Critical Evaluation of Implicit Solvent Models for Predicting Aqueous Oxidation Potentials of Neutral Organic Compounds

BODIPY-Based Macrostructures: A Design Strategy toward Enhancing the Efficiency of Dye-Sensitized Solar Cells

Among the metal-free dyes, boron dipyrromethene (BODIPY) has attracted much attention in the solar cell industry due to its thermal stability and tunable electronic and photophysical properties. However, the low power conversion efficiency of dye-sensitized solar cells based on BODIPY has limited their widespread application. Accordingly, different types of structural modifications have already been proposed to improve the photophysical properties of the BODIPY dyes. In this study, we used the strategy of constructing BODIPY-based covalent macrostructures by integrating two BODIPY subunits via a π-linker in linear and cyclic configurations. To this end, various types of the π-linkers including butadiyne, phenyl, and thiophene derivatives are considered. The structural, electronic, and optical properties as well as the photovoltaic performance of BODIPY dimers are theoretically calculated within DCM solvent. The results indicate that for a given linker, the BODIPY dimers with a linear configuration show better performance as compared to their macrocyclic counterparts. The reason is the enhancement of π-conjugation length, higher light harvesting ability, and proper charge carrier separation in linearly linked BODIPYs. In the cyclic series, the dyes incorporating phenyl linkers exhibit greater power conversion efficiency of up to 9%. For the dyes with a linear configuration, the involvement of a thienyl-thiophene bridge results in lower charge recombination and enhances the efficiency by up to 15%, which are expected to be potential candidates for organic dyes applied in DSSCs.

Mesoporous Single Atom-Cluster Fe-N/C Oxygen Evolution Electrocatalysts Synthesized with Bottlebrush Block Copolymer-Templated Rapid Thermal Annealing

Current electrocatalysts for oxygen evolution reaction (OER) are either expensive (such as IrO2, RuO2) or/and exhibit high overpotential as well as sluggish kinetics. This article reports mesoporous earth-abundant iron (Fe)-nitrogen (N) doped carbon electrocatalysts with iron clusters and closely surrounding Fe-N4 active sites. Unique to this work is that the mechanically stable mesoporous carbon-matrix structure (79 nm in pore size) with well-dispersed nitrogen-coordinated Fe single atom-cluster is synthesized via rapid thermal annealing (RTA) within only minutes using a self-assembled bottlebrush block copolymer (BBCP) melamine-formaldehyde resin composite template. The resulting porous structure and domain size can be tuned with the degree of polymerization of the BBCP backbone, which increases the electrochemically active surface area and improves electron transfer and mass transport for an effective OER process. The optimized electrocatalyst shows a required potential of 1.48 V (versus RHE) to obtain the current density of 10 mA/cm2 in 1 M KOH aqueous electrolyte and a small Tafel slope of 55 mV/decade at a given overpotential of 250 mV, which is significantly lower than recently reported earth-abundant electrocatalysts. Importantly, the Fe single-atom nitrogen coordination environment facilitates the surface reconstruction into a highly active oxyhydroxide under OER conditions, as revealed by X-ray photoelectron spectroscopy and in situ Raman spectroscopy, while the atomic clusters boost the single atoms reactive sites to prevent demetalation during the OER process. Density functional theory (DFT) calculations support that the iron nitrogen environment and reconstructed oxyhydroxides are electrocatalytically active sites as the kinetics barrier is largely reduced. This work has opened a new avenue for simple, rapid synthesis of inexpensive, earth-abundant, tailorable, mechanically stable, mesoporous carbon-coordinated single-atom electrocatalysts that can be used for renewable energy production.

A combined experimental-molecular modeling study of crown ether europium complexes: Effects of the coordinated anion on structural and luminescence properties

It is reported the synthesis, characterization by elemental analysis, thermogravimetry; electronic absorption, infrared, excitation, and emission spectroscopies of the [Eu(12C4)(phen)2(X)n]X2 complexes, where 12C4 = 12-crown-4, phen = 1,10-phenanthroline, and X  = F-, Cl-, Br-, SCN-, ClO4-, and NO3-. It is verified that the polarizability of the anion X- exerts remarkable effects on the emission process. As a general trend, lower wavenumbers for the 7F0→5L6, 7F0→5D2 and 7F0→5D1 transitions are associated with the anions with higher volumes and, consequently, higher polarizability. The molecular modeling results performed with quantum methods (RHF and DFT) suggest some relationships between the calculated structures, electronic, and luminescence properties with the presence of the LMCT (ligand-to-metal charge transfer) states, which explains the differences in the emission spectra of these complexes due to the coordinated anion.

Stability of the protactinium(V) mono-oxo cation probed by first-principle calculations

This study explores the distinctive behavior of protactinium (Z=91) within the actinide series. In contrast to neighboring elements like uranium or plutonium, protactinium in the pentavalent state diverges by not forming the typical dioxo protactinyl moiety PaO2 + in aqueous phase. Instead, it manifests as a monooxo PaO3+ cation or a Pa5+ . Employing first-principle calculations with implicit and explicit solvation, we investigate two stoichiometrically equivalent neutral complexes: PaO(OH)2 (X)(H2 O) and Pa(OH)4 (X), where X represents various monodentate and bidentate ligands. Calculating the Gibbs free energy for the reaction PaO(OH)2 (X)(H2 O)→Pa(OH)4 (X), we find that the PaO(OH)2 (X)(H2 O) complex is stabilized with Cl- , Br- , I- , NCS- , NO3 - , and SO4 2- ligands, while it is not favored with OH- , F- , and C2 O4 2- ligands. Quantum Theory of Atoms in Molecules (QTAIM) and Natural Bond Orbital (NBO) methods reveal the Pa mono-oxo bond as a triple bond, with significant contributions from the 5f and 6d shells. Covalency of the Pa mono-oxo bond increases with certain ligands, such as Cl- , Br- , I- , NCS- , and NO3 - . These findings elucidate protactinium's unique chemical attributes and provide insights into the conditions supporting the stability of relevant complexes.

DFT investigation on the structural and vibrational behaviours of the non-protein amino acids in hybrid explicit/continuum solvent: a case of the zwitterions γ-aminobutyric and α - aminoisobutyric acids

BACKGROUND

The influence of hybrid solvation models on the molecular structures and vibrational characteristics of g-aminobutyric acid (GABA) and a-aminoisobutyric acid (AIB) zwitterions was assessed by employing a variety of Density Functional Theory (DFT). The quantum chemical methods included the B3LYP and B3PW91 hybrid functionals and the 6‑311++G(d,p) basis set.

METHODS

The most stable conformation derived from the potential energy surface (PES) scans using the B3LYP/6-311++G(d,p) model chemistry for each studied molecule was predicted within a continuum environment represented by the COSMO and SMD solvation models. The stable structures were subsequently immersed in explicit/COSMO and explicit/SMD hybrid solvation models, where 10 and 8 water molecules were explicitly positioned around the functional groups of the GABA and AIB zwitterions, respectively. The number of water molecules chosen was sufficient to prevent proton transfer among the carboxylate group (COO-) and the ammonium group (NH3+) within each molecule under investigation. After optimizing the geometry of each hydrated complex, the normal vibrational modes were determined. The scaled theoretical frequencies obtained from the various model chemistries were then compared to available experimental data from infrared (IR) and Raman spectroscopy.

RESULTS

In the case of GABA and AIB molecules, the comparisons revealed that the B3LYP/6-311++G(d,p) model chemistry yielded wavenumber values that closely matched the experimental IR and Raman data, particularly when the explicit/SMD solvent was employed. The computed results indicate deviations of less than 4% when compared to the experimental data for the two molecules under investigation.

Unlocking the Potential: Predicting Redox Behavior of Organic Molecules, from Linear Fits to Neural Networks

Redox-active organic molecules, i.e., molecules that can relatively easily accept and/or donate electrons, are ubiquitous in biology, chemical synthesis, and electronic and spintronic devices, such as solar cells and rechargeable batteries, etc. Choosing the best candidates from an essentially infinite chemical space for experimental testing in a target application requires efficient screening approaches. In this Review, we discuss modern in silico techniques for predicting reduction and oxidation potentials of organic molecules that go beyond conventional first-principles computations and thermodynamic cycles. Approaches ranging from simple linear fits based on molecular orbital energy approximation and energy difference approximation to advanced regression and neural network machine learning algorithms employing complex descriptors of molecular compositions, geometries, and electronic structures are examined in conjunction with relevant literature examples. We discuss the interplay between ab initio data and machine learning (ML), i.e., whether it is better to base predictions on low-level quantum-chemical results corrected with ML or to bypass first-principles computations entirely and instead rely on elaborate deep learning architectures. Finally, we list currently available data sets of redox-active organic molecules and their experimental and/or computed properties to facilitate the development of screening platforms and rational design of redox-active organic molecules.

Berberine isolation from Coscinium fenestratum: optical, electrochemical, and computational studies

Berberine was extracted from Coscinium fenestratum (tree turmeric) and purified by column chromatography. The UV-Vis absorption spectroscopy of berberine was studied in acetonitrile and aqueous media. TD-DFT calculations employing the B3LYP functional were found to reproduce the general features of the absorption and emission spectra correctly. The electronic transitions to the first and second excited singlet states involve a transfer of electron density from the electron donating methylenedioxy phenyl ring to the electron accepting isoquinolium moiety. An estimate of the electrochemical gap (2.64 V) was obtained from microelectrode voltammetry and good agreement was found with quantum chemical calculations using the cc-pVTZ basis set and the B3LYP, CAM-B3LYP and wB97XD functionals. The calculations indicate spin density of the radical dication is delocalised over the molecule. These basic data are useful for assessment of the synthesis of donor-acceptor polymeric materials employing oxidative polymerization or co-polymerisation of berberine.

Factor analysis of error in oxidation potential calculation: A machine learning study

The conductor-like polarizable continuum model (C-PCM), which is a low-cost solvation model, cannot treat characteristic interactions between the solvent and substructure(s) of the solute. Moreover, the error in a charged system is significant. Using machine learning, we clarified that the systematic error of the oxidation potential calculated by the G3B3/C-PCM was correlated with the molecular size of a solute. The G3B3/C-PCM overestimated the Gibbs oxidation energy by averaging 6.94 kcal/mol. According to the performance of related methods reported in previous studies, this error is mainly due to the solvation energy of the charged solute. Additionally, we succeeded in reducing the error to 2.27 kcal/mol (32%)-3.2 kcal/mol (40%) by correction based on the substructure information of the solute. To modify the C-PCM, effects that correlate with the molecular size of the solute in the charged system should be incorporated.

Graphene-Supported Naphthalene-Based Polyimide Composite as a High-Performance Sodium Storage Cathode

Electroactive acid anhydride with multicarbonyl is highly promising for electrochemical energy storage because of its high specific capacity and environmental benignity. Its low electrical conductivity and high dissolution in organic electrolyte, however, result in poor cycling and rate capabilities. Here, we report a naphthalene polyimide derivative (NPI) synthesized by using anhydride under condensation polymerization conditions, along with its composite with graphene (NPI-G) fabricated via in situ polymerization. The composite delivers a high reversible capacity and outstanding cycling stability and rate capability as a cathode for sodium-ion batteries (SIBs) owing to the formation of a polymer, the improvement in the electrical conductivity brought about by the highly dispersed graphene sheets, and the enhancement of structural stability resulting from the π-π stacking interaction between the phenyl groups of NPI and the six-member carbon rings of graphene. This investigation sheds light on the development, design, and screening of next-generation organic electrode materials with high performance for SIBs.

Ionization Energies and Redox Potentials of Hydrated Transition Metal Ions: Evaluation of Domain-Based Local Pair Natural Orbital Coupled Cluster Approaches

Hydrated transition metal ions are prototypical systems that can be used to model properties of transition metals in complex chemical environments. These seemingly simple systems present challenges for computational chemistry and are thus crucial in evaluations of quantum chemical methods for spin-state and redox energetics. In this work, we explore the applicability of the domain-based pair natural orbital implementation of coupled cluster (DLPNO-CC) theory to the calculation of ionization energies and redox potentials for hydrated ions of all first transition row (3d) metals in the 2+/3+ oxidation states, in connection with various solvation approaches. In terms of model definition, we investigate the construction of a minimally explicitly hydrated quantum cluster with a first and second hydration layer. We report on the convergence with respect to the coupled cluster expansion and the PNO space, as well as on the role of perturbative triple excitations. A recent implementation of the conductor-like polarizable continuum model (CPCM) for the DLPNO-CC approach is employed to determine self-consistent redox potentials at the coupled cluster level. Our results establish conditions for the convergence of DLPNO-CCSD(T) energetics and stress the absolute necessity to explicitly consider the second solvation sphere even when CPCM is used. The achievable accuracy for redox potentials of a practical DLPNO-based approach is, on average, 0.13 V. Furthermore, multilayer approaches that combine a higher-level DLPNO-CCSD(T) description of the first solvation sphere with a lower-level description of the second solvation layer are investigated. The present work establishes optimal and transferable methodological choices for employing DLPNO-based coupled cluster theory, the associated CPCM implementation, and cost-efficient multilayer derivatives of the approach for open-shell transition metal systems in complex environments.

Acid Dissociation Constants of the Benzimidazole Unit in the Polybenzimidazole Chain: Configuration Effects

The acid dissociation constant of three benzimidazoles, namely 2,2′-bibenzo[d]imidazole, 2,5′-bibenzo[d]imidazole, and 5,5′-bibenzo[d]imidazole, have been investigated by means of density functional theory calculations in gas phase and in aqueous solution. The theoretical approach was validated by the comparing of predicted and experimentally determined pK_a values in imidazole, benzimidazole, and 2-phenylbenzimidazole. From the studied compounds, 2,2′-bibenzo[d]imidazole was found to be the most acidic, which made it a valuable candidate as a material for polymer electrolyte membrane fuel cells.

Structure-Energetics-Property Relationships Support Computational Design of Photodegradable Pesticides

Development of high-performing pesticides with tunable degradation properties is vital to increasing the safety and effectiveness of tomorrow's analogs. Chromophoric dissolved organic matter in the excited triple state (³CDOM*) is known to play a key role in the removal of pesticides via indirect photodegradation. However, the potential of these transformations to guide the design of safer chemicals has not yet been fully realized. Here, we report a two-tier computational framework developed to probe and predict both kinetics and thermodynamics of ³CDOM*-pesticide interactions. In the first tier, robust in silico models were constructed by fitting free energies obtained from density functional theory (DFT) calculations to cell potentials and second-order rate constants for the ³CDOM*-pesticide electron transfer. In the second tier, Gibbs free energies and corresponding free energy barriers, determined in solution using the Marcus theory, were applied to develop a quick yet accurate screening approach based on the frontier molecular orbital (FMO) Theory. Being highly mechanistic and spanning ca. 1500 unique ³CDOM*-pesticide interactions, our approach is both robust and broadly applicable. To that end, the outcomes of our computational models were integrated into an easy-to-use decision framework that can guide structure-based design of less persistent pesticide analogs.

Quantum chemical calculations of lithium-ion battery electrolyte and interphase species

Lithium-ion batteries (LIBs) represent the state of the art in high-density energy storage. To further advance LIB technology, a fundamental understanding of the underlying chemical processes is required. In particular, the decomposition of electrolyte species and associated formation of the solid electrolyte interphase (SEI) is critical for LIB performance. However, SEI formation is poorly understood, in part due to insufficient exploration of the vast reactive space. The Lithium-Ion Battery Electrolyte (LIBE) dataset reported here aims to provide accurate first-principles data to improve the understanding of SEI species and associated reactions. The dataset was generated by fragmenting a set of principal molecules, including solvents, salts, and SEI products, and then selectively recombining a subset of the fragments. All candidate molecules were analyzed at the ωB97X-V/def2-TZVPPD/SMD level of theory at various charges and spin multiplicities. In total, LIBE contains structural, thermodynamic, and vibrational information on over 17,000 unique species. In addition to studies of reactivity in LIBs, this dataset may prove useful for machine learning of molecular and reaction properties.

Analytical energy gradient for the second-order Møller-Plesset perturbation theory coupled with the reference interaction site model self-consistent field explicitly including spatial electron density distribution

Solvatochromic shifts of the activation free energies are important aspects to consider for reaction control. To predict the energies, the stationary points in a solution must be accurately determined along the reaction pathway. In this study, the second-order Møller-Plesset perturbation (MP2) theory combined with the reference interaction site model was applied using our fitting approach, and the MP2 analytical energy gradient was determined. The coupled-cluster energy and thermal correction were calculated using the MP2 optimized geometry with solvent effect, and the activation free energies of the Diels-Alder reaction between cyclopentadiene and methyl vinyl ketone are within an error of 2 kcal/mol compared with the experimental data.

Machine learning of free energies in chemical compound space using ensemble representations: Reaching experimental uncertainty for solvation

Free energies govern the behavior of soft and liquid matter, and improving their predictions could have a large impact on the development of drugs, electrolytes, or homogeneous catalysts. Unfortunately, it is challenging to devise an accurate description of effects governing solvation such as hydrogen-bonding, van der Waals interactions, or conformational sampling. We present a Free energy Machine Learning (FML) model applicable throughout chemical compound space and based on a representation that employs Boltzmann averages to account for an approximated sampling of configurational space. Using the FreeSolv database, FML's out-of-sample prediction errors of experimental hydration free energies decay systematically with training set size, and experimental uncertainty (0.6 kcal/mol) is reached after training on 490 molecules (80% of FreeSolv). Corresponding FML model errors are on par with state-of-the art physics based approaches. To generate the input representation for a new query compound, FML requires approximate and short molecular dynamics runs. We showcase its usefulness through analysis of solvation free energies for 116k organic molecules (all force-field compatible molecules in the QM9 database), identifying the most and least solvated systems and rediscovering quasi-linear structure-property relationships in terms of simple descriptors such as hydrogen-bond donors, number of NH or OH groups, number of oxygen atoms in hydrocarbons, and number of heavy atoms. FML's accuracy is maximal when the temperature used for the molecular dynamics simulation to generate averaged input representation samples in training is the same as for the query compounds. The sampling time for the representation converges rapidly with respect to the prediction error.

Fine-tuning pharmacological properties of mirtazapine antidepressant drug: a theoretical study

It has become obvious that fluorinated drugs have a significant role in medicinal applications. In this study, the fluorination of mirtazapine antidepressant drug was investigated using density functional theory calculations. We found that the intramolecular hydrogen bonding and charge transfers of the mirtazapine drug were influenced by fluorine substitution. Our results also reveal that the fluorination altered the stability, solubility, and molecular polarity of the mirtazapine antidepressant drug. Moreover, our results show that the electronic spectra of fluorinated derivatives of the mirtazapine exhibit a red shift toward higher wavelengths compared to the original antidepressant drug. Our calculations show that the difference between G value of the gas and water (ΔG) of fluorinated derivatives of the mirtazapine drug was negative. We also found that the fluorination can increases the first hyperpolarizability of the mirtazapine antidepressant drug. Our results present an efficient strategy to improve the nonlinear optical responses of the antidepressant drugs. Consequently, the results of present study show that the fluorination of mirtazapine could be considered as a promising strategy to design antidepressant drugs with better pharmacological properties.Communicated by Ramaswamy H. Sarma.

Dissolution Kinetics of Different Inorganic Oilfield Scales in Green Formulations

Scale mineral deposition is a critical problem that hinders the daily production of oil and gas fields. Chemical removal of these scales, based on the scale type, is common. In this paper, borax and diethylene tremaine penta acetic (DTPA) acid-based formulations are used for the removal of sulfides, carbonates, and sulfate scales. In particular, the dissolution rates of sulfide (pyrite, pyrrhotite, and galena), sulfate (celestite and barite), and carbonate (calcite) scales were investigated in a rotating disc apparatus at typical well conditions. Scanning electron microscopy-energy-dispersive X-ray and X-ray diffraction analyses were performed for characterizing scale composition and type. The effect of temperature, scale type, and formulation on the dissolution rate is studied. Even though borax formulation has been developed for the sulfide scale removal, it showed a high dissolution rate for the carbonate scale (7.23 × 10^-7 mol·L^-1·s^-1·cm^-2). For the sulfide scale, the highest dissolution in borax formulation was obtained with galena (lead sulfide, PbS), followed by pyrrhotite, and the lowest dissolution was reported for pyrite (1.55 × 10^-8 mol·L^-1·s^-1·cm^-2). Borax formulation was found to be inefficient in the removal of sulfate scales with a dissolution rate lower than carbonate and sulfide scales by 3 and 2 orders of magnitude, respectively. Similarly, DTPA-based formulation has yielded the highest dissolution for the carbonate scale (7.98 × 10^-6 mol·L^-1·s^-1·cm^-2). However, for sulfate, DTPA-based formulation showed better performance than borax. The increase in temperature leads to an increase in the dissolution rate for almost all types of scales; however, DTPA-based formulation showed improved performance with temperature. Both formulations are efficient in removing sulfate- and sulfide-rich scales. The experimental results of DTPA have been validated by density functional theory calculations of binding energies between DTPA and metal ions present in the mixed scale.

Dimethyl sulfoxide as a strongly coordinating solvent: 3′,4′-dihydroxyflavone-Cu(II)-DMSO system case study

Dimethyl sulfoxide (DMSO) is an aprotic organic solvent widely used in laboratory practice due to its ability to dissolve both polar and nonpolar compounds. However, DMSO is also commonly known as a strongly coordinating solvent, especially towards transition metal containing complexes. In this study, estimation of the coordination ability of DMSO towards the Cu(II) ion was attempted, employing a model system composed of 3′,4′-dihydroxyflavone-Cu(II) complex in the presence of explicit DMSO molecules, using the density functional theory (DFT). Nature of the Cu-DMSO chemical interaction (i.e. Cu-O bonding) was studied within the framework of quantum theory of atoms in molecules (QTAIM). Impact of DMSO coordination on the charge and spin distribution at Cu(II) ion was inspected using Mulliken population and QTAIM analysis.

Anion Association Strength as a Unifying Descriptor for the Reversibility of Divalent Metal Deposition in Nonaqueous Electrolytes

Developing next-generation battery chemistries that move beyond traditional Li-ion systems is critical to enabling transformative advances in electrified transportation and grid-level energy storage. In this work, we provide the first evidence for common descriptors for improved reversibility of metal plating/stripping in nonaqueous electrolytes for multivalent ion batteries. Focusing first on the specific role of chloride (Cl^-) in promoting electrochemical reversibility in multivalent systems, rotating disk (RDE) and ring-disk electrode (RRDE) investigations were performed utilizing a variety of divalent cations (Mg²⁺, Zn²⁺, and Cu²⁺) and the bis-(trifluoromethane sulfonyl) imide (TFSI^-) anion. By introducing varying concentrations of Cl^-, a cooperative effect is observed between TFSI^- and Cl^- that yields the more reversible behavior of mixed electrolytes relative to electrolytes containing only TFSI^-. This effect is shown to be general for Mg, Zn, and Cu electrodeposition, and mechanistic understanding of the role of Cl^- in improving reversibility of TFSI-based electrolytes is obtained through the combination of R(R)DE experimental results and density functional theory (DFT) evaluation of the redox activity and thermodynamic stability of various TFSI- and Cl-based solution complexes of metal ions. The cooperative anion effect is further generalized to other mixed-anion systems, where systematic variations in anion association strength predicted from DFT (i.e., Cl^- > OTf^- ≈ TFSI^- > BF₄^- > PF₆^-) yield corresponding trends in redox potentials and improvements of ≥200 mV in the reversibility of metal deposition/dissolution. These results identify anion association strength as a common descriptor for the reversibility of divalent metal anodes and suggest a set of general design principles for developing new electrolytes with improved activity and stability.

Gas Phase Computational Study of Diclofenac Adsorption on Chitosan Materials

Environmental pollution with non-steroidal anti-inflammatory drugs and their metabolites exposes living organisms on their long-lasting, damaging influence. Hence, the ways of non-steroidal anti-inflammatory drugs (NSAIDs) removal from soils and wastewater is sought for. Among the potential adsorbents, biopolymers are employed for their good availability, biodegradability and low costs. The first available theoretical modeling study of the interactions of diclofenac with models of pristine chitosan and its modified chains is presented here. Supermolecular interaction energy in chitosan:drug complexes is compared with the the mutual attraction of the chitosan dimers. Supermolecular interaction energy for the chitosan-diclofenac complexes is significantly lower than the mutual interaction between two chitosan chains, suggesting that the diclofenac molecule will encounter problems when penetrating into the chitosan material. However, its surface adsorption is feasible due to a large number of hydrogen bond donors and acceptors both in biopolymer and in diclofenac. Modification of chitosan material introducing long-distanced amino groups significantly influences the intramolecular interactions within a single polymer chain, thus blocking the access of diclofenac to the biopolymer backbone. The strongest attraction between two chitosan chains with two long-distanced amino groups can exceed 120 kcal/mol, while the modified chitosan:diclofenac interaction remains of the order of 20 to 40 kcal/mol.

Linear correlation models for the redox potential of organic molecules in aqueous solutions

In this study, we use the molecular orbital energy approximation (MOEA) and the energy difference approximation (EDA) to build linear correlation models for the redox potentials of 53 organic compounds in aqueous solutions. The molecules evaluated include nitroxides, phenols, and amines. Both the MOEA and EDA methods yield similar correlation models, however, the MOEA method is less computationally expensive. Correlation coefficients (R²) below 0.3 and mean absolute errors above 0.25 V were found for correlation models built without solvent effects. When explicit water molecules and a continuum solvent model are added to the calculations, correlation coefficients close to 0.8 are reached, and mean absolute errors below 0.18 V are obtained. The incorporation of solvent effects is necessary for good correlation models, particularly for redox processes of charged molecules in aqueous solutions. A comparison of the correlation models from different methodologies is provided. Graphical abstract.

Fast and accurate calculation of hydration energies of molecules and ions

An accurate and efficient method for calculation of hydration free energy of ions and neutral molecules is presented.

Accurate pKa Evaluations for Complex Bio-Organic Molecules in Aqueous Media

Despite the numerous computational efforts on estimating acid dissociation constant (pK_a's), an accurate estimation of pK_a's of bio-organic molecules in the aqueous medium is still a challenge. The major difficulty lies in the accurate description of the aqueous environment and the cost and accuracy of quantum mechanical (QM) methods. Herein, we report a well-defined quantum chemical protocol for accurately calculating pK_a's of a wide range of bio-organic molecules in aqueous media. The performance of our method has been assessed using test sets containing molecules with a range of sizes and a variety of functional groups, including alcohols, phenols, amines, and carboxylic acids, and obtained an impressive mean absolute accuracy of 0.5 pK_a units. For the smaller molecules, we use a high-level QM method (CBS-QB3) and a calibrated explicit-implicit solvation model that yields accurate pK_a values for a range of functional groups. For the larger molecules, we combine this approach with an efficient error-cancellation scheme that eliminates the systematic errors in different density functional methods to yield accurate pK_a values for simple to complex molecular systems. Our protocol is efficient, applicable to large molecules, covers all the common functional groups present in bio-organic molecules, and should find widespread applications in diverse research areas including drug-protein binding, catalysis, and chemical synthesis.

Micropollutant Oxidation Studied by Quantum Chemical Computations: Methodology and Applications to Thermodynamics, Kinetics, and Reaction Mechanisms

The abatement of organic micropollutants during oxidation processes has become an emerging issue for various urban water systems such as drinking water, wastewater, and water reuse. Reaction kinetics and mechanisms play an important role in terms of efficiency of these processes and the formation of transformation products, which are controlled by functional groups in the micropollutants and the applied oxidants. So far, the kinetic and mechanistic information on the underlying reactions was obtained by experimental studies; additionally, predictive quantitative structure-activity relationships (QSARs) were applied to determine reaction kinetics for the oxidation of emerging compounds. Since this experimental approach is very laborious and there are tens of thousands potential contaminants, alternative strategies need to be developed to predict the fate of micropollutants during oxidative water treatment. Due to significant developments in quantum chemical (QC) computations in recent years and increased computational capacity, QC-based methods have become an alternative or a supplement to the current experimental approach. This Account provides a critical assessment of the current state-of-the-art of QC-based methods for the assessment of oxidation of micropollutants. Starting from a given input structure, QC computations need to locate energetic minima on the potential energy surface (PES). Then, useful thermodynamic and kinetic information can be estimated by different approaches: Experimentally determined reaction mechanisms can be validated by identification of transition structures on the PES, which can be obtained for addition reactions, heavy atom transfer (Cl⁺, Br⁺, O·) and H atom transfer (simultaneous proton and electron transfer) reactions. However, transition structures in the PES cannot be obtained for e^--transfer reactions. Second-order rate constants k for the reactions of micropollutants with chemical oxidants can be obtained by ab initio calculations or by QSARs with various QC descriptors. It has been demonstrated that second-order rate constants from ab initio calculations are within factors 3-750 of the measured values, whereas QSAR-based methods can achieve factors 2-4 compared to the experimental data. The orbital eigenvalue of the highest occupied molecular orbital ( E_HOMO) is the most commonly used descriptor for QSAR-based computations of k-values. In combination with results from experimental studies, QC computations can also be applied to investigate reaction mechanisms for verification/understanding of oxidative mechanisms, calculation of branching ratios or regioselectivity, evaluation of the experimental product distribution and assessment of substitution effects. Furthermore, other important physical-chemical constants such as unknown equilibria for species, which are not measurable due to low concentrations, or p K_a values of reactive transient species can be estimated. With further development of QC-based methods, it will become possible to implement kinetic and mechanistic information from such computations in in silico models to predict oxidative transformation of micropollutants. Such predictions can then be complemented by tailored experimental studies to confirm/falsify the computations.

Multistep Explicit Solvation Protocol for Calculation of Redox Potentials

The calculation of molecular redox potentials in aqueous solution presents a challenge to quantum chemistry due to the need to calculate charged, open-shell species experiencing large solvent effects. Traditionally, redox potentials are calculated via the use of density functional theory and continuum solvation methods, but such protocols have been found to often suffer from large errors, particularly in the case of aqueous solution. While explicit solvation models hold promise of higher accuracy to describe solvent effects in general, their complicated use and lack of well-defined, reliable protocols has hindered their adoption. In this study, we present an explicit-solvation-based approach for the calculation of molecular redox potentials. We combine the use of affordable semiempirical QM/MM molecular dynamics (making use of the recently proposed GFN-xTB method by Grimme et al.) for both redox states and use the linear response approximation to relate vertical ionization energies to the adiabatic redox potential. Simulation length, averaging over snapshots, and accounting for bulk and polarization effects are systematically evaluated using phenol as a working example. We find that it is crucial to reliably account for bulk solvation effects in these calculations, as well as polarization effects which we divide up into short-range and long-range contributions. The short-range polarization contribution is accounted for via QM-region expansion, while the long-range contribution is accounted for via Drude-polarizable QM/MM. Our multistep protocol has been coded to be used in a fully automatic way in a local version of Chemshell. It has been evaluated on a test set of oxidation potentials of organic molecules and found to give gas-solution redox shifts with a mean absolute error of 0.13 eV with respect to experiment, compared to mean absolute errors of 0.26 and 0.21 eV with CPCM and SMD continuum models, respectively.

One-Electron Reduction Potentials: Calibration of Theoretical Protocols for Morita⁻Baylis⁻Hillman Nitroaromatic Compounds in Aprotic Media

Nitroaromatic compounds—adducts of Morita–Baylis–Hillman (MBHA) reaction—have been applied in the treatment of malaria, leishmaniasis, and Chagas disease. The biological activity of these compounds is directly related to chemical reactivity in the environment, chemical structure of the compound, and reduction of the nitro group. Because of the last aspect, electrochemical methods are used to simulate the pharmacological activity of nitroaromatic compounds. In particular, previous studies have shown a correlation between the one-electron reduction potentials in aprotic medium (estimated by cyclic voltammetry) and antileishmanial activities (measured by the IC₅₀) for a series of twelve MBHA. In the present work, two different computational protocols were calibrated to simulate the reduction potentials for this series of molecules with the aim of supporting the molecular modeling of new pharmacological compounds from the prediction of their reduction potentials. The results showed that it was possible to predict the experimental reduction potential for the calibration set with mean absolute errors of less than 25 mV (about 0.6 kcal·mol⁻¹).

DFT investigation on the metabolic mechanisms of theophylline by cytochrome P450 monooxygenase

Theophylline, one of the most commonly used bronchodilators and respiratory stimulators for the treatment of acute and chronic asthmatic conditions, can cause permanent neurological damage through chronic or excessive ingestion. In this work, DFT calculation was performed to identify the metabolic mechanisms of theophylline by cytochrome P450 (CYP450) monooxygenase. Two main metabolic pathways were investigated, namely, N₁- (path A) and N₃- (path B) demethylations, which proceeded through N-methyl hydroxylation followed by the decomposition of the generated carbinolamine species. N-methyl hydroxylation involved a hydrogen atom transfer (HAT) mechanism, which can be generalized as the N-demethylation mechanism of xanthine derivatives. The energy gap between the low-spin double state (LS) and the high-spin quartet state (HS) was low (<1 kcal mol^-1), indicating a two-state reactivity (TSR) mechanism. The generated carbinolamine species preferred to decompose through the adjacent heteroatom (O₆ for path A and O₂ for path B) mediated mechanism. Path B was kinetically more feasible than path A attributed to its relatively lower activation energy. 1-Methylxanthine therefore was the energetically favorable metabolite of theophylline. The observations obtained in the work were in agreement with the experimental observation, which can offer important implications for further pharmacological and clinic studies.

Solvent effect on the degree of (a)synchronicity in polar Diels-Alder reactions from the perspective of the reaction force constant analysis

In this work, we computationally evaluated the influence of six different molecular solvents, described as a polarizable continuum model at the M06-2X/6-31+G(d,p) level, on the activation barrier/reaction rate, overall energy change, TS geometry, and degree of (a)synchronicity of two concerted Diels-Alder cycloadditions of acrolein (R1) and its complex with Lewis acid acrolein···BH₃ (R2) to cyclopentadiene. In gas-phase, we found that both exothermicity and activation barrier are only reduced by about 2.0 kcal mol^-1, and the asynchronicity character of the mechanism is accentuated when BH₃ is included. An increment in the solvent's polarity lowers the activation energy of R1 by 1.3 kcal mol^-1, while for R2 the reaction rate is enhanced by more than 2000 times at room temperature (i.e., the activation energy decreases by 4.5 kcal mol^-1) if the highest polar media is employed. Therefore, a synergistic effect is achieved when both external agents, i.e., Lewis acid catalyst and polar solvent, are included together. This effect was ascribed to the ability of the solvent to favor the encounter between cyclopentadiene and acrolein···BH₃. This was validated by the asymmetry of the TS which becomes highly pronounced when either both or just BH₃ is considered or the solvent's polarity is increased. Finally, the reaction force constant κ(ξ) reveals that an increment in the solvent's polarity is able to turn a moderate asynchronous mechanism of the formation of the new C-C σ-bonds into a highly asynchronous one. Graphical abstract A synergistic effect is achieved when both external agents, i.e., Lewis acid catalyst and polar solvent, are included together: lowered energy barriers and increased asynchronicities.

In silico environmental chemical science: properties and processes from statistical and computational modelling

Quantitative structure-activity relationships (QSARs) have long been used in the environmental sciences. More recently, molecular modeling and chemoinformatic methods have become widespread. These methods have the potential to expand and accelerate advances in environmental chemistry because they complement observational and experimental data with "in silico" results and analysis. The opportunities and challenges that arise at the intersection between statistical and theoretical in silico methods are most apparent in the context of properties that determine the environmental fate and effects of chemical contaminants (degradation rate constants, partition coefficients, toxicities, etc.). The main example of this is the calibration of QSARs using descriptor variable data calculated from molecular modeling, which can make QSARs more useful for predicting property data that are unavailable, but also can make them more powerful tools for diagnosis of fate determining pathways and mechanisms. Emerging opportunities for "in silico environmental chemical science" are to move beyond the calculation of specific chemical properties using statistical models and toward more fully in silico models, prediction of transformation pathways and products, incorporation of environmental factors into model predictions, integration of databases and predictive models into more comprehensive and efficient tools for exposure assessment, and extending the applicability of all the above from chemicals to biologicals and materials.

Electrochemical Oxidation and Radical Cations of Structurally Non-rigid Hypervalent Silatranes: Theoretical and Experimental Studies

Using 18 silatranes XSi(OCH₂ CH₂ )₃ N (1) as examples, the potentials of electrochemical oxidation E⁰ of the hypervalent compounds of Si were calculated for the first time at the ab initio and DFT levels. The experimental peak potentials E_p (acetonitrile) show an excellent agreement (MAE=0.03) with the MP2//B3PW91 calculated E⁰ (C-PCM). Radical cations of 1 reveal a stretch isomerism of the N→Si dative bond. Localization of the spin density (SD) on the substituent X and the short (s) coordination contact Si⋅⋅⋅N (d_SiN <2.13 Å) along with the high five-coordinate character of Si are typical for the first isomer 1^+.(s) , whereas the second one, 1^+.(l) , has a longer (l) Si⋅⋅⋅N distance (d_SiN >3.0 Å), the four-coordinate Si and the SD localized on the silatrane nitrogen atom N_s . The vertical model of adiabatic ionization (1→1^+.(s) or 1→1^+.(l) ) was developed. It allows, in accordance with an original experimental test (electrooxidation of 1 in the presence of ferrocene), a reliable prediction of the most probable pathways of the silatrane oxidation. The reliable relationships of E⁰ (1) with the strength characteristics of the dative contact N→Si were revealed.

In search of the best DFT functional for dealing with organic anionic species

“And the winner is…” This work assesses the ability of different Density Functional Theory (DFT) functionals for a proper treatment of organic anionic species.

Free Energies of Redox Half-Reactions from First-Principles Calculations

Quantitative prediction of the energetics of redox half-reactions is still a challenge for modern computational chemistry. Here, we propose a simple scheme for reliable calculations of vertical ionization and attachment energies, as well as of redox potentials of solvated molecules. The approach exploits linear response approximation in the context of explicit solvent simulations with spherical boundary conditions. It is shown that both vertical ionization energies and vertical electron affinities, and, consequently redox potentials, exhibit linear dependence on the inverse radius of the solvation sphere. The explanation of the linear dependence is provided, and an extrapolation scheme is suggested. The proposed approach accounts for the specific short-range interactions within hybrid DFT and effective fragment potential approach as well as for the asymptotic system-size effects. The computed vertical ionization energies and redox potentials are in excellent agreement with the experimental values.