Variation of Activation Volume as an Indicator of the Difference in Clusterization Phenomenon Induced by H-Bonding and F-Π Stacking Interactions in Enantiomers and a Racemate of Flurbiprofen.

In this paper, X-ray diffraction (XRD), differential scanning calorimetry (DSC), broadband dielectric (BDS), and Fourier transform infrared (FTIR) spectroscopy supported by molecular dynamics (MD) simulations and quantum chemical computations were applied to investigate the structural and thermal properties, molecular dynamics, and H-bonding pattern of R-, S-, and RS-flurbiprofen (FLP). Experimental data indicated various spatial molecular arrangements in crystalline forms of examined systems, which seemed to disappear in the liquid state. Surprisingly, deeper analysis of high-pressure dielectric data revealed unexpected variation in the activation volume of pure enantiomers and a racemate. MD simulations showed that it is an effect of the clusterization phenomenon and a higher population of small associates in the former samples. Moreover, theoretical consideration exposed the particular role of unspecific F-Π interactions as a driving force underlying local molecular arrangements of molecules in the liquid and the crystal lattice of R-, S-, and RS-FLP.

A Hardware Encoder-Based Synchronization Method for a Fast Terahertz TDS Imaging System Based on the ECOPS Scheme.

In this paper, we report our use of a hardware encoder-based synchronization method for a fast terahertz time-domain spectroscopy raster scanner built with the commercially available TeraFlash Smart platform. We describe the principles of our method, including our incorporation of synchronization signals from various devices included in the scanner. We also describe its implementation in a microcontroller with a dedicated counter. By such means, a fast scanning mode was obtained, which was 35 times faster than a traditional step-by-step approach. To validate the proposed synchronization method, we carried out measurements using the USAF 1951 resolution test and a fiberglass plate with a set of intentionally introduced defects. Our results confirmed that the TDS scanner with the developed synchronization method was able to capture high-quality images with resolutions as high as those obtained using traditional step-by-step scanning, but with significantly reduced scanning times.

The existence of a strongly bonded layer in associating liquids within silica pores - a spectral and molecular dynamics study.

The properties of confined materials are assumed to be governed by the phenomena occurring at the interface, especially the formation of an irreversible adsorption layer (IAL), which has been widely discussed and detected in the case of thin polymer films and silica nanoparticles. In this paper, we present a novel experimental approach allowing us to reveal the formation of an IAL in two phenyl alcohols infiltrated into various mesoporous silica templates. The proposed methodology (based on evaporation) allowed us to detect the alterations in the OH and aromatic CH stretching vibration bands in infrared spectra, which were considered as evidence of the existence of IAL in constrained systems. Such interpretation was also confirmed by complementary molecular dynamics (MD) simulations that indicated the creation of much stronger hydrogen bonds between alcohols and silanol units than between alcohols themselves. Moreover, computation allowed us to identify additional enormously strong π-stacking interactions between phenyl rings stabilizing the interfacial layer. MD simulations also shed new light on the clustering process of both alcohols under confinement. Simulation and experimental data presented in this paper allowed a much deeper understanding of the processes occurring at the interface-formation of IAL and the association phenomenon at the nanoscale level.

The Impact of Various Poly(vinylpyrrolidone) Polymers on the Crystallization Process of Metronidazole.

In this paper, we propose one-step synthetic strategies for obtaining well-defined linear and star-shaped polyvinylpyrrolidone (linPVP and starPVP). The produced macromolecules and a commercial PVP K30 with linear topology were investigated as potential matrices for suppressing metronidazole (MTZ) crystallization. Interestingly, during the formation of binary mixtures (BMs) containing different polymers and MTZ, we found that linear PVPs exhibit maximum miscibility with the drug at a 50:50 weight ratio (w/w), while the star-shaped polymer mixes with MTZ even at a 30:70 w/w. To explain these observations, comprehensive studies of MTZ-PVP formulations with various contents of both components were performed using Fourier-transform infrared spectroscopy, differential scanning calorimetry, and X-ray diffraction. The obtained results clearly showed that the polymer's topology plays a significant role in the type of interactions occurring between the matrix and MTZ. Additionally, we established that for MTZ-PVP 50:50 and 75:25 w/w BMs, linear polymers have the most substantial impact on inhibiting the crystallization of API. The star-shaped macromolecule turned out to be the least effective in stabilizing amorphous MTZ at these polymer concentrations. Nevertheless, long-term structural investigations of the MTZ-starPVP 30:70 w/w system (which is not achievable for linear PVPs) demonstrated its complete amorphousness for over one month.

AlphaFold2 captures the conformational landscape of the HAMP signaling domain.

In this study, we present a conformational landscape of 5000 AlphaFold2 models of the Histidine kinases, Adenyl cyclases, Methyl-accepting proteins and Phosphatases (HAMP) domain, a short helical bundle that transduces signals from sensors to effectors in two-component signaling proteins such as sensory histidine kinases and chemoreceptors. The landscape reveals the conformational variability of the HAMP domain, including rotations, shifts, displacements, and tilts of helices, many combinations of which have not been observed in experimental structures. HAMP domains belonging to a single family tend to occupy a defined region of the landscape, even when their sequence similarity is low, suggesting that individual HAMP families have evolved to operate in a specific conformational range. The functional importance of this structural conservation is illustrated by poly-HAMP arrays, in which HAMP domains from families with opposite conformational preferences alternate, consistent with the rotational model of signal transduction. The only poly-HAMP arrays that violate this rule are predicted to be of recent evolutionary origin and structurally unstable. Finally, we identify a family of HAMP domains that are likely to be dynamic due to the presence of a conserved pi-helical bulge. All code associated with this work, including a tool for rapid sequence-based prediction of the rotational state in HAMP domains, is deposited at https://github.com/labstructbioinf/HAMPpred.

Pressure-Induced Aggregation of Associating Liquids as a Driving Force Enhancing Hydrogen Bond Cooperativity.

The behavior of hydrogen bonds under extreme pressure is still not well understood. Until now, the shift of the stretching vibration band of the X-H group (X = the donor atom) in infrared spectra has been attributed to the variation in the length of the covalent X-H bond. Herein, we combined infrared spectroscopy and X-ray diffraction experimental studies of two H-bonded liquid hexane derivatives, i.e., 2-ethyl-1-hexanol and 2-ethyl-1-hexylamine, in diamond anvil cells at pressures up to the GPa level, with molecular dynamics simulations covering similar thermodynamic conditions. Our findings revealed that the observed changes in the X-H stretching vibration bands under compression are not primarily due to H-bond shortening resulting from increased density but mainly due to cooperative enhancement of H-bonds caused by intensified molecular clustering. This sheds new light on the nature of H-bond interactions and the structure of liquid molecular systems under compression.

Visible-light-induced ATRP under high-pressure: synthesis of ultra-high-molecular-weight polymers.

In this study, a high-pressure-assisted photoinduced atom transfer radical polymerization (p ≤ 250 MPa) enabled the synthesis of ultra-high-molecular-weight polymers (UHMWPs) of up to 9 350 000 and low/moderate dispersity (1.10 < D < 1.46) in a co-solvent system (water/DMSO), without reaction mixture deoxygenation.

Experimental and Computational Approach to Studying Supramolecular Structures in Propanol and Its Halogen Derivatives.

A series of four alcohols, n-propanol and its halogen (Cl, Br, and I) derivatives, were selected to study the effects of variation in polarity and halogen-driven interactions on the hydrogen bonding pattern and supramolecular structure by means of experimental and theoretical methods. It was demonstrated on both grounds that the average strength of H-bonds remains the same but dissociation enthalpy, the size of molecular nanoassemblies, as well as long-range correlations between dipoles vary with the molecular weight of halogen atom. Further molecular dynamics simulations indicated that it is connected to the variation in the molecular order introduced by specific halogen-based hydrogen bonds and halogen-halogen interactions. Our results also provided important experimental evidence supporting the assumption of the transient chain model on the molecular origin of the structural process in self-assembling alcohols.

Mesoporous Matrices as a Promising New Generation of Carriers for Multipolymorphic Active Pharmaceutical Ingredient Aripiprazole.

The enhancement of the properties (i.e., poor solubility and low bioavailability) of currently available active pharmaceutical ingredients (APIs) is one of the major goals of modern pharmaceutical sciences. Among different strategies, a novel and innovative route to reach this milestone seems to be the application of nanotechnology, especially the incorporation of APIs into porous membranes composed of pores of nanometric size and made of nontoxic materials. Therefore, in this work, taking the antipsychotic API aripiprazole (APZ) infiltrated into various types of mesoporous matrices (anodic aluminum oxide, native, and silanized silica) characterized by similar pore diameters (d = 8-10 nm) as an example, we showed the advantage of incorporated systems in comparison to the bulk substance considering the crystallization kinetics, molecular dynamics, and physical stability. Calorimetric investigations supported by the temperature-dependent X-ray diffraction measurements revealed that in the bulk system the recrystallization of polymorph III, which next is converted to the mixture of forms IV and I, is visible, while in the case of confined samples polymorphic forms I and III of APZ are produced upon heating of the molten API with different rates. Importantly, the two-step crystallization observed in thermograms obtained for the API infiltrated into native silica templates may suggest crystal formation by the interfacial and core molecules. Furthermore, dielectric studies enabled us to conclude that there is no trace of crystallization of spatially restricted API during one month of storage at T = 298 K. Finally, we found that in contrast to the crystalline and amorphous bulk samples, all examined confined systems show a logarithmic increase in API dissolution over time (very close to a prolonged release effect) without any sign of precipitation. Our data demonstrated that mesoporous matrices appear to be interesting candidates as carriers for unstable amorphous APIs, like APZ. In addition to protecting them against crystallization, they can provide the desired prolonged release effect, which may increase the drug concentration in the blood (resulting in higher bioavailability). We believe that the "nanostructirization" in terms of the application of porous membranes as a novel generation of drug carriers might open unique perspectives in the further development of drugs characterized by prolonged release.

pLM-BLAST: distant homology detection based on direct comparison of sequence representations from protein language models.

MOTIVATION: The detection of homology through sequence comparison is a typical first step in the study of protein function and evolution. In this work, we explore the applicability of protein language models to this task. RESULTS: We introduce pLM-BLAST, a tool inspired by BLAST, that detects distant homology by comparing single-sequence representations (embeddings) derived from a protein language model, ProtT5. Our benchmarks reveal that pLM-BLAST maintains a level of accuracy on par with HHsearch for both highly similar sequences (with >50% identity) and markedly divergent sequences (with <30% identity), while being significantly faster. Additionally, pLM-BLAST stands out among other embedding-based tools due to its ability to compute local alignments. We show that these local alignments, produced by pLM-BLAST, often connect highly divergent proteins, thereby highlighting its potential to uncover previously undiscovered homologous relationships and improve protein annotation. AVAILABILITY AND IMPLEMENTATION: pLM-BLAST is accessible via the MPI Bioinformatics Toolkit as a web server for searching precomputed databases (https://toolkit.tuebingen.mpg.de/tools/plmblast). It is also available as a standalone tool for building custom databases and performing batch searches (https://github.com/labstructbioinf/pLM-BLAST).

Nature of Dielectric Response of Phenyl Alcohols.

Phenyl alcohols (PhAs) are an interesting class of materials, for which the dielectric response reveals only the presence of single prominent Debye-like (D) relaxation, interpreted as a genuine structural (α) process. Herein, we have performed dielectric and mechanical measurements on a series of PhAs characterized by the varying length of the alkyl chain and found that this interpretation is not valid. Analysis of the derivative of the real part of the complex permittivity together with the mechanical and light scattering data clearly indicated that the prominent dielectric D-like peak is actually a superposition of both cross-correlation between dipole-dipole (D-mode) and self-dipole correlation (α-process) and that the distinguished α-mode exhibits a similar ("generic") shape of PhAs independently to their molecular weight and applied experimental technique. Therefore, the data presented herein contribute to the whole discussion focused on the dielectric response function and universality (or diversity) of the spectral shape of the α-mode of polar liquids.

The Use of a Barley-Based Well to Define Cationic Betaglucan to Study Mammalian Cell Toxicity Associated with Interactions with Biological Structures.

Among potential macromolecule-based pharmaceuticals, polycations seem particularly interesting due to their proven antimicrobial properties and use as vectors in gene therapy. This makes an understanding of the mechanisms of these molecules' interaction with living structures important, so the goal of this paper was to propose and carry out experiments that will allow us to characterize these phenomena. Of particular importance is the question of toxicity of such structures to mammalian cells and, in the work presented here, two lines, normal fibroblasts 3T3-L1 and A549 lung cancer, were used to determine this. In this work, three well-defined cationic derivatives of barley-derived betaglucans obtained in a reaction with glycidyltrimethylammonium chloride (BBGGTMAC) with different degrees of cationization (50, 70, and 100% per one glucose unit) and electrostatic charge were studied. The studies address interactions of these polymers with proteins (bovine serum proteins and BSA), nucleic acids (DNA), glycosaminoglycans (heparin), and biological membranes. The results described in this study make it possible to indicate that toxicity is most strongly influenced by interactions with biological membranes and is closely related to the electrostatic charge of the macromolecule. The presentation of this observation was the goal of this publication. This paper also shows, using fluorescently labeled variants of polymers, the penetration and impact on cell structure (only for the polymer with the highest substitution binding to cell membranes is observed) by using confocal and SEM (for the polymer with the highest degree of substitution, and the appearance of additional structures on the surface of the cell membrane is observed). The labeled polymers are also tools used together with dynamic light scattering and calorimetric titration to study their interaction with other biopolymers. As for the interactions with biological membranes, lipid Langmuir monolayers as model membrane systems were used.

High-pressure studies in the supercooled and glassy state of the strongly associated active pharmaceutical ingredient-ticagrelor.

In this paper, the molecular dynamics at different thermodynamic conditions of hydrogen-bonded (H-bonded) active pharmaceutical ingredient-ticagrelor (TICA) have been investigated. Extensive high-pressure (HP) dielectric studies revealed surprising high sensitivity of the structural (α)-relaxation to compression. They also showed that unexpectedly the shape of the α-peak remains invariable at various temperature (T) and pressure (p) conditions at constant α-relaxation time. Further infrared measurements on the ordinary and pressure densified glasses of the examined compound indicated that the hydrogen-bonding pattern in TICA is unchanged by the applied experimental conditions. Such behavior was in contrast to that observed recently for ritonavir (where the organization of hydrogen bonds varied at high p) and explained the lack of changes in the width of α-dispersion with compression. Moreover, HP dielectric measurements performed in the glassy state of TICA revealed the high sensitivity of the slow secondary (ß)-relaxation (Johari-Goldstein type) to pressure and fulfillment of the isochronal superpositioning of α- and JG-ß-relaxation times. Additionally, it was found that the activation entropy for the ß-process, estimated from the Eyring equation (a high positive value at 0.1 MPa) slightly increases with compression. We suggested that the reason for that are probably small conformational variations of TICA molecules at elevated p.

Studies on Antifungal Properties of Methacrylamido Propyl Trimethyl Ammonium Chloride Polycations and Their Toxicity In Vitro.

The biological activity of polycations is usually associated with their biocidal properties. Their antibacterial features are well known, but in this work, observations on the antifungal properties of macromolecules obtained by methacrylamido propyl trimethyl ammonium chloride (MAPTAC) polymerization are presented. The results, not previously reported, make it possible to correlate antifungal properties directly with the structure of the macromolecule, in particular the molecular mass. The polymers described here have antifungal activity against some filamentous fungi. The strongest effect occurs for polymers with a mass of about 0.5 mDa which have confirmed activity against the multidrug-resistant species Scopulariopsis brevicaulis, Fusarium oxysporum, and Fusarium solani, as well as the dermatophytes Trichophyton mentagrophytes, Trichophyton rubrum, Trichophyton interdigitale, and Trichophyton tonsurans. In addition, this publication describes the effects of these macromolecular systems on serum and blood components and provides a preliminary assessment of toxicity on cell lines of skin-forming cells, i.e., fibroblasts and keratinocytes. Additionally, using a Franz diffusion chamber, a negligibly low transport of the active polymer through the skin was demonstrated, which is a desirable effect for externally applied antifungal drugs. IMPORTANCE Infectious diseases are a very big medical, social, and economic problem. Even before the COVID-19 pandemic, certain infections were among of the most common causes of death. The difficulties in the treatment of infectious diseases concern in particular fungal diseases, against which we have only a few classes of drugs represented by a few substances. The publication presents the preliminary results of the in vitro antifungal activity studies of four MAPTAC polymers on different fungal species and their cytotoxicity to human cells (fibroblasts and keratinocytes). The paper also compares these properties with analogous ones of two commonly used antifungal drugs, ciclopirox and terbinafine.

Studies on the nature and pressure evolution of phase transitions in 1-adamantylamine and 1-adamantanol.

In this paper, several experimental techniques, i.e., differential scanning calorimetry, X-ray diffraction, Fourier transform infrared, Raman, and broadband dielectric spectroscopy were applied to study the nature of the phase transitions in 1-adamantylamine (1-NH2-ADM, C10H17N) and 1-adamantanol (1-OH-ADM, C10H16O). Calorimetric measurements showed one and three endothermic peaks in thermograms for the latter and the former substance, respectively. Indeed, results of spectroscopic investigations indicated that the observed thermal events in 1-NH2-ADM correspond to transitions between various plastic crystal (PC) phases (I, II, III, IV), while the endothermic process in 1-OH-ADM can be assigned to a phase transition between the PC and the ordinary crystal (OC). Especially interesting were the outcomes of dielectric studies carried out both at ambient and high-pressure conditions, during heating and cooling cycles. They showed: i) noticeable changes in the frequency dependencies of the imaginary (ε'') and real (ε') parts of the complex dielectric permittivity that occurred around temperatures of the characteristic endothermic events detected by the calorimetry, and ii) significant fluctuations of ε'' and ε' at pressures attributed to the respective phase transitions. Moreover, the pressure coefficients of the phase transition temperatures were estimated to be approximately equal to 0.2 K/MPa for both compounds. In turn, volume variation (ΔV) at the PC (II)-PC (III) and PC (III)-PC (IV) transition temperatures for 1-NH2-ADM was essentially different than ΔV for the PC-OC transition in 1-OH-ADM.

On the relationship between the Debye process in dielectric response and a dissociation-association phenomenon in phenyl alcohols.

In this paper, we have examined a series of phenyl-substituted primary monohydroxy alcohols (phenyl alcohols, PhAs), from ethanol to hexanol by means of dielectric and Fourier transform infrared (FTIR) spectroscopies supported by the mechanical investigations. The combination of both dielectric and mechanical data allows calculation of the energy barrier, Ea, for dissociation by the Rubinstein approach developed to describe the dynamical properties of self-assembling macromolecules. It was observed that the determined activation energy remains constant, |Ea,RM| ∼ 12.9-14.2 kJ mol-1, regardless of the molecular weight of the examined material. Surprisingly, the obtained values agree very well with Ea of the dissociation process determined from the FTIR data analysed within the van't Hoff relationship, where Ea,vH ∼ 9.13-13.64 kJ mol-1. Thus, the observed agreement between Ea determined by both applied approaches clearly implies that in the case of the examined series of PhAs, the dielectric Debye-like process is governed by the association-dissociation phenomenon as proposed by the transient chain model.

Biological Properties of Heparins Modified with an Arylazopyrazole-Based Photoswitch.

Unfractionated heparin (UFH) and enoxaparin (Enox) were substituted with a photoswitch (PS) showing quantitative trans-cis and cis-trans photoisomerizations. Long half-life of the cis photoisomer enabled comparison of the properties of heparins substituted with both PS photoisomers. Hydrodynamic diameter, Dh, of UFH-PS decreased upon trans-cis photoisomerization, the change being more pronounced for UFH-PS with a higher degree of substitution (DS), while Dh of Enox-PS did not significantly change. The anticoagulative properties of substituted heparins were significantly attenuated compared to non-substituted compounds. The interaction of UFH-PS with HSA, lysozyme, and protamine was studied with ITC. Under serum-free conditions, UFH-PS-trans with a high DS stimulated proliferation of murine fibroblasts, while UFH-PS-cis decreased the viability of these cells. Under serum conditions, both UFH-PS-cis and UFH-PS-trans decreased cell viability, the reduction for UFH-PS-cis being higher than that for UFH-PS-trans. Neither Enox-PS-trans nor Enox-PS-cis influenced the viability at concentrations prolonging aPTT, while at higher concentrations their cytotoxicity did not differ.

Studying the Intermolecular Interactions, Structural Dynamics, and Non-Equilibrium Kinetics of Cilnidipine Infiltrated into Alumina and Silica Pores.

In the present study, the behavior of the calcium channel blocker cilnidipine (CLN) infiltrated into silica (SiO2) and anodic aluminum oxide (AAO) porous membranes characterized by a similar pore size (d = 8 nm and d = 10 nm, respectively) as well as the bulk sample has been investigated using differential scanning calorimetry, broadband dielectric spectroscopy (BDS), and Fourier-transform infrared spectroscopy (FTIR) techniques. The obtained data suggested the existence of two sets of CLN molecules in both confined systems (core and interfacial). They also revealed the lack of substantial differences in inter- and intramolecular dynamics of nanospatially restricted samples independently of the applied porous membranes. Moreover, the annealing experiments (isothermal time-dependent measurements) performed on the confined CLN clearly indicated that the whole equilibration process under confinement is governed by structural relaxation. It was also found that the ßanneal parameters obtained from BDS and FTIR data upon equilibration of both confined samples are comparable (within 10%) to each other, while the equilibration constants are significantly different. This finding strongly emphasizes that there is a close connection between the inter- and intramolecular dynamics under nanospatial restriction.

Automatic Speaker Recognition System Based on Gaussian Mixture Models, Cepstral Analysis, and Genetic Selection of Distinctive Features.

This article presents the Automatic Speaker Recognition System (ASR System), which successfully resolves problems such as identification within an open set of speakers and the verification of speakers in difficult recording conditions similar to telephone transmission conditions. The article provides complete information on the architecture of the various internal processing modules of the ASR System. The speaker recognition system proposed in the article, has been compared very closely to other competing systems, achieving improved speaker identification and verification results, on known certified voice dataset. The ASR System owes this to the dual use of genetic algorithms both in the feature selection process and in the optimization of the system's internal parameters. This was also influenced by the proprietary feature generation and corresponding classification process using Gaussian mixture models. This allowed the development of a system that makes an important contribution to the current state of the art in speaker recognition systems for telephone transmission applications with known speech coding standards.

Fast THz-TDS Reflection Imaging with ECOPS-Point-by-Point versus Line-by-Line Scanning.

We built a high-speed TDS setup with the use of electronically controlled optical sampling (ECOPS), which can measure up to 1600 terahertz pulses per second. The movement of the sample was provided by two fast-speed motorized linear stages constituting the gantry. We developed a flat-bar-based metal marker approach for the synchronization of continuous line-by-line scans. We carefully compared the performance of the terahertz reflection time-domain spectroscopy (TDS) scanner operating in a slow point-by-point and a one-hundred-times faster line-by-line imaging scheme. We analyzed images obtained for both schemes for a uniform metallic breadboard with holes, as well as a glass composite sample with defects. Although the measurement time was reduced by 100 times in terms of the line-by-line scheme, the overall performance in both schemes was almost identical in terms of the defects' sizes, shapes and locations. The results proved that the proposed ECOPS TDS system can provide uniform and extremely fast scanning without any deterioration in image quality.