Probing machine learning models based on high throughput experimentation data for the discovery of asymmetric hydrogenation catalysts.

Enantioselective hydrogenation of olefins by Rh-based chiral catalysts has been extensively studied for more than 50 years. Naively, one would expect that everything about this transformation is known and that selecting a catalyst that induces the desired reactivity or selectivity is a trivial task. Nonetheless, ligand engineering or selection for any new prochiral olefin remains an empirical trial-error exercise. In this study, we investigated whether machine learning techniques could be used to accelerate the identification of the most efficient chiral ligand. For this purpose, we used high throughput experimentation to build a large dataset consisting of results for Rh-catalyzed asymmetric olefin hydrogenation, specially designed for applications in machine learning. We showcased its alignment with existing literature while addressing observed discrepancies. Additionally, a computational framework for the automated and reproducible quantum-chemistry based featurization of catalyst structures was created. Together with less computationally demanding representations, these descriptors were fed into our machine learning pipeline for both out-of-domain and in-domain prediction tasks of selectivity and reactivity. For out-of-domain purposes, our models provided limited efficacy. It was found that even the most expensive descriptors do not impart significant meaning to the model predictions. The in-domain application, while partly successful for predictions of conversion, emphasizes the need for evaluating the cost-benefit ratio of computationally intensive descriptors and for tailored descriptor design. Challenges persist in predicting enantioselectivity, calling for caution in interpreting results from small datasets. Our insights underscore the importance of dataset diversity with broad substrate inclusion and suggest that mechanistic considerations could improve the accuracy of statistical models.

Cooperative Ligands in Dissolution of Gold.

Invited for the cover of this issue is the group of Timo Repo at the University of Helsinki. The image depicts a ligand-exchange reaction as a battle between hummingbirds and golden birds, which represent two different thiol ligands. Read the full text of the article at 10.1002/chem.202101028.

Role of Acetate Anions in the Catalytic Formation of Isocyanurates from Aromatic Isocyanates.

The formation of isocyanurates via cyclotrimerization of aromatic isocyanates is widely used to enhance the physical properties of a variety of polyurethanes. The most commonly used catalysts in industries are carboxylates for which the exact catalytically active species have remained controversial. We investigated how acetate and other carboxylates react with aromatic isocyanates in a stepwise manner and identified that the carboxylates are only precatalysts in the reaction. The reaction of carboxylates with an excess of aromatic isocyanates leads to irreversible formation of corresponding deprotonated amide species that are strongly nucleophilic and basic. As a result, they are active catalysts during the nucleophilic anionic trimerization, but can also deprotonate urethane and urea species present, which in turn catalyze the isocyanurate formation. The current study also shows how quantum chemical calculations can be used to direct spectroscopic identification of reactive intermediates formed during the active catalytic cycle with predictive accuracy.

Cooperative Ligands in Dissolution of Gold.

Development of new, environmentally benign dissolution methods for metallic gold is driven by needs in the circular economy. Gold is widely used in consumer electronics, but sustainable and selective dissolution methods for Au are scarce. Herein, we describe a quantitative dissolution of gold in organic solution under mild conditions by using hydrogen peroxide as an oxidant. In the dissolution reaction, two thiol ligands, pyridine-4-thiol and 2-mercaptobenzimidazole, work in a cooperative manner. The mechanistic investigations suggest that two pyridine-4-thiol molecules form a complex with Au0 that can be oxidized, whereas the role of inexpensive 2-mercaptobenzimidazole is to stabilize the formed AuI species through a ligand exchange process. Under optimized conditions, the reaction proceeds vigorously and gold dissolves quantitatively in two hours. The demonstrated ligand-exchange mechanism with two thiols allows to drastically reduce the thiol consumption and may lead to even more effective gold dissolution methods in the future.

Divergent Carbocatalytic Routes in Oxidative Coupling of Benzofused Heteroaryl Dimers: A Mechanistic Update.

Mildly thermal air or HNO3 oxidized activated carbons catalyse oxidative dehydrogenative couplings of benzo[b]fused heteroaryl 2,2'-dimers, e.g., 2-(benzofuran-2-yl)-1H-indole, to chiral 3,3'-coupled cyclooctatetraenes or carbazole-type migrative products under O2 atmosphere. DFT calculations show that the radical cation and the Scholl-type arenium cation mechanisms lead to different products with 2-(benzofuran-2-yl)-1H-indole, being in accord with experimental product distributions.

Dual H-bond activation of NHC-Au(i)-Cl complexes with amide functionalized side-arms assisted by H-bond donor substrates or acid additives.

Novel approach with amide-tethered H-bond donor NHC ligands enabled Au(i)-catalysis via H-bonding. The plain NHC-Au(i)-Cl complex catalysed conversions of terminal N-propynamides to oxazolines, and enyne cycloisomerization with an acid additive, in DCM at RT. DFT calculations enlightened the function of the side-arm in the activation.

Carbocatalytic Oxidative Dehydrogenative Couplings of (Hetero)Aryls by Oxidized Multi-Walled Carbon Nanotubes in Liquid Phase.

HNO3 -oxidized carbon nanotubes catalyze oxidative dehydrogenative (ODH) carbon-carbon bond formation between electron-rich (hetero)aryls with O2 as a terminal oxidant. The recyclable carbocatalytic method provides a convenient and an operationally easy synthetic protocol for accessing various benzofused homodimers, biaryls, triphenylenes, and related benzofused heteroaryls that are highly useful frameworks for material chemistry applications. Carbonyls/quinones are the catalytically active site of the carbocatalyst as indicated by model compounds and titration experiments. Further investigations of the reaction mechanism with a combination of experimental and DFT methods support the competing nature of acid-catalyzed and radical cationic ODHs, and indicate that both mechanisms operate with the current material.

Design Principles for Rational Polyurethane Catalyst Development.

Tertiary amine catalysts are essential components in manufacturing polyurethane materials. The low-emission requirements for indoor applications are typically achieved by employing tertiary amines with catalytically active N, N-dimethyl groups as the base catalyst and a longer alkyl substituent with a reactive end, that is, alcohol or amine, to incorporate it in the polyurethane matrix. N, N-dimethyl groups are, however, oxidized when exposed to air and lead to undesired formaldehyde emissions. Here, we employ modern quantum chemical methods to understand design principles how the structure of tertiary amine catalysts having N, N-dimethyl groups can be modified to avoid this source of formaldehyde formation but still preserve their catalytic activity. We found the pyrrolidine derivative of commonly used N, N-dimethylated catalysts to be the most promising candidate and developed design principles to rationalize why longer alkyl chains or larger ring sizes inhibit the catalytic activity. The computationally predicted catalyst performances were confirmed experimentally in model polyurethane systems for selected amine catalysts, and emission measurements showed that the formaldehyde emission was completely suppressed when pyrrolidine derivative was used as a catalyst. Our results further illustrate how condensed phase reactions can be predicted using quantum chemical methods and that to account for steric hindrance near the reaction center, it was also necessary to include conformational energy contributions in the calculated activation free energies.

Visible-Light-Photocatalyzed Reductions of N-Heterocyclic Nitroaryls to Anilines Utilizing Ascorbic Acid Reductant.

A photoreductive protocol utilizing [Ru(bpy)3]2+ photocatalyst, blue light LEDs, and ascorbic acid (AscH2) has been developed to reduce nitro N-heteroaryls to the corresponding anilines. Based on experimental and computational results and previous studies, we propose that the reaction proceeds via proton-coupled electron transfer between AscH2, photocatalyst, and the nitro N-heteroaryl. The method offers a green catalytic procedure to reduce, e.g., 4-/8-nitroquinolines to the corresponding aminoquinolines, substructures present in important antimalarial drugs.

Pyridinethiol-Assisted Dissolution of Elemental Gold in Organic Solutions.

Dissolution of elemental gold in organic solutions is a contemporary approach to lower the environmental burden associated with gold recycling. Herein, we describe fundamental studies on a highly efficient method for the dissolution of elemental Au that is based on DMF solutions containing pyridine-4-thiol (4-PSH) as a reactive ligand and hydrogen peroxide as an oxidant. Dissolution of Au proceeds through several elementary steps: isomerization of 4-PSH to pyridine-4-thione (4-PS), coordination with Au0 , and then oxidation of the Au0 thione species to AuI simultaneously with oxidation of free pyridine thione to elemental sulfur and further to sulfuric acid. The final dissolution product is a AuI complex bearing two 4-PS ligands and SO4 2- as a counterion. The ligand is crucial as it assists the oxidation process and stabilizes and solubilizes the formed Au cations.

Light-activated chemical probing of nucleobase solvent accessibility inside cells.

This corrects the article DOI: 10.1038/nchembio.2548.

Total Synthesis of (-)-Chromodorolide B By a Computationally-Guided Radical Addition/Cyclization/Fragmentation Cascade.

The first total synthesis of a chromodorolide marine diterpenoid is described. The core of the diterpenoid is constructed by a bimolecular radical addition/cyclization/fragmentation cascade that unites two complex fragments and forms two C-C bonds and four contiguous stereogenic centers of (-)-chromodorolide B in a single step. This coupling step is initiated by visible-light photocatalytic fragmentation of a redox-active ester, which can be accomplished in the presence of an iridium or a less-precious electron-rich dicyanobenzene photocatalyst, and employs equimolar amounts of the two addends. Computational studies guided the development of this central step of the synthesis and provide insight into the origin of the observed stereoselectivity.

Light-activated chemical probing of nucleobase solvent accessibility inside cells.

The discovery of functional RNAs that are critical for normal and disease physiology continues to expand at a breakneck pace. Many RNA functions are controlled by the formation of specific structures, and an understanding of each structural component is necessary to elucidate its function. Measuring solvent accessibility intracellularly with experimental ease is an unmet need in the field. Here, we present a novel method for probing nucleobase solvent accessibility, Light Activated Structural Examination of RNA (LASER). LASER depends on light activation of a small molecule, nicotinoyl azide (NAz), to measure solvent accessibility of purine nucleobases. In vitro, this technique accurately monitors solvent accessibility and identifies rapid structural changes resulting from ligand binding in a metabolite-responsive RNA. LASER probing can further identify cellular RNA-protein interactions and unique intracellular RNA structures. Our photoactivation technique provides an adaptable framework to structurally characterize solvent accessibility of RNA in many environments.

Mechanism of photocatalytic water oxidation on small TiO2 nanoparticles.

We present the first unconstrained nonadiabatic molecular dynamics (NAMD) simulations of photocatalytic water oxidation by small hydrated TiO2 nanoparticles using Tully surface hopping and time-dependent density functional theory. The results indicate that ultrafast electron-proton transfer from physisorbed water to the photohole initiates the photo-oxidation on the S1 potential energy surface. The new mechanism readily explains the observation of mobile hydroxyl radicals in recent experiments. Two key driving forces for the photo-oxidation reaction are identified: localization of the electron-hole pair and stabilization of the photohole by hydrogen bonding interaction. Our findings illustrate the scope of recent advances in NAMD methods and emphasize the importance of explicit simulation of electronic excitations.

That Little Extra Kick: Nonadiabatic Effects in Acetaldehyde Photodissociation.

The effect of nonadiabatic transitions on branching ratios, kinetic and internal energy distribution of fragments, and reaction mechanisms observed in acetaldehyde photodissociation is investigated by nonadiabatic molecular dynamics (NAMD) simulations using time-dependent hybrid density functional theory and Tully surface hopping. Homolytic bond breaking is approximately captured by allowing spin symmetry to break. The NAMD simulations reveal that nonadiabatic transitions selectively enhance the kinetic energy of certain internal degrees of freedom within approximately 50 fs. Branching ratios from NAMD and conventional "hot" Born-Oppenheimer molecular dynamics (BOMD) are similar and qualitatively agree with experiment. However, as opposed to the BOMD simulations, NAMD captures the high-energy tail of the experimental kinetic energy distribution. The extra "kick" of the nuclei in the direction of the nonadiabatic coupling vector results from nonadiabatic transitions close to conical intersections. From a mechanistic perspective, the nonadiabatic effects favor asynchronous over synchronous fragmentation and tend to suppress roaming.

Diastereoselective Coupling of Chiral Acetonide Trisubstituted Radicals with Alkenes.

The stereochemical outcome of reactions of chiral nucleophilic trisubstituted acetonide radicals with electron-deficient alkenes is dictated by a delicate balance between destabilizing non-bonding interactions and stabilizing hydrogen-bonding between substituents on the α and ß carbons.

Modeling the Charging of Highly Oxidized Cyclohexene Ozonolysis Products Using Nitrate-Based Chemical Ionization.

Several extremely low volatility organic compounds (ELVOCs) formed in the ozonolysis of endocyclic alkenes have recently been detected in laboratory and field studies. These experiments have been carried out with chemical ionization atmospheric pressure interface time-of-flight mass spectrometers (CI-APi-TOF) with nitrate ions as reagent ions. The nitrate ion binds to the detected species through hydrogen bonds, but it also binds very strongly to one or two neutral nitric acid molecules. This makes the measurement highly selective when there is an excess amount of neutral nitric acid in the instrument. In this work, we used quantum-chemical methods to calculate the binding energies between a nitrate ion and several highly oxidized ozonolysis products of cyclohexene. These were then compared with the binding energies of nitrate ion-nitric acid clusters. Systematic configurational sampling of the molecules and clusters was carried out at the B3LYP/6-31+G* and ωB97xD/aug-cc-pVTZ levels, and the final single-point energies were calculated with DLPNO-CCSD(T)/def2-QZVPP. The binding energies were used in a kinetic simulation of the measurement system to determine the relative ratios of the detected signals. Our results indicate that at least two hydrogen bond donor functional groups (in this case, hydroperoxide, OOH) are needed for an ELVOC molecule to be detected in a nitrate ion CI-APi-TOF. Also, a double bond in the carbon backbone makes the nitrate cluster formation less favorable.

Photoinduced charge transfer in a conformational switching chlorin dimer-azafulleroid in polar and nonpolar media.

In the present study, a biomimetic reaction center model, that is, a molecular triad consisting of a chlorin dimer and an azafulleroid, is synthesized and its photophysical properties are studied in comparison with the corresponding molecular dyad, which consists only of a chlorin monomer and an azafulleroid. As evidenced by (1) H NMR, UV/Vis, and fluorescence spectroscopy, the chlorin dimer-azafulleroid folds in nonpolar media into a C2 -symmetric geometry through hydrogen bonding, resulting in appreciable electronic interactions between the chlorins, whereas in polar media the two chlorins diverge from contact. Femtosecond transient absorption spectroscopy studies reveal longer charge-separated states for the chlorin dimer-azafulleroid; ≈1.6 ns in toluene, compared with the lifetime of ≈0.9 ns for the corresponding chlorin monomer-azafulleroid in toluene. In polar media, for example, benzonitrile, similar charge-separated states are observed, but the lifetimes are inevitably shorter: 65 and 73 ps for the dimeric and monomeric chlorin-azafulleroids, respectively. Nanosecond transient absorption and singlet oxygen phosphorescence studies corroborate that in toluene, the charge-separated state decays indirectly via the triplet excited state to the ground state, whereas in benzonitrile, direct recombination to the ground state is observed. Complementary DFT studies suggest two energy-minima conformations, that is, a folded chlorin dimer-azafulleroid, which is present in nonpolar media, and another conformation in polar media, in which the two hydrophobic chlorins wrap the azafulleroid. Inspection of the frontier molecular orbitals shows that in the folded conformation, the HOMO on each chlorin is equivalent and is shared owing to partial π-π overlap, resulting in delocalization of the conjugated π electrons, whereas the wrapped conformation lacks this stabilization. As such, the longer charge-separated lifetime for the dimer is rationalized by both the electron donor-acceptor separation distance and the stabilization of the radical cation through delocalization. The chlorin folding seems to change the photophysical properties in a manner similar to that observed in the chlorophyll dimer in natural photosynthetic reaction centers.

Regioselectivity of intermolecular Pauson-Khand reaction of aliphatic alkynes: experimental and theoretical study of the effect of alkyne polarization.

Generally judged poor electronic regioselectivity of alkyne insertion in intermolecular Pauson-Khand reaction (PKR) has severely restricted its synthetic applications. In our previous rational study concerning diarylalkynes (Fager-Jokela, E.; Muuronen, M.; Patzschke, M.; Helaja, J. J. Org. Chem. 2012, 77, 9134-9147), both experimental and theoretical results indicated that purely electronic factors, i.e., alkyne polarization via resonance effect, induced the observed modest regioselectivity. In the present work, we substantiate that the alkyne polarization via inductive effect can result notable, synthetically valuable regioselectivity. Computational study at DFT level was performed to disclose the electronic origin of the selectivity. Overall, the NBO charges of alkynes correlated qualitatively with regioisomer outcome. In a detailed computational PKR case study, the obtained Boltzmann distributions of the transition state (TS) populations correlate closely with experimental regioselectivity. Analysis of the TS-structures revealed that weak interactions, e.g., hydrogen bonding and steric repulsion, affect the regioselectivity and can easily override the electronic guidance.