Gaussian Process Regression-Based Near-Infrared d-Luciferin Analogue Design Using Mutation-Controlled Graph-Based Genetic Algorithm.

Molecular discovery is central to the field of chemical informatics. Although optimization approaches have been developed that target-specific molecular properties in combination with machine learning techniques, optimization using databases of limited size is challenging for efficient molecular design. We present a molecular design method with a Gaussian process regression model and a graph-based genetic algorithm (GB-GA) from a data set comprising a small number of compounds by introducing mutation probability control in the genetic algorithm to enhance the optimization capability and speed up the convergence to the optimal solution. In addition, we propose reducing the number of parameters in the conventional GB-GA focusing on efficient molecular design from a small database. We generated a target-specific database by combining active learning and iterative design in the evolutionary methodologies and chose Gaussian process regression as the prediction model for molecular properties. We show that the proposed scheme is more efficient for optimization toward the target properties from goal-directed benchmarks with several drug-like molecules compared to the conventional GB-GA method. Finally, we provide a demonstration whereby we designed D-luciferin analogues with near-infrared fluorescence for bioimaging, which is desirable for effective in vivo light sources, from a small-size data set.

Symmetry-Mismatched SBU Transformation in MOFs: Postsynthetic Metal Exchange from Zn to Fe and Its Effects on Gas Adsorption and Dye Selectivity.

This research explores the alteration of metal-organic frameworks (MOFs) using a method called postsynthetic metal exchange. We focus on the shift from a Zn-based MOF containing a [Zn4O(COO)6] secondary building unit (SBU) of octahedral site symmetry (ANT-1(Zn)) to a Fe-based one with a [Fe3IIIO(COO)6]+ SBU of trigonal prismatic site symmetry (ANT-1(Fe)). The symmetry-mismatched SBU transformation cleverly maintains the MOF's overall structure by adjusting the conformation of the flexible 1,3,5-benzenetribenzoate linker to alleviate the framework strain. The process triggers a decrease in the framework volume and pore size alongside a change in the framework's charge. These alterations influence the MOF's ability to adsorb gas and dye. During the transformation, core-shell MOFs (ANT-1(Zn@Fe)) are formed as intermediate products, demonstrating unique gas sorption traits and adjusted dye adsorption preferences due to the structural modifications at the core-shell interface. Heteronuclear clusters, located at the framework interfaces, enhance the heat of CO2 adsorption. Furthermore, they also influence the selectivity of the dye size. This research provides valuable insights into fabricating novel MOFs with unique properties by modifying the SBU of a MOF with flexible organic linkers from one site symmetry to another.

Spatial distribution modulation of mixed building blocks in metal-organic frameworks.

The placement of mixed building blocks at precise locations in metal-organic frameworks is critical to creating pore environments suitable for advanced applications. Here we show that the spatial distribution of mixed building blocks in metal-organic frameworks can be modulated by exploiting the different temperature sensitivities of the diffusion coefficients and exchange rate constants of the building blocks. By tuning the reaction temperature of the forward linker exchange from one metal-organic framework to another isoreticular metal-organic framework, core-shell microstructural and uniform microstructural metal-organic frameworks are obtained. The strategy can be extended to the fabrication of inverted core-shell microstructures and multi-shell microstructures and applied for the modulation of the spatial distribution of framework metal ions during the post-synthetic metal exchange process of a Zn-based metal-organic framework to an isostructural Ni-based metal-organic framework.

Scratch Properties of Clear Coat for Automotive Coating Comprising Molecular Necklace Crosslinkers with Silane Functional Groups for Various Environmental Factors.

Automotive coatings, which comprise multiple layers, i.e., primer, base coating, and clear coat layers, are exposed to various environmental conditions that pose various types of damages to them. In particular, the outer layer of the automotive coating, i.e., the clear coat, is affected significantly by such damages. Therefore, a reliable and durable clear coat must be developed to improve the appearance of automobiles. In this study, a new clear coat based on an acrylic-based clear coat modified using polyrotaxane crosslinkers, which are necklace-shaped supramolecules composed of ring-shaped host molecules, is developed and characterized. The effects of polyrotaxane and silane on the scratch properties and mechanisms of the clear coating are analyzed. It is observed that the critical loads of the clear coat from scratch tests can be improved by adding optimal molecular necklace crosslinkers comprising silane functional groups. The improvement in the scratch properties of the modified acrylic-based clear coat may be attributed to the crosslinking characteristics and dynamic molecular movements of the polyrotaxane. In addition, the effects of environmental factors on the scratch characteristics of the modified acrylic-based clear coat are investigated by addressing the scratch durability of the clear coat.

PyUNIxMD: A Python-based excited state molecular dynamics package.

Theoretical/computational description of excited state molecular dynamics is nowadays a crucial tool for understanding light-matter interactions in many materials. Here we present an open-source Python-based nonadiabatic molecular dynamics program package, namely PyUNIxMD, to deal with mixed quantum-classical dynamics for correlated electron-nuclear propagation. The PyUNIxMD provides many interfaces for quantum chemical calculation methods with commercial and noncommercial ab initio and semiempirical quantum chemistry programs. In addition, the PyUNIxMD offers many nonadiabatic molecular dynamics algorithms such as fewest-switch surface hopping and its derivatives as well as decoherence-induced surface hopping based on the exact factorization (DISH-XF) and coupled-trajectory mixed quantum-classical dynamics (CTMQC) for general purposes. Detailed structures and flows of PyUNIxMD are explained for the further implementations by developers. We perform a nonadiabatic molecular dynamics simulation for a molecular motor system as a simple demonstration.

Foldable and Extremely Scratch-Resistant Hard Coating Materials from Molecular Necklace-like Cross-Linkers.

A flexible hard coating material displaying extreme scratch resistance and foldable flexibility was developed via the design of an organic-inorganic hybrid coating material employing an alkoxysilyl-functionalized polyrotaxane cross-linker (PRX_Si1). PRX_Si1 has a molecular necklace-like structure that can form organic-inorganic cross-linking points and provide large molecular movements. It was postulated that the scratch resistance and flexibility could be simultaneously increased because of the hybrid cross-linking points and dynamic molecular movements. To confirm this hypothesis, the crystalline structure and mechanical properties of the PRX_Si1-based hard coating material were analyzed via transmission electron microscopy, small-angle X-ray diffraction, tensile, pencil hardness, and scratch tests. Finally, the PRX_Si1-based hard coating material could form homogeneously dispersed nanoscale siloxane crystalline domains, and the strain at the break point was 3 times higher than that of a commercial hard coating material, resulting in no defect formation even after 5000 folding test runs. Moreover, the material displayed extremely high pencil hardness (9H) and scratch resistance.