Takashi Kamachi

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.

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

Hydrolytic enantioselective protonation of dienyl esters and a β-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,β-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).

The Catalytic Mechanism of Fluoroacetate Dehalogenase: A Computational Exploration of Biological Dehalogenation

The biological dehalogenation of fluoroacetate carried out by fluoroacetate dehalogenase is discussed by using quantum mechanical/molecular mechanical (QM/MM) calculations for a whole-enzyme model of 10 800 atoms. Substrate fluoroacetate is anchored by a hydrogen-bonding network with water molecules and the surrounding amino acid residues of Arg105, Arg108, His149, Trp150, and Tyr212 in the active site in a similar way to haloalkane dehalogenase. Asp104 is likely to act as a nucleophile to attack the alpha-carbon of fluoroacetate, resulting in the formation of an ester intermediate, which is subsequently hydrolyzed by the nucleophilic attack of a water molecule to the carbonyl carbon atom. The cleavage of the strong C-F bond is greatly facilitated by the hydrogen-bonding interactions between the leaving fluorine atom and the three amino acid residues of His149, Trp150, and Tyr212. The hydrolysis of the ester intermediate is initiated by a proton transfer from the water molecule to His271 and by the simultaneous nucleophilic attack of the water molecule. The transition state and produced tetrahedral intermediate are stabilized by Asp128 and the oxyanion hole composed of Phe34 and Arg105.

Theoretical analysis of the diradical nature of adenosylcobalamin cofactor-tyrosine complex in B12-dependent mutases: inspiring PCET-driven enzymatic catalysis.

Detailed theoretical and X-ray based structural analysis has been carried out in order to unmask the role of the tyrosine residue (Y) in the activation of the Co-C bond in AdoCbl-dependent mutases. In particular, methylmalonyl-CoA mutase (MCM) and glutamate mutase (GLM) enzymes have been studied; in the case of MCM, the significance of the Y89 residue has been analyzed extensively. Three different theoretical platforms encompassing the DFT, CASSCF/QDPT2, and QM/MM frameworks have been employed to elucidate the energetics of the AdoCbl-Y(-) complex while taking into account a varied degree of structural complexity. The diradical state, [AdoCbl](*-)-Y*, has been found to be the lowest electronic state of the AdoCbl-Y(-) complex, providing strong evidence that electron transfer from the Y89 residue to the cofactor is feasible. Crystallographic analysis of the active sites of MCM and GLM enzymes reveals that substrate binding can play a critical role in displacing the hydroxyl proton of the Y residue (Y89 in the case of MCM enzyme and Y181 in the case of GLM enzyme) that will facilitate the electron transfer (ET), hence making the activation process a case of proton-coupled electron transfer (PCET). PCET-inspired enzymatic catalysis implies that the cleavage of the Co-C bond takes place via one-electron reduced form of the AdoCbl cofactor (i.e., [AdoCbl](*-)), rather than its neutral analogue, thus providing an efficient mode of cleavage that can help in understanding the origin of the catalytic effect in such enzymes.

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.

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.

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.

Selective carbon dioxide adsorption of ε-Keggin-type zincomolybdate-based purely inorganic 3D frameworks

Polyoxometalate-based 3D frameworks, Na1.5H11.4[ZnMo12O40{Zn2}]·5.5H2O and (NH4)1.5H8.5[ZnMo12O40{Zn2}]·6H2O, are synthesized in moderate yields. Rotation of the reactor under hydrothermal conditions is essential to improve the yield. The materials show zeolite-like selective molecule adsorption properties. Depending on the micropore aperture size of the materials, small molecules can be adsorbed in the materials, while large molecules cannot. The enthalpy of adsorption and DFT calculation indicate that the materials strongly interact with CO2, but weakly interact with CH4, due to electrostatic interactions between the materials and molecules. CO2/CH4 co-sorption experiments show that the materials can selectively adsorb CO2, and CO2 adsorption selectivity of the material with sodium cations is higher than that of the material with ammonium cations. The material with sodium ions can be utilized for gas chromatographic separation of CH4 and CO2.

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.

Catalytic roles of the metal ion in the substrate-binding site of coenzyme B12-dependent diol dehydratase.

Functions of the metal ion in the substrate-binding site of diol dehydratase are studied on the basis of quantum mechanical/molecular mechanical (QM/MM) calculations. The metal ion directly coordinates to substrate and is essential for structural retention and substrate binding. The metal ion has been originally assigned to the K(+) ion; however, QM/MM computations indicate that Ca(2+) ion is more reasonable as the metal ion because calculated Ca-O distances better fit to the coordination distances in X-ray crystal structures rather than calculated K-O distances. The activation energy for the OH group migration, which is essential in the conversion of diols to corresponding aldehydes, is sensitive to the identity of the metal ion. For example, the spectator OH group of substrate is fully deprotonated by Glu170 in the transition state for the OH group migration in the Ca-contained QM/MM model, and therefore the barrier height is significantly decreased in the model having Ca(2+) ion. On the other hand, the deprotonation of the spectator OH group cannot effectively be triggered by the K(+) ion. Moreover, in the hydrogen recombination, the most energy-demanding step is more favorable in the Ca-contained model. The proposal that the Ca(2+) ion should be involved in the substrate-binding site is consistent with an observed large deuterium kinetic isotope effect of 10, which indicates that C-H bond activation is involved in the rate-determining step. Asp335 is found to have a strong anticatalytic effect on the OH group migration despite its important role in substrate binding. The synergistic interplay of the O-C bond cleavage by Ca(2+) ion and the deprotonation of the spectator OH group by Glu170 is required to overcome the anticatalytic effect of Asp335.