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Search results for: molecular interactions
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Elucidating of oxidative distress in COVID-19 and methods of its prevention
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Protective effect of Aronia melanocarpa polyphenols against cadmium-induced disorders in bone metabolism: A study in a rat model of lifetime human exposure to this heavy metal
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Aqueous solutions of NMA, Na2HPO4 , and NaH2PO4 as models for interaction studies in phosphate–protein systems
PublicationPhosphate buffers are essential for many areas of studies. However, their influence on buffered systems is often ignored. The phosphate salts can interact with biologically important macromolecules (e.g. proteins) and stabilize or destabilize them. With our research, we want to answer question what kind of interactions, if any, occur between phosphate ions and a protein backbone model — N-methylacetamide (NMA). ATR-FTIR spectroscopy...
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Syntheses, spectroscopic and structural properties of phenoxysilyl compounds: X-ray structures, FT-IR and DFT calculations
PublicationThe reaction of silicon disulfide with alkylphenols leads to tetraphenoxysilane, cyclodisilthiane and silanethiol. The products of the reaction of silicon disulfide with phenols are characterized by FT-IR, NMR, X-ray diffraction and DFT calculations. The intramolecular interactions in the compounds are mainly XH---π (X = C, S) whereas the intermolecular interactions are either very weak CH---π/CH---O contacts found in aryloxysilane...
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Amides as models to study the hydration of proteins and peptides — spectroscopic and theoretical approach on hydration in various temperatures
PublicationInteractions with water are one of the key factors which determine protein stability and activity in aqueous solutions. However, the protein hydration is still insufficiently understood. N-methylacetamide (NMA) is regarded as a minimal part of the peptide backbone and the relative simplicity of its structure makes it a good model for studies on protein–water interactions. In this paper, the influence of NMA and N,N-dimethylacetamide...
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Weak hydrogen bonding interaction S-H···O=C studied by FT-IR spectroscopy and DFT calculations
PublicationInteractions between the thiolate group of tri-tert-butoxysilanethiol (TBST) and carbonyl group of acetone are studied with the use of FT-IR spectroscopy and DFT calculations.
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Cooperation of mono- and bi-articular muscles: human lower limb
PublicationObjectives: The aim of this study was to create and analyze a Pareto-optimal problem that would describe cooperation between mono- and bi-articulate lower limb muscles in sagittal plane. Methods: Equations describing the problem were derived and analyzed, additional constrains were introduced and experimental verification based on gait video analysis was performed. Results: Uncertainty of Pareto-optimal solution is shown for the...
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The hydration of selected biologically relevant molecules – the temperature effect on apparent molar volume and compression
PublicationThe densities and sound velocities at T = (288.15, 293.15, 298.15, 303.15 and 308.15) K were measured for aqueous solutions of glycine, trimethylamine-N-oxide, taurine and N-methylacetamide. From these data, the apparent molar volumes, V the apparent molar isentropic compressions, KS,, and the Passynski hydration numbers of solutes were determined. The concentration dependencies of the calculated quantities, their limiting values...
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Novel 2-(2-arylmethylthio-4-chloro-5-methylbenzenesulfonyl)-1-(1,3,5-triazin-2-ylamino)guanidine derivatives: Inhibition of human carbonic anhydrase cytosolic isozymes I and II and the transmembrane tumor-associated isozymes IX and XII, anticancer activity, and molecular modeling studies
PublicationA series of novel 2-(2-arylmethylthio-4-chloro-5-methylbenzenesulfonyl)-1-(6-substituted-4-chloro-1,3,5-triazin-2-ylamino)guanidine derivatives 9–20 have been synthesized by substitution of chlorine atom at the 1,3,5-triazine ring in compounds 5–8 with 3- or 4-aminobenzenesulfonamide and 4-(aminomethyl)benzenesulfonamide hydrochloride. All the synthesized compounds were evaluated for their inhibitory activity toward hCA I, II,...
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Quantum-classical calculations of the nanomechanical properties of metals
PublicationTradycyjnie symulacje komputerowe układów w skali atomowej prowadzone są przy użyciu klasycznej metody dynamiki molekularnej (MD) bądź kwantowych metod ab initio. Główną wadą ujęcia klasycznego jest jego empiryczna natura, a co za tym idzie - niewielka przenośność, jego prostota natomiast pozwala na przeprowadzanie symulacji układów zawierających miliony atomów. W wyniku zastosowania metod kwantowych otrzymuje się bardziej wiarygodne...
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Simplified AutoDock force field for hydrated binding sites
Publicationhas been extracted from the Protein Data Bank and used to test and recalibrate AutoDock force field. Since for some binding sites water molecules are crucial for bridging the receptor-ligand interactions, they have to be included in the analysis. To simplify the process of incorporating water molecules into the binding sites and make it less ambiguous, new simple water model was created. After recalibration of the force field on...
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Jahn-Teller and related conical intersections in the benzene radical cation and the monofluoro derivate
PublicationThe multi-state multi-mode vibronic interactions in the benzene radical cation and its monofluoro derivative have been investigated theoretically, based on high-level electronic structure calculations for the system parameters and a quantum treatment of the nuclear motion. The available experimental data are well reproduced. The interplay of different vibronic coupling mechanisms is pointed out leading to multiple nonadiabatic...
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Thermodynamic study of binary mixtures of toluene with ionic liquids, 1-butyl-1-methylpyrrolidinium bis(trifluoromethylsulfonyl)imide, 1-hexyl-1-methylpyrrolidinium bis(trifluoromethylsulfonyl)imide and 1-butylpyridinium bis(trifluoromethylsulfonyl)imide
PublicationDensities, refractive indices and viscosities at 293.15, 298.15, 303.15, 308.15 and 313.15 K of binary mixtures of toluene with 1-butyl-1-methylpyrrolidinium bis(trifluoromethylsulfonyl)imide, 1-hexyl-1-methylpyrrolidinium bis(trifluoromethylsulfonyl)imide and 1-butylpyridinium bis(trifluoromethylsulfonyl)imide have been measured over the miscible region at p = 0.1 MPa. From the experimental data, values of excess molar volume,...
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Interfacial water controls the process of adsorption of hyperactive antifreeze proteins onto the ice surface
PublicationA mechanism of interactions between the ice-binding surface of a hyperactive antifreeze protein molecule and the ice surface is proposed, involving the influence of water present between the two surfaces on the behavior of the approaching molecule. It is demonstrated that the interfacial water, even before its full solidification, can act as a factor that pushes away or pulls nearer the protein molecule to ensure its proper positioning....
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Effect of choline chloride based natural deep eutectic solvents on aqueous solubility and thermodynamic properties of acetaminophen
PublicationIn this work, natural deep eutectic solvents (NADESs) containing choline chloride as hydrogen bond acceptor and 1,2-propanediol, malic acid and tartaric acid as hydrogen bond donors have been synthesized and applied to enhance the aqueous solubility of model sparingly water-soluble drug – acetaminophen. The results indicate that the greatest impact on the solubility of acetaminophen have deep eutectic solvents based on 1,2-propanediol...
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Extractive detoxification of feedstocks for the production of biofuels using new hydrophobic deep eutectic solvents – Experimental and theoretical studies
PublicationThe paper presents a synthesis of novel hydrophobic deep eutectic solvents (DESs) composed of natural components, which were used for removal of furfural (FF) and 5-hydroxymethylfurfural (HMF) from lignocellulosic hydrolysates. The main physicochemical properties of DESs were determined, followed by explanation of the DES formation mechanism, using 1H NMR, 13C NMR and FT-IR analysis and density functional theory (DFT). The most...
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Effect of urea and glycine betaine on the hydration sphere of model molecules for the surface features of proteins
PublicationWater properties may significantly affect protein stability. Osmolytes are compounds that intrinsically affect water in many different ways and thus can influence proteins with this type of indirect mechanism. In this study, we characterize water properties in ternary solutions: model–water–osmolyte, with two model molecules: N-methylacetamide (NMA) and dimethyl sulfoxide (DMSO) and two osmolytes: glycine betaine (TMG)and urea....
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Investigation of tetrabutylammonium bromide-glycerol-based deep eutectic solvents and their mixtures with water by spectroscopic techniques
PublicationDeep eutectic solvents (DES) are formed by an acceptor and a donor of hydrogen bonds. They are generally considered as a possible alternative to hazardous organic solvents in various fields. Very recently they have also appeared in analytical chemistry, used mainly for the separation of analytes before instrumental quantification. For the development of new extraction procedures, it is important, among other things, to understand...
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Vapor correction of FTIR spectra – A simple automatic least squares approach
PublicationFTIR spectroscopy is one of the best techniques to study intermolecular interactions. However, such an application requires high quality spectra with as little noise as possible, which are often difficult to obtain. One of the main sources of unwanted interference is water vapor. Here a robust method is proposed for automatic, fast and reliable vapor correction of FTIR spectra. The presented least squares approach of vapor subtraction...
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Structural analysis and physico-chemical characterization of mononuclear manganese(II) and polynuclear copper(II) complexes with pyridine-based alcohol
PublicationTwo novel manganese(II) and copper(II) complexes, mononuclear [Mn(H2O)2(2-(CH2)2OHpy)2](NO3)2 (1) and polynuclear [Cu(SO4)(2-(CH2)2OHpy)2]n (2), based on 2-(hydroxyethyl)pyridine (2-(CH2)2OHpy) were synthesised and fully characterised using X-ray structure analysis as well as spectroscopic, magnetic and thermal methods. Both central metal ions Mn(1) and Cu(1) are coordinated by two N,O-donor 2-(CH2)2OHpy ligands and possess an...
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Solvent dependency of carbon dioxide Henry's constant in aqueous solutions of choline chloride-ethylene glycol based deep eutectic solvent
PublicationThe Henry's constants of carbon dioxide absorbed in aqueous solutions of ethaline (choline chloride-ethylene glycol) were determined for temperatures ranging from 303.15 to 323.15 K based on solubility measurement at CO2 pressure ranging from 0 to 6 bar (0.6 MPa). These studies revealed that the Henry's constant increased with the increase of temperature. Data indicated the highest capacity of CO2 absorption is obtained for ethaline...
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On the origin of surface imposed anisotropic growth of salicylic and acetylsalicylic acids crystals during droplet evaporation
PublicationIn this paper droplet evaporative crystallization of salicylic acid (SA) and acetylsalicylic acid (ASA) crystals on different surfaces, such as glass, polyvinyl alcohol (PVA), and paraffin was studied. The obtained crystals were analyzed using powder X-ray diffraction (PXRD) technique. In order to better understand the effect of the surface on evaporative crystallization, crystals deposited on glass were scraped off. Moreover,...
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Magnetic deep eutectic solvents as efficient media for extraction of furfural and 5-hydroxymethylfurfural from aqueous samples
PublicationThe extraction of furfural (FF) and 5-hydroxymethylfurfural (HMF) from hydrolysates is currently one of the main challenges in bio-refinery. In this work, the separation of FF and HMF from the aqueous phase was carried out using a new type of green solvents – Magnetic Deep Eutectic Solvents (MDES). A conductor-like screening model for realistic solvents (COSMO-RS) was used for the preselection of 400 MDES. MDES which exhibit the...
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Exploring the cocrystallization potential of urea and benzamide
PublicationThe cocrystallization landscape of benzamide and urea interacting with aliphatic and aromatic carboxylic acids was studied both experimentally and theoretically. Ten new cocrystals of benzamide were synthesized using an oriented samples approach via a fast dropped evaporation technique. Information about types of known bi-component cocrystals augmented with knowledge of simple binary eutectic mixtures was used for the analysis...
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Enhanced Activity of P4503A4 and UGT1A10 Induced by Acridinone Derivatives C-1305 and C-1311 in MCF-7 and HCT116 Cancer Cells: Consequences for the Drugs’ Cytotoxicity, Metabolism and Cellular Response
PublicationActivity modulation of drug metabolism enzymes can change the biotransformation of chemotherapeutics and cellular responses induced by them. As a result, drug-drug interactions can be modified. Acridinone derivatives, represented here by C-1305 and C-1311, are potent anticancer drugs. Previous studies in non-cellular systems showed that they are mechanism-based inhibitors of cytochrome P4503A4 and undergo glucuronidation via UDP-glucuronosyltranspherase...
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Potential of Silver Nanoparticles in Overcoming the Intrinsic Resistance of Pseudomonas aeruginosa to Secondary Metabolites from Carnivorous Plants
PublicationCarnivorous plants are exemplary natural sources of secondary metabolites with biological activity. However, the therapeutic antimicrobial potential of these compounds is limited due to intrinsic resistance of selected bacterial pathogens, among which Pseudomonas aeruginosa represents an extreme example. The objective of the study was to overcome the intrinsic resistance of P. aeruginosa by combining silver nanoparticles (AgNPs)...
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Effect of ectoine on hydration spheres of peptides–spectroscopic studies
PublicationIn this paper, we use FTIR spectroscopy to characterize the hydration water of ectoine, its interactions with two peptides–diglycine and NAGMA, and the properties of water molecules in the hydration spheres of both peptides changed by the presence of the osmolyte. We found that the interaction of ectoine with the peptide hydration shells had no effect on its own hydration sphere. However, the enhanced hydration layer of the osmolyte...
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Effect of temperature and composition on physical properties of deep eutectic solvents based on 2-(methylamino)ethanol – measurement and prediction
PublicationNovel deep eutectic solvents were synthesized using 2-(methylamino)ethanol as hydrogen bond donor with tetrabutylammonium bromide or tetrabutylammonium chloride or tetraethylammonium chloride as hydrogen bond acceptors. Mixtures were prepared at different molar ratios of 1:6, 1:8 and 1:10 salt to alkanolamine and then Fourier Transform Infrared Spectroscopy measurements were performed to confirm hydrogen bonds interactions between...
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Solvent Screening for Solubility Enhancement of Theophylline in Neat, Binary and Ternary NADES Solvents: New Measurements and Ensemble Machine Learning
PublicationTheophylline, a typical representative of active pharmaceutical ingredients, was selected to study the characteristics of experimental and theoretical solubility measured at 25 °C in a broad range of solvents, including neat, binary mixtures and ternary natural deep eutectics (NADES) prepared with choline chloride, polyols and water. There was a strong synergistic effect of organic solvents mixed with water, and among the experimentally...
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New Carvone-Based Deep Eutectic Solvents for Siloxanes Capture from Biogas
PublicationDuring biogas combustion, siloxanes form deposits of SiO2 on engine components, thus shortening the lifespan of the installation. Therefore, the development of new methods for the purification of biogas is receiving increasing attention. One of the most effective methods is physical absorption with the use of appropriate solvents. According to the principles of green engineering, solvents should be biodegradable, non-toxic, and...
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Conserved motifs of MutL proteins
PublicationtThe MutL protein is best known for its function in DNA mismatch repair (MMR). However, there isevidence to suggest that MutL is not only the linker connecting the functions of MutS and MutH in MMR,but that it also participates in other repair systems, such as Very Short Patch (VSP), Base Excision (BER)and Nucleotide Excision Repair (NER). This study set out to identify the most highly conserved aminoacid sequence motifs in MutL...
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Individual contributions of M X-ray line from Cu- and Co-like tungsten ions and L X-ray line from Ne-like molybdenum ions – Benchmarks for new approach to determine the high-temperature tokamak plasma parameters
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Energy shift of the Lβ2 line as an ionization diagnostic for the dense plasma in the PFRP
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Modeling of soft N, M and L X-ray lines from tungsten relevant to plasma parameters in the WEST tokamak
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Elastic cross-section calculations for electron collisions with XY4 (X=Si,Ge; Y=H, F, Cl, Br, I) molecules
PublicationObliczano elastyczne przekroje czynne dla tetraedrycznych związków krzemu i germanu. Otrzymane wyniki porównano z innymi dostępnymi wynikami obliczeń oraz z danymi doświadczalnymi; dla energii powyżej 100 eV uzyskano zadowalającą zgodność.
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Theoretical Auger and photoionization studies for open shell atoms andions.
PublicationWykorzystano program komputerowy RATIP do badań własności atomów i jonów o dowolnej konfiguracji. Położono nacisk na obliczenia szeregu własności elektronów Augera i fotojonizacji, aby dokonać porównań z ostatnio wykonywanymi doświadczeniami.
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Dissolution of Nb-doped hydroxyapatite prepared via low-temperature mechanochemical method: Spectroscopy studies
PublicationCalcium phosphate glass ceramics with nominal hydroxyapatite stoichiometry doped with niobium were synthesized using simple as well as low-temperature mechanochemical method and then in the form of compressed pellet were submitted to the static dissolution process in distilled water for one month. The results of structural analysis, performed mainly on the base of spectroscopic methods such as: infrared absorption spectroscopy,...
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Nano-structured Pt embedded in acidic salts of heteropolymolybdate matrices: MS EXAFS study
PublicationA structural study of Pt nano-catalysts is presented in the paper. The innovation in the case of the considered catalytic materials resides in the use a meso-microporous inorganic matrix of heteropolyacid salt of composition X2.5H0.5YMo12O40 where X = Rb, Cs and Y = P, Si as a catalyst support. Metallic nanoparticles were created by platinum ions reduction in a hot H2/Argon stream and were mainly located into matrix pores. As the...
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Storing Matter’technique in SIMS depth profile analysis
PublicationSecondary ion mass spectrometry (SIMS) is a very useful technique for the analysis of layered systems. It is based on the primary ion beam sputtering of solids and mass analysis of the emitted secondary ions. A main limitation of this technique results from the direct quantitative analysis, since the ionization efficiency of a given atom is highly influenced by the neighbouring atoms at the surface. This phenomenon is known as...
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Annihilation rates of low-energy positron scattering from simple diatomic molecules
PublicationWe discuss the calculations of Zeff coefficients for a series of diatomic molecules over the range of energies below the positronium formation. During the development of a general code for polyatomic, nonlinear molecules colliding with positrons, it was discovered that the earlier one, employed only for diatomic molecules, had an error. The error is corrected and the corrected results are presented here. We also discuss a way of...
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Correlation–polarization effects in electron/positron scattering from acetylene: A comparison of computational models
PublicationDifferent computational methods are employed to evaluate elastic (rotationally summed) integral and differential cross sections for low energy (below about 10 eV) positron scattering off gas-phase C2H2 molecules. The computations are carried out at the static and static-plus-polarization levels for describing the interaction forces and the correlation–polarization contributions are found to be an essential component for the correct...
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A natural deep eutectic solvent - protonated L-proline-xylitol - based stationary phase for gas chromatography
PublicationThe paper presents a new kind of stationary phase for gas chromatography based on deep eutectic solvents (DES) in the form of a mixture of L-proline (protonated with hydrochloric acid) as a hydrogen bond acceptor (HBA) and xylitol as a hydrogen bond donor (HBD) in a molar ratio of HBA:HBD 5:1. DES immobilized on a silanized chromatographic support was tested by gas chromatography (GC) in order to determine its resolving power for...
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Tuning Ferulic Acid Solubility in Choline-Chloride- and Betaine-Based Deep Eutectic Solvents: Experimental Determination and Machine Learning Modeling
PublicationDeep eutectic solvents (DES) represent a promising class of green solvents, offering particular utility in the extraction and development of new formulations of natural compounds such as ferulic acid (FA). The experimental phase of the study undertook a systematic investigation of the solubility of FA in DES, comprising choline chloride or betaine as hydrogen bond acceptors and six different polyols as hydrogen bond donors....
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Rengel Cane Sia Doctoral Candidate
PeopleI’m Rengel, born and raised in the Philippines. As an undergraduate I did kinetic modeling on Copper-catalyzed atom transfer radical addition (ATRA). Then I was inspired to do both theoretical and experimental studies, which led me to propose my master’s thesis on Synthesis, Computational, Electrochemical, and Photoconductivity Studies on Naphthalene and its derivatives. This led to a master’s degree in Chemistry in the Mindanao...