Molecular weight fractionation by confinement of polymer in one-dimensional pillar[5]arene channels.

Confinement of polymers in nano-spaces can induce unique molecular dynamics and properties. Here we show molecular weight fractionation by the confinement of single polymer chains of poly(ethylene oxide) (PEO) in the one-dimensional (1D) channels of crystalline pillar[5]arene. Pillar[5]arene crystals are activated by heating under reduced pressure. The activated crystals are immersed in melted PEO, causing the crystals to selectively take up PEO with high mass fraction. The high mass fractionation is caused by the greater number of attractive CH/π interactions between PEO C-H groups and the π-electron-rich 1D channel of the pillar[5]arene with increasing PEO chain length. The molecular motion of the confined PEO (PEO chain thickness of ~3.7 Å) in the 1D channel of pillar[5]arenes (diameter of ~4.7 Å) is highly restricted compared with that of neat PEO.

Lewis Acid-Catalyzed Selective [2 + 2]-Cycloaddition and Dearomatizing Cascade Reaction of Aryl Alkynes with Acrylates.

Combined Lewis acid, consisting of two or more Lewis acids, sometimes shows unique catalytic ability, and it may promote reactions which could not be catalyzed by any of the Lewis acids solely. On the other hand, the development of efficient methods for the facile synthesis of cyclobutenes and densely functionalized decalins is an attractive target for synthetic chemists due to their versatile synthetic utilities and widespread occurrence in natural products. Herein, we wish to report an efficient method for the assembly of cyclobutenes and densely functionalized decalin skeletons through In(tfacac)3-TMSBr catalyzed selective [2 + 2]-cycloaddition and dearomatizing cascade reaction of aryl alkynes with acrylates with high chemo- and stereoselectivity. The obtained cyclobutene could be easily converted into cyclobutane as well as synthetically useful 1,4- and 1,5-diketones with high chemo- and stereoselectivity. On the basis of mechanistic studies, plausible reaction mechanisms were proposed for both the [2 + 2]-cycloaddition and the dearomatizing cascade reaction. Finally, the computational studies of reaction mechanisms were conducted, and the results suggest that the combined Lewis acid could efficiently promote both reactions.

Alkane-length sorting using activated pillar[5]arene crystals.

We report a simple and easy-to-operate method for separating n-alkanes: when we immersed activated pillar[5]arene crystals into a mixture of n-alkanes with various chain lengths, the crystals preferentially took up n-alkanes with longer chain lengths.

A reaction mode of carbene-catalysed aryl aldehyde activation and induced phenol OH functionalization.

The research in the field of asymmetric carbene organic catalysis has primarily focused on the activation of carbon atoms in non-aromatic scaffolds. Here we report a reaction mode of carbene catalysis that allows for aromatic aldehyde activation and remote oxygen atom functionalization. The addition of a carbene catalyst to the aldehyde moiety of 2-hydroxyl aryl aldehyde eventually enables dearomatization and remote OH activation. The catalytic process generates a type of carbene-derived intermediate with an oxygen atom as the reactive centre. Inexpensive achiral urea co-catalyst works cooperatively with the carbene catalyst, leading to consistent enhancement of the reaction enantioselectivity. Given the wide presence of aromatic moieties and heteroatoms in natural products and synthetic functional molecules, we expect our reaction mode to significantly expand the power of carbene catalysis in asymmetric chemical synthesis.

The mechanism of an asymmetric ring-opening reaction of epoxide with amine catalyzed by a metal-organic framework: insights from combined quantum mechanics and molecular mechanics calculations.

We applied QM/MM calculations to the asymmetric ring-opening reaction of cyclohexene oxide with aniline catalyzed by a two-dimensional metal-organic framework (MOF) that contains a Cu-paddlewheel (Cu-PDW) unit, aiming to elucidate the reaction mechanism and to identify the factors that determine the enantioselectivity of the reaction. Our QM/MM calculations show that the reaction consists of two major steps. In the first step, ring-opening of the epoxide moiety occurs that leads to an intermediate having an alkoxide ion, and the strong binding of the alkoxide to the Cu(ii) center results in cleavage of one of the four coordination bonds of the copper with carboxylate ligands. In the second step of the reaction, there is a proton transfer from aniline to a distant site-i.e., the alkoxide oxygen atom-to form the ß-amino alcohol product, and the carboxylate ligands of the Cu-PDW unit assist this process. The first ring-opening step was calculated as the rate-limiting step, and the enantioselectivity arises from different degrees of CH-π interactions between aniline and a naphthol group in the transition states. The transition state for the ring-opening step in the formation of the (R,R)-isomer is stabilized by CH-π interactions, whereas such interactions are absent in the transition state for the (S,S)-isomer formation. Interestingly, QM/MM calculations also show that the Cu-PDW unit does not maintain a symmetric geometry during the reaction but rather is flexible enough to detach a carboxylate ligand from the copper center, thereby facilitating the reaction. These results illuminate the utility of multiscale QM/MM computations in identifying critical factors determining the reactivity and selectivity of MOF-catalyzed reactions.

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.

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.

[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.

Generation of adenosyl radical from S-adenosylmethionine (SAM) in biotin synthase.

A mechanism of the C-S bond activation of S-adenosylmethionine (SAM) in biotin synthase is discussed from quantum mechanical/molecular mechanical (QM/MM) computations. The active site of the enzyme involves a [4Fe-4S] cluster, which is coordinated to the COO(-) and NH(2) groups of the methionine moiety of SAM. The unpaired electrons on the iron atoms of the [4Fe-4S](2+) cluster are antiferromagnetically coupled, resulting in the S=0 ground spin state. An electron is transferred from an electron donor to the [4Fe-4S](2+)-SAM complex to produce the catalytically active [4Fe-4S](+) state. The SOMO of the [4Fe-4S](+)-SAM complex is localized on the [4Fe-4S] moiety and the spin density of the [4Fe-4S] core is calculated to be 0.83. The C-S bond cleavage is associated with the electron transfer from the [4Fe-4S](+) cluster to the antibonding σ* C-S orbital. The electron donor and acceptor states are effectively coupled with each other at the transition state for the C-S bond cleavage. The activation barrier is calculated to be 16.0 kcal/mol at the QM (B3LYP/SV(P))/MM (CHARMm) level of theory and the C-S bond activation process is 17.4 kcal/mol exothermic, which is in good agreement with the experimental observation that the C-S bond is irreversibly cleaved in biotin synthase. The sulfur atom of the produced methionine molecule is unlikely to bind to an iron atom of the [4Fe-4S](2+) cluster after the C-S bond cleavage from the energetical and structural points of view.

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.