Ichor: A Python library for computational chemistry data management and machine learning force field development

We present ichor, an open-source Python library that simplifies data management in computational chemistry and streamlines machine learning force field development. Ichor implements many easily extensible file management tools, in addition to a lazy file reading system, allowing efficient management of hundreds of thousands of computational chemistry files. Data from calculations can be readily stored into databases for easy sharing and post-processing. Raw data can be directly processed by ichor to create machine learning-ready datasets. In addition to powerful data-related capabilities, ichor provides interfaces to popular workload management software employed by High Performance Computing clusters, making for effortless submission of thousands of separate calculations with only a single line of Python code. Furthermore, a simple-to-use command line interface has been implemented through a series of menu systems to further increase accessibility and efficiency of common important ichor tasks. Finally, ichor implements general tools for visualization and analysis of datasets and tools for measuring machine-learning model quality both on test set data and in simulations. With the current functionalities, ichor can serve as an end-to-end data procurement, data management, and analysis solution for machine-learning force-field development.

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

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

NTO Degradation by Nitroreductase: A DFT Study

NTO (5-nitro-1,2,4-triazol-3-one), an energetic material used in military applications, may be released to the environment during manufacturing, transportation, storage, training, and disposal. A detailed investigation of the possible mechanism for all steps of reduction of NTO by oxygen-insensitive nitroreductase, as one of the pathways for NTO environmental degradation, was performed by computational study at the PCM(Pauling)/M06-2X/6-311++G(d,p) level. Obtained results reveal an overall sequence for NTO transformation into ATO (5-amino-1,2,4-triazol-3-one) with the flavin mononucleotide (FMN) cofactor of nitroreductase. Reduction of the nitro group to the nitroso group and the nitroso group to the hydroxylamino group follow a similar mechanism that consists of the sequential electron and proton transfer from the flavin cofactor. The hydride transfer mechanism may contribute to reduction of the nitroso group by the anionic form of the reduced flavin cofactor. Reduction of 5-(hydroxylamino)-1,2,4-triazol-3-one by the neutral form of the reduced flavin is impossible, whereas reduction of the hydroxylamino group to the amino group occurs with the anionic form of the reduced cofactor by a mechanism involving an initial proton transfer from the hydroxonium ion followed by two electrons and one proton transfers from the flavin cofactor. Small activation energies and high exothermicity support the significant contribution of oxygen-insensitive nitroreductase and other enzymes, containing FMN as a cofactor, to NTO degradation in the environment.

Method for the accurate prediction of electron transfer potentials using an effective absolute potential

A protocol for the accurate computation of electron transfer (ET) potentials from ab initio and density functional theory (DFT) calculations is described. The method relies on experimental pKa values, which can be measured accurately, to compute a computational setup dependent effective absolute potential. The effective absolute potentials calculated using this protocol display strong variations between the different computational setups and deviate in several cases significantly from the "generally accepted" value of 4.28 V. The most accurate estimate, obtained from CCSD(T)/aug-ccpvqz, indicates an absolute potential of 4.14 V for the normal hydrogen electrode (nhe) in water. Using the effective absolute potential in combination with CCSD(T) and a moderately sized basis, we are able to predict ET potentials accurately for a test set of small organic molecules (σ = 0.13 V). Similarly we find the effective absolute potential method to perform equally good or better for all considered DFT functionals compared to using one of the literature values for the absolute potential. For, M06-2X, which comprises the most accurate DFT method, standard deviation of 0.18 V is obtained. This improved performance is a result of using the most appropriate effective absolute potential for a given method.

Reduction of 1,2,3-trichloropropane (TCP): pathways and mechanisms from computational chemistry calculations

The characteristic pathway for degradation of halogenated aliphatic compounds in groundwater or other environments with relatively anoxic and/or reducing conditions is reductive dechlorination. For 1,2-dihalocarbons, reductive dechlorination can include hydrogenolysis and dehydrohalogenation, the relative significance of which depends on various structural and energetic factors. To better understand how these factors influence the degradation rates and products of the lesser halogenated hydrocarbons (in contrast to the widely studied per-halogenated hydrocarbons, like trichloroethylene and carbon tetrachloride), density functional theory calculations were performed to compare all of the possible pathways for reduction and elimination of 1,2,3-trichloropropane (TCP). The results showed that free energies of each species and reaction step are similar for all levels of theory, although B3LYP differed from the others. In all cases, the reaction coordinate diagrams suggest that β-elimination of TCP to allyl chloride followed by hydrogenolysis to propene is the thermodynamically favored pathway. This result is consistent with experimental results obtained using TCP, 1,2-dichloropropane, and 1,3-dichloropropane in batch experiments with zerovalent zinc (Zn⁰, ZVI) as a reductant.

A theoretical study on the pKa values of selenium compounds in aqueous solution

The pK_a values of different kinds of selenium compounds (R-SeH) were investigated by using the ωB97XD method with a SMD model.

Theoretical modeling of pKa's of thiol compounds in aqueous solution

The pK_a's of different kinds of thiols (R-SH) were investigated by using the M06-2X method with a SMD_sSAS model.

Thermodynamics of aqueous perfluorooctanoic acid (PFOA) and 4,8-dioxa-3H-perfluorononanoic acid (DONA) from DFT calculations: Insights into degradation initiation

Modern fluorosurfactants introduced during and after perfluoroalkyl carboxylates/sulfonates phase-out present chemical features designed to facilitate abatement, hence reducing persistence. However, the implications of such features on environmental partitioning and stability are yet to be fully appreciated, partly due to experimental difficulties inherent to the handling of their (diluted) aqueous solutions. In this work, rigorous quantum chemistry calculations were carried out in order to provide theoretical insights into the thermodynamics of hydroperfluorosurfactants in aqueous medium. Estimates of acid dissociation constant (pK_a), standard reduction potential (E⁰), and bond dissociation enthalpy (BDE) and free energy (BDFE) were computed for perfluorooctanoic acid (PFOA), 4,8-dioxa-3H-perfluorononanoic acid (DONA) and their anionic forms via ensemble averaging at density functional theory level with implicit solvent models. A ‹pK_a› in the neighborhood of zero and a E⁰ of about 2.2 V were obtained for PFOA. Predictions for the acidic function of DONA compare well with PFOA's, with a pK_a of 0.8-1.5 and a E⁰ of 2.07-2.15 V. Deprotonation thus represents the dominant phenomenon at environmental conditions. Calculations indicate that H-abstraction of the aliphatic proton of DONA by a hydroxyl radical is the thermodynamically favored reaction path in oxidative media, whereas hydrolysis is not a realistic scenario due to the high dissociation constant. Short intramolecular interactions available to the peculiar hydrophobic tail of DONA were also reviewed, and the relevance of the full conformational space of the fluorinated side chain discussed.

A quantum chemical based toxicity study of estimated reduction potential and hydrophobicity in series of nitroaromatic compounds

Nitroaromatic compounds and the products of their degradation are toxic to bacteria, cells and animals. Various studies have been carried out to better understand the mechanism of toxicity of aromatic nitrocompounds and their relationship to humans and the environment. Recent data relate cytotoxicity of nitroaromatic compounds to their single- or two-electron enzymatic reduction. However, mechanisms of animal toxicity could be more complex. This work investigates the estimated reduction and oxidation potentials of 34 nitroaromatic compounds using quantum chemical approaches. All geometries were optimized with density functional theory (DFT) using the solvation model based on density (SMD) and polarizable continuum model (PCM) solvent model protocols. Quantitative structure-activity/property (QSAR/QSPR) models were developed using descriptors obtained from quantum chemical optimizations as well as the DRAGON software program. The QSAR/QSPR equations developed consist of two to four descriptors. Correlations have been identified between electron affinity (E_LUMO) and hydrophobicity (log P).

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.

Structure-Activity Relationships for Rates of Aromatic Amine Oxidation by Manganese Dioxide

New energetic compounds are designed to minimize their potential environmental impacts, which includes their transformation and the fate and effects of their transformation products. The nitro groups of energetic compounds are readily reduced to amines, and the resulting aromatic amines are subject to oxidation and coupling reactions. Manganese dioxide (MnO2) is a common environmental oxidant and model system for kinetic studies of aromatic amine oxidation. In this study, a training set of new and previously reported kinetic data for the oxidation of model and energetic-derived aromatic amines was assembled and subjected to correlation analysis against descriptor variables that ranged from general purpose [Hammett σ constants (σ(-)), pKas of the amines, and energies of the highest occupied molecular orbital (EHOMO)] to specific for the likely rate-limiting step [one-electron oxidation potentials (Eox)]. The selection of calculated descriptors (pKa, EHOMO, and Eox) was based on validation with experimental data. All of the correlations gave satisfactory quantitative structure-activity relationships (QSARs), but they improved with the specificity of the descriptor. The scope of correlation analysis was extended beyond MnO2 to include literature data on aromatic amine oxidation by other environmentally relevant oxidants (ozone, chlorine dioxide, and phosphate and carbonate radicals) by correlating relative rate constants (normalized to 4-chloroaniline) to EHOMO (calculated with a modest level of theory).

Structure and electrochemical properties for complexes of nitrocompounds with inorganic ions: A theoretical approach

Reduction and oxidation (redox) reactions are widely used for removal of nitrocompounds from contaminated soil and water. Structures and redox properties for complexes of nitrocompounds, such as 2,4,6-trinitrotoluene (TNT), 2,4-dinitrotoluene (DNT), 2,4-dinitroanisole (DNAN), and 5-nitro-2,4-dihydro-3H-1,2,4-triazol-3-one (NTO), with common inorganic ions (Na(+) , Cl(-) , NO3-) were investigated at the SMD(Pauling)/PCM(Pauling)/MPWB1K/TZVP level of theory. Atoms in molecules (AIM) theory was applied to analyze the topological properties of the bond critical points involved in the interactions between the nitrocompounds and the ions. Topological analyses show that intermolecular interactions of the types O(N)…Na(+) , C-H…Cl(-) ( ONO2-), and C…Cl(-) ( ONO2-) may be discussed as noncovalent closed-shell interactions, while N-H···Cl(-) ( ONO2-) hydrogen bonds are partially covalent in nature. Complexation causes significant decrease of redox activity of the nitrocompounds. Analysis of the reduction potentials of the complexes obtained through application of the Pourbaix diagram of an iron/water system revealed that sodium complexes of NTO might be reduced by metallic iron. © 2016 Wiley Periodicals, Inc.

Ionization Energies and Aqueous Redox Potentials of Organic Molecules: Comparison of DFT, Correlated ab Initio Theory and Pair Natural Orbital Approaches

The calculation of redox potentials involves large energetic terms arising from gas phase ionization energies, thermodynamic contributions, and solvation energies of the reduced and oxidized species. In this work we study the performance of a wide range of wave function and density functional theory methods for the prediction of ionization energies and aqueous one-electron oxidation potentials of a set of 19 organic molecules. Emphasis is placed on evaluating methods that employ the computationally efficient local pair natural orbital (LPNO) approach, as well as several implementations of coupled cluster theory and explicitly correlated F12 methods. The electronic energies are combined with implicit solvation models for the solvation energies. With the exception of MP2 and its variants, which suffer from enormous errors arising at least partially from the poor Hartree-Fock reference, ionization energies can be systematically predicted with average errors below 0.1 eV for most of the correlated wave function based methods studies here, provided basis set extrapolation is performed. LPNO methods are the most efficient way to achieve this type of accuracy. DFT methods show in general larger errors and suffer from inconsistent behavior. The only exception is the M06-2X functional which is found to be competitive with the best LPNO-based approaches for ionization energies. Importantly, the limiting factor for the calculation of accurate redox potentials is the solvation energy. The errors in the predicted solvation energies by all continuum solvation models tested in this work dominate the final computed reduction potential, resulting in average errors typically in excess of 0.3 V and hence obscuring the gains that arise from choosing a more accurate electronic structure method.

Adsorption of 2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane (CL-20) on a soil organic matter. A DFT M05 computational study

Adsorption of 2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane (CL-20) by soil organic matter considering the Leonardite Humic Acid (LHA) model at the M05/tzvp level of Density Functional Theory (DFT) applying cluster approximation has been investigated. Different orientations of CL-20 toward LHA surface were examined. It was found that deprotonation of LHA is required to obtain stable complexes with CL-20. Hydrogen bonds between CL-20 and deprotonated LHA were analyzed applying the atoms in molecules (AIM) theory. An attachment or removal of an electron with respect to the complex does not have significant effect on mutual orientation of the adsorbent in complexes. It was shown that adsorbed CL-20 does not undergo redox transformation and, therefore, adsorption on soil organic matter may be responsible for decrease of the degradation rate of CL-20 in soil.

Structure and Redox Properties of 5-Amino-3-nitro-1H-1,2,4-triazole (ANTA) Adsorbed on a Silica Surface: A DFT M05 Computational Study

A cluster approximation was applied at the M05/tzvp level to model an adsorption of 5-amino-3-nitro-1H-1,2,4-triazole (ANTA) on the (001) surface of α-quartz. Structures of the obtained ANTA-silica complexes confirm a nearly parallel orientation of the nitro compound toward the surface. The atoms in molecules (AIM) method was applied to analyze binding between ANTA and the silica surface. Attachment or loss of an electron was found to lead to a significant deviation from coplanarity in the complexes and to a strengthening of a hydrogen bonding. Redox properties of the adsorbed ANTA were compared with those of gas-phase and hydrated species by calculation of the ionization potential, electron affinity, oxidation and reduction Gibbs free energies, and oxidation and reduction potentials. It was shown that the adsorbed ANTA has a lower ability to undergo redox transformations as compared to that of the hydrated one.

Are the reduction and oxidation properties of nitrocompounds dissolved in water different from those produced when adsorbed on a silica surface? A DFT M05-2X computational study

The reduction and oxidation properties of four nitrocompounds (trinitrotoluene [TNT], 2,4-dinitrotoluene, 2,4-dinitroanisole, and 5-nitro-2,4-dihydro-3H-1,2,4-triazol-3-one [NTO]) dissolved in water as compared with the same properties for compounds adsorbed on a silica surface were studied. To consider the influence of adsorption, cluster models were developed at the M05/tzvp level. A hydroxylated silica (001) surface was chosen to represent a key component of soil. The PCM(Pauling) and SMD solvation models were used to model water bulk influence. The following properties were analyzed: electron affinity, ionization potential, reduction Gibbs free energy, oxidation Gibbs free energy, and reduction and oxidation potentials. It was found that adsorption and solvation decrease gas phase electron affinity, ionization potential, and Gibbs free energy of reduction and oxidation, and thus, promote redox transformation of nitrocompounds. However, in case of solvation, the changes are more significant than for adsorption. This means that nitrocompounds dissolved in water are easier to transform by reduction or oxidation than adsorbed ones. Among the considered compounds, TNT was found to be the most reactive in an electron attachment process and the least reactive for an electron detachment transformation. During ionization, a deprotonation of adsorbed NTO was found to occur.

Predicting reduction rates of energetic nitroaromatic compounds using calculated one-electron reduction potentials

The evaluation of new energetic nitroaromatic compounds (NACs) for use in green munitions formulations requires models that can predict their environmental fate. Previously invoked linear free energy relationships (LFER) relating the log of the rate constant for this reaction (log(k)) and one-electron reduction potentials for the NAC (E1NAC) normalized to 0.059 V have been re-evaluated and compared to a new analysis using a (nonlinear) free-energy relationship (FER) based on the Marcus theory of outer-sphere electron transfer. For most reductants, the results are inconsistent with simple rate limitation by an initial, outer-sphere electron transfer, suggesting that the linear correlation between log(k) and E1NAC is best regarded as an empirical model. This correlation was used to calibrate a new quantitative structure-activity relationship (QSAR) using previously reported values of log(k) for nonenergetic NAC reduction by Fe(II) porphyrin and newly reported values of E1NAC determined using density functional theory at the M06-2X/6-311++G(2d,2p) level with the COSMO solvation model. The QSAR was then validated for energetic NACs using newly measured kinetic data for 2,4,6-trinitrotoluene (TNT), 2,4-dinitrotoluene (2,4-DNT), and 2,4-dinitroanisole (DNAN). The data show close agreement with the QSAR, supporting its applicability to other energetic NACs.

Computational electrochemistry: prediction of liquid-phase reduction potentials

This article reviews recent developments and applications in the area of computational electrochemistry. Our focus is on predicting the reduction potentials of electron transfer and other electrochemical reactions and half-reactions in both aqueous and nonaqueous solutions. Topics covered include various computational protocols that combine quantum mechanical electronic structure methods (such as density functional theory) with implicit-solvent models, explicit-solvent protocols that employ Monte Carlo or molecular dynamics simulations (for example, Car-Parrinello molecular dynamics using the grand canonical ensemble formalism), and the Marcus theory of electronic charge transfer. We also review computational approaches based on empirical relationships between molecular and electronic structure and electron transfer reactivity. The scope of the implicit-solvent protocols is emphasized, and the present status of the theory and future directions are outlined.

Toward understanding the redox properties of model chromophores from the green fluorescent protein family: an interplay between conjugation, resonance stabilization, and solvent effects

The redox properties of model chromophores from the green fluorescent protein family are characterized computationally using density functional theory with a long-range corrected functional, the equation-of-motion coupled-cluster method, and implicit solvation models. The analysis of electron-donating abilities of the chromophores reveals an intricate interplay between the size of the chromophore, conjugation, resonance stabilization, presence of heteroatoms, and solvent effects. Our best estimates of the gas-phase vertical/adiabatic detachment energies of the deprotonated (i.e., anionic) model red, green, and blue chromophores are 3.27/3.15, 2.79/2.67, and 2.75/2.35 eV, respectively. Vertical/adiabatic ionization energies of the respective protonated (i.e., neutral) species are 7.64/7.35, 7.38/7.15, and 7.70/7.32 eV, respectively. The standard reduction potentials (E(red)(0)) of the anionic (Chr•/Chr–) and neutral (Chr+•/Chr) model chromophores in acetonitrile are 0.34/1.40 V (red), 0.22/1.24 V (green), and −0.12/1.02 V (blue), suggesting, counterintuitively, that the red chromophore is more difficult to oxidize than the green and blue ones (in both neutral and deprotonated forms). The respective redox potentials in water follow a similar trend but are more positive than the acetonitrile values.

Theoretical Determination of One-Electron Oxidation Potentials for Nucleic Acid Bases

The oxidation potentials for N-methyl substituted nucleic acid bases guanine, adenine, cytosine, thymine, uracil, xanthine, and 8-oxoguanine were computed using B3LYP and CBS-QB3 with the SMD solvation model. Acid-base and tautomeric equilibria present in aqueous solution were accounted for by combining standard redox potentials with calculated pKa and tautomerization energies to produce an ensemble averaged pH dependent potential. Gas phase free energies were computed using B3LYP/aug-cc-pVTZ//B3LYP/6-31+G(d,p) and CBS-QB3. Solvation free energies were computed at the SMD/B3LYP/6-31+G(d,p) level of theory. Compared to experimental results, calculations with the CBS-QB3 level of theory have a mean absolute error (MAE) of ca. 1 kcal/mol for the gas phase proton affinity/gas phase basicity and an MAE of ca. 0.04 eV for the adiabatic/vertical ionization potentials. The B3LYP calculations have a MAE of ∼2 kcal/mol for the proton affinity/gas phase basicity data but systematically underestimated ionization potentials by 0.14-0.21 eV. Solvent cavities for charged solute species were rescaled uniformly by fitting computed pKa data to experimentally measured pKa values. After solvent cavity scaling, the MAEs for computed pKa's compared to experimental results are 0.7 for B3LYP and 0.9 for CBS-QB3. In acetonitrile, the computed E°(XH(+•)/XH) redox potentials are systematically lower than experimentally measured potentials by 0.21 V for CBS-QB3 and 0.33 V for B3LYP. However, the redox potentials relative to adenine are in very good agreement with experimental results, with MAEs of 0.10 V for CBS-QB3 and 0.07 V for B3LYP. In aqueous solution, B3LYP and CBS-QB3 have MAEs of 0.21 and 0.19 V for E7(X(•),H(+)/XH). Replacing the methyl substituent with ribose changes the calculated E7 potentials by 0.1-0.2 V. The calculated difference between the guanine and adenine oxidation potentials is too large compared to experimental results, but the calculated difference between guanine and 8-oxoguanine is in good agreement with the measured values.

Quantum Chemical Benchmarking, Validation, and Prediction of Acidity Constants for Substituted Pyridinium Ions and Pyridinyl Radicals

Sensibly modeling (photo)electrocatalytic reactions involving proton and electron transfer with computational quantum chemistry requires accurate descriptions of protonated, deprotonated, and radical species in solution. Procedures to do this are generally nontrivial, especially in cases that involve radical anions that are unstable in the gas phase. Recently, pyridinium and the corresponding reduced neutral radical have been postulated as key catalysts in the reduction of CO2 to methanol. To assess practical methodologies to describe the acid/base chemistry of these species, we employed density functional theory (DFT) in tandem with implicit solvation models to calculate acidity constants for 22 substituted pyridinium cations and their corresponding pyridinyl radicals in water solvent. We first benchmarked our calculations against experimental pyridinium deprotonation energies in both gas and aqueous phases. DFT with hybrid exchange-correlation functionals provide chemical accuracy for gas-phase data and allow absolute prediction of experimental pKas with unsigned errors under 1 pKa unit. The accuracy of this economical pKa calculation approach was further verified by benchmarking against highly accurate (but very expensive) CCSD(T)-F12 calculations. We compare the relative importance and sensitivity of these energies to selection of solvation model, solvation energy definitions, implicit solvation cavity definition, basis sets, electron densities, model geometries, and mixed implicit/explicit models. After determining the most accurate model to reproduce experimentally-known pKas from first principles, we apply the same approach to predict pKas for radical pyridinyl species that have been proposed relevant under electrochemical conditions. This work provides considerable insight into the pitfalls using continuum solvation models, particularly when used for radical species.

DFT M06-2X investigation of alkaline hydrolysis of nitroaromatic compounds

The nitroaromatic compounds 2,4,6-trinitrotoluene (TNT), 2,4-dinitrotoluene (DNT) and 2,4-dinitroanisole (DNAN) are potential environmental contaminants and their transformations under a variety of environmental conditions are consequently of great interest. One possible method to safely degrade these nitrocompounds is alkaline hydrolysis. A mechanism of the initial stages of this reaction was investigated computationally. Simulations of UV-VIS and NMR spectra for this mechanism were also produced. The results obtained were compared to available experimental data on the alkaline hydrolysis of TNT and suggest that the formation of Meisenheimer complexes and an anion of TNT are potential first-step intermediates in the reaction path. As the reaction proceeds, computational results indicate that polynegative complexes dominate the degradation pathway, followed by cycles of carbon chain opening and breaking. A second possible pathway was identified that leads to polymeric products through Janovsky complex formation. Results from this study indicate that the order of increasing resistance to alkaline hydrolysis is TNT, DNT and DNAN.

First-principle protocol for calculating ionization energies and redox potentials of solvated molecules and ions: theory and application to aqueous phenol and phenolate

The effect of hydration on the lowest vertical ionization energy (VIE) of phenol and phenolate solvated in bulk water was characterized using the equation-of-motion ionization potential coupled-cluster (EOM-IP-CCSD) and effective fragment potential (EFP) methods (referred to as EOM/EFP) and determined experimentally by valence photoemission measurements using microjets and synchrotron radiation. The computed solvent-induced shifts in VIEs (ΔVIEs) are -0.66 and +5.72 eV for phenol and phenolate, respectively. Our best estimates of the absolute values of VIEs (7.9 and 7.7 eV for phenol and phenolate) agree reasonably well with the respective experimental values (7.8 ± 0.1 and 7.1 ± 0.1 eV). The EOM/EFP scheme was benchmarked against full EOM-IP-CCSD using microsolvated phenol and phenolate clusters. A protocol for calculating redox potentials with EOM/EFP was developed based on linear response approximation (LRA) of free energy determination. The oxidation potentials of phenol and phenolate calculated using LRA and EOM/EFP are 1.32 and 0.89 V, respectively; they agree well with experimental values.