Search

Perchlorate compounds are well-known for their explosive and hazardous nature. Considering previously reported perchlorate crystals of salen-type manganese (III) complexes, our study aimed to identify the specific molecular/crystal structure responsible for their explosive properties. Employing deep learning, we conducted an analysis of the Hirschfeld surface for salen-type metal complexes within a crystal structure database. The results indicate that the salen-type complex site lacks distinctive structural features, attributing its explosive potential to the chemical bonding of the perchlorate ion and the surrounding intermolecular interactions.

The title copper(II) complex, [Cu(C18H19N3O3)(C3H4N2)], consists of a tridentate ligand synthesized from L-leucine and azobenzene-salicylaldehyde. One imidazole molecule 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.

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.

In this study, interviews with undergraduate and graduate students about incidents that did not result in an accident but felt dangerous (so-called near miss incidents) that occurred in the chemical laboratory at the university (to which the author belongs) in 2023 were conducted. An explanation of near-miss cases and the causes attributed to the experimenter is provided. Specifically, potential dangers related to (1) contact with hazardous chemicals, (2) handling of glassware, and (3) working spaces and electricity frequently occur. Comparing undergraduate and graduate students, it was found that the former tended to think about concrete and individual countermeasures, while the latter tended to discuss causes and countermeasures from a broader perspective; therefore, they were differentiated based on the description column. Comments from the graduate students were categorized into corresponding case categories and recorded in a discussion column. Furthermore, a summary section is included on who should be careful, their outlook, and their mindset.

Schiff bases are organic compounds that are often used as ligands in metal complexes. In addition to the C=N double bond, which is characteristic of Schiff bases, intermolecular hydrogen bonds are frequently observed in both the twisting of planar substituents in organic compounds and the geometric structure of the coordination environment in metal complexes. The results of the crystal structure analyses are stored in databases, which can be used to assess three-dimensional structures. To examine the important structural aspects for novel molecular and material designs, this review examines the important discussion of crystal structure “features” from various viewpoints based on papers on Schiff bases and Schiff base metal complexes from recent years.

Mycoplasma mobile is a parasitic bacterium that forms gliding machinery on the cell pole and glides on a solid surface in the direction of the cell pole. The gliding machinery consists of both internal and surface structures. The internal structure is divided into a bell at the front and chain structure extending from the bell. In this study, the internal structures prepared under several conditions were analyzed using negative-staining electron microscopy and electron tomography. The chains were constructed by linked motors containing two complexes similar to ATP synthase. A cylindrical spacer with a maximum diameter of 6 nm and a height of 13 nm, and anonymous linkers with a diameter of 0.9–8.3 nm and length of 14.7±6.9 nm were found between motors. The bell is bowl-shaped and features a honeycomb surface with a periodicity of 8.4 nm. The chains of the motor are connected to the rim of the bell through a wedge-shaped structure. These structures may play roles in the assembly and cooperation of gliding machinery units.

The title copper(II) complex, [Cu(C16H13NO4)(C3H4N2)], consists of a tridentate ligand synthesized from L-tyrosine and salicylaldehyde. One imidazole molecule 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.

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.

Abstract 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.

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

Electron microscopic visualization and movement analysis of the gliding machinery in Bacteroidetes provide insights into the mechanism of gliding motility, or the ability of these microbes to move on solid surfaces.

As a recent cutting-edge research target, the prediction of crystal systems or space groups using machine learning based on databases has been actively reported [...]

Alzheimer’s disease causes the destruction of cranial nerve cells and is said to be caused by neuronal cell death due to the accumulation of amyloid-β protein. One method for the treatment of Alzheimer’s disease is to reduce the toxicity of the amyloid beta protein. Among the possibilities is to reduce toxicity by changing the secondary structure of the protein. In this study, the secondary structure of the protein was verified by binding a zinc complex to the protein and irradiating it with an infrared free-electron laser (IR-FEL). By binding Salen-Type zinc complexes to human serum albumin (HSA) and irradiating it with IR-FEL, structural changes were observed in the α-helix and β-sheet, the secondary structure of HSA. In addition to researching the possibility of binding zinc complexes to small proteins, docking simulations were examined. GOLD docking simulations showed that it is possible to bind zinc complexes to lysozyme (Lyz), a small protein. These results suggest that binding zinc complexes to amyloid-β and inducing a secondary conformational change through IR-FEL irradiation could be used for the treatment of Alzheimer’s disease by making the complexes lose their toxicity.

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.

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

Mycoplasmas, a group of small parasitic bacteria, adhere to and move across host cell surfaces. The role of motility across host cell surfaces in pathogenesis remains unclear. Here, we used optical microscopy to visualize rheotactic behavior in three phylogenetically distant species of Mycoplasma using a microfluidic chamber that enabled the application of precisely controlled fluid flow. We show that directional movements against fluid flow occur synchronously with the polarized cell orienting itself to be parallel against the direction of flow. Analysis of depolarized cells revealed that morphology itself functions as a sensor to recognize rheological properties that mimic those found on host-cell surfaces. These results demonstrate the vital role of cell morphology and motility in responding to mechanical forces encountered in the native environment.

In the title complex, [Sm(NO3)3(C30H28N2O4)], the Sm atom is surrounded by ten O atoms. The (S,S)-2,2′-{[(1,2-diphenylethane-1,2-diyl)bis[(azaniumylylidene)methanylylidene]}bis(6-methoxyphenolate) ligand, obtained from o-vanillin and (1S,2S)-(−)-1,2-diphenylethylenediamine, exhibits a slightly distorted planar arrangement of the four coordinated O atoms. In the crystal, the complex shows intramolecular N—H...O hydrogen bonds and weak intermolecular C—H...O hydrogen bonds. The Hirshfeld surface analysis indicates that the most important contributions to the packing are from H...H (33.5%), O...H (34.1%) and C...H (21.7%) contacts.

The Fo ATP synthase, the bacterial flagellar motor, and the bacterial type 9 secretion system (T9SS) are the three known proton motive force driven biological rotary motors. In this review, we summarize the current information on the nuts and bolts of T9SS. Torque generation by T9SS, its role in gliding motility of bacteria, and the mechanism via which a T9SS-driven swarm shapes the microbiota are discussed. The knowledge gaps in our current understanding of the T9SS machinery are outlined.

Many cyanobacteria, which use light as an energy source via photosynthesis, show directional movement towards or away from a light source. However, the molecular and cell biological mechanisms for switching the direction of movement remain unclear. Here, we visualized type IV pilus-dependent cell movement in the rod-shaped thermophilic cyanobacterium Thermosynechococcus vulcanus using optical microscopy at physiological temperature and light conditions. Positive and negative phototaxis were controlled on a short time scale of 1 min. The cells smoothly moved over solid surfaces towards green light, but the direction was switched to backward movement when we applied additional blue light illumination. The switching was mediated by three photoreceptors, SesA, SesB, and SesC, which have cyanobacteriochrome photosensory domains and synthesis/degradation activity of the bacterial second messenger cyclic dimeric GMP (c-di-GMP). Our results suggest that the decision-making process for directional switching in phototaxis involves light-dependent changes in the cellular concentration of c-di-GMP. Direct visualization of type IV pilus filaments revealed that rod-shaped cells can move perpendicular to the light vector, indicating that the polarity can be controlled not only by pole-to-pole regulation but also within-a-pole regulation. This study provides insights into previously undescribed rapid bacterial polarity regulation via second messenger signalling with high spatial resolution.

Length control is a fundamental requirement for molecular architecture. Even small wall-less bacteria have specially developed macro-molecular structures to support their survival. Mycoplasma pneumoniae, a human pathogen, forms a polar extension called an attachment organelle, which mediates cell division, cytadherence, and cell movement at host cell surface. This characteristic ultrastructure has a constant size of 250–300 nm, but its design principle remains unclear. In this study, we constructed several mutants by genetic manipulation to increase or decrease coiled-coil regions of HMW2, a major component protein of 200 kDa aligned in parallel along the cell axis. HMW2-engineered mutants produced both long and short attachment organelles, which we quantified by transmission electron microscopy and fluorescent microscopy with nano-meter precision. This simple design of HMW2 acting as a molecular ruler for the attachment organelle should provide an insight into bacterial cellular organization and its function for their parasitic lifestyles. Author summary Mycoplasma pneumoniae, a pathogen of “walking pneumonia”, have a membrane protrusion with a precise length of 250–300 nm specially developed to support their parasitic lifestyles. To date, however, there has been no report focusing on the potential length-control mechanisms of this characteristic architecture called an attachment organelle. Here, we found that the coiled-coil domains of the 200-kDa protein HMW2 are aligned in parallel along the cell axis, and acts as a molecular ruler by the assembly into a physical scaffold. The molecular ruler could be engineered by genetic modification to produce both longer and shorter attachment organelle. The analyses of the length-controlled mutant highlight a simple design principle of cellular organization in a small bacterium.

Campylobacter jejuni rotates a flagellum at each pole to swim through the viscous mucosa of its hosts' gastrointestinal tracts. Despite their importance for host colonization, however, how C. jejuni coordinates rotation of these two opposing flagella is unclear. As well as their polar placement, C. jejuni's flagella deviate from the norm of Enterobacteriaceae in other ways: their flagellar motors produce much higher torque and their flagellar filament is made of two different zones of two different flagellins. To understand how C. jejuni's opposed motors coordinate, and what contribution these factors play in C. jejuni motility, we developed strains with flagella that could be fluorescently labeled, and observed them by high-speed video microscopy. We found that C. jejuni coordinates its dual flagella by wrapping the leading filament around the cell body during swimming in high-viscosity media and that its differentiated flagellar filament and helical body have evolved to facilitate this wrapped-mode swimming.

Abstract Photoanodes comprising Au nanoparticles (GNPs) and thin TiO2 layers with a stacked structure were fabricated by repeating the application of TiO2 paste and GNP solutions on conductive glass to vary the distribution of GNPs in the TiO2 layer. The plasmon-enhanced characteristics of dye-sensitized solar cells (DSSCs) with such photoanodes were investigated. Both the absorption of the TiO2 layer and the performance of the DSSC are found to be most increased by plasmonic enhancement when GNPs are concentrated near the position in the TiO2 layer, which is the penetration depth of the incident light of wavelength corresponding to the maximum absorption of the N719 dye (~ 520 nm). When a GNP layer with a relatively high density of 1.3 μg/cm2 density was formed at its position, and two GNP layers with a relatively low density of 0.65 μg/cm2 were formed near the front side of the incident light, the short-circuit current density (Jsc) and energy conversion efficiency (η) of the DSSC were found to be 10.8 mA/cm2 and 5.0%, increases of 15 and 11%, respectively, compared with those of the DSSC without GNPs. Our work suggests that optimization of the distribution of GNPs in the TiO2 layer is very important for improving the performance of DSSCs fabricated by utilizing GNPs.

Spherical zoospores of a rare actinomycete, Actinoplanes missouriensis, adhere to various hydrophobic solid surfaces by means of type IV pili. The purpose of this protocol is to provide detailed descriptions of the preparation of A. missouriensis zoospores and an assay for the adhesion of the zoospores to solid surfaces. This adhesion assay, which measures numbers of zoospores that adhered to the dish surface and swimming zoospores in a tunnel chamber by using a phase-contrast microscope, can also be used for swimming cells of other microorganisms.

ABSTRACT Mycoplasma mobile, a fish pathogen, glides on solid surfaces by repeated catch, pull, and release of sialylated oligosaccharides by a unique mechanism based on ATP energy. The gliding machinery is composed of huge surface proteins and an internal “jellyfish”-like structure. Here, we elucidated the detailed three-dimensional structures of the machinery by electron cryotomography. The internal “tentacle”-like structure hydrolyzed ATP, which was consistent with the fact that the paralogs of the α- and β-subunits of F1-ATPase are at the tentacle structure. The electron microscopy suggested conformational changes of the tentacle structure depending on the presence of ATP analogs. The gliding machinery was isolated and showed that the binding activity to sialylated oligosaccharide was higher in the presence of ADP than in the presence of ATP. Based on these results, we proposed a model to explain the mechanism of M. mobile gliding. IMPORTANCE The genus Mycoplasma is made up of the smallest parasitic and sometimes commensal bacteria; Mycoplasma pneumoniae, which causes human “walking pneumonia,” is representative. More than ten Mycoplasma species glide on host tissues by novel mechanisms, always in the direction of the distal side of the machinery. Mycoplasma mobile, the fastest species in the genus, catches, pulls, and releases sialylated oligosaccharides (SOs), the carbohydrate molecules also targeted by influenza viruses, by means of a specific receptor and using ATP hydrolysis for energy. Here, the architecture of the gliding machinery was visualized three dimensionally by electron cryotomography (ECT), and changes in the structure and binding activity coupled to ATP hydrolysis were discovered. Based on the results, a refined mechanism was proposed for this unique motility.

We studied supramolecular chirality induced by circularly polarized light. Photoresponsive azopolymers form a helical intermolecular network. Furthermore, studies on photochemical materials using optical vortex light will also attract attention in the future. In contrast to circularly polarized light carrying spin angular momentum, an optical vortex with a spiral wave front and carrying orbital angular momentum may impart torque upon irradiated materials. In this review, we summarize a few examples, and then theoretically and computationally deduce the differences in spin angular momentum and orbital angular momentum depending on molecular orientation not on, but in, polymer films. UV-vis absorption and circular dichroism (CD) spectra are consequences of electric dipole transition and magnetic dipole transition, respectively. However, the basic effect of vortex light is postulated to originate from quadrupole transition. Therefore, we explored the simulated CD spectra of azo dyes with the aid of conventional density functional theory (DFT) calculations and preliminary theoretical discussions of the transition of CD. Either linearly or circularly polarized UV light causes the trans–cis photoisomerization of azo dyes, leading to anisotropic and/or helically organized methyl orange, respectively, which may be detectable by CD spectroscopy after some technical treatments. Our preliminary theoretical results may be useful for future experiments on the irradiation of UV light under vortex.

ABSTRACT Mycoplasma mobile, a fish-pathogenic bacterium, features a protrusion that enables it to glide smoothly on solid surfaces at a velocity of up to 4.5 µm s−1 in the direction of the protrusion. M. mobile glides by a repeated catch-pull-release of sialylated oligosaccharides fixed on a solid surface by hundreds of 50-nm flexible “legs” sticking out from the protrusion. This gliding mechanism may be explained by a possible directed binding of each leg with sialylated oligosaccharides, by which the leg can be detached more easily forward than backward. In the present study, we used a polystyrene bead held by optical tweezers to detach a starved cell at rest from a glass surface coated with sialylated oligosaccharides and concluded that the detachment force forward is 1.6- to 1.8-fold less than that backward, which may be linked to a catch bond-like behavior of the cell. These results suggest that this directed binding has a critical role in the gliding mechanism. IMPORTANCE Mycoplasma species are the smallest bacteria and are parasitic and occasionally commensal, as represented by Mycoplasma pneumoniae, which causes so-called “walking pneumonia” in humans. Dozens of species glide on host tissues, always in the direction of the characteristic cellular protrusion, by novel mechanisms. The fastest species, Mycoplasma mobile, catches, pulls, and releases sialylated oligosaccharides (SOs), which are common targets among influenza viruses, by means of a specific receptor based on the energy of ATP hydrolysis. Here, force measurements made with optical tweezers revealed that the force required to detach a cell from SOs is smaller forward than backward along the gliding direction. The directed binding should be a clue to elucidate this novel motility mechanism.

Mycoplasma pneumoniae, a human pathogenic bacterium, glides on host cell surfaces by a unique and unknown mechanism. It forms an attachment organelle at a cell pole as a membrane protrusion composed of surface and internal structures, with a highly organized architecture. In the present study, we succeeded in isolating the internal structure of the organelle by sucrose-gradient centrifugation. The negative-staining electron microscopy clarified the details and dimensions of the internal structure, which is composed of terminal button, paired plates, and bowl complex from the end of cell front. Peptide mass fingerprinting of the structure suggested 25 novel components for the organelle, and 3 of them were suggested for their involvement in the structure through their subcellular localization determined by enhanced yellow fluorescent protein (EYFP) tagging. Thirteen component proteins including the previously reported ones were mapped on the organelle systematically for the first time, in nanometer order by EYFP tagging and immunoelectron microscopy. Two, three, and six specific proteins localized specifically to the terminal button, the paired plates, and the bowl, respectively and interestingly, HMW2 molecules were aligned parallel to form the plate. The integration of these results gave the whole image of the organelle and allowed us to discuss possible gliding mechanisms.

The title copper(II) complex, [Cu(C18H19N3O3)(C3H4N2)], consists of a tridentate ligand synthesized from l-leucine and azobenzene-salicylaldehyde. One imidazole molecule 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. [ABSTRACT FROM AUTHOR]

The title copper(II) complex, [Cu(C16H13NO4)(C3H4N2)], consists of a tridentate ligand synthesized from l-tyrosine and salicylaldehyde. One imidazole molecule 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. [ABSTRACT FROM AUTHOR]

The title copper(II) complex, [Cu(C16H13NO4)(C3H4N2)], consists of a tridentate ligand synthesized from L-tyrosine and salicylaldehyde. One imidazole molecule 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. [ABSTRACT FROM AUTHOR]