Mechanistic Study

One of the challenges in utilizing hydrogen gas (H₂) as a sustainable fossil fuel alternative is the inhibition of H₂ oxidation by carbon monoxide (CO), which is involved in the industrial production of H₂ sources. To solve this problem, a catalyst that selectively oxidizes either CO or H₂ or one that co-oxidizes H₂ and CO is needed. Recently, a NiIr catalyst [Ni^IICl(X)Ir^IIICl(η⁵-C₅Me₅)], (X = N,N'-dimethyl-3,7-diazanonane-1,9-dithiolate), which efficiently and selectively oxidizes either H₂ or CO depending on the pH, has been developed (Angew. Chem. Int. Ed. 2017, 56, 9723-9726). In the present work, density functional theory (DFT) calculations are employed to elucidate the pH-dependent reaction mechanisms of H₂ and CO oxidation catalyzed by this NiIr catalyst. During H₂ oxidation, our calculations suggest that dihydrogen binds to the Ir center and generates an Ir(III)-dihydrogen complex, followed by subsequent isomerization to an Ir(V)-dihydride species. Then, a proton is abstracted by a buffer base, CH₃COO^-, resulting in the formation of a hydride complex. The catalytic cycle completes with electron transfer from the hydride complex to a protonated 2,6-dichlorobenzeneindophenol (DCIP) and a proton transfer from the oxidized hydride complex to a buffer base. The CO oxidation mechanism involves three distinct steps, i.e., (1) formation of a metal carbonyl complex, (2) formation of a metallocarboxylic acid, and (3) conversion of the metallocarboxylic acid to a hydride complex. The formation of the metallocarboxylic acid involves nucleophilic attack of OH^- to the carbonyl-C followed by a large structural change with concomitant cleavage of the Ir-S bond and rotation of the COOH group along the NiIr axis. During the conversion of the metallocarboxylic acid to the hydride complex, intramolecular proton transfer followed by removal of CO₂ leads to the formation of the hydride complexes. In addition, the barrier heights for the binding of small molecules (H₂, OH^-, H₂O, and CO) to Ir were calculated, and the results indicated that dissociation from Ir is a faster process than the binding of H₂O and H₂. These calculations indicate that H₂ oxidation is inhibited by CO and OH^- and thus prefers acidic conditions. In contrast, the CO oxidation reactions occur more favorably under basic conditions, as the formation of the metallocarboxylic acid involves OH^- attack to a carbonyl-C and the binding of OH^- to Ni largely stabilizes the triplet spin state of the complex. Taken together, these calculations provide a rationale for the experimentally observed pH-dependent, selective oxidations of H₂ and CO.

Oligomerization of Silicic Acids in Neutral Aqueous Solution: A First-Principles Investigation

Crystallite aluminosilicates are inorganic microporous materials with well-defined pore-size and pore-structures, and have important industrial applications, including gas adsorption and separation, catalysis, etc. Crystallite aluminosilicates are commonly synthesized via hydrothermal processes, where the oligomerization of silicic acids is crucial. The mechanisms for the oligomerization of poly-silicic acids in neutral aqueous solution were systematically investigated by extensive first-principles-based calculations. We showed that oligomerization of poly-silicic acid molecules proceeds through the lateral attacking and simultaneously proton transfer from the approaching molecule for the formation of a 5-coordinated Si species as the transition state, resulting in the ejection of a water molecule from the formed poly-silicic acid. The barriers for this mechanism are in general more plausible than the conventional direct attacking of poly-silicic acid with reaction barriers in the range of 150–160 kJ/mol. The formation of linear or branched poly-silicic acids by intermolecular oligomerization is only slightly more plausible than the formation of cyclic poly-silicic acids via intramolecular oligomerization according to the reaction barriers (124.2–133.0 vs. 130.6–144.9 kJ/mol). The potential contributions of oligomer structures, such as the length of the linear oligomers, ring distortions and neighboring linear branches, etc., to the oligomerization were also investigated but found negligible. According to the small differences among the reaction barriers, we proposed that kinetic selectivity of the poly-silicic acids condensation would be weak in neutral aqueous solution and the formation of zeolite-like structures would be thermodynamics driven.

Novel Insights into Gallium's Mechanism of Therapeutic Action: A DFT/PCM Study of the Interaction between Ga3+ and Ribonucleotide Reductase Substrates

The broadly accepted mechanism of gallium's therapeutic action postulates the inactivation of the upregulated/hyperactive enzyme ribonucleotide reductase (RNR) in cancer cells by substituting the redox-active iron by redox-silent gallium in the enzyme active site. Recently, another hypothesis for the Ga³⁺ curative effect has been put forward: the metal cation can deactivate the enzyme by entrapping its substrates (nucleotide diphosphates; NDPs) into Ga³⁺-NDP complexes, lowering the free substrate levels in the cell. Several questions arise: Does gallium readily form complexes with NDPs? What are the preferable modes of metal binding to NDPs? Does, and if so, to what extent, the metal binding alter the native conformation of the substrate, thus influencing the process of substrate-enzyme recognition? Here, by employing density functional theory (DFT)/polarizable continuum model (PCM) calculations, we attempt to answer these questions. The results, which are in line with the available experimental data, lay support to the recent hypothesis about the curative effect of gallium, revealing that, by engaging the free NDPs in forming metal complexes, on the one side, and producing metal constructs that are not/poorly recognizable by the host enzyme, on the other side, gallium deprives RNR from its substrates, thus reducing the enzyme activity in malignant cells.

LigParGen web server: an automatic OPLS-AA parameter generator for organic ligands

The accurate calculation of protein/nucleic acid–ligand interactions or condensed phase properties by force field-based methods require a precise description of the energetics of intermolecular interactions. Despite the progress made in force fields, small molecule parameterization remains an open problem due to the magnitude of the chemical space; the most critical issue is the estimation of a balanced set of atomic charges with the ability to reproduce experimental properties. The LigParGen web server provides an intuitive interface for generating OPLS-AA/1.14*CM1A(-LBCC) force field parameters for organic ligands, in the formats of commonly used molecular dynamics and Monte Carlo simulation packages. This server has high value for researchers interested in studying any phenomena based on intermolecular interactions with ligands via molecular mechanics simulations. It is free and open to all at jorgensenresearch.com/ligpargen, and has no login requirements.

The multiple dissociation constants of glutathione disulfide: interpreting experimental pH-titration curves with ab initio MD simulations

The hexapeptide glutathione disulfide (GSSG) has six ionizable groups with six associated dissociation constants. The experimentally measured pH-titration curve, however, does not exhibit the six corresponding equivalence points and bears little resemblance to standard textbook examples of acid-base pH-titration curves. The curve highlights the difficulties in determining multiple pKa values of polyprotic acids - typically proteins and peptides - from experiment. The six pKa values of GSSG can, however, be estimated using Car-Parrinello molecular dynamics (CPMD) simulations in conjunction with metadynamics sampling of the underlying free energy landscape of the dissociation reactions. Ab initio MD simulations were performed on a GSSG molecule solvated by 200 water molecules. Using the estimated pKa values the theoretical titration curve was calculated and found to be in good agreement with experiment. The results clearly highlight how dissociation constants estimated from ab initio MD simulations can facilitate the interpretation of the pH-titration curves of complex chemical and biological systems.

C-F activation of perfluorophenazine at nickel: selectivity and mechanistic investigations

The reactivity of [Ni(cod)2] towards perfluorophenazine in the presence of phosphines is reported. When PiPr3 and PCy3 are used, an initial κ-(N) coordination of the nickel centre to the nitrogen atom of the perfluorophenazine ring occurs, forming the dark blue complexes [Ni{κ-(N)-C12N2F8}(PiPr3)2] (1) and [Ni{κ-(N)-C12N2F8}(PCy3)2] (2). Complex 1 was structurally characterized by X-ray diffraction analysis. The complexes rearranged by regioselective C-F activation of the perfluorophenazine ring in the 2-position to yield complexes trans-[NiF(2-C12N2F7)(PiPr3)2] (5) and trans-[NiF(2-C12N2F7)(PCy3)2] (6). The structure of 6 was also determined by X-ray diffraction analysis. Kinetic measurements for the decrease of 1 at different temperatures reveal a first order reaction with ΔH‡ = 19 ± 7 kcal mol-1. Initially, small amounts of an intermediate, assigned as [Ni(η2-1,2-C12N2F8)(PiPr3)2] (3), were observed, which exhibits a 1,2-η2 coordination of the perfluorophenazine. DFT calculations on the same transformation were also computed, which suggest that both a phosphine-assisted mechanism and an oxidative addition can be operating reaction pathways. The 1,2-η2 complex [Ni(η2-1,2-C12N2F8)(PEt3)2] (4) was obtained when PEt3 was used as ligand, and an unstable dark red complex trans-[NiF(2-C12N2F7)(PEt3)2] (7) formed rapidly by C-F activation. The reactivity of the perfluorophenazine was compared with those of perfluorodibenzo-p-dioxin. In this case, no prior coordination was observed and the C-F activation took place in a less selective manner forming trans-[NiF(1-C12O2F7)(PiPr3)2] (8) and trans-[NiF(2-C12O2F7)(PiPr3)2] (9), outlining the role of the nitrogen for the selectivity of the process. Treatment of two equivalents of [Ni(cod)2] and four equivalents of PiPr3 with perfluorophenazine afforded a double C-F activation to give [{trans-(PiPr3)2NiF}2(2,7-C12N2F6)] (10).

Solvation Entropy Made Simple

The entropies of molecules in solution are often calculated using gas phase formulas. It is assumed that, because implicit solvation models are fitted to reproduce free energies, this is sufficient for modeling reactions in solution. However, this procedure exaggerates entropic effects in processes that change molecularity. Here, computationally efficient (i.e., having similar cost as gas phase entropy calculations) approximations for determining solvation entropy are proposed to address this issue. The S_ω, S_ϵ, and S _ϵα models are nonempirical and rely only on physical arguments and elementary properties of the medium (e.g., density and relative permittivity). For all three methods, average errors as compared to experiment are within chemical accuracy for 110 solvation entropies, 11 activation entropies in solution, and 32 vaporization enthalpies. The models also make predictions regarding microscopic and bulk properties of liquids which prove to be accurate. These results imply that Δ H_sol and Δ S_sol can be described separately and with less reliance on parametrization by a combination of the methods presented here with existing, reparametrized, implicit solvation models.

Quantum Chemical Study of the Mechanism of Water Oxidation Catalyzed by a Heterotrinuclear Ru2 Mn Complex

The heterotrinuclear complex A {[Ru^II (H₂ O)(tpy)]₂ (μ-[Mn^II (H₂ O)₂ (bpp)₂ ])}⁴⁺ [tpy=2,2':6',2''-terpyridine, bpp=3,5-bis(2-pyridyl)pyrazolate] was found to catalyze water oxidation both electrochemically and photochemically with [Ru(bpy)₃ ]³⁺ (bpy=2,2'-bipyridine) as the photosensitizer and Na₂ S₂ O₈ as the electron acceptor in neutral phosphate buffer. The mechanism of water oxidation catalyzed by this unprecedented trinuclear complex was studied by density functional calculations. The calculations showed that a series of oxidation and deprotonation events take place from A, leading to the formation of complex 1 (formal oxidation state of Ru1^IV Mn^III Ru2^III ), which is the starting species for the catalytic cycle. Three sequential oxidations of 1 result in the generation of the catalytically competing species 4 (formal oxidation state of Ru1^IV Mn^V Ru2^IV ), which triggers the O-O bond formation. The direct coupling of two adjacent oxo ligands bound to Ru and Mn leads to the production of a superoxide intermediate Int1. This step was calculated to have a barrier of 7.2 kcal mol^-1 at the B3LYP*-D3 level. Subsequent O₂ release from Int1 turns out to be quite facile. Other possible pathways were found to be much less favorable, including water nucleophilic attack, the coupling of an oxo and a hydroxide, and the direct coupling pathway at a lower oxidation state (Ru^IV Mn^IV Ru^IV ).

Solvation Free Energy Calculation Using a Fixed-Charge Model: Implicit and Explicit Treatments of the Polarization Effect

In this work, IPolQ-Mod charges and the reference potential scheme are used to calculate the solvation free energies of a set of organic molecules. Both methods could capture the phase transfer of a solute with accompanying polarization cost utilizing a fixed-charge model. The IPolQ-Mod charges, which are the average of two charge sets fitted in a vacuum state and a condensed phase, take account of the polarization effect implicitly. For the reference potential method, the quantum mechanics polarization corrections are calculated explicitly by thermodynamic perturbation. The polarization effect captured by the IPolQ-Mod charges is an approximation to that of the reference potential method theoretically. In the present study, the reference potential method shows a slight improvement over the classical restrained electrostatic potential (RESP) charges, which perform pretty well in predicting the solvation free energy. However, IPolQ-Mod(MP2) shows a poor agreement with the experimental data. Compared with IPolQ-Mod(MP2), IPolQ-Mod(M06-2X) or IPolQ-Mod(ωB97X) is found to give more appropriate prediction of the molecule's dipole and the solvation free energies calculated by IPolQ-Mod(M06-2X) or IPolQ-Mod(ωB97X) are more compatible with those of the RESP charges. If the other force field parameters remain unchanged, M06-2X or ωB97X is recommended to derive the IPolQ-Mod charges.

Theoretical insights into the structural, photophysical and nonlinear optical properties of phenoxazin-3-one dyes

Here we investigate the structural, photophysical and nonlinear optical (NLO) properties of phenoxazin-3-one dyes, resazurin (Rz) and resorufin (Rf), by performing quantum chemical calculations using the DFT and TDDFT methods.

Atomic Charges in Highly Ionic Diatomic Molecules

Atomic charges were investigated as functions of detectable atomic and molecular constants at equilibrium structures. It was found based upon the variation idea that atomic charges in highly ionic molecules can be expressed as a function of molecular dipole moments, polarizabilities of free cations, and polarizabilities of free neutral atoms of the corresponding anions. The function can be given in the form of classical Rittner's relationship (J. Chem. Phys. 1951, 19, 1030). For the ground states of alkali halide molecules, the predicted atomic charges are close to an elementary charge e and the predicted dipole moments are in good agreement with the observed values; for spin-restricted high-ionic systems such as the lowest ⁹Σ electronic states of BN, AlN, GaN, BP, AlP, GaP, BAs, AlAs, and GaAs molecules, the predicted atomic charges are also near 1e and in good agreement with the results of natural population analysis at MRCI/cc-pvqz and HF/6-311+G(3df) levels. Polarizabilities for the lowest quintet states of B^-, Al^-, Ga^-, N⁺, P⁺, and As⁺ ions were also obtained based upon high-level ab initio computations. Atomic charges from other related methods are also investigated for comparison. The results demonstrate that high-quality atomic charges can be obtained with detectable variables, such as molecular dipole moment, vibrational frequency, as well as polarizabilities of the related free atoms and ions.

Theoretical study on the acidities of pyrrole, indole, carbazole and their hydrocarbon analogues in DMSO

SMD and IEF-PCM continuum solvation models have been used, in combination with three quantum chemistry methods (B3LYP, M062X, and CBS-QB3), to study the acidities of pyrrole, indole, and carbazole, as well as their hydrocarbon analogues in DMSO, following a direct thermodynamic method. Theoretical parameters such as aromaticity indices (HOMA and SA), molecular electrostatic potential (MEP), and atomic charges have been calculated using B3LYP/6-311++G(d,p) level of theory. Calculated pKa values indicate that there is generally good agreement with experimental data, with all deviations being less than the acceptable error for directly calculated pKa values. The M062X functional combined with the SMD solvation model provided the most accurate pKa values. The MEP surfaces clearly show the electron density change accompanying the deprotonation process and explain the relative stability of conjugate bases. The HOMA aromaticity indices seem to be directly related to acidity strength. The collected data have been used to elucidate the pKa trends for the series of molecules under consideration.

Metal-Substrate Cooperation Mechanism for Dehydrogenative Amidation Catalyzed by a PNN-Ru Catalyst

The pyridine-based PNN ruthenium pincer complex (PNN)Ru(CO)(H) can catalyze the well-known dehydrogenative amidation reaction, but the mechanism is not fully understood. In this work, we find there exists an alternative metal-substrate cooperation mechanism in this reaction system, which is more favorable than the aromatization-dearomatization mechanism. The possible reaction of the excess base t-BuO^- with catalyst species (PNN)Ru(CO)(H) is studied, indicating t-BuO^- is able to facilitate the ligand substitution and enhance catalytic activities. With the bifunctional Ru-N moiety, the imine-substituted species (PN)(imine)Ru(CO)(H) 5 could serve as an alternative catalytic species and efficiently facilitate some elementary steps such as the hydrogen transfer, hydrogen elimination, and C-N coupling. Meanwhile, the C-N coupling step proceeds via the split of aldehydic C-H bond across the Ru(II)-imine bond, which results in an amide bond directly. The hemiaminal is uninvolved in the C-N coupling process. Finally, the formation of linear peptides and cyclic dipeptides are unveiled by the newly proposed mechanism. The metal-substrate cooperation could widely exist in transition metal catalyst systems with a large influence on the reaction activity.

Polarizable Force Field for Molecular Ions Based on the Classical Drude Oscillator

Development of accurate force field parameters for molecular ions in the context of a polarizable energy function based on the classical Drude oscillator is a crucial step toward an accurate polarizable model for modeling and simulations of biological macromolecules. Toward this goal we have undertaken a hierarchical approach in which force field parameter optimization is initially performed for small molecules for which experimental data exists that serve as building blocks of macromolecular systems. Small molecules representative of the ionic moieties of biological macromolecules include the cationic ammonium and methyl substituted ammonium derivatives, imidazolium, guanidinium and methylguanidinium, and the anionic acetate, phenolate, and alkanethiolates. In the present work, parameters for molecular ions in the context of the Drude polarizable force field are optimized and compared to results from the nonpolarizable additive CHARMM general force field (CGenFF). Electrostatic and Lennard-Jones parameters for the model compounds are developed in the context of the polarizable SWM4-NDP water model, with emphasis on assuring that the hydration free energies are consistent with previously reported parameters for atomic ions. The final parameters are shown to be in good agreement with the selected quantum mechanical (QM) and experimental target data. Analysis of the structure of water around the ions reveals substantial differences between the Drude and additive force fields indicating the important role of polarization in dictating the molecular details of aqueous solvation. The presented parameters represent the foundation for the charged functionalities in future generations of the Drude polarizable force field for biological macromolecules as well as for drug-like molecules.

Quantum Chemistry Study on the Extraction of Trivalent Lanthanide Series by Cyanex301: Insights from Formation of Inner- and Outer-Sphere Complexes

The extraction of lanthanide series by Cyanex301, i.e., bis(2,4,4-trimethylpentyl)dithiophosphinic acid (HC301), has been modeled by density functional theory calculation, taking into account the formation of both inner- and outer-sphere complexes. The inner-sphere complex Ln(C301)₃ and the outer-sphere complex Ln(H₂O)₉(C301)₃ are optimized, followed by the analysis of interaction energy, bond length, Laplacian bond orders, and Mulliken populations. The covalency degree increases in Ln-S and Ln-O bonds in the inner- and outer-sphere complexes, respectively, as the lanthanide series is traversed. Mulliken population analysis indicates the important role of the 5d-orbital participation in bonding in the formation of inner- and outer-sphere complexes. Two thermodynamic cycles regarding the formation of inner- and outer-sphere complexes are established to calculate the extraction Gibbs free energies (ΔG _extr), and relaxed potential energy surface scan is utilized to model the kinetic complexation of C301 anion with hydrated metal ions. Light lanthanides can form both inner- and outer-sphere complexes, whereas heavy lanthanides only form outer-sphere complexes in biphasic extraction. After adopting the data of forming inner-sphere complex for light Ln(III) and that of forming outer-sphere complexes for heavy Ln(III), the trend of the calculated -ΔG _extr agrees very well with that of the experimental distribution ratios on crossing the Ln(III) series. Results from this work help to theoretically understand the extraction behavior of Cyanex301 with respect to different Ln(III).

Mechanism of Water Oxidation Catalyzed by a Mononuclear Iron Complex with a Square Polypyridine Ligand: A DFT Study

The mononuclear [Cl-Fe^III(dpa)-Cl]⁺ (1_Cl) complex containing a square planar tetradentate polypyridine ligand has been reported to catalyze water oxidation in pH = 1 aqueous medium with ceric ammonium nitrate (CAN) as a chemical oxidant. The reaction mechanism of the oxygen evolution driven by this catalyst was investigated by means of density functional calculations. The results showed that one chloride ligand of 1_Cl has to exchange with a water molecule to generate 1, [Cl-Fe^III(dpa)-OH₂]²⁺, as the starting species of the catalytic cycle. The initial one-electron oxidation of 1 is coupled with the release of two protons, generating [Cl-Fe^IV(dpa)═O]⁺ (2). Another one-electron transfer from 2 leads to the formation of an Fe^V═O complex [Cl-Fe^V(dpa)═O]²⁺ (3), which triggers the critical O-O bond formation. The electronic structure of 3 was found to be very similar to that of the high-valent heme-iron center of P450 enzymes, termed Compound I, in which a π-cation radical ligand is believed to support a formal iron(IV)-oxo core. More importantly, 3 and Compound I share the same tendency toward electrophilic reactions. Two competing pathways were suggested for the O-O bond formation based on the present calculations. One is the nitrate nucleophilic attack on the iron(V)-oxo moiety with a total barrier of 12.3 kcal mol^-1. In this case, nitrate functions as a co-catalyst for the dioxygen formation. The other is the water nucleophilic attack on iron(V)-oxo with a greater barrier of 16.5 kcal mol^-1. In addition, ligand degradation via methyl hydrogen abstraction was found to have a barrier similar to that of the O-O bond formation, while the aromatic carbon hydroxylation has a higher barrier.

Generalized Born implicit solvent models for small molecule hydration free energies

Hydration free energy estimation of small molecules from all-atom simulations was widely investigated in recent years, as it provides an essential test of molecular force fields and our understanding of solvation effects. While explicit solvent representations result in highly accurate models, they also require extensive sampling due to the high number of solvent degrees of freedom. Implicit solvent models, such as those based on the generalized Born model for electrostatic solvation effects and a solvent accessible surface area term for nonpolar contributions (GBSA), significantly reduce the number of degrees of freedom and the computational cost to estimate hydration free energies. However, a recent survey revealed a gap in the accuracy between explicit TIP3P solvent estimates and those computed with many common GBSA models. Here we address this shortcoming by providing a thorough comparison of the performance of three implicit solvent models with different nonpolar contributions and a generalized Born term to estimate experimental hydration free energies. Starting with a minimal set of only ten atom types, we demonstrate that a nonpolar term with atom type dependent surface tension coefficients in combination with an accurate generalized Born term and fully optimized parameters performs best in estimating hydration free energies, even yielding comparable results to the explicit TIP3P water model. Analysis of our results provides evidence that the asymmetric behavior of water around oppositely charged atoms is one of the main sources of error for two of the three implicit solvent models. Explicitly accounting for this effect in the parameterization reduces the corresponding errors, suggesting this as a general strategy for improving implicit solvent models. The findings presented here will help to improve the existing generalized Born based implicit solvent models implemented in state-of-the-art molecular simulation packages.

Origin of the overpotentials for HCOO− and CO formation in the electroreduction of CO2 on Cu(211): the reductive desorption processes decide

Potential-related free energy profiles of CO and HCOO⁻ pathways in CO₂RR on Cu(211) are computed with implicit solvent model.

Comparison of RESP and IPolQ-Mod Partial Charges for Solvation Free Energy Calculations of Various Solute/Solvent Pairs

The calculation of solvation free energies ΔG_solv by molecular simulations is of great interest as they are linked to other physical properties such as relative solubility, partition coefficient, and activity coefficient. However, shortcomings in molecular models can lead to ΔG_solv deviations from experimental data. Various studies have demonstrated the impact of partial charges on free energy results. Consequently, calculation methods for partial charges aimed at more accurate ΔG_solv predictions are the subject of various studies in the literature. Here we compare two methods to derive partial charges for the general AMBER force field (GAFF), i.e. the default RESP as well as the physically motivated IPolQ-Mod method that implicitly accounts for polarization costs. We study 29 solutes which include characteristic functional groups of drug-like molecules, and 12 diverse solvents were examined. In total, we consider 107 solute/solvent pairs including two water models TIP3P and TIP4P/2005. Comparison with experimental results yields better agreement for TIP3P, regardless of the partial charge scheme. The overall performance of GAFF/RESP and GAFF/IPolQ-Mod is similar, though specific shortcomings in the description of ΔG_solv for both RESP and IPolQ-Mod can be identified. However, the high correlation between free energies obtained with GAFF/RESP and GAFF/IPolQ-Mod demonstrates the compatibility between the modified charges and remaining GAFF parameters.

A DFT investigation of the blue bottle experiment: E∘half-cell analysis of autoxidation catalysed by redox indicators

The blue bottle experiment is a collective term for autoxidation reactions catalysed by redox indicators. The reactions are characterized by their repeatable cycle of colour changes when shaken/left to stand and intricate chemical pattern formation. The blue bottle experiment is studied based on calculated solution-phase half-cell reduction potential of related reactions. Our investigation confirms that the reaction in various versions of the blue bottle experiment published to date is mainly the oxidation of an acyloin to a 1,2-dicarbonyl structure. In the light of the calculations, we also propose new non-acyloin reducing agents for the experiment. These results can help guide future experimental studies on the blue bottle experiment.