The rational design of high-performance graphene-based single-atom electrocatalysts for the ORR using machine learning.

In this work, high-performance two-dimensional (2D) graphene-based single-atom electrocatalysts (ZZ/ZA-MNxCy) for the oxygen reduction reaction (ORR) were screened out using machine learning (ML). A model was built for the fast prediction of electrocatalysts and two descriptors valence electron correction (VEc) and degree of construction differences (DC) were proposed to improve the accuracy of the model prediction. Two evaluation criteria, high-performance catalyst retention rate rR and high-performance catalyst occupancy rate rO, were proposed to evaluate the accuracy of ML models in high-performance catalyst screening. The addition of VEc and DC in the model could change the mean absolute error (MAEtest) of the test set, the coefficient of determination (R2test) of the test set, rO, and rR from 0.334 V, 0.683, 0.222, and 0.360 to 0.271 V, 0.774, 0.421, and 0.671, respectively. The partially screened potential high-performance ORR electrocatalysts such as ZZ-CoN4 and ZZ-CoN3C1 were also further investigated using a Density Functional Theory (DFT) method, which confirmed the accuracy of the ML model (MAE = 0.157 V, R2 = 0.821).

A theoretical study on the hydrogenation of CO2 to methanol catalyzed by ruthenium pincer complexes.

Herein, a density functional theory (DFT) study was performed to investigate thoroughly the cascade reaction mechanism for the hydrogenation of carbon dioxide to methanol catalyzed by ruthenium pincer complex [RuH2(Me2PCH2SiMe2)2NH(CO)]. Three catalytic stages involving the hydrogenation of carbon dioxide (stage I), formic acid (stage II) and formaldehyde (stage III) were studied. The calculated results show that the dominant H2 activation strategy in the hydrogenation of CO2 to methanol may not be the methanol-assisted H2 activation, but the formate-assisted H2 activation. In this cascade reaction, all energy spans of stage I, II and III are 20.2 kcal mol-1 of the formate-assisted H2 activation. This implies that it could occur under mild conditions. Meanwhile, the catalyst is proposed to be efficient for the transfer hydrogenation using isopropanol as the hydrogen resource, and the ruthenium pincer complexes [RuH2(Me2PCH2SiMe2)2NH(CO)], [RuH2(Ph2PCH2SiMe2)2NH(CO)] and [RuH2(Me2PCH2SiMe2)2NH(CO)] exhibit similar catalytic activities for the hydrogenation of CO2 to methanol.

An experimental and theoretical study on the growth of plate-like ß-HMX crystals in the hydroxylated interlayer space.

Plate-like ß-HMX crystals are grown in the hydroxylated interlayer space using a crystallization technique combining the cooling crystallization and solvent-antisolvent methods. The obtained crystals have been investigated by X-ray diffraction (XRD), scanning electron microscopy (SEM), and atomic force microscopy (AFM). The experimental results indicate that the most morphologically important face of the plate-like ß-HMX crystals is the (011) face adopting a layer-by-layer growth mode. Meanwhile, molecular dynamics (MD) simulations were performed to study the crystal morphology in HMX crystal growth in the hydroxylated interlayer space based on a modified attachment energy (MAE) model. The calculated results show that the major face is the (011) face and the interaction energies between the crystal face and the hydroxylated interlayer are in the order of (011) > (110) > (020), which agree well with the experimental results above.

Asymmetric Induction with a Chiral Amine Catalyzed by a Ru-PNP Pincer Complex: Insight from Theoretical Investigation.

In this paper, the mechanism of asymmetric amination of a racemic alcohol with Ellman's sulfinamide and the origin of diastereoselectivity catalyzed by a Ru-PNP pincer complex were studied using density functional theory (DFT). The mechanism involves dehydrogenation of the racemic alcohol, C-N coupling, and hydrogen transfer from the catalyst to the in situ formed imine. The calculated results indicate that both the alcohol dehydrogenation and imine hydrogenation are stepwise. The hydride transfer from a Ru hydride complex to the imine is shown to be the chirality-determining step in the whole catalytic cycle. It was found that the diastereoselectivity mainly stems from the hydrogen bonding interactions between the oxygen atom of the sulfinyl moiety and the hydrogen atom of the NH group of the ligand.

pH-Dependent transfer hydrogenation or dihydrogen release catalyzed by a [(η6-arene)RuCl(κ2-N,N-dmobpy)]+ complex: a DFT mechanistic understanding.

The reaction mechanism of the pH-dependent transfer hydrogenation of a ketone or the dehydrogenation of formic acid catalyzed by a [(η6-arene)RuCl(κ2-N,N-dmobpy)]+ complex in aqueous media has been investigated using the density functional theory (DFT) method. The TM-catalyzed TH of ketones with formic acid as the hydrogen source proceeds via two steps: the formation of a metal hydride and the transfer of the hydride to the substrate ketone. The calculated results show that ruthenium hydride formation is the rate-determining step. This proceeds via an ion-pair mechanism with an energy barrier of 14.1 kcal mol-1. Interestingly, the dihydrogen release process of formic acid and the hydride transfer process that produces alcohols are competitive under different pH environments. The investigation explores the feasibility of the two pathways under different pH environments. Under acidic conditions (pH = 4), the free energy barrier of the dihydrogen release pathway is 4.5 kcal mol-1 that is higher than that of the hydride transfer pathway, suggesting that the hydride transfer pathway is more favorable than the dihydrogen release pathway. However, under strongly acidic conditions, the dihydrogen release pathway is more favorable compared to the hydride transfer pathway. In addition, the ruthenium hydride formation pathway is less favorable than the ruthenium hydroxo complex formation pathway under basic conditions.

Theoretical Study of the Histidine-catalyzed Asymmetric Aldol Reaction of Acetone and Benzaldehyde.

The mechanism of histidine-catalyzed asymmetrical aldol reaction of acetone with benzaldehyde was studied by using B3LYP method of density functional theory at the levels of 6-31G(d,p) and cc-pvdz basis sets. The calculation results showed that the reaction mechanism included four steps: (I) nucleophilic attack of histidine on acetone to form alcohol intermediate Inter-A through the transition state TS1 (considered a rate control step because the activation energy (49.95 kcal/mol) was relatively high); (II) dehydration of the alcohol intermediate to form the cis- or trans-enamine through the transition states TS3 and TS4 with the energy barriers of 36.12 and 38.15 kcal/mol; (III) electrophilic addition of cis-enamine or trans-enamine with benzaldehyde to form imine Inter-C or Inter-E through the transition states TS8, TS9, TS10, and TS11 (energy barriers 18.43, 22.34, 13.24, and 13.24 kcal/mol, respectively); (IV) after combination of the imine intermediate with water through the transition states TS12, TS13, TS14, and TS15 (energy barriers 22.79, 34.6, 28.2, 25.12 kcal/mol, respectively), removal of the histidine catalys to obtain the final S or R aldol product. Through analyzing the potential energy profile of reaction, we found that the histidine-catalyzed reaction of acetone with benzaldehyde was more energetically favorable to obtain the R-product (ee value >99%). Solvent effects computed with a polarizable continuum model (PCM) indicated that the DMSO and water can reduce the reaction energy barrier.

Computational study on the function of water within a beta-helix antifreeze protein dimer and in the process of ice-protein binding.

Antifreeze proteins (AFPs) help many organisms protect themselves from freezing in subzero temperatures. The most active AFPs found to date are those from insects, which possess exceptionally regular beta-helical structures. On the ice-binding surface of these proteins, regularly arrayed water molecules are observed within the repeating Thr-Xxx-Thr motif, but the exact role of these water molecules remains unknown. In this work, we have employed a number of computational methods to examine the role of these water molecules in an AFP from Tenebrio molitor (TmAFP). Our investigation involved a combination of molecular and quantum mechanical approaches. Properties such as stability, interaction energy, orbital overlap, and conformational analysis of various systems, including TmAFP-water, TmAFP-water-ice, and TmAFP-ice, were systematically evaluated and compared. The regularly arrayed water molecules were found to remain associated with TmAFP before ice binding, demonstrating that they are an intrinsic part of the protein. These water molecules may assist TmAFP in the process of ice recognition and binding. However, after facilitating the initial stages of ice recognition and binding, these water molecules are excluded in the final formation of the AFP-ice complex. The departure of these water molecules enables a better two-dimensional match between TmAFP and ice. These results agree with experimental observations showing that although these water molecules are aligned with the ice-binding hydroxyl groups of Thr residues in one dimension, they are in fact positioned slightly off in the second dimension, making a good two-dimensional match impossible.

Analysis of ice-binding sites in fish type II antifreeze protein by quantum mechanics.

Many organisms living in cold environments can survive subzero temperatures by producing antifreeze proteins (AFPs) or antifreeze glycoproteins. In this paper we investigate the ice-binding surface of type II AFP by quantum mechanical methods, which, to the best of our knowledge, represents the first time that molecular orbital computational approaches have been applied to AFPs. Molecular mechanical approaches, including molecular docking, energy minimization, and molecular dynamics simulation, were used to obtain optimal systems for subsequent quantum mechanical analysis. We selected 17 surface patches covering the entire surface of the type II AFP and evaluated the interaction energy between each of these patches and two different ice planes using semi-empirical quantum mechanical methods. We have demonstrated the weak orbital overlay phenomenon and the change of bond orders in ice. These results consistently indicate that a surface patch containing 19 residues (K37, L38, Y20, E22, Y21, I19, L57, T56, F53, M127, T128, F129, R17, C7, N6, P5, G10, Q1, and W11) is the most favorable ice-binding site for both a regular ice plane and an ice plane where water O atoms are randomly positioned. Furthermore, for the first time the computation results provide new insights into the weakening of the ice lattice upon AFP binding, which may well be a primary factor leading to AFP-induced ice growth inhibition.