Crystal structure and Hirshfeld surface analysis of (1H-imidazole-κN3)[4-methyl-2-({[2-oxido-5-(2-phenyl-diazen-1-yl)phen-yl]methyl-idene}amino)penta-noate-κ3O,N,O']copper(II).

The title copper(II) complex, [Cu(C18H19N3O3)(C3H4N2)], consists of a tridentate ligand synthesized from l-leucine and azo-benzene-salicyl-aldehyde. One imidazole mol-ecule is additionally coordinated to the copper(II) ion in the equatorial plane. The crystal structure features N-H⋯O hydrogen bonds. A Hirshfeld surface analysis indicates that the most important contributions to the packing are from H⋯H (52.0%) and C⋯H/H⋯C (17.9%) contacts.

The prediction of single-molecule magnet properties via deep learning.

This paper uses deep learning to present a proof-of-concept for data-driven chemistry in single-molecule magnets (SMMs). Previous discussions within SMM research have proposed links between molecular structures (crystal structures) and single-molecule magnetic properties; however, these have only interpreted the results. Therefore, this study introduces a data-driven approach to predict the properties of SMM structures using deep learning. The deep-learning model learns the structural features of the SMM molecules by extracting the single-molecule magnetic properties from the 3D coordinates presented in this paper. The model accurately determined whether a molecule was a single-molecule magnet, with an accuracy rate of approximately 70% in predicting the SMM properties. The deep-learning model found SMMs from 20 000 metal complexes extracted from the Cambridge Structural Database. Using deep-learning models for predicting SMM properties and guiding the design of novel molecules is promising.

Catalytic Oxidation of Methanol to Formaldehyde Catalyzed by Iron Complex with N3S3-type Tripodal Ligand.

A Fe3+ complex with N3S3-type tripod ligand, 1, reacts with O2 in CH3OH to generate formaldehyde, which has been studied structurally, spectroscopically, and electrochemically. Complex 1 crystallizes as an octahedral structure with crystallographic C3 symmetry around the metal, with Fe-N=2.2917(17) Å and Fe-S=2.3574(6) Å. UV-vis spectrum of 1 in CH3OH under Ar shows an intense band at 572 nm (ϵ 4,100 M-1cm-1), which shifts to 590 nm (ϵ 2,860 M-1cm-1) by the addition of O2, and a new peak appeared at 781 nm (ϵ 790 M-1cm-1). Such a spectral change is not observed in CH2Cl2. Cyclic voltammogram (CV) of 1 in CH2Cl2 under Ar gives reversible redox waves assigned to Fe2+/Fe3+ and Fe3+/Fe4+ couples at -1.60 V (ΔE=69 mV) and -0.53 V (ΔE=71 mV) vs Fc/Fc+, respectively. In contrast, in CH3OH, the reversible redox waves, albeit accompanied by a positive shift of the Fe2+/Fe3+ couple, are observed at -1.20 V (ΔE=85 mV) and -0.53 V (ΔE=64 mV) vs Fc/Fc+ under Ar. Interestingly, a catalytic current was observed for the CV of 1 in CH3OH in the presence of CH3ONa under Ar, when the sweep rate was slowed down.

Cell surface architecture of the cultivated DPANN archaeon Nanobdella aerobiophila.

The DPANN archaeal clade includes obligately ectosymbiotic species. Their cell surfaces potentially play an important role in the symbiotic interaction between the ectosymbionts and their hosts. However, little is known about the mechanism of ectosymbiosis. Here, we show cell surface structures of the cultivated DPANN archaeon Nanobdella aerobiophila strain MJ1T and its host Metallosphaera sedula strain MJ1HA, using a variety of electron microscopy techniques, i.e., negative-staining transmission electron microscopy, quick-freeze deep-etch TEM, and 3D electron tomography. The thickness, unit size, and lattice symmetry of the S-layer of strain MJ1T were different from those of the host archaeon strain MJ1HA. Genomic and transcriptomic analyses highlighted the most highly expressed MJ1T gene for a putative S-layer protein with multiple glycosylation sites and immunoglobulin-like folds, which has no sequence homology to known S-layer proteins. In addition, genes for putative pectin lyase- or lectin-like extracellular proteins, which are potentially involved in symbiotic interaction, were found in the MJ1T genome based on in silico 3D protein structure prediction. Live cell imaging at the optimum growth temperature of 65°C indicated that cell complexes of strains MJ1T and MJ1HA were motile, but sole MJ1T cells were not. Taken together, we propose a model of the symbiotic interaction and cell cycle of Nanobdella aerobiophila.IMPORTANCEDPANN archaea are widely distributed in a variety of natural and artificial environments and may play a considerable role in the microbial ecosystem. All of the cultivated DPANN archaea so far need host organisms for their growth, i.e., obligately ectosymbiotic. However, the mechanism of the ectosymbiosis by DPANN archaea is largely unknown. To this end, we performed a comprehensive analysis of the cultivated DPANN archaeon, Nanobdella aerobiophila, using electron microscopy, live cell imaging, transcriptomics, and genomics, including 3D protein structure prediction. Based on the results, we propose a reasonable model of the symbiotic interaction and cell cycle of Nanobdella aerobiophila, which will enhance our understanding of the enigmatic physiology and ecological significance of DPANN archaea.

Towards Industrially Important Applications of Enhanced Organic Reactions by Microfluidic Systems.

This review presents a comprehensive evaluation for the manufacture of organic molecules via efficient microfluidic synthesis. Microfluidic systems provide considerably higher control over the growth, nucleation, and reaction conditions compared with traditional large-scale synthetic methods. Microfluidic synthesis has become a crucial technique for the quick, affordable, and efficient manufacture of organic and organometallic compounds with complicated characteristics and functions. Therefore, a unique, straightforward flow synthetic methodology can be developed to conduct organic syntheses and improve their efficiency.

Recent Advances in Chiral Schiff Base Compounds in 2023.

Schiff bases (imine or azomethine -N=CH-), which were first obtained by a German chemist, H [...].

Crystal structure and Hirshfeld surface analysis of (1H-imidazole-κN3)[N-(2-oxido-benzyl-idene)tyrosinato-κ3O,N,O']copper(II).

The title copper(II) complex, [Cu(C16H13NO4)(C3H4N2)], consists of a tridentate ligand synthesized from l-tyrosine and salicyl-aldehyde. One imidazole mol-ecule is additionally coordinating to the copper(II) ion. The crystal structure features N-H⋯O, O-H⋯O and C-H⋯O hydrogen bonds. The Hirshfeld surface analysis indicates that the most important contributions to the packing are from H⋯H (37.9%), C⋯H (28.2%) and O⋯H/H⋯O (21.2%) contacts.

From Basics of Coordination Chemistry to Understanding Cisplatin-analogue Pt Drugs.

BACKGROUND: Cisplatin, a platinum complex discovered by Rosenberg in 1969, has long been known as the first metal-based anticancer agent. Since then, various similar derivatives of cisplatin have been investigated for pharmacological activity, and the approved complexes have been applied as drugs. OBJECTIVES: The aims of the current study are: 1) to summarize the advantages and dose-limiting effects of the approved and unapproved chemotherapy platinum cytostatics, 2) to develop new strategies for the development of platinum anticancer drugs, and 3) to clarify the important factors for the mechanism of action of platinum complexes. METHODS: A search was conducted in the literature databases, and the obtained information was summarized and analyzed. RESULTS: Myelosuppression is the main dose-limiting effect and the reason for the disapproval of platinum complexes, such as picoplatin, enloplatin, miboplatin, sebriplatin, zeniplatin, spiroplatin, iproplatin, and ormaplatin. From the basic point of view of inorganic coordination chemistry, such as theoretical calculations, crystal structures of model complexes, docking structures with nucleic acid molecules, spectroscopy, and biological aspects, the importance of physicochemical properties of inorganic platinum complexes for their mechanism of action has been indicated. Spectroscopic methods, such as FTIR, NMR, X-ray crystal structure analysis, and fluorescence microscopy, are important for the investigation of the conformational changes in the binding of platinum complexes and DNA. CONCLUSION: In the development of platinum complexes, strong anti-cancer drug activity, low toxicity, and resistance can be obtained by the application of polynuclear platinum agents, complexes with targeted activity, and nanoparticle formulations. Electronic structure, stereochemical, and thermodynamic properties are essential for understanding the reaction mechanism of platinum complexes.

Dehydrogenative Annulation of Silylated 1H-Indoles with Alkynes via Silyl Migration.

We investigated the dehydrogenative annulation of silylated 1H-indole derivatives with alkynes to synthesize a silole-fused indole. The addition of the in situ generated silylium ion to alkynes was followed by the sila-Friedel-Crafts reaction via silyl migration, realizing regioselective dehydrogenative annulation controlled by the steric bulkiness of a base. The optical properties of the obtained siloloindoles indicated fluorescence of which the intensity depends on the location of the fused silole.

Rheotaxis in Mycoplasma gliding.

This review describes the upstream-directed movement in the small parasitic bacterium Mycoplasma. Many Mycoplasma species exhibit gliding motility, a form of biological motion over surfaces without the aid of general surface appendages such as flagella. The gliding motility is characterized by a constant unidirectional movement without changes in direction or backward motion. Unlike flagellated bacteria, Mycoplasma lacks the general chemotactic signaling system to control their moving direction. Therefore, the physiological role of directionless travel in Mycoplasma gliding remains unclear. Recently, high-precision measurements under an optical microscope have revealed that three species of Mycoplasma exhibited rheotaxis, that is, the direction of gliding motility is lead upstream by the water flow. This intriguing response appears to be optimized for the flow patterns encountered at host surfaces. This review provides a comprehensive overview of the morphology, behavior, and habitat of Mycoplasma gliding, and discusses the possibility that the rheotaxis is ubiquitous among them.

Crystal structure and Hirshfeld surface analysis of mono/bis-(aqua-κO)[N-(2-oxido-benzyl-idene)valinato-κ3 O,N,O']copper(II): dimeric Schiff base copper(II) complexes having different numbers of coordinated water mol-ecules.

The mol-ecular structure of the title compound, [Cu(C12H13N2O3)(H2O)2]·[Cu(C12H13N2O3)(H2O)], consists of two different mol-ecules in the asymmetric unit. Both of the structures consist of a tridentate ligand synthesized from l-valine and salicyl-aldehyde, and one water mol-ecule or two water mol-ecules coordinating to CuII. They have a square-planar (mol-ecule 1) or a square-pyramidal (mol-ecule 2) coordination geometry. In the crystal, the mol-ecules form intra- and inter-molecular O-H⋯O hydrogen bonds involving the coordinated water mol-ecules and other sites. A Hirshfeld surface analysis indicated that the most important contributions to the packing are from H⋯H [52.9% (mol-ecule 1) and 51.1% (mol-ecule 2)] and H⋯O/ O⋯H [21.2% (mol-ecule 1) and 25.8% (mol-ecule 2)] contacts. In addition, an electrostatic potential map was also obtained from DFT calculations to support the discussion of the inter-molecular inter-actions.

A novel hybrid protein composed of superoxide-dismutase-active Cu(II) complex and lysozyme.

A novel hybrid protein composed of a superoxide dismutase-active Cu(II) complex (CuST) and lysozyme (CuST@lysozyme) was prepared. The results of the spectroscopic and electrochemical analyses confirmed that CuST binds to lysozyme. We determined the crystal structure of CuST@lysozyme at 0.92 Å resolution, which revealed that the His15 imidazole group of lysozyme binds to the Cu(II) center of CuST in the equatorial position. In addition, CuST was fixed in position by the weak axial coordination of the Thr89 hydroxyl group and the hydrogen bond between the guanidinium group of the Arg14 residue and the hydroxyl group of CuST. Furthermore, the combination of CuST with lysozyme did not decrease the superoxide dismutase activity of CuST. Based on the spectral, electrochemical, structural studies, and quantum chemical calculations, an O2- disproportionation mechanism catalyzed by CuST@lysozyme is proposed.

Isolation and Visualization of Gliding Motility Machinery in Bacteroidota.

Many members of the phylum Bacteroidota (formerly called Bacteroidetes) adhere to and move on solid surfaces. This type of bacterial motility is called gliding and does not involve the conventional bacterial motility machinery, such as flagella and pili. To understand the mechanism of gliding motility of some Bacteroidota bacteria such as a soil bacterium Flavobacterium johnsoniae and a marine bacterium Saprospira grandis, the gliding motility machines of these two bacteria have been analyzed by electron microscopy with negative staining. Here, we describe methods to directly observe the gliding motility machinery in Bacteroidota by transmission electron microscopy.

Live Cell Imaging of the Twitching Motility of Cyanobacteria by High-Resolution Microscopy.

Many cyanobacteria show directional movement either toward or away from light sources. The cell movement, also known as twitching motility, is usually driven by type IV pili (T4P), a bacterial molecular machine. The machine generates a propulsion force through repeated cycles of extension and retraction of pilus filaments. Here, I describe a phototaxis assay for observing Synechocystis sp. PCC6803 and Thermosynechococcus vulcanus at the single-cell level with optical microscopy. By adding fluorescent beads, I also describe a method how to visualize the asymmetric activation of T4P during phototaxis.

Live Cell Imaging of Gliding Motility of Flavobacterium johnsoniae Under High-Resolution Microscopy.

Many phylum Bacteroidetes bacteria are motile without either flagella or pili. These cells move on surfaces such as glass or agar, and a motor generates a propulsion force for the cells via a proton motive force across the cytoplasmic membrane. The gliding motility depends on the helical track of cell adhesin along the longer axis of the cell body. Here, we describe live-cell imaging of gliding motility under optical microscopy, as well as an immunofluorescent labeling method for visualizing helical trajectories.

Swimming Motility Assays of Spiroplasma.

Spiroplasma swim in liquids without the use of the bacterial flagella. This small helical bacterium propels itself by generating kinks that travel down the cell body. The kink translation is unidirectional, from the leading pole to the lagging pole, during cell swimming in viscous environments. This protocol describes a swimming motility assay of Spiroplasma eriocheiris for visualizing kink translations of the absolute handedness of the body helix with optical microscopy.

Filamentous structures in the cell envelope are associated with bacteroidetes gliding machinery.

Many bacteria belonging to the phylum Bacteroidetes move on solid surfaces, called gliding motility. In our previous study with the Bacteroidetes gliding bacterium Flavobacterium johnsoniae, we proposed a helical loop track model, where adhesive SprB filaments are propelled along a helical loop on the cell surface. In this study, we observed the gliding cell rotating counterclockwise about its axis when viewed from the rear to the advancing direction of the cell and revealed that one labeled SprB focus sometimes overtook and passed another SprB focus that was moving in the same direction. Several electron microscopic analyses revealed the presence of a possible multi-rail structure underneath the outer membrane, which was associated with SprB filaments and contained GldJ protein. These results provide insights into the mechanism of Bacteroidetes gliding motility, in which the SprB filaments are propelled along tracks that may form a multi-rail system underneath the outer membrane. The insights may give clues as to how the SprB filaments get their driving force.

Improvement of the SOD activity of the Cu2+ complexes by hybridization with lysozyme and its hydrogen bond effect on the activity enhancement.

We prepared L-amino acids (L-valine and L-serine, respectively) based on the Schiff base Cu2+ complexes CuSV and CuSS in the absence/presence of hydroxyl groups and their imidazole-bound compounds CuSV-Imi and CuSS-Imi to reveal the effects of hydroxyl groups on SOD activity. The structural and spectroscopic features of the Cu2+ complexes were evaluated using X-ray crystallography, UV-vis spectroscopy, and EPR spectroscopy. The spectroscopic behavior upon addition of lysozyme indicated that both CuSV and CuSS were coordinated by the imidazole group of His15 in lysozyme at their equatorial position, leading to the formation of hybrid proteins with lysozyme. CuSS-Imi showed a higher SOD activity than CuSV-Imi, indicating that the hydroxyl group of CuSS-Imi played an important role in the disproportionation of O2 - ion. Hybridization of the Cu2+ complexes CuSV and CuSS with lysozyme resulted in higher SOD activity than that of CuSV-Imi and CuSS-Imi. The improvements in SOD activity suggest that there are cooperative effects between Cu2+ complexes and lysozyme.

Interference of flagellar rotation up-regulates the expression of small RNA contributing to Bordetella pertussis infection.

Bacterial small RNAs (sRNAs) posttranscriptionally regulate gene expressions involved in various biological processes, including pathogenicity. Our previous study identified sRNAs, the expression of which was up-regulated in Bordetella pertussis, the causative agent of whooping cough, upon tracheal colonization of the bacteria; however, their roles in bacterial infection remain unknown. Here, we found that one sRNA, Bpr4, contributes to B. pertussis infection by posttranscriptionally up-regulating filamentous hemagglutinin (FHA), a major adhesin of the bacteria. Bpr4 bound to the 5' untranslated region of fhaB mRNA encoding FHA and inhibited its degradation mediated by RNaseE. Our results demonstrated that Bpr4 up-regulation was triggered by the interference of flagellar rotation, which caused the disengagement of MotA, a flagellar stator. Subsequently, MotA activated a diguanylate cyclase to generate cyclic di-GMP, which plays a role in Bpr4 up-regulation through the RisK/RisA two-component system. Our findings indicate that a flagellum-triggered sensory system contributes to B. pertussis infection.