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Department of Physical Chemistry
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Year 2017
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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...
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Indirect Determination of MCPD Fatty Acid Esters in Lipid Fractions of Commercially Available Infant Formulas for the Assessment of Infants’ Health Risk
PublicationMCPD esters are intensively investigated food lipid contaminants for over a decade. Concern related to their presence in various types of food products is related to the fact that possible free MCPD release from its esterified form during digestion may lead to elevated daily intake of these toxicants.Special attention should be devoted into powdered infant formulas, which contain significant amounts of refined vegetable oils, likely...
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Intercalation complex of imidazoacridinone C-1311, a potential anticancer drug, with DNA helix d(CGATCG)2: stereostructural studies by 2D NMR spectroscopy.
PublicationImidazoacridinone C-1311 (Symadex®) is a powerful antitumor agent, which successfully made its way through the Phase I clinical trials and has been recommended for Phase II few a years ago. It has been shown experimentally that during the initial stage of its action C-1311 forms a relatively stable intercalation complex with DNA, yet it has shown no base-sequence specificity while binding to DNA. In this paper, the d(CGATCG)2:C-1311...
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Intramolecular transformation of an antifungal antibiotic nystatin A1 into its isomer, iso-nystatin A1 - structural and molecular modeling studies
PublicationNystatin A1, a polyene macrolide antifungal antibiotic, in a slightly basic or acidic solution undergoes an intramolecular transformation, yielding a structural isomer, the translactonization product, iso-nystatin A1 with lactone ring diminished by two carbon atoms. Structural evidence is provided by advanced NMR and Mass Spectrometry (MS) studies. Molecular dynamics simulations and quantum mechanics calculations gave the insight...
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Iron–Sulfur Cluster Biogenesis Chaperones: Evidence for Emergence of Mutational Robustness of a Highly Specific Protein–Protein Interaction
PublicationBiogenesis of iron–sulfur clusters (FeS) is a highly conserved process involving Hsp70 and J-protein chaperones. However, Hsp70 specialization differs among species. In most eukaryotes, including Schizosaccharomyces pombe, FeS biogenesis involves interaction between the J-protein Jac1 and the multifunctional Hsp70 Ssc1. But, in Saccharomyces cerevisiae and closely related species, Jac1 interacts with the specialized Hsp70 Ssq1,...
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Membrane Sterols Modulate the Binding Mode of Amphotericin B without Affecting Its Affinity for a Lipid Bilayer
PublicationMembrane-active antibiotics are known to selectively target certain pathogens based on cell membrane properties, such as fluidity, lipid ordering, and phase behavior. These are in turn modulated by the composition of a lipid bilayer and in particular by the presence and type of membrane sterols. Amphotericin B (AmB), the golden standard of antifungal treatment, exhibits higher activity toward ergosterol-rich fungal membranes, which...
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Molecular basis of the osmolyte effect on protein stability: a lesson from the mechanical unfolding of lysozyme
PublicationOsmolytes 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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Molecular dynamics simulations reveal the balance of forces governing the formation of a guanine tetrad—a common structural unit of G-quadruplex DNA
PublicationG-quadruplexes (G4) are nucleic acid conformations of guanine-rich sequences, in which guanines are arranged in the square-planar G-tetrads, stacked on one another. G4 motifs form in vivo and are implicated in regulation of such processes as gene expression and chromosome maintenance. The structure and stability of various G4 topologies were determined experimentally; however, the driving forces for their formation are not fully...
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Principles and Developments of Solid-Phase Microextraction
PublicationSample preparation has been commonly considered a critical step of the analytical process. In this sense, remarkable efforts have been made to develop efficient sample preparation techniques which could overcome the limitations of conventional approaches. Since its inception in the early 1990’s, solid-phase microextraction (SPME) has become a widespread miniaturized sample preparation technique for extraction and preconcentration...
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Protein thermal stabilization in aqueous solutions of osmolytes
PublicationProteins’ thermal stabilization is a significant problem in various biomedical, biotechnological, and technological applications. We investigated thermal stability of hen egg white lysozyme in aqueous solutions of the following stabilizing osmolytes: Glycine (GLY), N-methylglycine (NMG), N,N-dimethylglycine (DMG), N,N,N-trimethylglycine (TMG), and trimethyl-N-oxide (TMAO). Results of CD-UV spectroscopic investigation were compared...
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Solvation of alkaline earth metal ions in N,N-dimethylformamide and N,N-dimethylacetamide – A volumetric and acoustic study
PublicationDensities and sound velocities at temperatures (298.15, 303.15, 308.15, 313.15 and 318.15) K of magnesium(II), calcium(II) and strontium(II) rifluoromethanesulfonates (triflates), as well as barium(II) perchloratein N,N-dimethylformamide (dmf) and N,N-dimethylacetamide (dma) have been measured over the composition range studied. From these results, apparent molar volumes and apparent molar isentropic compressibilities at infinite...
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Structure of solvation water around the active and inactive regions of a type III antifreeze protein and its mutants of lowered activity
PublicationWater molecules from the solvation shell of the ice-binding surface are considered important for the antifreeze proteins to perform their function properly. Herein, we discuss the problem whether the extent of changes of the mean properties of solvation water can be connected with the antifreeze activity of the protein. To this aim, the structure of solvation water of a type III antifreeze protein from Macrozoarces americanus (eel...
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Synthesis and properties of carboxy derivative of Epidian 6 monomethacrylate (in English)
PublicationWe present the synthesis of an oligomer with carboxy and methacrylic groups based on Epidian 6. The effect of the catalyst nature and amount, solvent nature and process temperature on the rate of the reaction between Epidian6 monomethacrylate and adipic acid was examined at 313, 323 and 333 K in the presence of 4-dimethylaminopyridine, 1,4-diazobicyclo[2.2.2]octane, and benzyltriammonium chloride. The synthesized oligomer was characterized...
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Thermodynamics and kinetics of amphotericin B self-association in aqueous solution characterized in molecular detail
PublicationAmphotericin B (AmB) is a potent but toxic drug commonly used to treat systemic mycoses. Its efficiency as a therapeutic agent depends on its ability to discriminate between mammalian and fungal cell membranes. The association of AmB monomers in an aqueous environment plays an important role in drug selectivity, as oligomers formed prior to membrane insertion – presumably dimers – are believed to act differently on fungal (ergosterol-rich)...
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Układy uC szansą na masową popularyzację elektroniki
PublicationFelieton popularnonaukowy dotyczący przyszłości elektroniki.
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Water-mediated influence of a crowded environment on internal vibrations of a protein molecule
PublicationThe influence of crowding on the protein inner dynamics is examined by putting a single protein molecule close to one or two neighboring protein molecules. The presence of additional molecules influences the amplitudes of protein fluctuations. Also, a weak dynamical coupling of collective velocities of surface atoms of proteins separated by a layer of water is detected. The possible mechanisms of these phenomena are described....
Year 2015
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Are stabilizing osmolytes preferentially excluded from the protein surface? FTIR and MD studies
PublicationInteractions 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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Determination of Hydroxy Groups in the Modified Epoxy Oligomers Using IR-Spectroscopy
PublicationThe use of IR-spectroscopy has been proposed to determine the content of hydroxy groups in the modified functional oligomers based on bisphenol A diglycidyl ether. Apart from hydroxy groups the investigated oligomers contain epoxy or peroxy, carboxy or acrylic groups.
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Effect of temperature and ionic strength on volumetric and acoustic properties of solutions of urea alkil derivatives in aqueous NaCl
PublicationThe present work was undertaken to study volumetric and acoustic properties for diluted solutions of tetramethylurea in pure water and for urea, n-propylurea, n-butylurea and tetramethylurea in 0.5 or 1 moldm3 aqueous solutions of sodium chloride. This paper presents measured values of densities and sound velocities at T = (288.15, 298.15 and 308.15) K. From these data the apparent molar volumes, , adiabatic compressibilities,...
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Evaluation of polycaprolactone as a new sorbent coating for determination of polar organic compounds in water samples using membrane–SPME
PublicationCommercially available solid-phase microextraction fibers used for isolation of polar analytes are based on the adsorption phenomenon. In consequence, typical limitations bonded with analytes displacement and matrix effects are very frequent. In the present study, alternative solution is described. Polycaprolactone (PCL) was used for the first time as sorbent to isolate polar organic compounds from water samples using the membrane–solid-phase...
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Hydration of amino acids: FTIR spectra and molecular dynamics studies
PublicationThe 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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Interaction of cisplatin and two potential antitumoral platinum(ii) complexes with a model lipid membrane: a combined NMR and MD study
PublicationIn this study, the interaction of cisplatin (1) and two potential antitumoral Pt(II) complexes (2 and 3) with a model DMPC bilayer was investigated by multinuclear NMR spectroscopy and MD simulations in order to understand its implication for the different antitumoral properties shown by the three complexes. In particular, 31P, 13C and 2H solid state NMR experiments were performed to obtain information on the phase structure, phase...
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Ionogel fibres of bis(trifluoromethanesulfonyl)imide anion-based ionic liquids for the headspace solid-phase microextraction of chlorinated organic pollutants
PublicationIonogels, a family of hybrid materials in which ionic liquids (ILs) are confined in a sol–gel network, are receiving much attention in a variety of scientific and technological fields. In this work, ionogels derived from three different ILs based on the anion bis(trifluoromethanesulfonyl)imide (TFSI), namely 1-butyl- 3-methylpyridinium bis(trifluoromethanesulfonyl)imide ([C4C1Py][TFSI]), 1-butyl-1-methylpyrrolidinium bis(trifluoromethanesulfonyl)imide...
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Molecular hydrogen solvated in water – A computational study
PublicationThe 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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Nowe rozwiązania metodyczne i techniczne w zakresie techniki mikroekstrakcji do fazy stracjonarnej
PublicationSample preparation has been recognized as a critical step of the analytical process, being even considered as the bottleneck of the overall process. Enrichment of target compounds, transfer of the analytes into a solvent compatible with the analytical instrumentation, minimization of potential interferences, and efficient sample clean-up, are among the main aims of sample preparation techniques. In this regard, liquid-liquid extraction...
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Opportunities and shortcomings of ionic liquids in single-drop microextraction
PublicationThe synergistic combination of ionic liquids (ILs) and single-drop microextraction (SDME) involves a powerful coupling toward the development of sustainable analytical methodologies. This overview provides a survey of the literature regarding the IL-SDME, including a database on relevant physicochemical properties of ILs for their application in SDME, the strategies implemented to combine IL-based SDME methods efficiently with...
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Perspectives on the replacement of harmful organic solvents in analytical methodologies: a framework toward the implementation of a generation of eco-friendly alternatives
PublicationVolatile organic solvents derived from non-renewable fossil feedstocks are commonplace in analytical laboratories. In spite of their convenient performance in countless unit operations, their environmental, health and safety issues represent a major area of concern. The progressive replacement of organic solvents obtained from fossil resources by eco-friendly alternatives would involve remarkable advances within the framework of...
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Solvation of ionic liquids based on N-methyl-N-alkyl morpholinium cations in dimethylsulfoxide – volumetric and compressibility studies
PublicationThe density and sound velocity of the solutions of ionic liquids based on N-alkyl-N-methyl-morpholinium cations, N-ethyl-N-methylmorpholinium bis(trifluoromethanesulfonyl)imide, N-butyl-N-methylmorpholinium bis(trifluoromethanesulfonyl)imide, N-methyl-N-octyl-morpholinium bis(trifluoromethanesulfonyl)imide and N-decyl-N-methylmorpholinium bis(trifluoromethanesulfonyl)imide in dimethylsulfoxide were measured at T = (298.15 to 318.15)...
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Specific Binding of Cholesterol to the Amyloid Precursor Protein: Structure of the Complex and Driving Forces Characterized in Molecular Detail
PublicationC99 is the C-terminal membrane-bound fragment of the amyloid precursor protein that is cleaved by γ-secretase to release Aβ peptides, the hallmark of Alzheimer’s disease (AD). Specific interactions of C99 with cholesterol have been proposed to underlie the recognized role of cholesterol in promoting amyloidogenesis. By using molecular dynamics simulations, we studied cholesterol binding to C99 in a lipid bilayer. We determined...
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Unusual dynamic properties of water near the ice-binding plane of hyperactive antifreeze protein
PublicationThe dynamical properties of solvation water of hyperactive antifreeze protein from Choristoneura fumiferana (CfAFP) are analyzed and discussed in context of its antifreeze activity. The protein comprises of three well-defined planes and one of them binds to the surface of ice. The dynamical properties of solvation water around each of these planes were analyzed separately; the results are compared with the dynamical properties...
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Water-mediated long-range interactions between the internal vibrations of remote proteins
PublicationIt is generally acknowledged that the mobility of protein atoms and the mobility of water molecules in the solvation layer are connected. In this article, we answer the question whether a similar interdependence exists between the motions of atoms of proteins separated by the hydration layers of variable thickness. The system consisted of a kinesin catalytic domain and a tubulin dimer. It was studied using molecular dynamics simulations....
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Wykorzystanie cieczy jonowych jako materiałów sorpcyjnych w technice mikroekstrakcji do fazy stacjonarnej
PublicationW rozprawie doktorskiej przedstawiono podsumowanie wyników badań prowadzonych w okresie od 2011 do 2015 roku w ramach studium doktoranckiego. Prowadzone prace były ukierunkowane na sprawdzenie możliwości wykorzystania cieczy jonowych jako składników materiałów sorpcyjnych do pokrycia włókna ekstrakcyjnego w urządzeniu do SPME.
Year 2014
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A first-principles study of electron attachment to the fully hydrated bromonucleobases
PublicationDegradation mechanism of four brominated nucleobases (BrX), potential DNA radiosensitizers, is studied in explicit water solution, using ab initio molecular dynamics. Several fs long dynamics is needed to localize an electron on the nucleobase. Produced by electron attachment BrX anion radical degrades through the bromide anion abstraction, barrier-free (purines) or with low barrier (pyrimidines), to a reactive nucleobase radical....
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Apparent Molar Volumes and Expansivities of Ionic Liquids Based on N-Alkyl-N-methylmorpholinium Cations in Acetonitrile
PublicationDensities of some acetonitrile solutions of ionic liquids based on N-alkyl-N-methyl-morpholinium cations, N-ethyl-N-methylmorpholinium bis(trifluoromethanesulfonyl)imide, N-butyl-N-methylmorpholinium bis(trifluoromethanesulfonyl)imide, N-methyl-N-octylmorpholinium bis(trifluoromethanesulfonyl)imide and N-decyl-N-methylmorpholinium bis(trifluoromethanesulfonyl)imide were measured at T = (298.15− 318.15) K and at atmospheric pressure....