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Search results for: solvation water
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Why the solvation water around proteins is more dense than bulk water
PublicationThe main aim of this work is to propose a rational explanation of commonly observed phenomenon of increasing water density within solvation shell of proteins. We have observed that geometry of the water-water hydrogen bond network within solvation layer differs from the one in bulk water and it is the effect of interactions of water molecules with protein surface. Altered geometry of the network reflects changes in the structure...
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Why the Solvation Water around Proteins Is More Dense than Bulk Water
PublicationThe main aim of this work is to propose a rational explanation of the commonly observed phenomenon of increasing water density within solvation shell of proteins. We have observed that the geometry of the water–water hydrogen bond network within solvation layer differs from the one in bulk water, and it is the result of interactions of water molecules with protein surface. Altered geometry of the network reflects changes in the...
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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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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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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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Structural and dynamic properties of water within the solvation layer around various conformations of the glycine-based polypeptide
PublicationSeveral conformations of the solvated glycine-based polypeptides were investigated using molecular dynamics simulations. Some properties of water in the neighbouring space around these molecules were investigated. It was found, that water forms a well-defined layer - the first solvation shell - around the peptide molecule, and thickness of this layer is independent of the peptide structure, and it equals to approximately 0.28 nm....
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Structural and Dynamic Properties of Water within the Solvation Layer around Various Conformations of the Glycine-based Polypeptide
PublicationSeveral conformations of the solvated glycine-based polypeptides were investigated using molecular dynamics simulations. Some properties of water in the neighboring space around these molecules were investigated. It was found that water forms a well-defined layer—the first solvation shell—around the peptide molecule, and thickness of this layer is independent of the peptide structure and is equal to approximately 0.28 nm. Within...
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Revealing the Frank–Evans “Iceberg” Structures within the Solvation Layer around Hydrophobic Solutes
PublicationUsing computer simulations, the structural properties of solvation water of three model hydrophobic molecules, methane and two fullerenes (C60 and C80), were studied. Systems were simulated at temperatures in the range of 250−298 K. By analyzing both the local ordering of the molecules of water in the solvation layers and the structure of hydrogen bond network, it is shown that in the solvation layer of hydrophobic molecules, ordered...
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Mechanism of antifreeze protein functioning and the “anchored clathrate water” concept
PublicationIn liquid water, there is a natural tendency to form aggregates that consist of water molecules linked by hydrogen bonds. Such spontaneously formed aggregates are surrounded by a "sea" of disordered water molecules, with both forms remaining in equilibrium. The process of creating water aggregates also takes place in the solvation water of proteins, but in this case the interactions of water molecules with the protein surface shift...
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Unusual structural properties of water within the hydration shell of hyperactive antifreeze protein
PublicationMany hypotheses can be encountered explaining the mechanism of action of antifreeze proteins. One widespread theory postulates that the similarity of structural properties of solvation water of antifreeze proteins to ice is crucial to the antifreeze activity of these agents. In order to investigate this problem, the structural properties of solvation water of the hyperactive antifreeze protein from Choristoneura fumiferana were...
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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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Structural properties of hydration shell around various conformations of simple polypeptides
PublicationIn this paper we investigate structural properties of water within the solvation shell around the peptide core created by a well-defined conformation of polypeptide chain. The following secondary structures are investigated: linear (straight chain), and three helices PII (polyproline-like), 310, and α. We propose using the two-particle contribution to entropy as a rational measure of the water structural ordering within the solvation...
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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
PublicationSingle 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
PublicationA 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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Properties of water in the region between a tubulin dimer and a single motor head of kinesin
PublicationA kinesin is a molecular motor that can perform movement on a microtubule track in a stepping-like manner. This motion is connected with processes of association and dissociation of kinesin and tubulin. Water is an important participant in these kinds of molecular interactions. This is why we have decided to investigate the dynamical and structural properties of water in the region between the kinesin catalytic domain and the tubulin...
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Can cooperativity in hydrophobic association be reproduced correctly by implicit solvation models?
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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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Solvation of N-methylformamide by ethanol: a comparison of molecular dynamics calculations with the experimental data
PublicationWykonano obliczenia metodami dynamiki molekularnej dla tytułowego układu. Rezultaty porównano z uzyskanymi wcześniej wynikami pomiarów termodynamicznych oraz wnioskami z nich wyciągniętymi.
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Solvation of multivalent cations in methanol - apparent molar volumes, expansibilities, and isentropic compressibilities
PublicationWyznaczono gęstości roztworów trifluorometanosulfonianów galu, itru, lantanu, gadolinu i lutetu w metanolu w zakresie temperatur (283.15 to 313.15) K. Zmierzono prędkości dźwięku dla tych układów w temperaturze T = 298.15 K. Z uzyskanych danych wyznaczono standardowe cząstkowe objętości molowe i ich pochodne temperaturowe oraz standardowe cząstkowe molowe ściśliwości adiabatyczne badanych jonów. Wyniki omówiono stosując klasyczny...
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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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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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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....
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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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Analysis of the enthalpies of transfer of Co(II) ion in mixed solvents by means of the theory of preferential solvation.
PublicationZa pomocą teorii solwatacji preferencyjnej zanalizowano entalpie przeniesienia jonu Co(II) w kilku mieszaninach wodno-organicznych i organicznych, wyznaczając parametry, które w sposób ilościowy opisują solwatację preferencyjną jonu i jego wpływ na oddziaływania między cząsteczkami rozpuszczalnika. Przeprowadzono porównanie właściwości solwatacyjnych mieszanin. Wyznaczono także średni skład sfery solwatacyjnej jonu w zależności...
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Calculating the Partition Coefficients of Organic Solvents in Octanol/Water and Octanol/Air
PublicationPartition coefficients define how a solute is distributed between two immiscible phases at equilibrium. The experimental estimation of partition coefficients in a complex system can be an expensive, difficult, and time-consuming process. Here a computational strategy to predict the distributions of a set of solutes in two relevant phase equilibria is presented. The octanol/water and octanol/air partition coefficients are predicted...
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The hydrogen bond network structure within the hydration shell around simple osmolytes: Urea, tetramethylurea, and trimethylamine-N-oxide, investigated using both a fixed charge and a polarizable water model
PublicationDespite numerous experimental and computer simulation studies, a controversy still exists regarding the effect of osmolytes on the structure of surrounding water. There is a question, to what extent some of the contradictory results may arise from differences in potential models used to simulate the system or parameters employed to describe physical properties of the mixture and interpretation of the results. Bearing this in mind,...
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The hydrogen bond network structure within the hydration shell around simple osmolytes: Urea, tetramethylurea, and trimethylamine-N-oxide, investigated using both a fixed charge and a polarizable water model
PublicationDespite numerous experimental and computer simulation studies, a controversy still exists regarding the effect of osmolytes on the structure of surrounding water. There is a question, to what extent some of the contradictory results may arise from differences in potential models used to simulate the system or parameters employed to describe physical properties of the mixture and interpretation of the results. Bearing this in mind,...
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Solvation and partial molar volumes of some transition metal cations in N,N-dimethylacetamide, triethylphosphate and acetonitrile.
PublicationW oparciu o precyzyjne pomiary gęstości roztworów nadchloranów metali przejściowych szeregu Mn(II)-Zn(II) w DMA, TEP i AN wyznaczono pozorne molowe oraz graniczne wartości cząstkowych molowych objętości sole w temperaturach 293, 298 i 303,15 K. Wyznaczone wartości rozdzielono na udziały jonowe. Przeanalizowano czynniki decydujące o wielkości cząstkowych molowych objętości solwatowanych kationów.
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Solvation numbers of manganese(II) and zinc(II) perchlorates in methanol obtained from volumetric and compressibility properties
PublicationZmierzono gęstości roztworów nadchloranów manganu(II) i cynku(II) w metanolu w temperaturach: 283.15, 288.15, 293.15, 298.15, 303.15, 308.15, 313.15 K. Ponadto wyznaczono szybkości rozchodzenia się dźwięku w badanych roztworach w 298.15 K. Uzyskane wielkości pozwoliły na obliczenie pozornych objętości molowych oraz pozornych molowych ściśliwości adiabatycznych elektrolitów w metanolu. Oszacowane wielkości graniczne wykorzystane...
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Chemometric determination of solute-affected solvent vibrational spectra as a superior way of information extraction on solute solvation phenomena
PublicationW pracy zaprezentowano dwie chemometryczne metody wyznaczania widm zaburzonych rozpuszczalnika oraz liczby cząsteczek zaburzonych, na podstawie zmierzonych serii wibracyjnych widm FT-IR roztworów substancji. Pierwsza z metod została stworzona na podstawie Namiarowej Analizy Faktorowej (ang. Target Factor Analysis). Druga z nich wykorzystuje algorytm izolacji widm czystych składników z serii widm mieszanin. Działanie obu metod zostało...
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Solvation of cobalt(II) ion in N,N-dimethylformamide-methanol mixed solvent: calorimetry and VIS spectroscopy studies
PublicationZmierzono entalpie rozpuszczania trifluorometanosulfonianów Co(II) i Na(I) w mieszaninie N,N-dimetyloformamid(DMF)-metanol(MeOH) w całym zakresie jej składu. Z danych tych wyznaczono entalpie przeniesienia jonu Co(II) i jonu trifluorometanosulfonowego. Wyniki zanalizowano za pomocą teorii solwatacji preferencyjnej. Zmierzono również widma w zakresie widzialnym roztworów jonu Co(II) w mieszaninie DMF-MeOH i zanalizowano je, stosując...
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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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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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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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Solvation of cobalt(II) and trifluoromethanesulfonate ions in N,N-dimethylformamide-methanol mixed solvent studied by means of FT-IR spectroscopy
PublicationWidma FT-IR roztworów Co(CF3SO3)2-N,N-dimetyloformamid-metanol były analizowane w zakresie pasm CO i OH za pomocą metody widm różnicowych. Wyznaczono liczbę cząsteczek DMF i MeOH w pierwszej sferze solwatacji jonu Co(II) w zależności od składu rozpuszczalnika. Stwierdzono także obecność drugiej sfery solwatacji jonu Co(II) i scharakteryzowano ją ilościowo. Zbadano również solwatację jonu tifluorometanosulfonowego oraz asocjację...
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Solvation of 2-(hydroxymethyl)-2,5,7,8-tetramethyl-chroman-6-ol revealed by circular dichroism: a case of chromane helicity rule breaking
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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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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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Performance of the AMOEBA Water Model in the Vicinity of QM Solutes: A Diagnosis Using Energy Decomposition Analysis
PublicationThe importance of incorporating solvent polarization effects into the modeling of solvation processes has been well-recognized, and therefore a new generation of hybrid quantum mechanics/molecular mechanics (QM/MM) approaches that accounts for this effect is desirable. We present a fully self-consistent, mutually polarizable QM/MM scheme using the AMOEBA force field, in which the total energy of the system is variationally minimized...
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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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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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Preferential solvation in (amide+alcohol) binary mixtures. Part 2. The N-methylpyrrolidinone+methanol mixture at T = 313.15 K: thermodynamic resultsand molecular dynamics calculations.
PublicationBadano zjawisko preferencyjnej solwatacji amidu (N-metylopyrrolidonu) przez metanol wykorzystując dwie uzupełniające się metody: bezpośrednich pomiarów własności termodynamicznych roztworu oraz symulacji komputerowych. W metodzie pierwszej dokonano pomiarów wielkości termodynamicznych takich jak: nadmiarowa energia swobodna mieszania, nadmiarowa objętość mieszania oraz współczynnika ściśliwości izotermicznej mieszaniny,...
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Preferential solvation in (amide+alcohol) binary mixtures. Part 1. The N- methylpyrrolidinone+ethanol mixture at T = 313.15 K: thermodynamic resultsand molecular dynamics calculations.
PublicationBadano zjawisko preferencyjnej solwatacji amidu (N-metylopyrrolidonu) przez etanol wykorzystując dwie uzupełniające się metody: bezpośrednich pomiarów własności termodynamicznych roztworu oraz symulacji komputerowych. W metodzie pierwszej dokonano pomiarów wielkości termodynamicznych takich jak: nadmiarowa energia swobodna mieszania, nadmiarowa objętość mieszania oraz współczynnika ściśliwości izotermicznej mieszaniny,...
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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...
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The influence of intermolecular correlations on the infrared spectrum of liquid dimethyl sulfoxide
PublicationDimethyl sulfoxide (DMSO) is routinely applied as an excellent, water-miscible solvent and chemical reagent. Some of the most important data concerning its liquid structure were obtained using infrared (IR) spectroscopy. However, the actual extent of intermolecular correlations that connect the isolated monomer spectrum to the IR response of the bulk liquid is poorly studied thus far. Using ab initio molecular dynamics (AIMD) simulations,...
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Electronically Excited States in Solution via a Smooth Dielectric Model Combined with Equation-of-Motion Coupled Cluster Theory
PublicationWe present a method for computing excitation energies for molecules in solvent, based on the combination of a minimal parameter implicit solvent model and the equation-of-motion coupled-cluster singles and doubles method (EOM-CCSD). In this method, the solvent medium is represented by a smoothly varying dielectric function, constructed directly from the quantum mechanical electronic density using only two tunable parameters. The...
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Mutually polarizable QM/MM model with in situ optimized localized basis functions
PublicationWe extend our recently developed quantum-mechanical/molecular mechanics (QM/MM) approach [Dziedzic et al., J. Chem. Phys. 145, 124106 (2016)] to enable in situ optimization of the localized orbitals. The quantum subsystem is described with ONETEP linear-scaling density functional theory and the classical subsystem – with the AMOEBA polarizable force field. The two subsystems interact via multipolar electrostatics and are fully...
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Solvent dependency of carbon dioxide Henry's constant in aqueous solutions of choline chloride-ethylene glycol based deep eutectic solvent
PublicationThe Henry's constants of carbon dioxide absorbed in aqueous solutions of ethaline (choline chloride-ethylene glycol) were determined for temperatures ranging from 303.15 to 323.15 K based on solubility measurement at CO2 pressure ranging from 0 to 6 bar (0.6 MPa). These studies revealed that the Henry's constant increased with the increase of temperature. Data indicated the highest capacity of CO2 absorption is obtained for ethaline...
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Albumin–Hyaluronan Interactions: Influence of Ionic Composition Probed by Molecular Dynamics
PublicationThe lubrication mechanism in synovial fluid and joints is not yet fully understood. Nevertheless, intermolecular interactions between various neutral and ionic species including large macromolecular systems and simple inorganic ions are the key to understanding the excellent lubrication performance. An important tool for characterizing the intermolecular forces and their structural consequences is molecular dynamics. Albumin...
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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...