Solvent- and Light-Sensitive AIEE-Active Azo Dye: From Spherical to 1D and 2D Assemblies

Fluorescent molecular assembly systems provide an exciting platform for creating stimuli-responsive nano- and microstructured materials with optical, electronic, and sensing functions. To understand the relationship between (i) the plausible molecular structures preferentially adopted depending on the solvent polarity (such as N,N-dimethylformamide [DMF], tetrahydrofuran [THF], and toluene), (ii) the resulting spectroscopic features, and (iii) self-assembled nano-, micro-, and macrostructures, we chose a sterically crowded triangular azo dye (3Bu) composed of a polar molecular core and three peripheral biphenyl wings. The chromophore changed the solution color from yellow to pink-red depending on the solvent polarity. In a yellow DMF solution, a considerable amount of the twisted azo form could be kept stable with the help of favorable intermolecular interactions with the solvent molecules. By varying the concentration of the DMF solution, the morphology of self-assembled structures was transformed from nanoparticles to micrometer-sized one-dimensional (1D) structures such as sticks and fibers. In a pink-red toluene solution, the periphery of the central ring became more planar. The resulting significant amount of the keto-hydrazone tautomer grew into micro- and millimeter-sized 1D structures. Interestingly, when THF-H2O (1:1) mixtures were stored at a low temperature, elongated fibers were stacked sideways and eventually developed into anisotropic two-dimensional (2D) sheets. Notably, subsequent exposure of visible-light-irradiated sphere samples to solvent vapor resulted in reversible fluorescence off↔on switching accompanied by morphological restoration. These findings suggest that rational selection of organic dyes, solvents, and light is important for developing reusable fluorescent materials.

Microwave-Assisted Desulfation of the Hemolytic Saponins Extracted from Holothuria scabra Viscera

Saponins are plant and marine animal specific metabolites that are commonly considered as molecular vectors for chemical defenses against unicellular and pluricellular organisms. Their toxicity is attributed to their membranolytic properties. Modifying the molecular structures of saponins by quantitative and selective chemical reactions is increasingly considered to tune the biological properties of these molecules (i) to prepare congeners with specific activities for biomedical applications and (ii) to afford experimental data related to their structure–activity relationship. In the present study, we focused on the sulfated saponins contained in the viscera of Holothuria scabra, a sea cucumber present in the Indian Ocean and abundantly consumed on the Asian food market. Using mass spectrometry, we first qualitatively and quantitatively assessed the saponin content within the viscera of H. scabra. We detected 26 sulfated saponins presenting 5 different elemental compositions. Microwave activation under alkaline conditions in aqueous solutions was developed and optimized to quantitatively and specifically induce the desulfation of the natural saponins, by a specific loss of H2SO4. By comparing the hemolytic activities of the natural and desulfated extracts, we clearly identified the sulfate function as highly responsible for the saponin toxicity.

High-Throughput Computational Screening of Ionic Liquids for Butadiene and Butene Separation

The separation of 1,3-butadiene (1,3-C4H6) and 1-butene (n-C4H8) is quite challenging due to their close boiling points and similar molecular structures. Extractive distillation (ED) is widely regarded as a promising approach for such a separation task. For ED processes, the selection of suitable entrainer is of central importance. Traditional ED processes using organic solvents suffer from high energy consumption. To tackle this issue, the utilization of ionic liquids (ILs) can serve as a potential alternative. In this work, a high-throughput computational screening of ILs is performed to find proper entrainers, where 36,260 IL candidates comprising of 370 cations and 98 anions are involved. COSMO-RS is employed to calculate the infinite dilution extractive capacity and selectivity of the 36,260 ILs. In doing so, the ILs that satisfy the prespecified thermodynamic criteria and physical property constraints are identified. After the screening, the resulting IL candidates are sent for rigorous process simulation and design. 1,2,3,4,5-pentamethylimidazolium methylcarbonate is found to be the optimal IL solvent. Compared with the benchmark ED process where the organic solvent N-methyl-2-pyrrolidone is adopted, the energy consumption is reduced by 26%. As a result, this work offers a new IL-based ED process for efficient 1,3-C4H6 production.

DFT Study of the Molecular and Electronic Structure of Metal-Free Tetrabenzoporphyrin and Its Metal Complexes with Zn, Cd, Al, Ga, In

The electronic and molecular structures of metal-free tetrabenzoporphyrin (H2TBP) and its complexes with zinc, cadmium, aluminum, gallium and indium were investigated by density functional theory (DFT) calculations with a def2-TZVP basis set. A geometrical structure of ZnTBP and CdTBP was found to possess D4h symmetry; AlClTBP, GaClTBP and InClTBP were non-planar complexes with C4v symmetry. The molecular structure of H2TBP belonged to the point symmetry group of D2h. According to the results of the natural bond orbital (NBO) analysis, the M-N bonds had a substantial ionic character in the cases of the Zn(II) and Cd(II) complexes, with a noticeably increased covalent contribution for Al(III), Ga(III) and In(III) complexes with an axial –Cl ligand. The lowest excited states were computed with the use of time-dependent density functional theory (TDDFT) calculations. The model electronic absorption spectra indicated a weak influence of the nature of the metal on the Q-band position.

The SwissSimilarity 2021 Web Tool: Novel Chemical Libraries and Additional Methods for an Enhanced Ligand-Based Virtual Screening Experience

Hit finding, scaffold hopping, and structure–activity relationship studies are important tasks in rational drug discovery. Implementation of these tasks strongly depends on the availability of compounds similar to a known bioactive molecule. SwissSimilarity is a web tool for low-to-high-throughput virtual screening of multiple chemical libraries to find molecules similar to a compound of interest. According to the similarity principle, the output list of molecules generated by SwissSimilarity is expected to be enriched in compounds that are likely to share common protein targets with the query molecule and that can, therefore, be acquired and tested experimentally in priority. Compound libraries available for screening using SwissSimilarity include approved drugs, clinical candidates, known bioactive molecules, commercially available and synthetically accessible compounds. The first version of SwissSimilarity launched in 2015 made use of various 2D and 3D molecular descriptors, including path-based FP2 fingerprints and ElectroShape vectors. However, during the last few years, new fingerprinting methods for molecular description have been developed or have become popular. Here we would like to announce the launch of the new version of the SwissSimilarity web tool, which features additional 2D and 3D methods for estimation of molecular similarity: extended-connectivity, MinHash, 2D pharmacophore, extended reduced graph, and extended 3D fingerprints. Moreover, it is now possible to screen for molecular structures having the same scaffold as the query compound. Additionally, all compound libraries available for screening in SwissSimilarity have been updated, and several new ones have been added to the list. Finally, the interface of the website has been comprehensively rebuilt to provide a better user experience. The new version of SwissSimilarity is freely available starting from December 2021.

Application of Nucleic Acid Frameworks in the Construction of Nanostructures and Cascade Biocatalysts: Recent Progress and Perspective

Nucleic acids underlie the storage and retrieval of genetic information literally in all living organisms, and also provide us excellent materials for making artificial nanostructures and scaffolds for constructing multi-enzyme systems with outstanding performance in catalyzing various cascade reactions, due to their highly diverse and yet controllable structures, which are well determined by their sequences. The introduction of unnatural moieties into nucleic acids dramatically increased the diversity of sequences, structures, and properties of the nucleic acids, which undoubtedly expanded the toolbox for making nanomaterials and scaffolds of multi-enzyme systems. In this article, we first introduce the molecular structures and properties of nucleic acids and their unnatural derivatives. Then we summarized representative artificial nanomaterials made of nucleic acids, as well as their properties, functions, and application. We next review recent progress on constructing multi-enzyme systems with nucleic acid structures as scaffolds for cascade biocatalyst. Finally, we discuss the future direction of applying nucleic acid frameworks in the construction of nanomaterials and multi-enzyme molecular machines, with the potential contribution that unnatural nucleic acids may make to this field highlighted.

Interactions of Biobased Rheology Modifying Agents with Superplasticizer in Cement Paste

Organic admixtures are an indispensable component of modern concrete. Thus, their purposeful application is not only technically and economically viable but in addition an inevitable tool to make concrete more environmentally friendly. In this context, the use of polysaccharides has increasingly gained interest in the built environment as sustainable resource for performance enhancement. However, due to its origin, biopolymers possess a vast variety of molecular structures which can result in incompatibilities with other polymers present in concrete, such as superplasticizers. The present study highlights effects of the joint application of different types of starches and polycarboxylates with respect to their influence on cement hydration and structural build-up of cement pastes.

Bringing Chemical Structures to Life with Augmented Reality, Machine Learning and Quantum Chemistry

Visualizing 3D molecular structures is crucial to understanding and predicting their chemical behavior. However, static 2D hand-drawn skeletal structures remain the preferred method of chemical communication. Here, we combine cutting-edge technologies in augmented reality (AR), machine learning, and computational chemistry to develop MolAR, a mobile application for visualizing molecules in AR directly from their hand-drawn chemical structures. Users can also visualize any molecule or protein directly from its name or PDB ID, and compute chemical properties in real time via quantum chemistry cloud computing. MolAR provides an easily accessible platform for the scientific community to visualize and interact with 3D molecular structures in an immersive and engaging way.