Testing the TPSS meta-generalized-gradient-approximation exchange-correlation functional in calculations of transition states and reaction barriers

We have studied the performance of local and semilocal exchange-correlation functionals [meta-generalized-gradient-approximation (GGA)-TPSS, GGA-Perdew-Burke-Ernzerhof (PBE), and local density approximation (LDA)] in the calculation of transition states, reaction energies, and barriers for several molecular and one surface reaction, using the plane-wave pseudopotential approach. For molecular reactions, these results have been compared to all-electron Gaussian calculations using the B3LYP hybrid functional, as well as to experiment and high level quantum chemistry calculations, when available. We have found that the transition state structures are accurately identified irrespective of the level of the exchange-correlation functional, with the exception of a qualitatively incorrect LDA prediction for the H-transfer reaction in the hydrogen bonded complex between a water molecule and a OH radical. Both the meta-GGA-TPSS and the GGA-PBE functionals improve significantly the calculated LDA barrier heights. The meta-GGA-TPSS further improves systematically, albeit not always sufficiently, the GGA-PBE barriers. We have also found that, on the Si(001) surface, the meta-GGA-TPSS barriers for hydrogen adsorption agree significantly better than the corresponding GGA-PBE barriers with quantum Monte Carlo cluster results and experimental estimates.     

Facile synthesis of biphenyl-fused BODIPY and its property

A biphenyl-fused BODIPY was synthesized through a facile oxidative cyclization of peripheral aryl-substituents at the β-position of the BODIPY unit. The extended π-system of the fused BODIPY induces near-infrared (NIR) absorption and strong π-π interactions in the solid state. These features are beneficial for the application of the dye as a functional material. The biphenyl-fused BODIPY dye was demonstrated to exhibit photocurrent conversion ability on the basis of its n-type semiconducting property.     

Selective synthesis of a [3]rotaxane consisting of size-complementary components and its stepwise deslippage

An α-cyclodextrin-based size-complementary [3]rotaxane with an alkylene axle was selectively synthesized in one pot via an end-capping reaction with 2-bromophenyl isocyanate in water. Thermal degradation of the [3]rotaxane product yielded not only the original components but also the [2]rotaxane. Thermodynamic studies suggested a stepwise deslippage process.     

One‐Handed Helical Screw Direction of Homopeptide Foldamer Exclusively Induced by Cyclic α‐Amino Acid Side‐Chain Chiral Centers

Chiral cyclic α,α‐disubstituted amino acids, (3S,4S)‐ and (3R,4R)‐1‐amino‐3,4‐(dialkoxy)cyclopentanecarboxylic acids ((S,S)‐ and (R,R)‐Ac₅c^dOR; R: methyl, methoxymethyl), were synthesized from dimethyl L ‐(+)‐ or D ‐(?)‐tartrate, and their homochiral homoligomers were prepared by solution‐phase methods. The preferred secondary structure of the (S,S)‐Ac₅c^dOMe hexapeptide was a left‐handed (M) 3₁₀ helix, whereas those of the (S,S)‐Ac₅c^dOMe octa‐ and decapeptides were left‐handed (M) α helices, both in solution and in the crystal state. The octa‐ and decapeptides can be well dissolved in pure water and are more α helical in water than in 2,2,2‐trifluoroethanol solution. The left‐handed (M) helices of the (S,S)‐Ac₅c^dOMe homochiral homopeptides were exclusively controlled by the side‐chain chiral centers, because the cyclic amino acid (S,S)‐Ac₅c^dOMe does not have an α‐carbon chiral center but has side‐chain γ‐carbon chiral centers.     

Pulse radiolysis studies of intermolecular charge transfers involving tryptophan and three-electron-bonded intermediates derived from methionine

The oxidation processes of the radiation-generated, three-electron-bonded intermediates AcMet₂ [S??S]⁺ and AcMet [S??Br] were investigated by pulse radiolysis via their reactions with tryptophan (TrpH). These intermediates were derived from N-acetyl-methionine amide (N-AcMetNH₂) and N-acetyl-methionine methyl ester (N-AcMetOMe). The bimolecular rate constant k of the reaction between each intermediate and l-tryptophan (TrpH) was measured. For N-AcMetNH₂, k for the reaction of AcMet₂ [S??S]⁺ with TrpH were 3.4?×?10⁸ and 2.2?×?10⁸?dm³?mol^?1?s^?1 at pH?=?1 and 4.5, respectively. For N-AcMetOMe, k for the reaction of AcMet₂ [S??S]⁺ with TrpH were 4.0?×?10⁸ and 2.8?×?10⁸?dm³?mol^?1?s^?1 at pH 1 and 4.5, respectively. The rate constants for the intermolecular transformation of Met [S??Br] into TrpH⁺ or Trp were also estimated. For N-AcMetNH₂, k for the reaction of AcMet₂ [S??Br] with TrpH were 2.6?×?10⁸ and 3.3?×?10⁸?dm³?mol^?1?s^?1 at pH 1 and 4.5, respectively. Related mechanisms were discussed.     

The concentration fluctuations and the mutual diffusion coefficient in the supercritical solution

Molecular dynamics simulations on Lennard-Jones mixture in the supercritical region are performed. The number of the molecules in the unit cell is 23328 and the mole fraction is 0.5. The concentration fluctuations near the critical point are large compared to the ideal mixing. The mutual diffusion coefficient normalized by the self-diffusion coefficient has a small value near the critical density because of the large concentration fluctuation. The heat capacity, partial molar volume and correlation lengths of density and concentration in the supercritical region are compared with those at the normal density.     

Cationic Ring-Opening Polymerization of 1,3-Dehydroadamantanes

Ring-opening polymerizations of [3.3.1]propellane derivatives, 1,3-dehydroadamantane ( 1 ) and 5-butyl-1,3-dehydroadamantane ( 2 ), were carried out with CF₃SO₃H in CH₂Cl₂ at 0 °C for 6–42 h. The central σ-bonds in 1 and 2 were exclusively opened to afford novel poly([3.3.1]propellane)s, poly(1,3-adamantane)s, in 52–95% yields. The resulting poly( 2 ) possessing flexible butyl substituent was soluble in chloroform, THF, and 1,2-dichlorobenzene, and the degree of polymerization was estimated to be greater than 30, while the poly( 1 ) was hardly soluble in the common organic solvents. All aliphatic poly( 1 ) and poly( 2 ) showed high thermal stability, their 10% weight loss temperatures were 421 and 486 °C, respectively.     

Fluorescence Response and Self-Assembly of a Tweezer-Type Synthetic Receptor Triggered by Complexation with Heme and Its Catabolites

There is increasing interest in the development and applications of synthetic receptors that recognize target biomolecules in aqueous media. We have developed a new tweezer-type synthetic receptor that gives a significant fluorescence response upon complexation with heme in aqueous solution at pH 7.4. The synthetic receptor consists of a tweezer-type heme recognition site and sulfo-Cy5 as a hydrophilic fluorophore. The receptor–heme complex exhibits a supramolecular amphiphilic character that facilitates the formation of self-assembled aggregates, and both the tweezer moiety and the sulfo-Cy5 moiety are important for this property. The synthetic receptor also exhibits significant fluorescence responses to biliverdin and bilirubin, but shows very weak fluorescence responses to flavin mononucleotide, folic acid, and nicotinamide adenine dinucleotide, which contain smaller π-scaffolds.     

New efficient method of alkoxymethyl etherification of secondary alcohols

A new efficient method of MOM etherification of secondary alcohols using 2-(chloromethyl)-3,5-dioxahex-1-ene (Okahara's reagent) is reported.