Efficient Search for Energetically Favorable Molecular Conformations against Metastable States via Gray-Box Optimization

In order to accurately understand and estimate molecular properties, finding energetically favorable molecular conformations is the most fundamental task for atomistic computational research on molecules and materials. Geometry optimization based on quantum chemical calculations has enabled the conformation prediction of arbitrary molecules, including de novo ones. However, it is computationally expensive to perform geometry optimizations for enormous conformers. In this study, we introduce the gray-box optimization (GBO) framework, which enables optimal control over the entire geometry optimization process, among multiple conformers. Algorithms designed for GBO roughly estimate energetically preferable conformers during their geometry optimization iterations. They then preferentially compute promising conformers. To evaluate the performance of the GBO framework, we applied it to a test set consisting of seven dipeptides and mycophenolic acid to determine their stable conformations at the density functional theory level. We thus preferentially obtained energetically favorable conformations. Furthermore, the computational costs required to find the most stable conformation were significantly reduced (approximately 1% on average, compared to the naive approach for the dipeptides)

Inhibition of Epidermal Growth Factor Receptor and PI3K/Akt Signaling Suppresses Cell Proliferation and Survival through Regulation of Stat3 Activation in Human Cutaneous Squamous Cell Carcinoma

Recent studies have emphasized the important role of Stat3 activation in a number of human tumors from the viewpoint of its oncogenic and antiapoptotic activity. In this study, we examined the role and related signaling molecules of Stat3 in the carcinogenesis of human cutaneous squamous cell carcinoma (SCC). In 35 human cutaneous SCC samples, 86% showed overexpression of phosphorylated (p)-Stat3, and most of those simultaneously overexpressed p-EGFR or p-Akt. Constitutive activation of EGFR and Stat3 was observed in three SCC cell lines and four of five SCC tissues. AG1478, an inhibitor of the EGFR, downregulated Stat3 activation in HSC-1 human SCC cells. AG1478 inhibited cell proliferation and induced apoptosis of HSC-1 cells but did not inhibit the growth of normal human epidermal keratinocytes that did not show Stat3 activation. Furthermore, a PI3K inhibitor also suppressed Stat3 activation in HSC-1 cells to some degree. Combined treatment with the PI3K inhibitor and AG1478 strongly suppressed Stat3 activity and dramatically induced apoptosis of HSC-1 cells. These data suggest that Stat3 activation through EGFR and/or PI3K/Akt activation plays a critical role in the proliferation and survival of human cutaneous SCC

Wood-mimetic skins prepared using horseradish peroxidase catalysis to induce surface wrinkling of chitosan film upon drying

We previously developed bio-based wrinkled surfaces induced by wood-mimetic skins upon drying in which microscopic wrinkles were fabricated on a chitosan (CS) film by immersing it in a phenolic acid solution, followed by horseradish peroxidase (HRP)-catalyzed surface reaction and drying. However, the detailed structure of the resulting wood-mimetic skins, including crosslinking mode and thickness, has not been clarified due to the difficulty of the analysis. Here, we prepare wrinkled films using ferulic acid (FE), vanillic acid (VA), and homovanillic acid (HO) and characterize their structures to clarify the unknown characteristics of wood-mimetic skin. Chemical and structural analyses of wood-mimetic skins prepared using VA and HO indicate that the crosslinking structure in the skin is composed of ionic bonds between CS and an oligophenolic residue generated by the HRP-catalyzed reaction on the CS surface. Moreover, the quantity of these ionic bonds is related to the skin hardness and wrinkle size. Finally, SEM and TOF-SIMS analyses indicate that the skin thickness is on the submicron order (<200 nm)

Novel 1,8-Naphthalimide derivative with an open space for an anion: Unique fluorescence behaviour depending on the binding anion’s electrophilic property

We have designed a novel 1,8-naphthalimide derivative with an open space for an anion. Computational calculation has predicted that the space could trap various anion species and photo-induced charge transfer depending on the anion's electrophilic properties. Indeed, the fluorescence behaviour of the 1,8-naphthalimide derivative complexes with each anion is consistent with the computational prediction

Pushing property limits in materials discovery via boundless objective-free exploration

Materials chemists develop chemical compounds to meet often conflicting demands of industrial applications. This process may not be properly modeled by black-box optimization because the target property is not well defined in some cases. Herein, we propose a new algorithm for automated materials discovery called BoundLess Objective-free eXploration (BLOX) that uses a novel criterion based on kernel-based Stein discrepancy in the property space. Unlike other objective-free exploration methods, a boundary for the materials properties is not needed; hence, BLOX is suitable for open-ended scientific endeavors. We demonstrate the effectiveness of BLOX by finding light-absorbing molecules from a drug database. Our goal is to minimize the number of density functional theory calculations required to discover out-of-trend compounds in the intensity–wavelength property space. Using absorption spectroscopy, we experimentally verified that eight compounds identified as outstanding exhibit the expected optical properties. Our results show that BLOX is useful for chemical repurposing, and we expect this search method to have numerous applications in various scientific disciplines

Theoretical study on naphthobischalcogenadiazole conjugated polymer systems and C61 derivative as organic photovoltaic semiconductors

We investigated the charge-transfer reactions of solar cells including a quaterthiophene copolymer with naphtho-bis-thiadiazole (PNTz4T) and naphtho-bis-oxadiazole (PNOz4T) using constrained density functional theory (CDFT). According to our calculations, the high electron-transfer rate results in a highly efficient solar cell, and the stable charge-transfer state results in low energy loss. Our computations imply that the following three factors are crucial to improve the performance of semiconducting polymers: (i) large structural changes following charge-transfer, (ii) narrow band gap, and (iii) spatially delocalized lowest unoccupied molecular orbital (LUMO) of the ground state

De novo creation of a naked eye–detectable fluorescent molecule based on quantum chemical computation and machine learning

Designing fluorescent molecules requires considering multiple interrelated molecular properties, as opposed to properties that straightforwardly correlated with molecular structure, such as light absorption of molecules. In this study, we have used a de novo molecule generator (DNMG) coupled with quantum chemical computation (QC) to develop fluorescent molecules, which are garnering significant attention in various disciplines. Using massive parallel computation (1024 cores, 5 days), the DNMG has produced 3643 candidate molecules. We have selected an unreported molecule and seven reported molecules and synthesized them. Photoluminescence spectrum measurements demonstrated that the DNMG can successfully design fluorescent molecules with 75% accuracy (n = 6/8) and create an unreported molecule that emits fluorescence detectable by the naked eye

Augmented Lagrangian Method for Optimizing Non-Orthogonal Orbitals

We applied augmented Lagrangian method to optimize molecular wave function based on non-orthogonal orbitals (Spin coupled wave function; SCWF) for its grand-state energy. In contrast to the orthogonal-orbital-based electronic structure theory, SCWF includes spin eigenfunctions to satisfy the eigen states as the operator of the square of the spin. To obtain the ground-state energy of SCWF, therefore, it is necessary to optimize the orbital and the spin-coupling coefficients simultaneously. In this study, the spin-coupling and the orbital coefficients are optimized with the augmented Lagrangian method under the constrain of normality of the wave function.We employed this SCWF method to compute dissociative potential energy surfaces (PESs) of H2, H2-, He2+, and HLi. The obtained PESs by the SCWF method are close to these by full configuration interaction theory. These results indicate that the augmented Lagrangian method is effective to optimize SCWF.</p