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1. The impact of interface modification on the behavior of phenyl alcohols within silica templates

Author

Soszka, Natalia, Tarnacka, Magdalena, Hachula, Barbara, Geppert-Rybczynska, Monika, Prusik, Krystian, and Kaminski, Kamil

Subjects
Condensed Matter - Mesoscale and Nanoscale Physics
Abstract

Herein, thermal, dynamical properties, host-guest intermolecular interactions, and wettability of a series of monohydroxy phenyl-substituted alcohols (PhAs) infiltrated into native and silanized silica mesopores (d = 4 nm) were investigated by means of Dielectric and Infrared (IR) Spectroscopy, Differential Scanning Calorimetry as well as the contact angle measurements. Calorimetric data showed the occurrence of the two glass transition temperatures, Tg. Importantly, around the one detected at higher temperatures (Tg interfacial), strong deviation in the temperature evolution of the relaxation time of the main process was observed for all systems. Moreover, an additional process unrelated to the mobility of interface layer and core molecules was revealed most likely connected to either SAP or "new" confinement-induced nanoassociates. Further, IR investigations showed that the applied nanoconfinement had little impact on hydrogen bonds' strength, but it influenced the HBs distribution (including "new" population of HB) and the degree of association. Additionally, for the first time, we calculated the activation energy values of the dissociation process for PhAs in mesopores, which turned out to be lower with respect to those estimated for bulk samples. Thus, our research clearly showed the impact of the spatial geometrical restriction on the association process in alcohols having significant steric hindrance.

Published
2023

2. Is there a relationship between wettability and rates of equilibration of the H-bonded oligomer PMMS under confinement?

Author

Zimny, Sara, Tarnacka, Magdalena, Geppert-Rybczyńska, Monika, and Kamiński, Kamil

Subjects
Condensed Matter - Mesoscale and Nanoscale Physics, Physics - Chemical Physics
Abstract

In this paper, we investigated the annealing experiments of poly(mercaptopropylmethylsiloxane, PMMS) confined within two types of porous templates (anodic aluminium oxide, AAO, and silica) characterized by different pore diameter, d= 8-120nm, using different thermal protocols (varying significantly in cooling/heating rate) by means of Broadband Dielectric Spectroscopy (BDS) supported by the complementary Differential Scanning Calorimetry (DSC) and temperature-dependent contact angle, {\theta}, measurements. It was found that relaxation times obtained from routine temperature-dependent dielectric investigations deviate from the bulk behavior when approaching the glass transition temperature. Importantly, this confinement induced effect can be easily removed by the annealing experiments performed at some specific range of temperatures. The analysis of the dielectric data collected during isothermal experiments of confined samples that was beforehand cooled with different rates revealed that (i) constant rates of annealing gets longer with cooling and weakly depend on the rate of cooling, and (ii) activation energy of the equilibration process, E_a, varies with the reduction of the pore diameter and material the porous template is made of. In fact, there is significant reduction in E_a from ~62 to ~23 kJ/mol obtained for the annealing process carried out in AAO (d= 10 nm) and silica (d= 8 nm) membranes, respectively. Such significant change in E_a can be explained taking into account temperature-dependence of {\theta} of PMMS indicating a notable change in wettability between both surfaces upon cooling. As a consequence, one can expect that the mass exchange between interfacial and core molecules as well as adsorption-desorption processes occurring at the interface at lower temperatures must be affected.

Published
2023

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

Author

Łucak, Kinga, primary, Szeremeta, Anna Z., additional, Wrzalik, Roman, additional, Grelska, Joanna, additional, Jurkiewicz, Karolina, additional, Soszka, Natalia, additional, Hachuła, Barbara, additional, Kramarczyk, Daniel, additional, Grzybowska, Katarzyna, additional, Yao, Beibei, additional, Kamiński, Kamil, additional, and Pawlus, Sebastian, additional

Published
2023
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32. High-pressure studies in the supercooled and glassy state of the strongly associated active pharmaceutical ingredient—ticagrelor.

Author

Jesionek, Paulina, Heczko, Dawid, Hachuła, Barbara, Kamiński, Kamil, and Kamińska, Ewa

Subjects
TICAGRELOR, DIELECTRIC measurements, MOLECULAR dynamics, HYDROGEN bonding, PRESSURE measurement
Abstract

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 (β)-relaxation (Johari–Goldstein type) to pressure and fulfillment of the isochronal superpositioning of α- and JG-β-relaxation times. Additionally, it was found that the activation entropy for the β-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. [ABSTRACT FROM AUTHOR]

Published
2023
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36. Influence of Annealing in the Close Vicinity of Tg on the Reorganization within Dimers and Its Impact on the Crystallization Kinetics of Gemfibrozil

Author

Kamińska, Ewa, Minecka, Aldona, Tarnacka, Magdalena, Hachuła, Barbara, Kamiński, Kamil, and Paluch, Marian

Subjects
Ritonavir, Calorimetry, Differential Scanning, chemical modifications, Hydrogen Bonding, HIV Protease Inhibitors, Molecular Dynamics Simulation, Article, Phase Transition, Kinetics, Absorption, Physicochemical, amorphous state, gemfibrozil, Dielectric Spectroscopy, Spectroscopy, Fourier Transform Infrared, H-bonds, dimeric structures, Transition Temperature, crystallization kinetics, Glass, Crystallization, Dimerization, Hypolipidemic Agents
Abstract

In this paper, broadband dielectric spectroscopy (BDS) has been applied to study the molecular dynamics and crystallization kinetics of the antihyperlipidemic active pharmaceutical ingredient (API), gemfibrozil (GEM), as well as its deuterated (dGEM) and methylated (metGEM) derivatives, characterized by different types and strengths of intermolecular interactions. Moreover, calorimetric and infrared measurements have been carried out to characterize the thermal properties of examined samples and to probe a change in the H-bonding pattern in GEM, respectively. We found that the dielectric spectra of all examined compounds, collected below the glass transition temperature (Tg), reveal the presence of two secondary relaxations (β, γ). According to the coupling model (CM) predictions, it was assumed that the slower process (β) is of JG type, whereas the faster one (γ) has an intramolecular origin. Interestingly, the extensive crystallization kinetics measurements performed after applying two paths, i.e., the standard procedure (cooling and subsequently heating up to the appropriate temperature, Tc), as well as annealing at two temperatures in the vicinity of Tg and further heating up to Tc, showed that the annealing increases the crystallization rate in the case of native API, while the thermal history of the sample has no significant impact on the pace of this process in the two derivatives of GEM. Analysis of the dielectric strength (Δε) of the α-process during annealing, together with the results of Fourier transform infrared spectroscopy (FTIR) measurements, suggested that the reorganization within dimeric structures formed between the GEM molecules is responsible for the observed behavior. Importantly, our results differ from those obtained by Tominaka et al. (TominakaS.; KawakamiK.; FukushimaM.; MiyazakiA.Physical Stabilization of Pharmaceutical Glasses Based on Hydrogen Bond Reorganization under Sub-Tg TemperatureMol. Pharm.20171426427310.1021/acs.molpharmaceut.6b00866.28043129), who demonstrated that the sub-Tg annealing of ritonavir (RTV), which is able to form extensive supramolecular hydrogen bonds, protects this active substance against crystallization. Therefore, based on these contradictory reports, one can hypothesize that materials forming H-bonded structures, characterized by varying architecture, may behave differently after annealing in the vicinity of the glass transition temperature.

Published
2020

37. Self-Organized Nanoparticles of Random and Block Copolymers of Sodium 2-(acrylamido)-2-methyl-1-propanesulfonate and Sodium 11-(acrylamido)undecanoate as Safe and Effective Zika Virus Inhibitors

Author

Botwina, Pawel, primary, Obłoza, Magdalena, additional, Zatorska-Płachta, Maria, additional, Kamiński, Kamil, additional, Mizusaki, Masanobu, additional, Yusa, Shin-Ichi, additional, Szczubiałka, Krzysztof, additional, Pyrc, Krzysztof, additional, and Nowakowska, Maria, additional

Published
2022
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50. Rossmann-toolbox: a deep learning-based protocol for the prediction and design of cofactor specificity in Rossmann fold proteins.

Author

Kamiński, Kamil, Ludwiczak, Jan, Jasiński, Maciej, Bukala, Adriana, Madaj, Rafal, Szczepaniak, Krzysztof, and Dunin-Horkawicz, Stanisław

Subjects
*DEEP learning, *PROTEIN folding, *NICOTINAMIDE adenine dinucleotide phosphate, *FLAVIN adenine dinucleotide, *AMINO acid metabolism, *NICOTINAMIDE, *OXIDOREDUCTASES, *FLAVOPROTEINS
Abstract

The Rossmann fold enzymes are involved in essential biochemical pathways such as nucleotide and amino acid metabolism. Their functioning relies on interaction with cofactors, small nucleoside-based compounds specifically recognized by a conserved βαβ motif shared by all Rossmann fold proteins. While Rossmann methyltransferases recognize only a single cofactor type, the S-adenosylmethionine, the oxidoreductases, depending on the family, bind nicotinamide (nicotinamide adenine dinucleotide, nicotinamide adenine dinucleotide phosphate) or flavin-based (flavin adenine dinucleotide) cofactors. In this study, we showed that despite its short length, the βαβ motif unambiguously defines the specificity towards the cofactor. Following this observation, we trained two complementary deep learning models for the prediction of the cofactor specificity based on the sequence and structural features of the βαβ motif. A benchmark on two independent test sets, one containing βαβ motifs bearing no resemblance to those of the training set, and the other comprising 38 experimentally confirmed cases of rational design of the cofactor specificity, revealed the nearly perfect performance of the two methods. The Rossmann-toolbox protocols can be accessed via the webserver at https://lbs.cent.uw.edu.pl/rossmann-toolbox and are available as a Python package at https://github.com/labstructbioinf/rossmann-toolbox. [ABSTRACT FROM AUTHOR]

Published
2022
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