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Wyniki wyszukiwania dla: hydration, noncovalent interactions, urea, macromolecules,water
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Hydration of amino acids: FTIR spectra and molecular dynamics studies
PublikacjaThe hydration of selected amino acids, alanine, glycine, proline, valine, isoleucine and phenylalanine, has been studied in aqueous solutions by means of FTIR spectra of HDO isotopically diluted in H2O. The difference spectra procedure and the chemometric method have been applied to remove the contribution of bulk water and thus to separate the spectra of solute-affected HDO. To support interpretation of obtained spectral results,...
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General Mechanism of Osmolytes’ Influence on Protein Stability Irrespective of the Type of Osmolyte Cosolvent
PublikacjaThe stability of proteins in an aqueous solution can be modified by the presence of osmolytes. The hydration sphere of stabilizing osmolytes is strikingly similar to the enhanced hydration sphere of a protein. This similarity leads to an increase in the protein stability. Moreover, the hydration sphere of destabilizing osmolytes is significantly different. These solutes generate in their surroundings so-called “structurally different...
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Electrical conductivity relaxation measurements - water uptake of BaCe0.6Zr0.2Y0.1Tb0.1O3-δ
Dane BadawczeFor Electrical Conductivity Relaxation (ECR) measurements, platinum reversible electrodes were applied in a four-probe arrangement and the BaCe0.6Zr0.2Y0.1Tb0.1O3-δ sample was measured in the ProboStat™ measurement system. The ECR measurements were performed in air in the temperature range of 450-800 ℃ after switching water partial pressure between...
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Understanding ion–ion and ion–solvent interactions in aqueous solutions of morpholinium ionic liquids with N-acetyl-L-alaninate anion through partial molar properties and molecular dynamics simulations
PublikacjaAmino acid ionic liquids (AAILs) provide a low toxicity, biodegradable alternative to conventional ionic liquids, while also maintaining solubility in water. Densities and sound velocities of aqueous solutions of four amino acid ionic liquids (AAILs), based on the N-alkyl-N-methylmorpholinium ([Mor1,R], R = 2, 3, 6, 8) cation and N-acetyl-L-alaninate ([N-Ac-L-Ala]) anion were measured at T = (293.15–313.15) K and at atmospheric...
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Systematic Water Uptake Energetics of Yttrium-Doped Barium Zirconate—A High Resolution Thermochemical Study
PublikacjaA combination of surface area analyzer and microcalorimetry was employed to investigate the in situ water uptake energetics and the mechanism of proton incorporation in yttrium-doped barium zirconate in the temperature range 200–400 °C. The BaZr1–xYxO3 solid solutions are made with variable yttrium content (x = 10, 20, and 30 mol %) by a controlled oxidant-peroxo synthesis method. The water uptake increases as the partial pressure...
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Aggregation of nonionic surfactants in imidazolium ionic liquids
PublikacjaMicellar aggregation of surfactants in aqueous solutions has been described in terms of the balance between dispersive interactions of the hydrocarbon part of the amphiphilic molecule, and the hydration and electrostatic repulsive effects of hydrophilic head group. Changing the interactions by replacing water with another polar solvent, such as amides or glycols, has been studied to a smaller extent (Singh, Saleem et al. 1980;...
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Two-particle entropy and structural ordering in liquid water
PublikacjaEntropies of simple point charge (SPC) water were calculated over the temperature range 278-363 K using the two-particle correlation function approximation. Then, the total two-particle contribution to the entropy of the system was divided into three parts, which we call translational, configurational, and orientational. The configurational term describes the contribution to entropy, which originates from spatial distribution of...
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Paweł Możejko dr hab.
Osoby -
Weakly Hydrated Solute of Mixed Hydrophobic–Hydrophilic Nature
PublikacjaInfrared (IR) spectroscopy is a commonly used and invaluable tool in studies of solvation phenomena in aqueous solutions. Concurrently, density functional theory calculations and ab initio molecular dynamics simulations deliver the solvation shell picture at the molecular detail level. The mentioned techniques allowed us to gain insights into the structure and energy of the hydrogen bonding network of water molecules around methylsulfonylmethane...
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Design and Analysis of Artificial Neural Network (ANN) Models for Achieving Self-Sustainability in Sanitation
PublikacjaThe present study investigates the potential of using fecal ash as an adsorbent and demonstrates a self-sustaining, optimized approach for urea recovery from wastewater streams. Fecal ash was prepared by heating synthetic feces to 500 °C and then processing it as an adsorbent for urea adsorption from synthetic urine. Since this adsorption approach based on fecal ash is a promising alternative for wastewater treatment, it increases...
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Effectiveness of various types of coating materials applied in reinforced concrete exposed to freeze–thaw cycles and chlorides
PublikacjaThis study assesses the durability of coated and uncoated concrete surfaces protected with four Different coating materials: water-soluble (BW), solvent-based (BR), mineral (MI), and epoxy (EP). The durability assessment includes evaluating the absorption rate of water, pull-of adhesion strength, and coating material thickness. Concrete samples were subjected to immersion in regular water and a 7% urea solution, followed by cyclic...
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Effectiveness of various types of coating materials applied in reinforced concrete exposed to freeze–thaw cycles and chlorides
PublikacjaThis study assesses the durability of coated and uncoated concrete surfaces protected with four different coating materials: water-soluble (BW), solvent-based (BR), mineral (MI), and epoxy (EP). The durability assessment includes evaluating the absorption rate of water, pull-off adhesion strength, and coating material thickness. Concrete samples were subjected to immersion in regular water and a 7% urea solution, followed by...
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Exploring the cocrystallization potential of urea and benzamide
PublikacjaThe 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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The importance of the shape of the protein-water interface of a kinesin motor domain for dynamics of the surface atoms of the protein
PublikacjaSingle kinesin motor domain immersed in water has been investigated using molecular dynamics. It has been found that local properties of water in solvation shell change along with the nature of neighboring protein surface. However, a detailed analysis leads to the conclusion that the geometrical features of hydrogen bonds and overall structure of kinesin hydration water is not very different from bulk water. The local values of...
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The importance of the shape of the protein–water interface of a kinesin motor domain for dynamics of the surface atoms of the protein
PublikacjaA single kinesin motor domain immersed in water has been investigated using molecular dynamics. It has been found that local properties of water in the solvation shell change along with the nature of the neighboring protein surface. However, a detailed analysis leads to the conclusion that the geometrical features of hydrogen bonds and overall structure of kinesin hydration water are not very different from bulk water. The local...
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Amyloid fibril formation in the presence of water structure-affecting solutes
PublikacjaThe impact of the differently hydrated non-electrolytes (protein structure destabilizers) on the fibrillation of hen egg white lysozyme (HEWL) was investigated. Two isomeric urea derivatives i.e. butylurea (BU) and N,N,N′,N′-tetramethylurea (TMU) were chosen as a tested compounds. The obtained results show that butylurea exerts greater impact on HEWL and its fibrillation than tetramethylurea. Both substances decrease the time of...
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Wykorzystanie wiązań niekowalencyjnych do otrzymywania jedno- i dwuskładnikowych struktur supramolekularnych
PublikacjaPrzedstawiona rozprawa doktorska dotyczy badań nad wykorzystaniem oddziaływań międzycząsteczkowych do projektowania i syntezy uporządkowanych struktur krystalicznych, ze szczególnym uwzględnieniem wiązań halogenowych i chalkogenowych jako stosunkowo nowych i bardzo atrakcyjnych z punktu widzenia inżynierii kryształu. Praca podzielona jest na kilka części. Pierwsza z nich stanowi wstęp teoretyczny obejmujący opis, założenia oraz...
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Hydration of Oxometallate Ions in Aqueous Solution
PublikacjaThe strength of hydrogen bonding to and structure of hydrated oxometallate ions in aqueous solution have been studied by double difference infrared (DDIR) spectroscopy and large-angle X-ray scattering (LAXS), respectively. Anions are hydrated by accepting hydrogen bonds from the hydrating water molecules. The oxygen atom of the permanganate and perrhenate ions form weaker and longer hydrogen bonds to water than the hydrogen bonds...
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Water uptake analysis of acceptor-doped lanthanum orthoniobates
PublikacjaIn this work, lanthanum orthoniobates doped with either antimony, calcium, or both have been synthesized and studied. The water uptake of the investigated materials has been analyzed by means of thermogravimetric studies. The results show the difference between the thermodynamics of hydration between the lanthanum orthoniobate system and other proton conducting ceramics. The relation between the water uptake and effective acceptor...
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Aggregation of imidazoacridinones - spectroscopic and microcalorimetric approach
PublikacjaImidazoacridinones (IA) belong to a group of polycyclic heteroaromatic antitumor compounds. IA create the aggregated form in water solution. Self-association of substances is a very important phenomenon in many fields of applied chemistry. It is also fundamental model reaction of many kinds of molecular interactions such as the micelle formation of amphiphilic substances and the binding of small organic molecules to macromolecules....
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Effect of osmolytes on the thermal stability of proteins: replica exchange simulations of Trp-cage in urea and betaine solutions
PublikacjaAlthough osmolytes are known to modulate the folding equilibrium, the molecular mechanism of their effect on thermal denaturation of proteins is still poorly understood. Here, we simulated the thermal denaturation of a small model protein (Trp-cage) in the presence of denaturing (urea) and stabilizing (betaine) osmolytes, using the all-atom replica exchange molecular dynamics simulations. We found that urea destabilizes Trp-cage...
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Organic solvents aggregating and shaping structural folding of protein, a case study of the protease enzyme
PublikacjaLow solubility of reactants or products in aqueous solutions can result in the enzymatic catalytic reactions that can occur in non-aqueous solutions. In current study we investigated aqueous solutions containing different organic solvents / deep eutectic solvents (DESs) that can influence the protease enzyme's activity, structural, and thermal stabilities. Retroviral aspartic protease enzyme is responsible for the cleavage of the...
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Novel complexes possessing Hg–(Cl, Br, I)⋯O=C halogen bonding and unusual Hg₂S₂(Br/I)₄ kernel. The usefulness of τ₄′ structural parameter
PublikacjaOne mononuclear and two binuclear Hg(II) complexes have been synthesized and characterized by X-ray diffraction, ATR IR and Hirshfeld surface analysis. Single-crystal X-ray diffraction showed that binuclear compounds are centrosymmetric and isostructural. All complexes form bifurcated intermolecular N–H···O hydrogen bonds that contribute to a formation of the centrosymmetric dimers. In binuclear complexes, sulfur atoms of thiourea...
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Influence of Cement Replacement with Sewage Sludge Ash (SSA) on the Heat of Hydration of Cement Mortar
PublikacjaThe amount of fly ash from the incineration of sewage sludge is increasing all over the world, and its utilization is becoming a serious environmental problem. In the study, a type of sewage sludge ash (SSA) collected directly from the municipal sewage treatment plant was used. Five levels of cement replacement (2.5%, 5%, 7.5%, 10% and 20%) and unchanged water-to-binder (w/b) ratio (0.55) were used. The purpose of the study was...
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Molecular dynamics study on the role of solvation water in the adsorption of hyperactive AFP to the ice surface
PublikacjaUsing computer simulations, the early stages of the adsorption of the CfAFP molecule to the ice surface were analyzed. We found that the ice and the protein interact at least as early as when the protein is about 1 nm away from the ice surface. These interactions are mediated by interfacial solvation water and are possible thanks to the structural ordering of the solvent. This ordering leads to positional preference of the protein...
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Influence of Osmolytes on Protein and Water Structure: A Step To Understanding the Mechanism of Protein Stabilization
PublikacjaResults concerning the thermostability of hen egg white lysozyme in aqueous solutions with stabilizing osmolytes, trimethylamine-N-oxide (TMAO), glycine (Gly), and its N-methyl derivatives, N-methylglycine (NMG), N,N-dimethylglycine (DMG), and N,N,N-trimethylglycine (betaine, TMG), have been presented. The combination of spectroscopic (IR) and calorimetric (DSC) data allowed us to establish a link between osmolytes’ influence on...
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Molecular basis of the osmolyte effect on protein stability: a lesson from the mechanical unfolding of lysozyme
PublikacjaOsmolytes are a class of small organic molecules that shift the protein folding equilibrium. For this reason, they are accumulated by organisms under environmental stress, and find applications in biotechnology where proteins need to be stabilized or dissolved. However, despite years of research, debate continues over the exact mechanisms underpinning the stabilizing and denaturing effect of osmolytes. Here, we simulated the mechanical...
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Are stabilizing osmolytes preferentially excluded from the protein surface? FTIR and MD studies
PublikacjaInteractions between osmolytes and hen egg white lysozyme in aqueous solutions were studied by means of FTIR spectroscopy and molecular dynamics. A combination of difference spectra method and chemometric analysis of spectroscopic data was used to determine the number of osmolyte molecules interacting with the protein, and the preferential interaction coefficient in presented systems. Both osmolytes – L-proline and trimethylamine-N-oxide...
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Double layer adhesive silicone dressing as a potential dermal drug delivery film in scar treatment
PublikacjaThe present studies focused on the evaluation of design of an adhesive silicone film intended for scar treatment. Developed silicone double layer film was examined in terms of its future relevance to therapy and applicability on the human skin considering properties which included in vitro permeability of water vapor and oxygen. In order to adapt the patches for medical use in the future there were tested such properties as...
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The hydration of the protein stabilizing agents: trimethylamine-N-oxide, glycine and its N-methylderivatives - the volumetric and compressibility studies
PublikacjaThe densities at T = (288.15, 293.15, 298.15, 303.15, and 308.15) K and sound velocities at T = 298.15 K have been measured for aqueous solutions of trimethylamine-N-oxide, glycine, N-methylglycine (sarcosine), N,N-dimethylglycine, N,N,N-trimethylglycine (betaine). From these data the apparent molar volumes, VΦ, the apparent molar isentropic compressions, KS,Φ, and the solvation numbers of solutes have been determined. The concentration...
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Water Behavior Near the Lipid Bilayer
PublikacjaIn this chapter, we focus on the dynamics of water molecules situated in the vicinity of a phospholipid bilayer. Using a molecular dynamics simulation method, we studied interactions between water and the bilayer and tracked trajectories of the water molecules. Based on the hypothesis that molecules trapped inside the bilayer make different motions than the ones which are either attached to the surface or move freely in the water...
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Adsorption-assisted transport of water vapour in super-hydrophobic membranes filled with multilayer graphene platelets
PublikacjaThe effects of confinement of multilayer graphene platelets in hydrophobic microporous polymeric membranes are here examined. Intermolecular interactions between water vapour molecules and nanocomposite membranes are envisaged to originate assisted transport of water vapour in membrane distillation processes when a suitable filler-polymer ratio is reached. Mass transport coefficients are estimated under different working conditions,...
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The importance of individual spray properties in performance improvement of a urea-SCR system employing flash-boiling injection
PublikacjaThe appropriate mixing of a urea–water solution (UWS) with exhaust gases in a selective catalytic reduction system is crucial to efficiently reduce nitrogen oxides and diminish the deposition of liquid wall film. One of the methods to enhance the mixing of the UWS with the exhaust gases is a flash-boiling injection. Its positive effect has been linked with a reduced Sauter mean diameter (SMD) and improved evaporation, but the...
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Structure and water uptake in BaLnCo2O6−δ (Ln =La, Pr, Nd, Sm, Gd, Tb and Dy)
PublikacjaThe structure of BaLnCo2O6-δ (Ln =La, Pr, Nd, Sm, Gd, Tb and Dy) was studied by the means of synchrotron radiation powder X-ray diffraction, neutron powder diffraction and Transmission Electron Microscopy (TEM), while water uptake properties were analysed with the use of thermogravimetry (TG) and water adsorption isotherms. The structure refinement revealed that the dominant phase in all compositions was orthorhombic with an ordering...
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Closer look into the structures of tetrabutylammonium bromide–glycerol-based deep eutectic solvents and their mixtures with water
PublikacjaIn recent years, deep eutectic solvents (DES) and it’s mixture with water have become more and more attention as green solvents used in chemistry. However, there are only a few theoretical studies on the mechanisms of pure DES and DES-water complex formation. Therefore, the structural properties of tetrabutylammonium bromide–glycerol-based deep eutectic solvents and their mixtures with water have been investigated by means of Molecular...
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Terbium Substituted Lanthanum Orthoniobate: Electrical and Structural Properties
PublikacjaThe results of electrical conductivity studies, structural measurements and thermogravimetric analysis of La1−xTbxNbO4+δ (x = 0.00, 0.05, 0.1, 0.15, 0.2, 0.3) are presented and discussed. The phase transition temperatures, measured by high-temperature x-ray diffraction, were 480 °C, 500 °C, and 530 °C for La0.9Tb0.1NbO4+δ, La0.8Tb0.2NbO4+δ, and La0.7Tb0.3NbO4+δ, respectively. The impedance spectroscopy results suggest mixed conductivity...
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Molecular hydrogen solvated in water – A computational study
PublikacjaThe aqueous hydrogen molecule is studied with molecular dynamics simulations at ambient temperature and pressure conditions, using a newly developed flexible and polarizable H2 molecule model. The design and implementation of this model, compatible with an existing flexible and polarizable force field for water, is presented in detail. The structure of the hydration layer suggests that first-shell water molecules accommodate the...
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Structural changes of a simple peptide—Trpzip-1—in aqueous solutions and the corresponding hydration phenomena under the influence of temperature
PublikacjaTrpzip-1, a simple β-hairpin, is a rare example of peptide with stable secondary structure and can be a convenient model to study temperature-related processes that potential prion or amyloid proteins undergo. Although its sequence is simple, the exact processes which the peptide undergoes in aqueous solutions are quite complex and not well understood. The selection of well-established experimental (DSC, FTIR) and theoretical methods...
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Electrochemical Stability of Few-Layered Phosphorene Flakes on Boron-Doped Diamond: A Wide Potential Range of Studies in Aqueous Solutions
PublikacjaTwo-dimensional phosphorene has attracted great interest since its discovery as a result of its extraordinary properties. Two-dimensional single crystals of phosphorene can be useful for electrochemical (EC) sensing applications due to their enhanced surface-to-volume ratio. We proposed to investigate the electrochemical performance of phosphorene deposited directly on boron-doped diamond (BDD) electrodes. Noncovalent interaction...
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Structure of Microemulsion Formulated with Monoacylglycerols in the Presence of Polyols and Ethanol
PublikacjaThe influence of polyols as cosurfactants (propylene glycol PG; glycerol G) and short chain alcohol as a cosolvent (ethanol EtOH) on the formation and solubilization capacity of the systems: hexadecane/monoacylglycerols (MAG)/polyol/water:EtOH, at 60C, was investigated. Electrical conductivity measurement, and the DSC method were applied to determine the structure and type of microemulsions formed. The dimension of the droplets...
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g-C3N4 for Photocatalytic Degradation of Parabens: Precursors Influence, the Radiation Source and Simultaneous Ozonation Evaluation
PublikacjaGraphitic carbon nitride (g-C3N4) is a promising catalyst for contaminants of emerging concern removal applications, especially as a visible-light-driven material. In this study, g-C3N4 catalysts were effectively synthesized through a simple thermal polymerization method, using melamine, urea, and thiourea as precursors to elucidate the influence of these compounds on the final product’s photocatalytic performance. The degradation...
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Hydrogen Bonds in Blends of Poly(N-isopropylacrylamide), Poly(N-ethylacrylamide) Homopolymers, and Carboxymethyl Cellulose
PublikacjaRecently, it was reported that the physical crosslinking exhibited by some biopolymers could provide multiple benefits to biomedical applications. In particular, grafting thermoresponsive polymers onto biopolymers may enhance the degradability or offer other features, as thermothickening behavior. Thus, different interactions will affect the different hydrogen bonds and interactions from the physical crosslinking of carboxymethyl...
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Influence of iron content on water uptake and charge transport in BaCe0.6Zr0.2Y0.2−xFexO3−δ triple-conducting oxides
PublikacjaIn this work, we studied the BaCe0.6Zr0.2Y0.2−xFexO3−δ system which belongs to the triple-conducting oxides (TCOs) group. The electrochemical properties of BaCe0.6Zr0.2Y0.2−xFexO3−δ were investigated using electrochemical impedance spectroscopy (EIS) and the water uptake was analyzed using thermogravimetry (TG). All investigated materials exhibited water uptake, with proton concentration increasing with decreasing iron content....
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Simplified AutoDock force field for hydrated binding sites
Publikacjahas 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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Simulations of wave propagation and attenuation in fields of colliding ice floes
Dane BadawczeThis dataset contains results of numerical smulations of sea ice-wave interactions, corresponding to laboratory experiments conducted at the Large Ice Model Basin (LIMB) at the Hamburg Ship Model Basin (HSVA) as part of the LS-WICE ("Loads on Structure and Waves in Ice"; https://zenodo.org/record/1067170#.XrLt_dhpxhE) project. THe simulations were conducted...
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Water uptake and energetics of the formation of barium zirconate based multicomponent oxides
PublikacjaA group of multi-component oxides based on BaZrO3 have been prepared using a solid-state reaction method and examined in terms of their water uptake and thermodynamics of formation. Depending on the type and amount of acceptor substitution, the synthesized compounds exhibit various proton defect concentrations, reaching up to 0.2 mol/mol for a compound containing 10 different elements in the B-sublattice, where 50% of them are...
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Photocatalytic activity of nitrogen doped TiO2 nanotubes prepared by anodic oxidation: The effect of applied voltage, anodization time and amount of nitrogen dopant
PublikacjaNitrogen doped TiO2 nanotube arrays were prepared by anodizing Ti foils in an organic electrolyte containing specified amounts of urea as nitrogen precursor. The photocatalytic activity of the samples was evaluated by analyzing the degradation kinetics of phenol in water. The influence of tubes’ length, tubes’ surface morphology and amount of nitrogen in the TiO2 lattice on hydroxyl radical formation efficiency, photocatalytic...
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Influence of temperature and anion type on thermophysical properties of aqueous solutions of morpholine based amino acid ionic liquids
PublikacjaDensities and sound velocities of aqueous solutions of N-butyl-N-methylmorpholine based amino acid ionic liquids (AAILs), including N-acetyl-L-alanine, N-acetyl-Lvalinate, N-acetyl-L-leucinate, and N-acetyl-L-izoleucinate anions were measured at a temperature from 293.15 to 313.15 K at 5 K intervals and atmospheric pressure. These data were used to calculate the apparent molar volumes and the apparent molar compressibilities in...
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Solubility enhancement of metronidazole using natural deep eutectic solvents: Physicochemical and thermodynamic studies
PublikacjaThis research aimed to explore the utility of natural deep eutectic solvents (NADES) as the co-solvents for slightly water-soluble metronidazole (MNZ). After testing 70 wt% (percentage by weight) aqueous mixtures of seven NADESs, it was found that MNZ had the highest solubility in water solutions of NADES composed of choline chloride (ChCl) and citric acid (CA). The solubility of MNZ (expressed as 103 mol fraction) increased with...
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Interactions in Ternary Aqueous Solutions of NMA and Osmolytes—PARAFAC Decomposition of FTIR Spectra Series
PublikacjaIntermolecular interactions in aqueous solutions are crucial for virtually all processes in living cells. ATR-FTIR spectroscopy is a technique that allows changes caused by many types of such interactions to be registered; however, binary solutions are sometimes difficult to solve in these terms, while ternary solutions are even more difficult. Here, we present a method of data pretreatment that facilitates the use of the Parallel...