Prediction of Stable Surfaces of Metal Oxides through the Unsaturated Coordination Index.

This study proposes the unsaturated coordination index, σ, as a potential descriptor of the stability of metal-oxide surfaces cleaved from bulk. The value of σ, the number of missing bonds per unit area, can be obtained very quickly using only crystallographic data, namely, the bulk geometry. The surface energies of various binary oxides, with and without atom relaxation, were calculated. Their correlations with σ had good coefficients of determination (R2) values, particularly in high-symmetry crystals. The proposed descriptor is very useful for an initial evaluation of stable metal-oxide surfaces without conducting any surface model calculations.

Theoretical Mechanistic Investigation of the Dynamic Kinetic Resolution of N-Protected Amino Acid Esters using Phase-Transfer Catalysts.

A detailed theoretical mechanistic investigation on the dynamic kinetic resolution of N-protected amino acid esters using phase-transfer catalysts is described. Semiautomatic exhaustive conformation search of transition state (TS)-like structures were carried out using the ConFinder program and the pseudo-TS conformational search (PTSCS) method. This conformational search method successfully provided reasonable TS structures for determining the stereoselectivity in the asymmetric base hydrolysis of hexafluoroisopropyl (HFIP) esters as well as the racemization mechanism. Furthermore, the independent gradient model (IGM) analysis of the TS structures suggested that the H-bonding interactions with the oxyanion hole and π-stacking interactions are the common important features of the proposed TS structures that determine the stereoselectivity.

Oxidative Addition of Methane and Reductive Elimination of Ethane and Hydrogen on Surfaces: From Pure Metals to Single Atom Alloys.

Oxidative addition of CH4 to the catalyst surface produces CH3 and H. If the CH3 species generated on the surface couple with each other, reductive elimination of C2H6 may be achieved. Similarly, H's could couple to form H2. This is the outline of nonoxidative coupling of methane (NOCM). It is difficult to achieve this reaction on a typical Pt catalyst surface. This is because methane is overoxidized and coking occurs. In this study, the authors approach this problem from a molecular aspect, relying on organometallic or complex chemistry concepts. Diagrams obtained by extending the concepts of the Walsh diagram to surface reactions are used extensively. C-H bond activation, i.e., oxidative addition, and C-C and H-H bond formation, i.e., reductive elimination, on metal catalyst surfaces are thoroughly discussed from the point of view of orbital theory. The density functional theory method for structural optimization and accurate energy calculations and the extended Hückel method for detailed analysis of crystal orbital changes and interactions play complementary roles. Limitations of monometallic catalysts are noted. Therefore, a rational design of single atom alloy (SAA) catalysts is attempted. As a result, the effectiveness of the Pt1/Au(111) SAA catalyst for NOCM is theoretically proposed. On such an SAA surface, one would expect to find a single Pt monatomic site in a sea of inert Au atoms. This is desirable for both inhibiting overoxidation and promoting reductive elimination.

Factors determining surface oxygen vacancy formation energy in ternary spinel structure oxides with zinc.

Spinel oxides are an important class of materials for heterogeneous catalysis including photocatalysis and electrocatalysis. The surface O vacancy formation energy (EOvac) is a critical quantity for catalyst performance because the surface of metal oxide catalysts often acts as a reaction site, for example, in the Mars-van Krevelen mechanism. However, experimental evaluation of EOvac is very challenging. We obtained the EOvac for (100), (110), and (111) surfaces of normal zinc-based spinel oxides ZnAl2O4, ZnGa2O4, ZnIn2O4, ZnV2O4, ZnCr2O4, ZnMn2O4, ZnFe2O4, and ZnCo2O4. The most stable surface is (100) for all compounds. The smallest EOvac for a surface is the largest in the (100) surface except for ZnCo2O4. For (100) and (110) surfaces, there is a good correlation, over all spinels, between the smallest EOvac for the surface and bulk formation energy, while the ionization potential correlates well in (111) surfaces. Machine learning over EOvac of all surface sites in all orientations and for all compounds to find the important factors, or descriptors, that decide the EOvac revealed that bulk and surface-dependent descriptors are the most important, namely the bulk formation energy, a Boolean descriptor of whether the surface is (111) or not, and the ionization potential, followed by geometrical descriptors that are different in each O site.

Rhenium-Loaded TiO2 : A Highly Versatile and Chemoselective Catalyst for the Hydrogenation of Carboxylic Acid Derivatives and the N-Methylation of Amines Using H2 and CO2.

Herein, we report a heterogeneous TiO2 -supported Re catalyst (Re/TiO2 ) that promotes various selective hydrogenation reactions, which includes the hydrogenation of esters to alcohols, the hydrogenation of amides to amines, and the N-methylation of amines, by using H2 and CO2 . Initially, Re/TiO2 was evaluated in the context of the selective hydrogenation of 3-phenylpropionic acid methyl ester to afford 3-phenylpropanol (pH2 =5 MPa, T=180 °C), which revealed a superior performance over other catalysts that we tested in this study. In contrast to other typical heterogeneous catalysts, hydrogenation reactions with Re/TiO2 did not produce dearomatized byproducts. DFT studies suggested that the high selectivity for the formation of alcohols in favor of the hydrogenation of aromatic rings is ascribed to the higher affinity of Re towards the COOCH3 group than to the benzene ring. Moreover, Re/TiO2 showed a wide substrate scope for the hydrogenation reaction (19 examples). Subsequently, this Re/TiO2 catalyst was applied to the hydrogenation of amides, the N-methylation of amines, and the N-alkylation of amines with carboxylic acids or esters.

Redox Potentials of Cobalt Corrinoids with Axial Ligands Correlate with Heterolytic Co-C Bond Dissociation Energies.

We investigate the correlations between the redox potentials of nonalkylated cobalt corrinoids and the Co-C bond dissociation energies (BDEs) of the methylated species with an aqua or histidine axial ligand. A set of cobalt corrinoids, cobalamin, and its model systems, which include new version of myoglobin reconstituted with cobalt didehydrocorrin, are investigated. The Co(III)/Co(II) and Co(II)/Co(I) redox potentials of myoglobin reconstituted with cobalt tetradehydrocorrin and didehydrocorrin and the bare cofactors were determined. Density functional theory (DFT) calculations were performed to estimate the Co-C BDEs of the methylated species. It is found that the redox potentials correlate well with the heterolytic BDEs, which are dependent on the electronegativity of the corrinoid frameworks. The present study offers two important insights into our understanding of how enzymes promote the reactions: (i) homolysis is promoted by strong axial ligation and (ii) heterolysis is controlled by the redox potentials, which are regulated by the saturated framework and axial ligation in the enzyme.

TiO2 -Supported Re as a General and Chemoselective Heterogeneous Catalyst for Hydrogenation of Carboxylic Acids to Alcohols.

TiO2 -supported Re, Re/TiO2 , was found to promote selective hydrogenation of carboxylic acids having aromatic and aliphatic moieties to the corresponding alcohols. Re/TiO2 showed superior results compared to other transition-metal-loaded TiO2 and supported Re catalysts for selective hydrogenation of 3-phenylpropionic acid. 3-phenylpropanol was produced in 97 % yield under mild conditions (5 MPa H2 at 140 °C). Contrary to typical heterogeneous catalysts, Re/TiO2 does not lead to the formation of dearomatized byproducts. The catalyst is recyclable and shows a wide substrate scope in the synthesis of alcohols (22 examples; up to 97 % isolated yield).

Thermally Induced Intra-Carboxyl Proton Shuttle in a Molecular Rack-and-Pinion Cascade Achieving Macroscopic Crystal Deformation.

Proton transport via dynamic molecules is ubiquitous in chemistry and biology. However, its use as a switching mechanism for properties in functional molecular assemblies is far less common. In this study, we demonstrate how an intra-carboxyl proton shuttle can be generated in a molecular assembly akin to a rack-and-pinion cascade via a thermally induced single-crystal-to-single-crystal phase transition. In a triply interpenetrated supramolecular organic framework (SOF), a 4,4'-azopyridine (azpy) molecule connects to two biphenyl-3,3',5,5'-tetracarboxylic acid (H4 BPTC) molecules to form a functional molecular system with switchable mechanical properties. A temperature change reversibly triggers a molecular movement akin to a rack-and-pinion cascade, which mainly involves 1) an intra-carboxyl proton shuttle coupled with tilting of the azo molecules and azo pedal motion and 2) H4 BPTC translation. Moreover, both the molecular motions are collective, and being propagated across the entire framework, leading to a macroscopic crystal expansion and contraction.

Superior thermoelasticity and shape-memory nanopores in a porous supramolecular organic framework.

Flexible porous materials generally switch their structures in response to guest removal or incorporation. However, the design of porous materials with empty shape-switchable pores remains a formidable challenge. Here, we demonstrate that the structural transition between an empty orthorhombic phase and an empty tetragonal phase in a flexible porous dodecatuple intercatenated supramolecular organic framework can be controlled cooperatively through guest incorporation and thermal treatment, thus inducing empty shape-memory nanopores. Moreover, the empty orthorhombic phase was observed to exhibit superior thermoelasticity, and the molecular-scale structural mobility could be transmitted to a macroscopic crystal shape change. The driving force of the shape-memory behaviour was elucidated in terms of potential energy. These two interconvertible empty phases with different pore shapes, that is, the orthorhombic phase with rectangular pores and the tetragonal phase with square pores, completely reject or weakly adsorb N2 at 77 K, respectively.

Possible Peroxo State of the Dicopper Site of Particulate Methane Monooxygenase from Combined Quantum Mechanics and Molecular Mechanics Calculations.

Enzymatic methane hydroxylation is proposed to efficiently occur at the dinuclear copper site of particulate methane monooxygenase (pMMO), which is an integral membrane metalloenzyme in methanotrophic bacteria. The resting state and a possible peroxo state of the dicopper active site of pMMO are discussed by using combined quantum mechanics and molecular mechanics calculations on the basis of reported X-ray crystal structures of the resting state of pMMO by Rosenzweig and co-workers. The dicopper site has a unique structure, in which one copper is coordinated by two histidine imidazoles and another is chelated by a histidine imidazole and primary amine of an N-terminal histidine. The resting state of the dicopper site is assignable to the mixed-valent Cu(I)Cu(II) state from a computed Cu-Cu distance of 2.62 Å from calculations at the B3LYP-D/TZVP level of theory. A µ-η(2):η(2)-peroxo-Cu(II)2 structure similar to those of hemocyanin and tyrosinase is reasonably obtained by using the resting state structure and dioxygen. Computed Cu-Cu and O-O distances are 3.63 and 1.46 Å, respectively, in the open-shell singlet state. Structural features of the dicopper peroxo species of pMMO are compared with those of hemocyanin and tyrosinase and synthetic dicopper model compounds. Optical features of the µ-η(2):η(2)-peroxo-Cu(II)2 state are calculated and analyzed with TD-DFT calculations.

Low-Mode Conformational Search Method with Semiempirical Quantum Mechanical Calculations: Application to Enantioselective Organocatalysis.

A conformational search program for finding low-energy conformations of large noncovalent complexes has been developed. A quantitatively reliable semiempirical quantum mechanical PM6-DH+ method, which is able to accurately describe noncovalent interactions at a low computational cost, was employed in contrast to conventional conformational search programs in which molecular mechanical methods are usually adopted. Our approach is based on the low-mode method whereby an initial structure is perturbed along one of its low-mode eigenvectors to generate new conformations. This method was applied to determine the most stable conformation of transition state for enantioselective alkylation by the Maruoka and cinchona alkaloid catalysts and Hantzsch ester hydrogenation of imines by chiral phosphoric acid. Besides successfully reproducing the previously reported most stable DFT conformations, the conformational search with the semiempirical quantum mechanical calculations newly discovered a more stable conformation at a low computational cost.

Crystal Structures and Coordination Behavior of Aqua- and Cyano-Co(III) Tetradehydrocorrins in the Heme Pocket of Myoglobin.

Myoglobins reconstituted with aqua- and cyano-Co(III) tetradehydrocorrins, rMb(Co(III)(OH2)(TDHC)) and rMb(Co(III)(CN)(TDHC)), respectively, were prepared and investigated as models of a cobalamin-dependent enzyme. The former protein was obtained by oxidation of rMb(Co(II)(TDHC)) with K3[Fe(CN)6]. The cyanide-coordinated Co(III) species in the latter protein was prepared by ligand exchange of rMb(Co(III)(OH2)(TDHC)) with exogenous cyanide upon addition of KCN. The X-ray crystallographic study reveals the hexacoordinated structures of rMb(Co(III)(OH)(TDHC)) and rMb(Co(III)(CN)(TDHC)) at 1.20 and 1.40 Å resolution, respectively. The (13)C NMR chemical shifts of the cyanide in rMb(Co(III)(CN)(TDHC)) were determined to be 108.6 and 110.6 ppm. IR measurements show that the cyanide of rMb(Co(III)(CN)(TDHC)) has a stretching frequency peak at 2151 cm(-1) which is higher than that of cyanocobalamin. The (13)C NMR and IR measurements indicate weaker coordination of the cyanide to Co(III)(TDHC) relative to cobalamin, a vitamin B12 derivative. Thus, the extent of π-back-donation from the cobalt ion to the cyanide ion is lower in rMb(Co(III)(CN)(TDHC)). Furthermore, the pK(1/2) values of rMb(Co(III)(OH2)(TDHC)) and rMb(Co(III)(CN)(TDHC)) were determined by a pH titration experiment to be 3.2 and 5.5, respectively, indicating that the cyanide ligation weakens the Co-N(His93) bond. Theoretical calculations also demonstrate that the axial ligand exchange from water to cyanide elongates the Co-N(axial) bond with a decrease in the bond dissociation energy. Taken together, the cyano-Co(III) tetradehydrocorrin in myoglobin is appropriate for investigation as a structural analogue of methylcobalamin, a key intermediate in methionine synthase reaction.

Intraprotein transmethylation via a CH3-Co(iii) species in myoglobin reconstituted with a cobalt corrinoid complex.

Myoglobin reconstituted with a cobalt tetradehydrocorrin derivative, rMb(Co(TDHC)), was investigated as a hybrid model to replicate the reaction catalyzed by methionine synthase. In the heme pocket, Co(I)(TDHC) is found to react with methyl iodide to form the methylated cobalt complex, CH3-Co(III)(TDHC), although it is known that a similar nucleophilic reaction of a cobalt(i) tetradehydrocorrin complex does not proceed effectively in organic solvents. Furthermore, we observed a residue- and regio-selective transmethylation from the CH3-Co(III)(TDHC) species to the Nε2 atom of the His64 imidazole ring in myoglobin at 25 °C over a period of 48 h. These findings indicate that the protein matrix promotes the model reaction of methionine synthase via the methylated cobalt complex. A theoretical calculation provides support for a plausible reaction mechanism wherein the axial histidine ligation stabilizes the methylated cobalt complex and subsequent histidine-flipping induces the transmethylation via heterolytic cleavage of the Co-CH3 bond in the hybrid model.

Assembling an alkyl rotor to access abrupt and reversible crystalline deformation of a cobalt(II) complex.

Harnessing molecular motion to reversibly control macroscopic properties, such as shape and size, is a fascinating and challenging subject in materials science. Here we design a crystalline cobalt(II) complex with an n-butyl group on its ligands, which exhibits a reversible crystal deformation at a structural phase transition temperature. In the low-temperature phase, the molecular motion of the n-butyl group freezes. On heating, the n-butyl group rotates ca. 100° around the C-C bond resulting in 6-7% expansion of the crystal size along the molecular packing direction. Importantly, crystal deformation is repeatedly observed without breaking the single-crystal state even though the shape change is considerable. Detailed structural analysis allows us to elucidate the underlying mechanism of this deformation. This work may mark a step towards converting the alkyl rotation to the macroscopic deformation in crystalline solids.

Formation and nitrile hydrogenation performance of Ru nanoparticles on a K-doped Al2O3 surface.

Decarbonylation-promoted Ru nanoparticle formation from Ru3(CO)12 on a basic K-doped Al2O3 surface was investigated by in situ FT-IR and in situ XAFS. Supported Ru3(CO)12 clusters on K-doped Al2O3 were converted stepwise to Ru nanoparticles, which catalyzed the selective hydrogenation of nitriles to the corresponding primary amines via initial decarbonylation, the nucleation of the Ru cluster core, and the growth of metallic Ru nanoparticles on the surface. As a result, small Ru nanoparticles, with an average diameter of less than 2 nm, were formed on the support and acted as efficient catalysts for nitrile hydrogenation at 343 K under hydrogen at atmospheric pressure. The structure and catalytic performance of Ru catalysts depended strongly on the type of oxide support, and the K-doped Al2O3 support acted as a good oxide for the selective nitrile hydrogenation without basic additives like ammonia. The activation of nitriles on the modelled Ru catalyst was also investigated by DFT calculations, and the adsorption structure of a nitrene-like intermediate, which was favourable for high primary amine selectivity, was the most stable structure on Ru compared with other intermediate structures.

Molecular motor-driven abrupt anisotropic shape change in a single crystal of a Ni complex.

Many molecular machines with controllable molecular-scale motors have been developed. However, transmitting molecular movement to the macroscopic scale remains a formidable challenge. Here we report a single crystal of a Ni complex whose shape changes abruptly and reversibly in response to thermal changes at around room temperature. Variable-temperature single-crystal X-ray diffraction studies show that the crystalline shape change is induced by an unusual 90° rotation of uniaxially aligned oxalate molecules. The oxalate dianions behave as molecular-scale rotors, with their movement propagated through the entire crystalline material via intermolecular hydrogen bonding. Consequently, the subnanometre-scale changes in the oxalate molecules are instantly amplified to a micrometre-scale contraction or expansion of the crystal, accompanied by a thermal hysteresis loop. The shape change in the crystal was clearly detected under an optical microscope. The large directional deformation and prompt response suggest a role for this material in microscale or nanoscale thermal actuators.

Enantioselective alkylation by binaphthyl chiral phase-transfer catalysts: a DFT-based conformational analysis.

A conformational search method based on the density functional theory (DFT) was successfully applied to explore a mechanism for the highly enantioselective alkylation by binaphthyl-modifed chiral phase-transfer catalysts. Key interactions that govern the enantioselectivity were analyzed. The computational results are encouraging for further application of the DFT-based conformational search toward the rational design of next-generation asymmetric phase transfer catalysts.

Hydrolytic enantioselective protonation of cyclic dienyl esters and a ß-diketone with chiral phase-transfer catalysts.

Hydrolytic enantioselective protonation of dienyl esters and a ß-diketone catalyzed by phase-transfer catalysts are described. The latter reaction is the first example of an enantio-convergent retro-Claisen condensation. Corresponding various optically active α,ß-unsaturated ketones having tertiary chiral centers adjacent to carbonyl groups were obtained in good to excellent yields and enantiomeric ratios (83-99%, up to 97.5:2.5 er).

[Computational mutation analysis of enzymatic reaction].

Density functional theory (DFT) calculations are established as a useful research tool to investigate the structures and reactivity of biological systems; however, their high computational costs still restrict their applicability to systems of several tens up to a few hundred atoms. Recently, a combined quantum mechanical/molecular mechanical (QM/MM) approach has become an important method to study enzymatic reactions. In the past several years, we have investigated B12-dependent diol dehydratase using QM/MM calculations. The enzyme catalyzes chemically difficult reactions by utilizing the high reactivity of free radicals. In this paper, we explain our QM/MM calculations for the structure and reactivity of diol dehydratase and report key findings with respect to the catalytic roles of the active-site amino acid residues, computational mutational analysis of the active-site amino acid residues, assignment of the central metal ion, and function of the central metal ion. Our QM/MM calculations can correctly describe the structures and activation barriers of intermediate and transition states in the protein environment. Moreover, predicted relative activities of mutants are consistent with experimentally observed reactivity. These results will encourage the application of QM/MM research to the mechanistic study of enzymatic reactions, functional analysis of active-site residues, and rational design of enzymes with new catalytic functions.

Inactivation mechanism of glycerol dehydration by diol dehydratase from combined quantum mechanical/molecular mechanical calculations.

Inactivation of diol dehydratase during the glycerol dehydration reaction is studied on the basis of quantum mechanical/molecular mechanical calculations. Glycerol is not a chiral compound but contains a prochiral carbon atom. Once it is bound to the active site, the enzyme adopts two binding conformations. One is predominantly responsible for the product-forming reaction (G(R) conformation), and the other primarily contributes to inactivation (G(S) conformation). Reactant radical is converted into a product and byproduct in the product-forming reaction and inactivation, respectively. The OH group migrates from C2 to C1 in the product-forming reaction, whereas the transfer of a hydrogen from the 3-OH group of glycerol to C1 takes place during the inactivation. The activation barrier of the hydrogen transfer does not depend on the substrate-binding conformation. On the other hand, the activation barrier of OH group migration is sensitive to conformation and is 4.5 kcal/mol lower in the G(R) conformation than in the G(S) conformation. In the OH group migration, Glu170 plays a critical role in stabilizing the reactant radical in the G(S) conformation. Moreover, the hydrogen bonding interaction between Ser301 and the 3-OH group of glycerol lowers the activation barrier in G(R)-TS2. As a result, the difference in energy between the hydrogen transfer and the OH group migration is reduced in the G(S) conformation, which shows that the inactivation is favored in the G(S) conformation.