AutoSolvate: A Toolkit for Automating Quantum Chemistry Design and Discovery of Solvated Molecules

The availability of large, high-quality data sets is crucial for artificial intelligence design and discovery in chemistry. Despite the essential roles of solvents in chemistry, the rapid computational data set generation of solution-phase molecular properties at the quantum mechanical level of theory was previously hampered by the complicated simulation procedure. Software toolkits that can automate the procedure to set up high-throughput explicit-solvent quantum chemistry (QC) calculations for arbitrary solutes and solvents in an open-source framework are still lacking. We developed AutoSolvate, an open-source toolkit to streamline the workflow for QC calculation of explicitly solvated molecules. It automates the solvated-structure generation, force field fitting, configuration sampling, and the final extraction of microsolvated cluster structures that QC packages can readily use to predict molecular properties of interest. AutoSolvate is available through both a command line interface and a graphical user interface, making it accessible to the broader scientific community. To improve the quality of the initial structures generated by AutoSolvate, we investigated the dependence of solute-solvent closeness on solute/solvent identities and trained a machine learning model to predict the closeness and guide initial structure generation. Finally, we tested the capability of AutoSolvate for rapid data set curation by calculating the outer-sphere reorganization energy of a large data set of 166 redox couples, which demonstrated the promise of the AutoSolvate package for chemical discovery efforts.

Abiotic Reactivity of De Novo Designed Artificial Copper Peptides (ArCuPs): The Case of C-H Activation

We report a series of de novo designed Artificial Cu Peptides (ArCuPs) that oxidize and peroxygenate C-H bonds of model abiotic substrates via electrochemically generated Cu-oxygen species using H2O2 as the terminal oxidant, akin to native Cu enzymes. Detailed assessment of kinetic parameters established the catalytic nature of the ArCuPs. Selective alteration of outer sphere steric at the d layers above and below the Cu site allows facilitated access of substrates, where a more pronounced effect on catalysis is observed when space is created at the d layer below the Cu site via Ile to Ala mutation producing a kcat of 6.2 s-1, TONmax of 14800 and catalytic proficiency (kcat/KM/kuncat) of 340 M-1 for the oxidation of benzyl alcohol. Independent spectroscopic studied revealed that the rate of formation of the Cu-oxygen species and the spectroscopic feature of the most active variant is distinct compared to the other ArCuPs. Systematic alteration of outer sphere hydrophobicity led to a correlated tuning of the T2 Cu site redox potentials by ~80 mV. The enhanced activity of the ArCuP variant is attributed to a combination of steric effect that allows easy access of substrates, the nature of Cu-oxygen species, and stability of this construct compared to others, where Ile to Ala mutation unexpectedly leads to a higher thermostability which is further augmented by Cu binding.

Revisiting the Assignment of Innocent and Non-Innocent Counter ions in Lanthanide(III) Solution Chemistry

Lanthanides are found in critical applications from display technology to renewable energy. Often these rare earth elements are used as alloys or functional materials, yet the access to them are trough solution processes. In aqueous solution the rare earths are found predominantly as trivalent ions and charge balance dictates that counter ions are present. The fast ligand exchange and lack of directional bonding in lanthanides complexes has led to questions regarding the speciation of Ln3+ solvates in the presence of various counter ions, and to the distinction between innocent = non-coordinating, and non-innocent = coordinating counter ions. There is limited agreement as to which counter ions that belong to each group, which lead to this report. By using Eu3+ luminescence, it was possible to clearly distinguish between coordinating and non-coordinating ions. To interpret the results it was required to bridge the descriptions of ion pairing and coordination. The da-ta—in form of Eu3+ luminescence spectra and luminescence lifetimes from solutions with varying concentrations of acetate, chloride, nitrate, fluoride, sulfate, perchlorate and triflate—were contrasted to those obtained with ethylenediaminetet-raaceticacid (EDTA), which allowed for the distinction between three Ln3+-anion interaction types. It was possible to con-clude which counter ions are truly innocent (e.g. ClO4- and OTf-), and which clearly coordinate (e.g. NO3- and AcO-). Finally, the considerate amount of data from systems studied under similar conditions allowed the minimum perturbation arising from inner sphere or outer sphere coordination in Eu3+ complexes to be identified.

Abiotic Reactivity of De Novo Designed Artificial Copper Peptides (ArCuPs): The Case of C-H Activation

We report a series of de novo designed Artificial Cu Peptides (ArCuPs) that oxidize and peroxygenate C-H bonds of model abiotic substrates via electrochemically generated Cu-oxygen species using H2O2 as the terminal oxidant, akin to native Cu enzymes. Detailed assessment of kinetic parameters established the catalytic nature of the ArCuPs. Selective alteration of outer sphere steric at the d layers above and below the Cu site allows facilitated access of substrates, where a more pronounced effect on catalysis is observed when space is created at the d layer below the Cu site via Ile to Ala mutation producing a kcat of 6.2 s-1, TONmax of 14800 and catalytic proficiency (kcat/KM/kuncat) of 340 M-1 for the oxidation of benzyl alcohol. Independent spectroscopic studied revealed that the rate of formation of the Cu-oxygen species and the spectroscopic feature of the most active variant is distinct compared to the other ArCuPs. Systematic alteration of outer sphere hydrophobicity led to a correlated tuning of the T2 Cu site redox potentials by ~80 mV. The enhanced activity of the ArCuP variant is attributed to a combination of steric effect that allows easy access of substrates, the nature of Cu-oxygen species, and stability of this construct compared to others, where Ile to Ala mutation unexpectedly leads to a higher thermostability which is further augmented by Cu binding.

Abiotic Reactivity of De Novo Designed Artificial Copper Peptides (ArCuPs): The Case of C-H Activation

We report a series of de novo designed Artificial Cu Peptides (ArCuPs) that oxidize and peroxygenate C-H bonds of model abiotic substrates via electrochemically generated Cu-oxygen species using H2O2 as the terminal oxidant, akin to native Cu enzymes. Detailed assessment of kinetic parameters established the catalytic nature of the ArCuPs. Selective alteration of outer sphere steric at the d layers above and below the Cu site allows facilitated access of substrates, where a more pronounced effect on catalysis is observed when space is created at the d layer below the Cu site via Ile to Ala mutation producing a kcat of 6.2 s-1, TONmax of 14800 and catalytic proficiency (kcat/KM/kuncat) of 340 M-1 for the oxidation of benzyl alcohol. Independent spectroscopic studied revealed that the rate of formation of the Cu-oxygen species and the spectroscopic feature of the most active variant is distinct compared to the other ArCuPs. Systematic alteration of outer sphere hydrophobicity led to a correlated tuning of the T2 Cu site redox potentials by ~80 mV. The enhanced activity of the ArCuP variant is attributed to a combination of steric effect that allows easy access of substrates, the nature of Cu-oxygen species, and stability of this construct compared to others, where Ile to Ala mutation unexpectedly leads to a higher thermostability which is further augmented by Cu binding.

Synthetic Zeolites Modified with Salts of Transition Metals in the Reaction of Chemisorption-catalytic Oxidation of Sulphur Dioxide by Air Oxygen

The effect of the nature and concentration of d-metal salts attached to synthetic zeolites NaA and KA on the kinetic and stoichiometric parameters of the chemisorption-catalytic oxidation of sulphur dioxide with air oxygen at ambient temperature was studied. It was found that the adsorption capacity of NaA zeolite relative to SO2 is 100 times higher than that of KA zeolite; the time of protective action of NaA and KA zeolites increases upon modification with transition metal salts and with an increase of their content in the compositions. It was shown that the formation of inner and outer sphere complexes and the relationship between them is determined by the nature and concentration of metal ions and by the nature of the carrier. It was proven that the chemisorption-catalytic process ends with the oxidation of SO2 to H2SO4.

Antioxidative Reactivity of L-Ascorbic Acid and D-Isoascorbic Acid Species towards Reduction of Hexachloroiridate (IV)

The pair [IrCl6]2–/[IrCl6]3– has been demonstrated to be a good redox probe in biological systems while L-ascorbic acid (AA) is one of the most important antioxidants. D-isoascorbic acid (IAA) is an epimer of AA and is widely used as an antioxidant in various foods, beverages, meat, and fisher products. Reductions of [IrCl6]2– by AA and IAA have been analyzed kinetically and mechanistically in this work. The reductions strictly follow overall second-order kinetics and the observed second-order rate constants were collected in the pH region of 0 ≤ pH ≤ 2.33 at 25.0°C. Spectrophotometric titration experiments revealed a well-defined 1 : 2 stoichiometry, namely Δ[AA] : Δ[Ir(IV)] or Δ[IAA] : Δ[Ir(IV)] = 1 : 2, indicating that L-dehydroascorbic acid (DHA) and D-dehydroisoascorbic acid (DHIA) were the oxidation products of AA and IAA, respectively. A reaction mechanism is suggested involving parallel reactions of [IrCl6]2– with three protolysis species of AA/IAA (fully protonated, monoanionic, and dianionic forms) as the rate-determining steps and formation of ascorbic/isoascorbic and ascorbate/isoascorbate radicals; in each of the steps, [IrCl6]2– acquires an electron via an outer-sphere electron transfer mode. Rate constants of the rate-determining steps have been derived or estimated. The fully protonated forms of AA and IAA display virtually identical reactivity whereas ascorbate and isoascorbate monoanions have a significant reactivity difference. The ascorbate and isoascorbate dianions are extremely reactive and their reactions with [IrCl6]2– proceed with the diffusion-controlled rate. The species versus pH and the species reactivity versus pH distribution diagrams were constructed endowing that the ascorbate/isoascorbate monoanionic form dominated the total reactivity at physiological pH. In addition, the value of pKa1 = 3.74 ± 0.05 for IAA at 25.0°C and 1.0 M ionic strength was determined in this work.

Binding of Gold(III) from Solutions by the [Ag6{S2CN(CH2)6}6] Cluster: Synthesis, Thermal Behavior, and Self-Organization of the Supramolecular Structure of the Double Complex [Au{S2CN(CH2)6}2]2[AgCl2]Cl·2CHCl3 (Role of Secondary Au⋅⋅⋅Cl, Ag⋅⋅⋅S, and Cl⋅⋅⋅Cl Interactions)

The capability of silver(I) cyclo-hexamethylenedithiocarbamate to concentrate gold(III) from solutions characterized by a high level of salinity (5.15 M NaCl) into the solid phase has been established. The double chloroform-solvated Au(III)–Ag(I) complex [Au{S2CN(CH2)6}2]2[AgCl2]Cl·2CHCl3 (I) was preparatively isolated as an individual form of binding of [AuCl4]– anions. The composition of the ionic structural units of compound I indicates that gold(III) binding from a solution to the solid phase is accompanied by the complete redistribution of the HmDtc ligands between the coordination spheres of Ag(I) and Au(III). Complex I characterized by IR spectroscopy, simultaneous thermal analysis, and X-ray structure analysis (CIF file CCDC no. 2051654) exhibits the supramolecular structure containing two oppositely charged pseudo-polymeric subsystems. Complex cations [Au{S2CN(CH2)6}2]+ and anions [AgCl2]– (in a ratio of 2 : 1) form a complicatedly organized cation-anionic pseudo-polymeric ribbon ({[Au(HmDtc)2]⋅⋅⋅[AgCl2]⋅⋅⋅[Au(HmDtc)2]}+)n due to secondary interactions Ag⋅⋅⋅S (3.2613 Å) and Au⋅⋅⋅Cl (3.2765 Å). The pseudo-polymeric ribbon consists of two rows of cations and a row of anions. The outer-sphere chloride ions combine the solvate chloroform molecules by two equivalent hydrogen bonds Cl⋅⋅⋅H–C yielding anion-molecular triads [Cl3CH⋅⋅⋅Cl⋅⋅⋅HCCl3]–, which are involved in the formation of the supramolecular ribbon due to the secondary Cl⋅⋅⋅Cl interactions (3.4058 Å) between the nonequivalent chlorine atoms of the nearest solvate molecules. The study of the thermal behavior of complex I makes it possible to determine the character of thermolysis and conditions for the quantitative regeneration of bound gold.