Search Results (42)

The pressure response and structural stability of fluoranthene crystals up to 8 GPa are investigated using Raman spectroscopy. The vast majority of the Raman peaks upshift with pressure, either sublinearly (intermolecular modes) or quasilinearly (intramolecular modes), reflecting the bond hardening upon volume contraction. The frequency shifts, accompanied by intensity redistribution among the Raman peaks, are by far larger for the former than those for the latter vibrations, compatible with their nature: weak intermolecular van der Waals interactions and strong intramolecular covalent bonds. For pressures higher than 2 GPa, changes in the linear pressure coefficients of the Raman peak frequencies, mainly towards lower values, are observed. These are more pronounced for intermolecular and C–H stretching vibrations. For P > 4.7 GPa, the pressure coefficients are further reduced, while all the observed pressure-induced changes are fully reversible upon pressure release. These changes may be interpreted either as two structural transitions at ~2 and ~4.7 GPa or as a single, but sluggish, structural phase transition in the pressure range 2–4.7 GPa, featuring the reorientation and different stacking of the molecules. From the high-pressure Raman data in the low-pressure phase, a bulk modulus of ~7 GPa at ambient pressure is estimated for solid fluoranthene. Full article

The dynamic characteristics of single DNA molecules translocating within micro/nano-channels are fundamental for a wide range of applications such as stretching, separating, mapping, and even sequencing of DNA molecules. In this study, a type of tapered microchannel chip with uniform height for all configurations was fabricated, with the major tapered structure having a length of 13 μm and a width that tapers from 5 μm to 20 μm. The dynamic characteristics such as the trajectories and velocities of λ-DNA molecules translocating from different positions driven by an external DC electric field force were systematically investigated by single-molecule fluorescence imaging technology. Some dynamic characteristics of DNA molecules translocation were found. Considering simply the effects of electrophoretic force and electro-osmotic force on the DNA molecules, the dynamic characteristics of DNA molecules are well understood. For example, the velocity of the DNA molecule is inversely proportional to the diameter of the tapered channel and the turning phenomena of the trajectory of the DNA molecules translocating through microchannels. This study is helpful and proposes new ideas for the design and development of microfluidic chips for the quantitative manipulation of DNA molecules. Full article

Coarse-grained molecular dynamic simulations are employed to investigate the spatiotemporal evolution of vesicles (polymersomes) via self-assembly of randomly distributed amphiphilic diblock copolymers PB-PEO (Poly(Butadiene)-b-Poly(Ethylene Oxide)) in water. The vesiculation pathway consists of several intermediate structures, such as spherical/rodlike aggregates, wormlike micelles, lamellae, and cavities. The lamella-to-vesicle transition occurs at a constant aggregation number and is accompanied by a reduction in the solvent-accessible surface area. Simulation predictions are in qualitative agreement with the mechanism of vesicle formation in which the unfavorable hydrophobic interactions between water molecules and polymer segments, along the edge of the lamella, are eliminated at the expense of gaining curvature energy. However, rod–lamella–vesicle transition is accompanied by an increase in copolymer packing density. Hence, the change in the surface area accompanying vesiculation predicted by the simulations is significantly lower than theoretical estimates. Changes in information entropy, quantified by the expectation of the logarithm of the probability distribution function of the segmental stretch parameter s, defined as the difference between the maximum and instantaneous segmental extension, are statistically insignificant along the vesiculation pathway. For rods, lamellae, and polymersomes, s follows a log normal distribution. This is explained based on the configurational dynamics of a single diblock chain in water. Full article

This work systematically examines the interactions between a single argon atom and the edges and faces of cyclic H${}_2$O clusters containing three–five water molecules (Ar(H${}_2$O)${}_{n=3–5}$). Full geometry optimizations and subsequent harmonic vibrational frequency computations were performed using MP2 with a triple-$\zeta$ correlation consistent basis set augmented with diffuse functions on the heavy atoms (cc-pVTZ for H and aug-cc-pVTZ for O and Ar; denoted as haTZ). Optimized structures and harmonic vibrational frequencies were also obtained with the two-body–many-body (2b:Mb) and three-body–many-body (3b:Mb) techniques; here, high-level CCSD(T) computations capture up through the two-body or three-body contributions from the many-body expansion, respectively, while less demanding MP2 computations recover all higher-order contributions. Five unique stationary points have been identified in which Ar binds to the cyclic water trimer, along with four for (H${}_2$O)${}_4$ and three for (H${}_2$O)${}_5$. To the best of our knowledge, eleven of these twelve structures have been characterized here for the first time. Ar consistently binds more strongly to the faces than the edges of the cyclic (H${}_2$O)${}_n$ clusters, by as much as a factor of two. The 3b:Mb electronic energies computed with the haTZ basis set indicate that Ar binds to the faces of the water clusters by at least 3 kJ mol${}^{-1}$ and by nearly 6 kJ mol${}^{-1}$ for one Ar(H${}_2$O)${}_5$ complex. An analysis of the interaction energies for the different binding motifs based on symmetry-adapted perturbation theory (SAPT) indicates that dispersion interactions are primarily responsible for the observed trends. The binding of a single Ar atom to a face of these cyclic water clusters can induce perturbations to the harmonic vibrational frequencies on the order of 5 cm${}^{-1}$ for some hydrogen-bonded OH stretching frequencies. Full article

A novel hydrogen-bonded supramolecular crown-ether-based inclusion compound, [(DL-α-Phenylglycine)(18-crown-6)]⁺[(CoCl₄)_0.5]⁻(1), was obtained via evaporation in a methanolic solution at room temperature using DL-α-phenylglycine, 18-crown-6, cobalt chloride (CoCl₂), and hydrochloric acid. Its structure, thermal properties, and electrical properties were characterized via elemental analysis, single-crystal X-ray diffraction, variable-temperature infrared spectroscopy, thermogravimetric analysis, differential scanning calorimetry, and variable temperature–variable frequency dielectric constant testing. The compound was a monoclinic crystal system in the C₂ space group at low temperature (100 K) and room temperature (293 K). Analysis of the single crystal structure showed that [(CoCl₄)_0.5]⁻ presented an edge-sharing ditetrahedral structure in the disordered state, while the protonated DL-α-phenylglycine molecule in the disordered state and intramolecular hydroxyl group (-OH) underwent dynamic rocking, causing a significant stretching motion of the O-H···Cl-type one-dimensional hydrogen bond chain. This resulted in dielectric anomalies in the three axes of the crystal, thus showing significant dielectric anisotropy. Full article

The myelin sheath provides insulation to the brain’s neuron cells, which aids in signal transmission and communication with the body. Degenerated myelin hampers the connection between the glial cells, which are the front row responders during traumatic brain injury mitigation. Thus, the structural integrity of the myelin layer is critical for protecting the brain tissue from traumatic injury. At the molecular level, myelin consists of a lipid bilayer, myelin basic proteins (MBP), proteolipid proteins (PLP), water and ions. Structurally, the myelin sheath is formed by repeatedly wrapping forty or more myelin layers around an axon. Here, we have used molecular dynamic simulations to model and capture the tensile response of a single myelin layer. An openly available molecular dynamic solver, LAMMPS, was used to conduct the simulations. The interatomic potentials for the interacting atoms and molecules were defined using CHARMM force fields. Following a standard equilibration process, the molecular model was stretched uniaxially at a deformation rate of 5 Å/ps. We observed that, at around 10% applied strain, the myelin started to cohesively fail via flaw formation inside the bilayers. Further stretching led to a continued expansion of the defect inside the bilayer, both radially and transversely. This study provides the cellular-level mechanisms of myelin damage due to mechanical load. Full article

Chitin is one of the most common polysaccharides and is abundant in the cell walls of fungi and the shells of insects and aquatic organisms as a skeleton. The mechanism of how chitin responds to pH is essential to the precise control of brewing and the design of smart chitin materials. However, this molecular mechanism remains a mystery. Results from single-molecule studies, including single-molecule force spectroscopy (SMFS), AFM imaging, and molecular dynamic (MD) simulations, have shown that the mechanical and conformational behaviors of chitin molecules show surprising pH responsiveness. This can be compared with how, in natural aqueous solutions, chitin tends to form a more relaxed spreading conformation and show considerable elasticity under low stretching forces in acidic conditions. However, its molecular chain collapses into a rigid globule in alkaline solutions. The results show that the chain state of chitin can be regulated by the proportions of inter- and intramolecular H-bonds, which are determined via the number of water bridges on the chain under different pH values. This basic study may be helpful for understanding the cellular activities of fungi under pH stress and the design of chitin-based drug carriers. Full article

Hydrogels are soft materials constructed of physically or chemically crosslinked polymeric net-works with abundant water. The crosslinkers, as the mechanophores that bear and respond to mechanical forces, play a critical role in determining the mechanical properties of hydrogels. Here, we use a polyprotein as the crosslinker and mechanophore to form covalent polymer hydrogels in which the toughness and fatigue fracture are controlled by the mechanical unfolding of polyproteins. The protein Parvimonas sp. (ParV) is super stable and remains folded even at forces > 2 nN; however, it can unfold under loading forces of ~100 pN at basic pH values or low calcium concentrations due to destabilization of the protein structures. Through tuning the protein unfolding by pH and calcium concentrations, the hydrogel exhibits differences in modulus, strength, and anti-fatigue fracture. We found that due to the partially unfolding of ParV, the Young’s modulus decreased at pH 9.0 or in the presence of EDTA (Ethylene Diamine Tetraacetic Acid), moreover, because partially unfolded ParV can be further completely unfolded due to the mechanically rupture of ester bond, leading to the observed hysteresis of the stretching and relaxation traces of the hydrogels, which is in line with single-molecule force spectroscopy experiments. These results display a new avenue for designing pH- or calcium-responsive hydrogels based on proteins and demonstrate the relationship between the mechanical properties of single molecules and macroscopic hydrogel networks. Full article

The molecular structure of the liquid–vapor interfaces of aqueous solutions of alkali metal halides and methyl isobutyl carbinol (MIBC, (CH₃)₂CHCH₂COCH₃) is determined by using molecular dynamics simulations with polarizable force fields for the first time. The salts are chlorides, and iodides, some of which are found in raw and partially desalinated seawater increasingly used in flotation operations in regions affected by severe and prolonged drought. The density profiles at the interfaces show that all ions prefer the interface; however, with MIBC, non-polarizable ions, generally small ones, are increasingly pushed into the liquid bulk. A few ions of comparatively less ionic NaCl than KCl and CsCl, persist at the interface, consistent with spectroscopy observations. On the other hand, strongly polarizable ions such as I⁻ always share the interface with MIBC. In the presence of chlorides, the frother chains at the interface stretch slightly more toward vapor than in freshwater; however, in the presence of iodides, the chains stretch so much that they become orthogonal to the interface, giving rise to a well-packed monolayer, which is the most effective configuration. The dominant water configurations at the interface are double donor and single donor, with hydrogen atoms pointing toward the liquid, consistent with studies with sum-frequency generation experiments and extensive ab initio simulations. This picture changes radically in the presence of MIBC and salts. Depending on the halide and MIBC concentration, the different molecular configurations at the interface lead to very different surface tensions. The structure and properties of these new salt-rich interfaces and their impact on the location and arrangement of frother molecules should serve the flotation practitioner, especially in the search for the best frother and dosing in poor-quality water. Full article

The crystal structure of a naturally occurring layered double hydroxide mineral—desautelsite from San Benito County, California, USA—was refined using single-crystal X-ray diffraction data in the space group R-3m, a = 3.1238(2) Å, c = 23.528(3) Å, V = 198.83(4) ų, and Z = 3/8. The Mg and Mn cations are disordered occurring in one M site with occupancy Mg_0.77Mn_0.23. According to the electron microprobe analysis supported by Raman spectroscopy, the empirical formula is Mg_6.20(Mn^III_1.78Al_0.01Fe^III_0.01)_Σ1.80(OH)₁₆(CO₃)_0.90·5.35H₂O that shows higher content of interlayer (H₂O) molecules in comparison to the ideal formula that also agrees with the structure refinement. The Raman spectroscopy of two samples indicated O–H vibrations (3650/3640 cm⁻¹, ~3500 sh cm⁻¹), symmetric C–O (1055/1057 cm⁻¹), Mg–O–Mg (533/533 cm⁻¹) and Mn–O–Mn (439/438 cm⁻¹) stretching vibrations and lattice vibrations (284/287 cm⁻¹). Summing up our data and that of the current literature, we show a correlation (R² = 0.91) between the averaged effective ionic radius (x) and a unit cell parameter (y) of hydrotalcite group minerals, $y=1.9871x+1.4455$. Desautelsite follows this correlation, being the species with one of the largest a unit cell parameters among the group. The correlation can be applied for control of cation intercalation during synthesis. Full article

Synthesis of sulfonamide through an indirect method that avoids contamination of the product with no need for purification has been carried out using the indirect process. Here, we report the synthesis of a novel sulfonamide compound, ({4-nitrophenyl}sulfonyl)tryptophan (DNSPA) from 4-nitrobenzenesulphonylchloride and L-tryptophan precursors. The slow evaporation method was used to form single crystals of the named compound from methanolic solution. The compound was characterized by X-ray crystallographic analysis and spectroscopic methods (NMR, IR, mass spectrometry, and UV-vis). The sulfonamide N-H NMR signal at 8.07–8.09 ppm and S-N stretching vibration at 931 cm⁻¹ indicate the formation of the target compound. The compound crystallized in the monoclinic crystal system and P2₁ space group with four molecules of the compound in the asymmetric unit. Molecular aggregation in the crystal structure revealed a 12-molecule aggregate synthon sustained by O-H⋯O hydrogen bonds and stabilised by N-H⋯O intermolecular contacts. Experimental studies were complemented by DFT calculations at the B3LYP/6-311++G(d,p) level of theory. The computed structural and spectroscopic data are in good agreement with those obtained experimentally. The energies of interactions between the units making up the molecule were calculated. Molecular docking studies showed that DNSPA has a binding energy of −6.37 kcal/mol for E. coli DNA gyrase (5MMN) and −6.35 kcal/mol for COVID-19 main protease (6LU7). Full article

Bacterial adhesion to dental implants is the onset for the development of pathological biofilms. Reliable characterization of this initial process is the basis towards the development of anti-biofilm strategies. In the present study, single-cell force spectroscopy (SCFS), by means of an atomic force microscope connected to a microfluidic pressure control system (FluidFM), was used to comparably measure adhesion forces of different oral bacteria within a similar experimental setup to the common implant material titanium. The bacteria selected belong to different ecological niches in oral biofilms: the commensal pioneers Streptococcus oralis and Actinomyces naeslundii; secondary colonizer Veillonella dispar; and the late colonizing pathogens Porphyromonas gingivalis as well as fimbriated and non-fimbriated Aggregatibacter actinomycetemcomitans. The results showed highest values for early colonizing pioneer species, strengthening the link between adhesion forces and bacteria’s role in oral biofilm development. Additionally, the correlation between biophysical cellular characteristics and SCFS results across species was analyzed. Here, distinct correlations between electrostatically driven maximum adhesion force, bacterial surface elasticity and surface charge as well as single-molecule attachment points, stretching capability and metabolic activity, could be identified. Therefore, this study provides a step towards the detailed understanding of oral bacteria initial adhesion and could support the development of infection-resistant implant materials in future. Full article

Because of rising traumatic accidents and diseases, the number of patients suffering from nerve injury is increasing. Without effective rehabilitation therapy, the patients will get motor or sensory function losses or even a lifelong disability. As for amputees, neural interface technology can be used to splice nerves and electrical wires together in a way that allows them to control an artificial limb as if it was a natural extension of the body. However, the means the need for an autologous nerve to stimulate axonal regeneration and extension into target tissues, which are limited by the supply of donor nerves. Based on the principle of mechanical force regulating axon growth, in this paper, we developed a three-dimensional nerve stretch growth device for an implantable neural interface. The device consists of three motors controlled by single chip microcomputer and some mechanical parts. The stability and reliability of the device were tested. Then, we used neurons derived from human pluripotent stem cells by small chemical molecules to explore the optimal three-dimensional stretch culture parameters. Furthermore, we found that the axons were intact through 10 rotations per day and 1 mm of horizontal pulling per day. The results of this research will provide convenience for patients treated through an implantable neural interface. Full article

Nanoarchitectural control of matter is crucial for next-generation technologies. DNA origami templates are harnessed to accurately position single molecules; however, direct single molecule evidence is lacking regarding how well DNA origami can control the orientation of such molecules in three-dimensional space, as well as the factors affecting control. Here, we present two strategies for controlling the polar (θ) and in-plane azimuthal (ϕ) angular orientations of cyanine Cy5 single molecules tethered on rationally-designed DNA origami templates that are physically adsorbed (physisorbed) on glass substrates. By using dipolar imaging to evaluate Cy5′s orientation and super-resolution microscopy, the absolute spatial orientation of Cy5 is calculated relative to the DNA template. The sequence-dependent partial intercalation of Cy5 is discovered and supported theoretically using density functional theory and molecular dynamics simulations, and it is harnessed as our first strategy to achieve θ control for a full revolution with dispersion as small as ±4.5°. In our second strategy, ϕ control is achieved by mechanically stretching the Cy5 from its two tethers, being the dispersion ±10.3° for full stretching. These results can in principle be applied to any single molecule, expanding in this way the capabilities of DNA as a functional templating material for single-molecule orientation control. The experimental and modeling insights provided herein will help engineer similar self-assembling molecular systems based on polymers, such as RNA and proteins. Full article

Acoustic shockwaves are of interest as a possible means of the selective inactivation of viruses. It has been proposed that such inactivation may be enhanced by driving the virus particles at frequencies matching the characteristic frequency corresponding to acoustic modes of the viral structures, setting up a resonant response. Characteristic frequencies of viruses have been previously studied through opto-mechanical techniques. In contrast to optical excitation, shockwaves may be able to probe acoustic modes without the limitation of optical selection rules. This work explores molecular dynamics simulations of shockwaves interacting with a single STMV virus structure, in full atomistic detail, in order to measure the frequency of the response of the overall structure. Shockwaves of varying energy were set up in a water box containing the STMV structure by assigning water molecules at the edge of the box with an elevated velocity inward—in the direction of the virus. It was found that the structure compressed and stretched in a periodic oscillation of frequency 65 ± 6.5 GHz. This measured frequency did not show strong dependency on the energy of the shockwave perturbing the structure, suggesting the frequency is a characteristic of the structure. The measured frequency is also consistent with values predicted from elastic theory. Additionally, it was found that subjecting the virus to repeated shockwaves led to further deformation of the structure and the magnitude of the overall deformation could be altered by varying the time delay between repeated shockwave pulses. Full article