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Year 2020
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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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Ionic liquids in the microextraction techniques: the influence of ILs structure and properties
PublicationIonic liquids (ILs) are composed entirely of ions thus they possess unique properties, including negligible volatility, a liquid state in a broad range of temperatures and ability to change them depending on the chosen type of anion and cation, which make ILs unique and useful for many applications in sample preparation techniques. A deeper understanding of the nature of ILs and the impact of their structure on their parameters...
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Mapping the Structural and Dynamic Determinants of pH-Sensitive Heparin Binding to Granulocyte Macrophage Colony Stimulating Factor
PublicationGranulocyte macrophage colony stimulating factor (GMCSF) is an immunomodulatory cytokine that is harnessed as a therapeutic. GMCSF is known to interact with other clinically important molecules, such as heparin, suggesting that endogenous and administered GMCSF has the potential to modulate orthogonal treatment outcomes. Thus, molecular level characterization of GMCSF and its interactions with biologically active compounds is critical...
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Measurements of Activity Coefficients at Infinite Dilution for Organic Solutes in the Ionic Liquids N-Ethyl- and N-Octyl-N-methylmorpholinium Bis(trifluoromethanesulfonyl)imide. A Useful Tool for Solvent Selection
PublicationIn recent years, many papers describing ionic liquids (IL) as promising solvents in separation techniques have been published. The conscious choice of appropriate ionic liquid as absorption media in effective extraction of selected types of analytes requires deeper understanding of the analyte−IL interactions. Therefore, intensive research is conducted to determine the values of activity coefficient at infinite dilution, which...
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Mikrofiltrowany koncentrat soku brzozowego jako innowacyjny, trwały środek spożywczy o wysokiej wartości odżywczej
PublicationIntroduction. The forest environment becomes an increasingly popular place of obtaining raw materials, and one of the most promising product is birch sap. The market for bottled birch sap in Poland is monotonous, relying exclusively on pasteurized, acidified and sweetened drinks. A chance to change this situation is to develop a birch sap concentrate obtained by reverse osmosis. It has a sweet taste desired by consumers and particularly...
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Molywood: streamlining the design and rendering of molecular movies
PublicationMotivation High-quality dynamic visuals are needed at all levels of science communication, from the conference hall to the classroom. As scientific journals embrace new article formats, many key concepts – particularly in structural biology – are also more easily conveyed as videos than still frames. Notwithstanding, the design and rendering of a complex molecular movie remain an arduous task. Here, we introduce Molywood, a robust...
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Powrót Duchów
PublicationFelieton popularno-naukowy dotyczący technologii rzeczywistości rozszerzonej i sztucznej inteligencji.
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Pulsowo-różnicowa woltamperometria jako narzędzie pozwalające na wyznaczenie wartości mocy przeciwutleniającej
PublicationStandardowy potencjał redukcji (E0) jako parametr określający zdolność przeciwutleniaczy, jak np. flawan-3-oli do przyjmowania elektronów wykazywał wysoką korelację z ich aktywnością biologiczną. Jednak, w przypadku oceny całkowitej aktywności przeciwutleniającej mieszanin tych związków, parametr ten może okazać się być niewystarczającym. Bowiem do określenia tzw. mocy przeciwutleniającej ang. antioxidant power (AOP) powinny być...
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Rola wody solwatacyjnej w kształtowaniu aktywności białek z grupy krioprotektantów
PublicationBiałka przeciwdziałające zamarzaniu (AFP) posiadają zdolność do hamowania wzrostu kryształów lodu powstających w płynach ustrojowych organizmów żywych narażonych na działanie temperatur niższych od 0°C, poprzez wiązanie się z powierzchnią tych kryształów. W ramach mojej pracy, stosując metody dynamiki molekularnej, starałam się poznać szczegóły mechanizmu zachodzenia tego procesu. Aby to osiągnąć, przeprowadziłam szereg symulacji...
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Telomere uncapping by common oxidative guanine lesions: Insights from atomistic models
PublicationOxidative damage to DNA is widely known to contribute to aging and disease. This relationship has been extensively studied for telomeres – structures that cap chromosome ends – due to their role in cell proliferation and senescence, and exceptional susceptibility to oxidation. Indeed, the repetitive telomeric DNA sequence contains the 5′-GGG-3′ motif that has the lowest ionization potential of all trinucleotides. Accordingly, experiments...
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The hydration properties of protein stabilizer, trimethylamine-N-oxide in aqueous solutions of N-methylacetamide – The volumetric and compressibility studies between 288.15 and 308.15 K
PublicationApparent molar volumes and apparent molar isentropic compressions of the protein stabilizer, trimethylamine-N-oxide (TMAO) were determined from the densities and speed of sound measured at T = (288.15, 298.15 and 308.15) K in aqueous solutions of N-methylacetamide (NMA) at four different concentrations (2, 4, 6 and 8 mol/kg). The concentration dependencies of the calculated quantities extrapolated to the infinite dilution lead...
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The interaction parameters for solutions of n-butylurea in aqueous solutions of N-methylacetamide – The volumetric and compressibility studies between 288.15 K and 308.15 K
PublicationDensities and speed of sound were measured for solutions of n-butylurea in aqueous solution of Nmethylacetamide 2, 4, 6 and 8 (mol/kg) at T = (288.15, 298.15 and 308.15) K. From these data the apparent molar volumes, Vf, the apparent molar isentropic compressions, KSf, of the solute were determined. The concentration dependencies of the calculated quantities have been used to obtain the standard partial molar parameters. The latter...
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The new silica-based coated SPME fiber as universal support for the confinement of ionic liquid as an extraction medium
PublicationThe new silica-based SPME fiber coating is reported for the first time as universal support purposed to confinement of ionic liquid as an extraction medium. Fiber coating was prepared by the sol-gel process, using potassium silicate (K2SiO3) as a precursor and dimethylformamide (DMF) as a pore-forming medium. The concept of synthesis assumes obtaining a solid porous material on the surface of the glass rod and, being characterized...
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The Product of Matrix Metalloproteinase Cleavage of Doxorubicin Conjugate for Anticancer Drug Delivery: Calorimetric, Spectroscopic, and Molecular Dynamics Studies on Peptide–Doxorubicin Binding to DNA
PublicationMatrix metalloproteinases (MMPs) are extracellular matrix degradation factors, promoting cancer progression. Hence, they could provide an enzyme-assisted delivery of doxorubicin (DOX) in cancer treatment. In the current study, the intercalation process of DOX and tetrapeptide-DOX, the product of the MMPs' cleavage of carrier-linked DOX, into dsDNA was investigated using stationary and time-resolved fluorescence spectroscopy, UV-Vis...
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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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Thermophysical study of the binary mixtures of triethyl phosphate with N-methylformamide, N,N-dimethylformamide and N,N-dimethylacetamide – Experimental and theoretical approach
PublicationDensities at (293.15, 298.15, 303.15 and 308.15) K, and viscosities and ultrasonic velocities at 298.15 K of binary liquid mixtures of triethyl phosphate with N-methylformamide, N,N-dimethylformamide and N,N-dimethylacetamide have been measured over the entire range of composition at p = 0.1 MPa. From the experimental data, values of excess molar volume, excess isentropic compressibility, viscosity deviation and excess Gibbs energy...
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Tuning the extraction properties of ionogel-coated Solid-phase microextraction fibers based on the solvation properties of the ionic liquids
PublicationA silica-based network was used to immobilize ionic liquid-based ionogels and applied as a fiber coating forsolid-phase microextraction (SPME). The ionogels were prepared by a sol–gel process, using two ionic liquids,triethylsulfonium bis(trifluoromethylsulfonyl)imide ([Set3][TFSI]) and 1-butyl-1-methylpiperidinium bis(tri-fluoromethylsulfonyl)imide ([C4C1Pip][TFSI]), as well as their equimolar mixture. Methyltrimethoxysilane wasused...
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Two-step mechanism of J-domain action in driving Hsp70 function
PublicationJ-domain proteins (JDPs), obligatory Hsp70 cochaperones, play critical roles in protein homeostasis. They promote key allosteric transitions that stabilize Hsp70 interaction with substrate polypeptides upon hydrolysis of its bound ATP. Although a recent crystal structure revealed the physical mode of interaction between a J-domain and an Hsp70, the structural and dynamic consequences of J-domain action once bound and how Hsp70s...
Year 2019
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A Three-Step Approach to Estimation of Reduction Potentials of Natural Mixtures of Antioxidants Based on DPPH Test; Illustration for Catechins and Cocoa
PublicationThe aim of this study is to propose a methodology to assess electrochemical properties of complex mixtures of antioxidants, such as plant extracts, based on the results of simple and popular DPPH test. The first, most difficult step, involves determinations of standard reduction potentials (E0) for the series of purified compounds (here catechins). The next step is the calculation of stoichiometric values (n10) based on the results...
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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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Amyloid fibril formation in the presence of water structure-affecting solutes
PublicationThe 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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Analytical applications and physicochemical properties of ionic liquid-based hybrid materials: A review
PublicationIonic liquids with their unique properties found so far numerous analytical applications. Among them ionic liquids immobilized on the surface or within the pores of a solid support were successfully utilized in extraction techniques dedicated to preconcentration of the analytes from food, environmental and biological samples. In this review we focus on comprehensive summarizing of available literature data on the examples of ionic...
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ANTIOXIDANT POWER SERIES (APS) AS A TOOL FOR RATIONAL DESIGN AND ASSESSMENT OF HEALTH PROMOTING PROPERTIES OF FUNCTONAL FOODS BASED ON ANTIOXIDANT PHYTOCHEMICALS
PublicationOver past decades, plantborne antioxidants dominated so called "translational research" in the area of food, nutrition, and disease prevention. Among consumers and producers, such phytochemicals are synonyms of nutriceuticals. Popularity and commercial success of antioxidants stems from mechanistic studies suggesting the involvement of reactive oxygen species in etiology of chronic diseases. However, epidemiology failed to provide...
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Application of ionic liquids in microextraction techniques: Current trends and future perspectives
PublicationIonic liquids (ILs) with their unique properties found so far numerous analytical applications. Among them ILs both in their liquid form and immobilized on the surface or within the pores of a solid support were successfully utilized in microextraction techniques. The scope of this review will cover a comprehensive summarizing of available literature data on selected properties of ILs playing a key role in analytical purposes,...
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Are the short cationic lipopeptides bacterial membrane disruptors? Structure-Activity Relationship and molecular dynamic evaluation
PublicationShort cationic lipopeptides are amphiphilic molecules that exhibit antimicrobial activity mainly against Grampositives. These compounds bind to bacterial membranes and disrupt their integrity. Here we examine the structure-activity relation (SAR) of lysine-based lipopeptides, with a prospect to rationally design more active compounds. The presented study aims to explain how antimicrobial activity of lipopeptides is affected by...
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"Big data" i Wielki Brat
PublicationFelieton popularnonaukowy dotyczący ochrony prywatności danych.
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Ciecze jonowe jako medium sorpcyjne w mikroekstrakcji do pojedynczej kropli Cz. I. Podstawy teoretyczne zagadnienia
PublicationTechnika mikroekstrakcji do pojedynczej kropli stanowi sztandarowy przykład rozwiązania technicznego spełniającego wymogi stawiane przez ideę zielonej chemii analitycznej.
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Ciecze jonowe jako medium sorpcyjne w mikroekstrakcji do pojedynczej kropli. Cz.II. Praktyka analityczna
PublicationPomimo rosnącego zainteresowania metodami analitycznymi opartymi na użyciu cieczy jonowych ich sprzężenie wraz z techniką mikroekstrakcji do pojedynczej kropli nie osiągnęło zadowalającej popularności oraz akceptacji ze strony środowiska naukowego.
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Density, sound velocity, viscosity, and refractive index of new morpholinium ionic liquids with amino acid-based anions: Effect of temperature, alkyl chain length, and anion
PublicationIn this work, room temperature synthesis of twenty new ionic liquids (ILs) based on the N-alkyl-N-methylmorpholinium ([Mor1,R], R = 2, 3, 4, 6, 8) cation and N-acetyl-L-amino acid anions (L-alaninate, L-valinate, L-leucinate, L-isoleucinate) was described. The synthesized ILs were characterized by various spectroscopic techniques and high-resolution mass spectrometry. Furthermore, density (ρ), sound velocity (v), viscosity (η)...
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Determination of Antioxidant Activity of Vitamin C by Voltammetric Methods
PublicationVoltammetric methods—cyclic (CV) and differential pulse voltammetry (DPV) are considered the most appropriate way to evaluate antioxidant activity of redox active compounds. They provide information about both mechanism and kinetics of electrochemical oxidation of antioxidants as well as their physical and chemical properties such as the redox potential or the number of electrons transferred. These methods are helpful for understanding...
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Development and validation of a model that includes two ultrasound parameters and the plasma D-dimer level for predicting malignancy in adnexal masses: an observational study
PublicationBackground: Pre-operative discrimination of malignant from benign adnexal masses is crucial for planning additional imaging, preparation, surgery and postoperative care. This study aimed to define key ultrasound and clinical variables and develop a predictive model for calculating preoperative ovarian tumor malignancy risk in a gynecologic oncology referral center. We compared our model to a subjective ultrasound assessment (SUA)...
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DMSO hydration redefined: Unraveling the hydrophobic hydration of solutes with a mixed hydrophilic–hydrophobic characteristic
PublicationHydrophobic hydration of solutes with a mixed hydrophilic--hydrophobic characteristics is still poorly understood. This is because both experimental and theoretical methods find it difficult to see the ice-like water structure around the nonpolar solute groups, unlike hydrogen bonds with the hydrophilic groups. In order to unravel this problem, we have investigated DMSO hydration by means of infrared spectroscopy and theoretical...
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Ewolucja od węgla do krzemu
PublicationFelieton popularnonaukowy dotyczący filozofii techniki.
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General, Mild, and Metal-Free Functionalization of Indole and Its Derivatives Through Direct C3-Selenylation
PublicationA very mild method for the introduction of functionalized alkylselenyl group at C-3 position of the indole ring was developed. The proposed procedure consists of an electrophilic substitution of indole and its derivatives with bis(O,O-diisopropoxyphosphorothioyl) diselenide and subsequent cleavage of the P–Se bond with tetrabutylammonium fluoride in the presence of various electrophilic reagents. This method can be successfully...
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How green are ionic liquids? – A multicriteria decision analysis approach
PublicationDue to various desirable physicochemical properties, ionic liquids (ILs) are still gaining in popularity. ILs have been recurrently considered green solvents. However, environmental, health and safety assessments of ILs have raised certain doubts about their benignness, and their greenness status is currently unclear. To clarify the situation on their greenness, we perform a comprehensive assessment of more than 300 commercially...
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How to stop salami science: promotion of healthy trends in publishing behavior
PublicationThe career of scientists often depends on the number of their published works. This fact leads to the overproduction of low quality papers burying the important articles and making the knowledge less accessible. One of the methods to counteract these negative aspects might lie in the promotion of healthy trends in publishing behavior. In the present work, the theoretical analysis of a new bibliometric measure is presented, and...
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Influence of the ionic strength on the amyloid fibrillogenesis of hen egg white lysozyme
PublicationThe study investigates the role of the electrostatic interactions in the fibrillation of the hen egg white lysozyme (HEWL). In order to achieve this aim the influence of the cations Na+, Mg2+ and Al3+ on the amyloid fibril formation and amorphous aggregation was tested. The amyloids are formed in the solution without added salt but the Thioflavin T fluorescence gives the false-negative result. In these conditions, the HEWL fibrils...
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Interactions of N-alkyl-N-methylmorpholinium based ionic liquids with acetonitrile studied by density and velocity of sound measurements and molecular dynamics simulations
PublicationMorpholinium-based ionic liquids (ILs) and their mixtures with polar co-solvents are an interesting class of emerging electrolytes in electrochemistry that is relatively poorly studied. In this work, densities and sound velocities of four ILs, N-ethyl-N-methylmorpholinium tetrafluoroborate, N-butyl-N-methylmorpholinium tetrafluoroborate, N-octyl-N-methylmorpho-linium tetrafluoroborate and N-decyl-N-methylmorpholinium tetrafluoroborate...
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Interactions of telomeric proteins with nucleic acids: sequence recognition on intact and oxidatively damaged telomeres
PublicationTelomeres are complex nucleoprotein assemblies that play a vital role in the maintenance of functional ends of linear chromosomes. Telomeric DNA, composed of tandem repeats of the 5'-TTAGGG-3' motif, solves the so-called end replication problem: as chromosomes shorten with each cell division, no information is lost, and the telomere can be re-extended. In the cell, many protein factors regulate telomere length, nuclear positioning...
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Medium-sized cyclic bis(anisylphosphonothioyl)- disulfanes and their corresponding cyclic sulfane-structures and most characteristic reactions
PublicationCyclic 8-, 9-, 10-, and 12-membered bis(anisylphosphonothioyl)disulfanes were synthesized. Next, structurally related 7 to 9-membered cis and trans sulfanes were isolated as a result of sulfur atom extrusion from the parent cyclic disulfanes. The results of the desulfurization of the disulfanes were compared to the results obtained for desulfurization of the respective bis(anisylphosphodithioates). Cyclic disulfanes predominantly...
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Monitoring of lysozyme thermal denaturation by volumetric measurements and nanoDSF technique in the presence of N-butylurea
PublicationThe results of thermal studies of denaturation of hen egg white lysozyme (HEWL) in water and an aqueous solution of N-butylurea (BU) are presented. High-precision densimetric measurements were used to characterize and analyze the changes of the specific volume, v, during temperature elevation. The temperature of the midpoint of protein denaturation was also determined by nanoDSF technique (differential scanning fluorimetry). The...
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Nanoconfined Ionic Liquids. Properties and analytical applications
PublicationThe synergistic combination of ionic liquids (ILs) and solid‐like matrices involves a powerful coupling towards the development of new sustainable analytical methodologies. Here we survey the literature regarding such ionic liquid‐based hybrid materials, including a database on relevant physicochemical properties of ionic liquids confined in a solid network. Furthermore, this chapter presents the strategies implemented to combine...
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Obtaining of Coumarone-Indene Resins Based on Light Fraction of Coal Tar. 4. Bitumen-Polymer Blends with Participation of Coumarone-Indene Resins with Epoxy Groups
PublicationUsing light fraction of coal tar (5.75 wt % of coumarone and 44.45 wt % of indene), glycidyl methacrylate and styrene, the coumarone-indene resin with epoxy groups (CIRE) has been synthesized. Monoperoxy derivative of diglycidyl ether Bisphenol A (PO) was used as an initiator. The possible formation of CIRE has been studied on the model systems consisting of PO, glycidyl methacrylate, indene or coumarone, or styrene, or mixture...
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Role of the Solvation Water in Remote Interactions of Hyperactive Antifreeze Proteins with the Surface of Ice
PublicationMost protein molecules do not adsorb onto ice, one of the exceptions being so-called antifreeze proteins. In this paper, we describe that there is a force pushing an antifreeze protein molecule away from the ice surface when it is not oriented with its ice-binding plane toward the ice and that this pushing force may be also present even when the protein is oriented with its ice-binding plane toward the ice. This force is absent...
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Strach przed nieznanym błędem
PublicationFelieton popularnonaukowy dotyczący algorytmu genetycznego.
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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
PublicationTrpzip-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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Structure and evolution of the 4-helix bundle domain of Zuotin, a J-domain protein co-chaperone of Hsp70
PublicationThe J-domain protein Zuotin is a multi-domain eukaryotic Hsp70 co-chaperone. Though it is primarily ribosome-associated, positioned at the exit of the 60S subunit tunnel where it promotes folding of nascent polypeptide chains, Zuotin also has off-ribosome functions. Domains of Zuotin needed for 60S association and interaction with Hsp70 are conserved in eukaryotes. However, whether the 4-helix bundle (4HB) domain is conserved remains...
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Symulacje biomolekularne jako narzędzie do badania mechanizmów rozpoznania i wiązania pomiędzy białkami
PublicationBiałka pełnią wielorakie funkcje w organizmach żywych, jednak rzadko działają samodzielnie. W zdecydowanej większości przypadków współpracują one między sobą tworząc makrokompleksy o precyzyjnie zorientowanych podjednostkach. Oddziaływania międzybiałkowe wzbudzają więc duże zainteresowanie, jako że w istotny sposób odpowiadają za aktywność biologiczną białek. Choć do tej pory opracowano wiele metod doświadczalnych badania oddziaływań...
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Termodynamika oddziaływań i przejść strukturalnych DNA w układach wodnych na podstawie symulacji metodą dynamiki molekularnej
PublicationKwas deoksyrybonukleinowy jest jednym z najistotniejszych elementów każdej żywej komórki ze względu na rolę głównego nośnika informacji genetycznej. Posiada on instrukcje potrzebne do wzrostu, budowy, funkcjonowania oraz namnażania się wielu żywych organizmów, w tym także wirusów. Okazuje się, że w zależności od warunków środowiskowych, DNA może przyjmować wiele różnych struktur drugorzędowych, z których większość stanowi formy...
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Termodynamika oddziaływań substancji tetrafenylowych z wodą w świetle teorii funkcjonału gęstości
PublicationW termodynamice roztworów elektrolitów istotne jest zagadnienie podziału eksperymentalnie wyznaczanych wielkości termodynamicznych na udziały jonowe. Z uwagi na niemożność niezależnego wyznaczenia jonowych wielkości cząstkowych, podział wielkości charakteryzujących elektrolit musi być z konieczności dokonany w oparciu o założenie pozatermodynamiczne. Obecnie przyjmuje się, że najbardziej uzasadnionym teoretycznie i eksperymentalnie...
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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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The interpretation of the parameters of the equation used for the extrapolation of apparent molar volumes of the non-electrolyte (solutes) to the infinite dilution
PublicationThe paper discusses how to interpret the parameters of the basic equation used for the extrapolation of the apparent molar volume of the solute to infinite dilution. The common misunderstandings and oversimplifications have been pointed out. We present the alternative ways of the data interpretation that can be used to eliminate these obvious but frequent mistakes.
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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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Why do G-quadruplexes dimerize through the 5’-ends? Driving forces for G4 DNA dimerization examined in atomic detail
PublicationG-quadruplexes (G4) are secondary structures formed by guanine-rich nucleic acid sequences and shown to exist in living cells where they participate in regulation of gene expression and chromosome maintenance. G-quadruplexes with solvent-exposed guanine tetrads show the tendency to associate together through cofacial stacking, which may be important for packaging of G4-forming sequences and allows for the design of higher-order...
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Why is the cubic structure preferred in newly formed ice?
PublicationMolecular dynamics was employed to explain the preference for the cubic structure in newly formed crystals of ice. The results showed that in supercooled liquid water the molecules connected by hydrogen bonds are more likely to adopt relative orientations similar to the ones characteristic for cubic ice. The observed preference for certain relative orientations of molecules in the hydrogen-bonded pairs results in the higher probability...
Year 2018
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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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Birch sap concentrate as a potential modern food product
PublicationThis paper presents birch sap concentrate obtained by the reverse osmosis method. It is characterized by sweet taste, high content of minerals and no risk to consumers in terms of content of heavy metals standardized in the European Union food legislation. This beverage has all the features of a modern food product, i.e. it has an attractive taste, is obtained using new technology, meets the clean label requirements and can be...
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Communication: Inside the water wheel: Intrinsic differences between hydrated tetraphenylphosphonium and tetraphenylborate ions
PublicationTetraphenylphosphonium tetraphenylborate (TPTB) is a common reference electrolyte in physical chemistry of solutions allowing for a convenient partitioning of thermodynamic properties into single-ion contributions. Here, we compute on the basis of ab initio molecular dynamics simulations the infrared (IR) spectra for hydrated constituent ions of the TPTB assumption. Using spectral decomposition techniques, we extract important...
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Effect of Amino Acids and Sodium Chloride on d-Sorbitol in Aqueous Solutions at Different Temperatures: Volumetric and Acoustic Approach
PublicationApparent molar volumes and apparent molar compressibilities for d-sorbitol in (0.05, 0.1, 0.2 and 0.3) mol·kg−1 aqueous solutions of l-alanine, l-cysteine and l-histidine and NaCl have been determined from measurements of solution density at T = (288.15, 298.15, 308.15 and 318.15) K and sound velocity at T = 298.15 K, as a function of the concentration of the sugar alcohol. The data were used to obtain the limiting apparent molar...
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Effect of osmolytes of different type on DNA behavior in aqueous solution. Experimental and theoretical studies
PublicationOsmolytes, the small organic molecules accumulated in cells under environmental stress, can modulate the stability of biopolymers such as proteins and DNA. In spite of many years of research, there is no established molecular mechanism of the influence of osmolytes on DNA structure. Here, we used two model osmolytes that denature (urea) or stabilize (trimethylglycine, TMG) proteins to study their effect on DNA in aqueous solutions...
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Effect of osmolytes on the thermal stability of proteins: replica exchange simulations of Trp-cage in urea and betaine solutions
PublicationAlthough 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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Ludzkość-technologia: organizm symbiotyczny
PublicationFelieton popularnonaukowy dotyczący filozofii techniki.
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Mechanism of Binding of Antifungal Antibiotic Amphotericin B to Lipid Membranes: An Insight from Combined Single-Membrane Imaging, Microspectroscopy, and Molecular Dynamics
PublicationAmphotericin B is a lifesaving polyene antibiotic used in the treatment of systemic mycoses. Unfortunately, the pharmacological applicability of this drug is limited because of its severe toxic side effects. At the same time, the lack of a well-defined mechanism of selectivity hampers the efforts to rationally design safer derivatives. As the drug primarily targets the biomembranes of both fungi and humans, new insights into the...
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Molecular dynamics study on the role of solvation water in the adsorption of hyperactive AFP to the ice surface
PublicationUsing 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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New data acquisition system for birch sap concentrate production using the reverse osmosis technology
PublicationThe work presents a simple electronic device that helps to monitor the basic parameters of the reverse osmosis (RO) system during the concentration of birch tree sap. The construction costs are low (around 150 Euro) but the functionality of the device is high. It has an in-build two channel conductometer and can measure the volumetric flow rate of two streams of liquids. The collected data are transmitted wirelessly via Bluetooth...
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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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On the relationship between the structural and volumetric properties of solvated metal ions in O-donor solvents using new structural data in amide solvents
PublicationThe structures of the N,N-dimethylformamide (dmf), N,N-dimethylacetamide (dma), and N,N-dimethylpropionamide (dmp) solvated strontium and barium ions have been determined in solution using large angle X-ray scattering and EXAFS spectroscopy. The strontium ion has a mean coordination number (CN) between 6.2 and 6.8, and the barium ion has a mean CN between 7.1 and 7.8 in these amide solvents. The non-integer numbers indicates that...
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Preparation and characterization of dummy-template molecularly imprinted polymers as potential sorbents for the recognition of selected polybrominated diphenyl ethers
PublicationThe main aim of this work was to conduct the preliminary/basic research concerning the preparation process of a new dummy molecularly imprinted polymer (DMIP) materials. Developed DMIPs were proposed as a sorption material in solid-phase extraction (SPE) technique for recognition of selected low mass polybrominated diphenyl ethers (PBDEs) e PBDE-47 and PBDE-99. Four new DMIPs were synthesized employing bulky polymerization technique...
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Solvation of ionic liquids based on N -methyl- N -alkylmorpholinium cations in N,N -dimethylformamide and N,N -dimethylacetamide – Volumetric and compressibility studies
PublicationDensity and sound velocity of the solutions of ionic liquids based on N-alkyl-N-methyl- morpholinium cations: N-ethyl- -methylmorpholinium bis(trifluoromethanesulfonyl)imide, N-butyl-Nmethylmorpholinium bis(trifluoromethanesulfonyl)imide, N-octyl-N-methyl -morpholinium bis(trifluor omethanesulfonyl)imide and N-decyl-N-methylmorpholinium bis(trifluoromethanesulfonyl)imide in N, N-dimethylformamide and N,N-dimethylacetamide were...
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Structural changes of water caused by non-electrolytes: Volumetric and compressibility approach for urea-like analogues
PublicationHydration of thiourea (TU), hydroxyurea (HU, hydroxycarbamide), acetone (AC, 2-propanone) and dimethyl sulfoxide (DMSO) has been investigated with the help of the volumetric and compression measurement. The apparent molar volumes and the apparent molar isentropic (adiabatic) compression have been calculated from the density and speed of sound data at temperatures ranging from 288.15 to 308.15 K at atmospheric pressure (0.1 MPa)....
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Taurine as a water structure breaker and protein stabilizer
PublicationThe enhancing effect on the water structure has been confirmed for most of the osmolytes exhibiting both stabilizing and destabilizing properties in regard to proteins. The presented work concerns osmolytes, which should be classified as “structure breaking” solutes: taurine and N,N,N-trimethyltaurine (TMT). Here, we combine FTIR spectroscopy, DSC calorimetry and DFT calculations to gain an insight into the interactions between...
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The energy consumption during the birch tree sap concentration process using the reverse osmosis system
PublicationBirch tree sap was concentrated by mens of the reversed osmosis technique. The energy consumption in a small-scale pilot apparatus was estimated. The threshold value for the water removal above which the specific energy consumption significantly increased was identified. Below the threshold value the reversed osmosis had low energy demand and could be an attractive method for the production of birch tree sap-based beverages.
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The relationship between standard reduction potentials of catechins and biological activities involved in redox control
PublicationRedox homeostasis involves factors that ensure proper function of cells. The excess reactive oxygen species (ROS) leads to oxidative stress and increased risk of oxidative damage to cellular components. In contrast, upon reductive stress, insufficient ROS abundance may result in faulty cell signalling. It may be expected that dietary antioxidants, depending on their standard reduction potentials (E°), will affect both scenarios....
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The significance of the properties of water for the working cycle of the kinesin molecular motor
PublicationExplicit solvent molecular dynamics simulations were performed in this study to investigate and discuss several aspects of the influence of the properties of water on the working cycle of a molecular motor from the kinesin superfamily. The main objects of attention were: the binding of the neck linker and the association of the kinesin and the tubulin. The docking of the neck linker is considered a crucial event during the working...
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Unusual Influence of Fluorinated Anions on the Stretching Vibrations of Liquid Water
PublicationInfrared (IR) spectroscopy is a commonly used and invaluable tool in the studies of solvation phenomena in aqueous solutions. Concurrently, ab initio molecular dynamics (AIMD) simulations deliver the solvation shell picture at a molecular detail level and allow for a consistent decomposition of the theoretical IR spectrum into underlying spatial correlations. Here, we demonstrate how the novel spectral decomposition techniques...
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Wpływ osmolitów na stabilność białek w oparciu o metodę dynamiki molekularnej
PublicationCelem niniejszej pracy było zbadanie molekularnego mechanizmu wpływu biologicznie znaczących związków, tzw. osmolitów na stabilność białek. Aby zweryfikować istniejące hipotezy i dostarczyć spójnego obrazu działania osmolitów na poziomie molekularnym, wykorzystano metodę dynamiki molekularnej do zasymulowania mechanicznej denaturacji modelowych białek – lizozymu i ubikwityny. W tym podejściu odtworzony został efekt stabilizujący...
Year 2017
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Characteristic of Morpholinium Ionic Liquids as Gas Chromatography Stationary Phases with McReynolds Constants and Activity Coefficients at Infinite Dilution
PublicationIn this work, four ionic liquids based on N-alkyl-N-methylmorpholinium cation ([Mor1,R] where R= 2, 4, 8, 10) and bis(trifluoromethanesulfonyl)imide anion [TFSI] were synthesized. Using gas-liquid chromatography a number of parameters describing the sorption properties of the investigated ionic liquids were determined. The values of Kovats indices, McReynolds constants, and activity coefficients at infinite dilution were the basis...
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Dominant Pathways of Adenosyl Radical-Induced DNA Damage Revealed by QM/MM Metadynamics
PublicationBrominated nucleobases sensitize double stranded DNA to hydrated electrons, one of the dominant genotoxic species produced in hypoxic cancer cells during radiotherapy. Such radiosensitizers can therefore be administered locally to enhance treatment efficiency within the solid tumor while protecting the neighboring tissue. When a solvated electron attaches to 8-bromoadenosine, a potential sensitizer, the dissociation of bromide...
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Evaluation of Gas Chromatography Stationary Phases Based on Morpholinium Ionic Liquids by McReynolds Constants and Activity Coefficients at Infinite Dilution
PublicationIn this work, four ionic liquids (ILs) based on the N-alkyl-N-methylmorpholinium cation ([Mor1,R], in which R = 2, 4, 8, or 10) and bis (trifluoromethanesulfonyl)imide anion were synthesized. Using GLC, a number of parameters describing the sorption properties of the investigated ILs were determined. The values of Kovats indices, McReynolds constants, and activity coefficients at infinite dilution were the basis for the evaluation...
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Excess molar volume and viscosity deviation for binary mixtures of gamma-butyrolactone with dimethyl sulfoxide
PublicationThe densities of binary liquid mixtures of dimethyl sulfoxide and gamma-butyrolactone at (293.15, 298.15, 303.15 and 313.15) K and viscosity at T=298.15 K have been measured at atmospheric pressure over theentire range of concentration. From these data the excess molar volumes VE at (293.15, 298.15, 303.15 and 313.15) K and the viscosity deviation, the excess entropy, and the excess Gibbs energy of activation for viscous flow at...
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How proteins bind to DNA: target discrimination and dynamic sequence search by the telomeric protein TRF1
PublicationTarget search as performed by DNA-binding proteins is a complex process, in which multiple factors contribute to both thermodynamic discrimination of the target sequence from overwhelmingly abundant off-target sites and kinetic acceleration of dynamic sequence interrogation. TRF1, the protein that binds to telomeric tandem repeats, faces an intriguing variant of the search problem where target sites are clustered within short fragments...
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How water mediates the long-range interactions between remote protein molecules
PublicationThe high crowding of macromolecules in the cytoplasm affects the processes that occur inside a living cell. It can, for example, promote the forming of various loosely connected structures of proteins. It also means that bulk water is, essentially, not present there. The relatively thin layer of solvent that separates macromolecules may be able to participate in the long-range interactions between them and make them respond to...
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Localization and Orientation of Xanthophylls in a Lipid Bilayer
PublicationXanthophylls (polar carotenoids) play diverse biological roles, among which are modulation of the physical properties of lipid membranes and protection of biomembranes against oxidative damage. Molecular mechanisms underlying these functions are intimately related to the localization and orientation of xanthophyll molecules in lipid membranes. In the present work, we address the problem of localization and orientation of two xanthophylls...
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Mechanochemical Energy Transduction during the Main Rotary Step in the Synthesis Cycle of F1-ATPase
PublicationF1-ATPase is a highly efficient molecular motor that can synthesize ATP driven by a mechanical torque. Its ability to function reversibly in either direction requires tight mechanochemical coupling between the catalytic domain and the rotating central shaft, as well as temporal control of substrate binding and product release. Despite great efforts and significant progress, the molecular details of this synchronized and fine-tuned...
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Prosty aparat wykorzystujący technologię osmozy odwróconej do zagęszczania rodzimego soku brzozowego
PublicationW pracy przedstawiono prosty aparat laboratoryjny wykorzystujący technikę osmozy odwróconej, przewidziany do zagęszczania wiosennego soku brzozowego. Wyznaczono punkt pracy urządzenia i przetestowano go na syntetycznym soku drzewnym. Dokonano trójetapowego zagęszczenia pięciu próbek soku naturalnego przy jednoczesnym monitorowaniu procesu. Uzyskano ponad trzykrotne zagęszczenie soku, co dało produkt finalny zawierający 3,7 % suchej...
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Przegląd technik stosowanych do pomiaru potencjału redoks
PublicationPotencjał oksydacyjno-redukcyjny (redoks) charakteryzuje właściwości danej pary redoks, czyli zdolność, jaką posiada substancja do oddawania bądź przyjmowania elektronów. W ostatnich latach pojęcie to zyskuje rosnące zainteresowanie wśród naukowców, zajmujących się stresem oksydacyjnym. Niniejsza praca stanowi przegląd wybranych technik stosowanych do pomiaru potencjału oksydacyjno-redukcyjnego: w tym miareczkowania potencjometrycznego...
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Role of the disulfide bond in stabilizing and folding of the fimbrial protein DraE from uropathogenic Escherichia coli
PublicationDr fimbriae are homopolymeric adhesive organelles of uropathogenic Escherichia coli composed of DraE subunits, responsible for the attachment to host cells. These structures are characterized by enormously high stability resulting from the structural properties of an Ig-like fold of DraE. One feature of DraE and other fimbrial subunits that makes them peculiar among Ig-like domain-containing proteins is a conserved disulfide bond...
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Solvation of ionic liquids based on N-alkyl-N-methylmorpholinium cations in N,N-dimethylformamide and dimethyl sulfoxide – A volumetric and acoustic study
PublicationApparent molar volumes and molar isentropic compressibilities for N-ethyl-N-methylmorpholinium and N-decyl-N-methylmorpholinium tetrafluoroborates in N,N-dimethylformamide (DMF) and dimethyl sulfoxide (DMSO) have been determined from density and speed of sound measurements over the temperature range T = (298.15, 303.15, 308.15, 313.15, 318.15 and 328.15) K at experimental pressure p = 0.1 MPa. This data has been used to calculate...
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The accretion of the new ice layer on the surface of hexagonal ice crystal and the influence of the local electric field on this process
PublicationThe process of creation of a new layer of ice on the basal plane and on the prism plane of a hexagonal ice crystal is analyzed. It is demonstrated that the ordering of water molecules in the already existing crystal affects the freezing. On the basal plane, when the orientations of water molecules in the ice block are random, the arrangement of the new layer in a cubic manner is observed more frequently — approximately 1.7 times...
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Unique agreement of experimental and computational infrared spectroscopy: a case study of lithium bromide solvation in an important electrochemical solvent
PublicationInfrared (IR) spectroscopy is a widely used and invaluable tool in the studies of solvation phenomena in electrolyte solutions. Using state-of-the-art chemometric analysis of a spectral series measured in a concentration-dependent manner, the spectrum of the solute-affected solvent can be extracted, providing a detailed view of the structural and energetic states of the solvent molecules influenced by the solute. Concurrently,...
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Visualizing spatially decomposed intermolecular correlations in the infrared spectra of aprotic liquids
PublicationInfrared (IR) spectroscopy is commonly used to study intermolecular interactions in the liquid phase, including solvation phenomena. On the other hand, ab initio molecular dynamics (AIMD) simulations offer the possibility to obtain IR spectra from first principles. Surpassing the experiment, AIMD simulations can deliver additional information on the spatial intermolecular correlations underlying the IR spectrum of the liquid. Although...
Year 2016
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Anion–water interactions of weakly hydrated anions: molecular dynamics simulations of aqueous NaBF4 and NaPF6
PublicationIn aqueous ionic solutions, both the structure and the dynamics of water are altered dramatically with respect to the pure solvent. The emergence of novel experimental techniques makes these changes accessible to detailed investigations. At the same time, computational studies deliver unique possibilities for the interpretation of the experimental data at the molecular level. Here, using molecular dynamics simulations, we demonstrate...
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Apparent Molar Volumes and Isentropic Compressibilities of Tetraalkylammonium Bromides in Aqueous Propane-1,2-diol. An Attempt to Design Hydraulic Liquids
PublicationApparent molar volumes and apparent molar compressibilities for tetramethylammonium, tetraethylammonium, tetrapropylammonium, and tetrabutylammonium bromides in water, propane-1,2-diol, and water−propane-1,2-diol mixtures (mass fraction: 0.25, 0.50, and 0.75) have been determined from solution density measurements at T = 288.15, 293.15, 298.15, 303.15, 308.15, 313.15, and 318.15 K and sound velocity measurements at T = 298.15 K...
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Application of Ionic Liquids in Amperometric Gas Sensors
PublicationThis article presents an analysis of available literature data on metrological parameters of the amperometric gas sensors containing ionic liquids as an electrolyte. Four mechanism types of signal generation in amperometric sensors with ionic liquid are described. Moreover, this article describes the influence of selected physico-chemical properties of the ionic liquids on the metrological parameters of these sensors. Some metrological...
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Ciecze jonowe w technikach mikroekstrakcyjnych - cz. I. Struktura i właściwości fizykochemiczne
PublicationCiecze jonowe stanowią bradzo rozbudowaną grupę substancji, cechującą się ogromnym potencjałem zastosowania w różnych dziedzinach chemii.
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Ciecze jonowe w technikach mikroekstrakcyjnych. Cz. II. Praktyka analityczna.
PublicationRosnące od lat zainteresowanie cieczami jonowymi, wynikające z ich unikalnych właściwości fizykochemicznych, znalazło odzwierciedlenie w ich wykorzystaniu jako rozpuszczalników w chemii analitycznej, w tym szczególnie w wielu technikach przygotowania próbek do analizy. Ciecze jonowe zastosowano jako materiał sorpcyjny w takich technikach jak: mikroekstrakcja do fazy stacjonarnej SPME; mikroekstrakcja do pojedynczej kropli, SDME...
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Correlated Particle Motion and THz Spectral Response of Supercritical Water
PublicationMolecular dynamics simulations of supercritical water reveal distinctly different distance-dependent modulations of dipolar response and correlations in particle motion compared to ambient conditions. The strongly perturbed H-bond network of water at supercritical conditions allows for considerable translationaland rotational freedom of individual molecules. These changes give rise to substantially different infrared spectra and...
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Correlation between the number of Pro-Ala repeats in the EmrA homologue of Acinetobacter baumannii and resistance to netilmicin, tobramycin, imipenem and ceftazidime
PublicationAcinetobacter baumannii coccobacilli are dangerous to patients in intensive care units because of their multidrug resistance to antibiotics, developed mainly in the past decade. This study aimed to examine whether there is a significant correlation between the number of Pro-Ala repeats in the CAP01997 protein, the EmrA homologue of A. baumannii, and resistance to antibiotics. A total of 79 multidrug-resistant A. baumannii strains...
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Cross-linked epoxy-isocyanate blends containing Epidian-6 modified by glycols
PublicationPolymeric films of cross-linked structure may be formed using epoxy-isocyanate blends composed of Epidian-5 epoxy resin, 4,4’-diphenylmethanediisocyanate (MDI), Z-1 polyamine hardener and Epidian-6 epoxy resin modified by glycols. The effect of the component natures and ratio, process temperature and time on the gel-fraction content, as well as film hardness, was examined. The chemistry of the film forming process was determined...
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General Mechanism of Osmolytes’ Influence on Protein Stability Irrespective of the Type of Osmolyte Cosolvent
PublicationThe 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...