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.     

Controlled Dynamic Helicity of a Folded Macrocycle Based on a Bisterephthalamide with a Twofold Z‐Shaped Structure

Dynamic helicity in a folded macrocycle and control of the helical preference are described. We designed macrocycle 1 with a dual mode of folding through the integration of two flexible units that are arranged twice to form a cyclic structure. As a folding unit, we used a terephthalamide skeleton and a Z‐shaped hydrocarbon: the former acted as a control unit to induce a preference of a particular sense of dynamic helicity and the latter was just a spacer. A terephthalamide unit provided a binding site for capturing a ditopic hydrogen‐bonding guest when it adopted helically folded syn forms (M/P). Thus, only the terephthalamide unit controlled the helical sense of dynamic helicity in a folded macrocycle through the supramolecular transmission of chirality upon complexation with a chiral ditopic guest. In addition, chirality on a host could also contribute to the control of the helical preference in a folded macrocycle, which led to exceptionally enhanced chiroptical signals.     

Synthesis, π‐Face‐Selective Aggregation,and π‐Face Chiral Recognition of Configurationally Stable C3‐Symmetric Propeller‐Chiral Molecules with a π‐Core

The C₃‐symmetric propeller‐chiral compounds (P,P,P)‐ 1 and (M,M,M)‐ 1 with planar π‐cores perpendicular to the C₃‐axis were synthesized in optically pure states. (P,P,P)‐ 1 possesses two distinguishable propeller‐chiral π‐faces with rims of different heights named the (P/L)‐face and (P/H)‐face. Each face is configurationally stable because of the rigid structure of the helicenes contained in the π‐core. (P,P,P)‐ 1 formed dimeric aggregates in organic solutions as indicated by the results of ¹H NMR, CD, and UV/Vis spectroscopy and vapor pressure osmometry analyses. The (P/L)/(P/L) interactions were observed in the solid state by single‐crystal X‐ray analysis, and they were also predominant over the (P/H)/(P/H) and (P/L)/(P/H) interactions in solution, as indicated by the results of ¹H and 2D NMR spectroscopy analyses. The dimerization constant was obtained for a racemic mixture, which showed that the heterochiral (P,P,P)‐ 1 /(M,M,M)‐ 1 interactions were much weaker than the homochiral (P,P,P)‐ 1 /(P,P,P)‐ 1 interactions. The results indicated that the propeller‐chiral (P/L)‐face interacts with the (P/L)‐face more strongly than with the (P/H)‐face, (M/L)‐face, and (M/H)‐face. The study showed the π‐face‐selective aggregation and π‐face chiral recognition of the configurationally stable propeller‐chiral molecules.     

Inter-atomic distance and temperature dependence of correlation effects among thermal displacements

Diffuse neutron scattering from a powder AgCl was measured from 10 to 260 K. The correlation effects among thermal displacements of atoms were obtained from the diffraction data. The values of the correlation effects decrease rapidly with the increase of the inter-atomic distance. The values also decrease with the decrease of temperature. The similar tendency was also obtained in AgBr and CuI. The temperature dependence of the values of correlation effects agrees with the result by a simple Debye model of lattice vibrations.     

Self-oscillation of polymer chains with rhythmical soluble-insoluble changes

Self-oscillation of polymer chains in an aqueous solution has been achieved. The ruthenium catalyst for the Belousov-Zhabotinsky reaction was polymerized by using N-isopropylacrylamide and dissolved into the solution containing the BZ substrates. Periodical soluble-insoluble changes of the polymer chain were spontaneously induced by the BZ reaction. The conformational oscillations of the polymer were measured as the optical transmittance changes of the solution. This is the first report that rhythmical and reversible soluble-insoluble changes of polymer chains are realized under constant and homogeneous conditions. The transducing system from chemical energy of the BZ reaction to optical information has been constructed.     

Materials science of the gel to fluid phase transition in a supported phospholipid bilayer

We report the results of in situ AFM measurements examining the phase transition of bilayers formed from the zwitterionic phospholipid, DMPC, 1,2-dimyristoyl-sn-glycero-3-phosphocholine, supported on mica. The images show that the fluid to gel phase transition process features substantial tearing of the bilayer due to the density change between the two phases. The gel to fluid transition is strongly affected by the resultant stress introduced into the gel phase, which changes the degree of cooperativity, the shape of developing fluid phase regions, and the course of the transition.     

Crystalline inclusion compounds constructed through self-assembly of isonicotinic acid and thiocyanato coordination bridges

The synthesis, crystal structures, inclusion ability, and structural robustness of novel crystalline inclusion compounds of [Ni(SCN)2(isoH)2].xG (isoH = isonicotinic acid; G = aromatic guest) are described. The inclusion compounds are constructed by stacking identical 2D host layers that consist of SCN-, isoH, and Ni2+ with van der Waals contact separation. In the layer, two types of rectangular cavities (A-type and B-type) are formed, and the guests are included in the former cavity. The inclusion compounds were categorized into four stacking modes according to the difference in the stacking mode of the layers. A systematic investigation of the crystal structures of the 21 inclusion compounds clarified the close relationship between the molecular structure of the guest and the resultant stacking mode of the layers.