Physchem, Volume 4, Issue 2 (June 2024) – 6 articles

Crustacean shells, waste from the seafood industry, have been identified as a potential sustainable material for the adsorption of lead, a potent heavy metal found in the discharge of industrial processes. The dynamics and kinetics of its performance were evaluated in batch experiments under pH, temperature, time, and initial concentration. A unique and non-intuitive key finding was that among the native components of the crab shell matrix, i.e., chitin, protein, and calcium carbonate, calcium carbonate was instrumental in sequestration. The role of protein was minimal, whereas the efficiency of chitin in lead complexation was linked to the lead atomic radius, which, of the crab shell components, we determined was very prone to interacting with chitin. Full article

Rates of fast reactions are inversely proportional to the solvent viscosity (η). However, a quantitative study demonstrates that dynamic viscosity η is often a crude reflection of a viscous drug exerted on a molecule or radical. This paper aims to present an accurate dependence of the rates of fast bi- and monomolecular reactions upon the viscous drug of a media. Different correction coefficients f_micro are discussed, which should lead to a dependence rate ∝ (f_microη)⁻¹. Microviscosity is viscosity, leading to the expected rate dependence upon shear viscosity. In many cases, experimentally measured diffusion coefficients of molecules of a similar structure to the reactive radicals lead to the correct prediction of radicals’ diffusion coefficients and the rate constants of radicals recombination. Microviscosity of complex non-Newtonian liquids (biological liquids, polymeric solutions) can be measured using low MW molecular probes. Usually, the measured η_micro is much lower than the shear η of complex biological or polymeric liquids. Cis–trans isomerization of bulky groups in monomolecular reactions is often described with Kramers’ theory. An example of such isomerization of a cyanine dye studied experimentally and theoretically is presented. It is demonstrated in the selected case that Kramers’ theory adequately describes the dependence of cis–trans isomerization of organic compounds upon η. Full article

In this study, the mechanism of the reaction between 4-methyl aniline and hydroxyl free radicals was computed using the M06-2X and CCSD(T) methods, along with the 6-311++G(3df,2p) basis set. The kinetics of the reaction were calculated utilizing the transition state theory and the microcanonical Rice–Ramsperger–Kassel–Marcus theory. The calculated results revealed that NH-C₆H₄-CH₃ was the key product of the system. The total rate coefficient of the system, k__total = 2.04 × 10⁻¹⁸ T^2.07 exp[(11.2 kJ/mol)/RT] cm³/s, was found under the 300–2000 K interval, with P = 760 Torr. At the ambient conditions, the velocity of this reaction was about ten times larger than that of the reaction between C₆H₅CH₃ and hydroxyl free radicals, but it was smaller than the aniline + OH rate. Full article

The geometrical r_e parameters of trans-azobenzene (E-AB) free molecule were refined by gas electron diffraction (GED) method using available experimental data obtained previously by S. Konaka and coworkers. Structural analysis was carried out by various techniques. First of all, these included the widely used molecular orbital constrained gas electron diffraction method and regularization method. The results of the refinements using different models were also compared—a semirigid model, three variants of one-dimensional dynamic models, and a two-dimensional pseudoconformer model. Several descriptions have been used due to the fact that E-AB has a shallow potential energy surface along the rotation coordinates of phenyl groups. Despite this, it turned out that the semirigid model is suitable for use for E-AB and allows good agreement with experimental data to be achieved. According to the results of GED structural analysis, coupled with the results of DLPNO-CCSD(T0) calculations, E-AB has a planar structure. Based only on GED data, it is impossible to unambiguously determine the rotational angle of the phenyl group due to the facts that (i) with rotation over a wide range of angles, the bonded distances in the molecule change insignificantly and (ii) potential function in a structural analysis within a dynamic model is not determined with the necessary accuracy. This work also examines the sensitivity of the GED method to structural changes caused by trans-cis isomerization. The paper also analyzes the applicability of different variants of density functional theory (DFT) calculations in GED structural analysis using E-AB as an example. There are not enough similar methodological works in the literature. This experimental and methodological information is especially important and relevant for planning and implementing GED experiments and corresponding processing of the results for azobenzene derivatives, in which the conformer and isomeric diversity are even more complicated due to the presence of different substituents. Full article

A special type of Streptococcus mutans expressing collagen-binding proteins (CBPs), Cnm, and Cbm, on the cell surface has been shown to be highly pathogenic. It is believed that S. mutans with CBPs that has entered the blood vessel attaches to collagen molecules exposed from the damaged blood vessel, inhibiting aggregation by platelets and increasing bleeding. Therefore, it is crucial to understand the molecular characteristic features of CBPs to protect against and cure S. mutans-related diseases. In this work, we highlighted the Cbm/collagen-binding domain (CBD) and examined its binding ability and thermal stability using its domain/region exchange variants in more detail. The CBD comprises the N1-domain, a linker, N2-domain, and a latch (N1–N2~), where the latch interacts with the N1-domain to form a β-sheet. The collagen-binding activity of the Cbm/CBD domain/region exchange variants was investigated using ELISA. Binding assays demonstrated that the N-domain_linker_N-domain composition is necessary for collagen binding as previously reported, newly that the latch is involved in binding through the β-sheet with the N1-domain when the N1-domain is present at the N-terminal position, and that the N2-domain is particularly important for collagen binding at both the N- and C-terminal positions. Thermal denaturation experiments newly revealed that the linker and latch bound to the N-domain contribute to N-domain stabilization but have no effect on the N-domain_linker_N-domain molecule, which contains two N-domains. It has also been shown that the N-terminal N2-domain destabilizes the N-domain_linker_N-domain structure. The results of this study will contribute to the rapid detection of CBP, development of CBP-targeted therapies, and application of CBPs to protein engineering using their collagen-binding ability. Full article

The menthol sensor transient receptor potential melastatin-8 (TRPM8) can be activated by cold and, thus, serves as a biothermometer in a primary afferent sensory neuron for innocuous-to-noxious cold detection. However, the precise structural origins of specific temperature thresholds and sensitivity have remained elusive. Here, a grid thermodynamic model was employed, to examine if the temperature-dependent noncovalent interactions found in the 3-dimensional (3D) structures of thermo-gated TRPM8 could assemble into a well-organized fluidic grid-like mesh network, featuring the constrained grids as the thermorings for cold-sensing in response to PIP₂, Ca²⁺ and chemical agents. The results showed that the different interactions of TRPM8 with PIP₂ during the thermal incubation induced the formation of the biggest grids with distinct melting temperature threshold ranges. Further, the overlapped threshold ranges between open and pre-open closed states were required for initial cold activation with the matched thermo-sensitivity and the decrease in the systematic thermal instability. Finally, the intact anchor grid near the lower gate was important for channel opening with the active selectivity filter. Thus, PIP₂-dependent thermorings in TRPM8 may play a pivotal role in cold sensing. Full article