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.     

Hydrolysis of ionized deoxycholic acid in the aqueous phase and rate analysis for transfer of neutralized deoxycholic acid into the benzene phase across the benzene/water interface

Sodium deoxycholate in water dissociates into sodium cation and deoxycholate anion in the aqueous phase, and then, the latter anions partially hydrolyze to form deionized deoxycholic acids. The acids move into the benzene phase, when liquid benzene is placed upon the aqueous phase, and finally the partition equilibrium is reached. The above processes were traced by pH change in the aqueous phase by a pH meter or the change in [OH-] with time, from which the rate for transfer of neutralized acid to the organic phase was analyzed. From the trace, the rate constants for hydrolysis of acid anion ( kf), neutralization of acid ( kb), transfer of neutralized acid from the aqueous phase to the organic phase ( kin*), and its back-transfer from the organic phase to the aqueous phase ( kut*) were evaluated; kf = 2.18 x 10 (-4) mol (-1) dm (3) min (-1), kb = 1.24 x 10 (5) mol (-1) dm (3) min (-1), kin* = 4.06 x 10 (-1) min (-1) cm (-2), and kout*) = 8.00 x 10 (-2) min (-1) cm (-2). The above values are supported by the partition constant of deoxycholic acid between the benzene phase and the aqueous phase.     

Direction control of chemical wave propagation in self-oscillating gel array

A chemomechanical actuator utilizing a reaction-diffusion wave across gap junction was constructed toward a novel mircoconveyer by micropatterned self-oscillating gel array. Unidirectional propagation of the chemical wave of the Belousov-Zhabotinsky (BZ) reaction was induced on gel arrays. In the case of using a triangle-shaped gel as an element of the array, the chemical wave propagated from the corner side of the triangle gel to the plane side of the other gel (C-to-P) across the gap junction, whereas it propagated from the plane side to the corner side (P-to-C) in the case of the pentagonal gel array. Numerical analysis based on the Keener-Tyson model was done for understanding the mechanism of unidirectional propagation in triangle and pentagonal gel arrays. The swelling and deswelling changes of the gels followed the unidirectional propagation of the chemical wave.     

Phase separation of gas–liquid and liquid–liquid microflows in microchips

Phase separation of gas–liquid and liquid–liquid microflows in microchannels were examined and characterized by interfacial pressure balance. We considered the conditions of the phase separation, where the phase separation requires a single phase flow in each output of the microchannel. As the interfacial pressure, we considered the pressure difference between the two phases due to pressure loss in each phase and the Laplace pressure generated by the interfacial tension at the interface between the separated phases. When the pressure difference between the two phases is balanced by the Laplace pressure, the contact line between the two phases is static. Since the contact angle characterizing the Laplace pressure is restricted to values between the advancing and receding contact angles, the Laplace pressure has a limit. When the pressure difference between the two phases exceeds the limiting Laplace pressure, one of the phases leaks into the output channel of the other phase, and the phase separation fails. In order to experimentally verify this physical picture, microchips were used having a width of 215 μm and a depth of 34 μm for the liquid–liquid microflows, a width of 100 μm and a depth of 45 μm for the gas–liquid microflows. The experimental results of the liquid–liquid microflows agreed well with the model whilst that of the gas–liquid microflows did not agree with the model because of the compressive properties of the gas phase and evaporation of the liquid phase. The model is useful for general liquid–liquid microflows in continuous flow chemical processing.     

In-situ FTIR studies on self-assembled monolayers of surfactant molecules adsorbed on H-terminated Si(111) surfaces in aqueous solutions

The adsorption of a surfactant, sodium di-2-ethylhexyl sulfosuccinate (SDES), [C4H9CH(C2H5)CH2OCO][C4H9CH(C2H5)CH2OCOCH2]CHSO3- Na+, in an aqueous solution on an atomically flat H-terminated Si(111) [abbreviated as H-Si(111)] surface with a hydrophobic property was investigated by in-situ FTIR measurements. Immersion of the H-Si(111) surface in a solution of 1.0 x 10(-2) M SDES for more than 2 h led to formation of a self-assembled monolayer (SAM) with the alkyl chains having a tendency to be assembled perpendicular to the Si surface. The in-situ FTIR observation revealed that the adsorption was nearly complete about 60 min after the start of the immersion, and after that the adsorbed molecules changed their arrangement into an ordered mode. The Si-H peak in the FTIR spectrum remained unchanged with time in aqueous surfactant solution, in contrast to the case of immersion in pure water, indicating that the adsorbed surfactant protects the H-Si(111) surface from oxidation. No structural change in the SAM was observed when a negative potential of -700 mV vs Ag/AgCl was applied to the Si, whereas the adsorbed molecules changed their arrangement, accompanied by their substantial desorption and oxidation of the Si surface, when a positive potential of +700 mV was applied.     

Formation of double helix self-assembled monolayers of ethynylhelicene oligomer disulfides on gold surfaces

Optically active ethynylhelicene pentamers and hexamers linked by disulfide bonds were synthesized. They formed self-assembled monolayers (SAMs) with double helix structure on gold surfaces, which were analyzed by infrared reflection-absorption spectroscopy (IR-RAS), quartz crystal microbalance (QCM), surface plasmon resonance (SPR), and circular dichroism (CD). Double helix SAMs could be formed on gold surfaces either from double helices or random coils in solution. The double helices on the surface were more stable than in solution. This result suggested the presence of strong intercomplex interactions between double helix complexes on the surface.     

Recent topics of gold catalyst featuring Z-type ligands

In the long history regarding the development of the transition metal-catalyzed reactions, almost all ligands in metals are classified as the covalent X-type and/or dative L-type ligands. Therefore, exploring the reactivity of the metal complexes bearing the σ-acceptor, i.e., the Z-ligand, is required. This digest briefly describes our recent results regarding 1) the syntheses of gold complexes featuring the Z-type ligand, and 2) their catalytic reactions, which would be speculated that the electron-withdrawing effect of the Z-ligand on the neighboring gold activated the catalytic reactivity due to the increase in the Lewis acidity.     

Flapping Peryleneimide as a Fluorogenic Dye with High Photostability and Strong Visible‐Light Absorption

Flapping fluorophores (FLAP) with a flexible 8π ring are rapidly gaining attention as a versatile photofunctional system. Here we report a highly photostable “flapping peryleneimide” with an unprecedented fluorogenic mechanism based on a bent‐to‐planar conformational change in the S₁ excited state. The S₁ planarization induces an electronic configurational switch, almost quenching the inherent fluorescence (FL) of the peryleneimide moieties. However, the FL quantum yield is remarkably improved with a prolonged lifetime upon a slight environmental change. This fluorogenic function is realized by sensitive π‐conjugation design, as a more π‐expanded analogue does not show the planarization dynamics. With strong visible‐light absorption, the FL lifetime response synchronized with the flexible flapping motion is useful for the latest optical techniques such as FL lifetime imaging microscopy (FLIM).     

pH-responsive aqueous foams stabilized by hairy latex particles

Polystyrene (PS) latex particles carrying pH-responsive poly[2-(diethylamino)ethyl methacrylate] (PDEA) hair (PDEA-PS particles) were synthesized by dispersion polymerization and characterized in terms of diameter, diameter distribution, morphology, chemical composition, surface chemistry, and pH-response using scanning electron microscopy (SEM), elemental microanalysis, (1)H nuclear magnetic resonance spectroscopy, the laser diffraction method, and zeta potential measurements. The hairy particles can act as pH-responsive stabilizers of aqueous foams by adsorption at the air-water surface. Above pH 8.0, where particles have nonprotonated PDEA hair, which is relatively hydrophobic, particle-stabilized foams are stable for at least 1 month. Optical microscopy and SEM confirmed that flocculated PDEA-PS latex particles were adsorbed at the air-water interface and stabilized the aqueous foams. At pH 6.1 and 7.1, relatively stable foams can be prepared that remain stable for at least 24 h. SEM studies indicated that the PDEA-PS particles were adsorbed at the air-water interface as a monolayer at pH 6.1. At pH 5.1 and 3.1, where the particles have cationic water-soluble PDEA hairs with hydrophilic character, no foam was formed. Rapid defoamation can be induced by lowering the solution pH; the addition of acid caused the in situ protonation of 2-(diethylamino)ethyl methacrylate residues, which impart water-soluble hydrophilic character to the PDEA hair, and the PDEA-PS particles desorbed from the air-water interface. The foaming and defoaming cycles could be repeated at least five times.