Vibronic Structures in Absorption and Fluorescence Spectra of Firefly Oxyluciferin in Aqueous Solutions

To elucidate the factors determining the spectral shapes and widths of the absorption and fluorescence spectra for keto and enol oxyluciferin and their conjugate bases in aqueous solutions, the intensities of vibronic transitions between their ground and first electronic excited states were calculated for the first time via estimation of the vibrational Franck–Condon factors. The major normal modes, overtones and combination tones in absorption and fluorescence spectra are similar for all species. The theoretical full widths at half maximum of absorption spectra are 0.4–0.7 eV and those for the fluorescence spectra are 0.4–0.5 eV, except for phenolate‐keto that exhibits exceptionally sharp peak widths due to the dominance of the 0–0′ or 0′–0 band. These spectral shapes and widths explain many relevant features of the experimentally observed spectra.     

Solid‐Phase Combinatorial Synthesis and Biological Evaluation of Destruxin E Analogues

The solid‐phase combinatorial synthesis of cyclodepsipeptide destruxin E has been demonstrated. The combinatorial synthesis of cyclization precursors 8 was achieved by using a split and pool method on SynPhase Lanterns. The products were successfully macrolactonized in parallel in the solution phase by using 2‐methyl‐6‐nitrobenzoic anhydride and 4‐(dimethylamino)pyridine N‐oxide to afford macrolactones 9 , and the subsequent formation of an epoxide in the side chain gave 18 member destruxin E analogues 6 . Biological evaluation of analogues 6 indicated that the N‐MeAla residue was crucial to the induction of morphological changes in osteoclast‐like multinuclear cells (OCLs). Based on structure–activity relationships, azido‐containing analogues 15 were then designed for use as a molecular probe. The synthesis and biological evaluation of analogues 15 revealed that 15 b , in which the Ile residue was replaced with a Lys(N₃) residue, induced morphological changes in OCLs at a sufficient concentration, and modification around the Ile residue would be tolerated for attachment of a chemical tag toward the target identification of destruxin E ( 1 ).     

Bayesian molecular design with a chemical language model

The aim of computational molecular design is the identification of promising hypothetical molecules with a predefined set of desired properties. We address the issue of accelerating the material discovery with state-of-the-art machine learning techniques. The method involves two different types of prediction; the forward and backward predictions. The objective of the forward prediction is to create a set of machine learning models on various properties of a given molecule. Inverting the trained forward models through Bayes’ law, we derive a posterior distribution for the backward prediction, which is conditioned by a desired property requirement. Exploring high-probability regions of the posterior with a sequential Monte Carlo technique, molecules that exhibit the desired properties can computationally be created. One major difficulty in the computational creation of molecules is the exclusion of the occurrence of chemically unfavorable structures. To circumvent this issue, we derive a chemical language model that acquires commonly occurring patterns of chemical fragments through natural language processing of ASCII strings of existing compounds, which follow the SMILES chemical language notation. In the backward prediction, the trained language model is used to refine chemical strings such that the properties of the resulting structures fall within the desired property region while chemically unfavorable structures are successfully removed. The present method is demonstrated through the design of small organic molecules with the property requirements on HOMO-LUMO gap and internal energy. The R package iqspr is available at the CRAN repository.     

Matching Extension Missing Vertices and Edges in Triangulations of Surfaces

Let G be a 5‐connected triangulation of a surface Σ different from the sphere, and let be the Euler characteristic of Σ. Suppose that with even and M and N are two matchings in of sizes m and n respectively such that . It is shown that if the pairwise distance between any two elements of is at least five and the face‐width of the embedding of G in Σ is at least , then there is a perfect matching M₀ in containing M such that .     

Structural properties of charge-transfer complexes of multilayered [3.3]paracyclophanes

In the solid state, multilayered [3.3]paracyclophanes (PCPs) 2-6 and tetracyanoethylene (TCNE) form charge-transfer (CT) complexes with a 1:1 stoichiometry. All the benzene rings overlapped each other. All the [3.3]PCP units and dione units assume chair conformations and the transannular distances are shorter than those of the corresponding free multilayered [3.3]PCP except for the dione unit in the four-layered dione 6. In the crystal-packing diagrams, the PCP and TCNE are located in alternating donor-acceptor stacking in columns, and effective short contacts are observed in the neighboring molecules.     

Rhenium complex-catalyzed acylative cleavage of ethers with acyl chlorides

It was found that rhenium complex was an efficient catalyst for the acylative cleavage of C-O bond of ethers with acyl chlorides. When acyclic ethers were allowed to react with acyl chlorides in the presence of a catalytic amount of ReBr(CO)₅, acylative cleavage of C-O bond of acyclic ethers smoothly proceeded to give the corresponding esters in moderate to good yields. Similarly, cyclic ethers were acylative cleaved by acyl chlorides to give the corresponding chloro substituted esters in good yields by the use of Re₂O₇ catalyst.     

Nick sealing by T4 DNA ligase on a modified DNA template: tethering a functional molecule on D-threoninol

Efficient DNA nick sealing catalyzed by T4 DNA ligase was carried out on a modified DNA template in which an intercalator such as azobenzene had been introduced. The intercalator was attached to a D-threoninol linker inserted into the DNA backbone. Although the structure of the template at the point of ligation was completely different from that of native DNA, two ODNs could be connected with yields higher than 90% in most cases. A systematic study of sequence dependence demonstrated that the ligation efficiency varied greatly with the base pairs adjacent to the azobenzene moiety. Interestingly, when the introduced azobenzene was photoisomerized to the cis form on subjection to UV light (320-380 nm), the rates of ligation were greatly accelerated for all sequences investigated. These unexpected ligations might provide a new approach for the introduction of functional molecules into long DNA strands in cases in which direct PCR cannot be used because of blockage of DNA synthesis by the introduced functional molecule. The biological significance of this unexpected enzymatic action is also discussed on the basis of kinetic analysis.     

Image printing on the surface of anti-biofouling zwitterionic polymer brushes by ion beam irradiation

A CMB monomer was polymerized on a glass plate with a surface-confined ATRP initiator containing a 2-bromoisobutyryl group. The glass plate modified with a PCMB brush was highly hydrophilic and showed a strong resistance against non-specific adsorption of proteins and cell adhesion. Upon ion beam irradiation, furthermore, the PCMB brush was ablated and a hollow space with a designed shape could be made to which HEK293 cells (from human embryonic kidney) and Hep G2 (from human hepatoma) cells non-specifically adhered, while no adhesion of these cells to the non-treated area on the brush was observed. The present results clearly indicate the usefulness of ion beam-printed patterns of anti-biofouling zwitterionic polymer brushes in the biomedical field.     

Enantioselective total synthesis of (+)-lysergic acid, (+)-lysergol, and (+)-isolysergol by palladium-catalyzed domino cyclization of allenes bearing amino and bromoindolyl groups

Enantioselective total synthesis of the biologically important indole alkaloids (+)-lysergol, (+)-isolysergol, and (+)-lysergic acid is described. Key features of these total synthesis include (1) a facile synthesis of a chiral 1,3-amino alcohol via the Pd(0)- and In(I)-mediated reductive coupling reaction between L-serine-derived 2-ethynylaziridine and formaldehyde; (2) the Cr(II)/Ni(0)-mediated Nozaki-Hiyama-Kishi (NHK) reaction of an indole-3-acetaldehyde with iodoalkyne; and (3) Pd(0)-catalyzed domino cyclization of an allene bearing amino and bromoindolyl groups. This domino cyclization enabled direct construction of the C/D ring system of the ergot alkaloids skeleton, as well as the creation of the C5 stereogenic center with transfer of the allenic axial chirality to the central chirality.     

Infrared photodissociation spectroscopy of H(+)(H2O)6·M(m) (M = Ne, Ar, Kr, Xe, H2, N2, and CH4): messenger-dependent balance between H3O(+) and H5O2(+) core isomers

Although messenger mediated spectroscopy is a widely-used technique to study gas phase ionic species, effects of messengers themselves are not necessarily clear. In this study, we report infrared photodissociation spectroscopy of H(+)(H(2)O)(6)·M(m) (M = Ne, Ar, Kr, Xe, H(2), N(2), and CH(4)) in the OH stretch region to investigate messenger(M)-dependent cluster structures of the H(+)(H(2)O)(6) moiety. The H(+)(H(2)O)(6), the protonated water hexamer, is the smallest system in which both the H(3)O(+) (Eigen) and H(5)O(2)(+) (Zundel) hydrated proton motifs coexist. All the spectra show narrower band widths reflecting reduced internal energy (lower vibrational temperature) in comparison with bare H(+)(H(2)O)(6). The Xe-, CH(4)-, and N(2)-mediated spectra show additional band features due to the relatively strong perturbation of the messenger. The observed band patterns in the Ar-, Kr-, Xe-, N(2)-, and CH(4)-mediated spectra are attributed mainly to the "Zundel" type isomer, which is more stable. On the other hand, the Ne- and H(2)-mediated spectra are accounted for by a mixture of the "Eigen" and "Zundel" types, like that of bare H(+)(H(2)O)(6). These results suggest that a messenger sometimes imposes unexpected isomer-selectivity even though it has been thought to be inert. Plausible origins of the isomer-selectivity are also discussed.