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Wyniki wyszukiwania dla: solvation
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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
PublikacjaDespite 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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Theoretical investigation of the structural insights of the interactions of γ-Fe2O3 nanoparticle with (EMIM TFSI) ionic liquid
PublikacjaOne of the possible applications of ionic liquids is to produce electricity from heat. The iron oxide nanoparticle is a potent electrical particle, which is expected to improve the heat’s efficiency to electricity conversion, however, it is prone to aggregation and sedimentation, which hamper its application. One of the methods to enhance the nanoparticle’s solubility and electrical properties is the use of a stabilizing component...
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Structural changes of water caused by non-electrolytes: Volumetric and compressibility approach for urea-like analogues
PublikacjaHydration 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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The influence of intermolecular correlations on the infrared spectrum of liquid dimethyl sulfoxide
PublikacjaDimethyl 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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Micelle formation of Tween 20 nonionic surfactant in imidazolium ionic liquids
PublikacjaAggregation behavior of polyoxyethylene (POE)-type nonionic surfactant Tween 20 in imidazolium ionic liquids with varying chain length and different anions, such as tetrafluoroborate, hexafluorophosphate, bis(trifluoromethanesulfonyl)imide, and trifluoromethanesulfonate, was investigated by means of surface tension, conductivity and dynamic light scattering measurements. The role of the chain length, anion size as well as interactions...
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Photoinduced electron transfer in 5-bromouracil labeled DNA. A contrathermodynamic mechanism revisited by electron transfer theories
PublikacjaThe understanding of the 5-bromouracil (BrU) based photosensitization mechanism of DNA damage is of large interest due to the potential applications in photodynamic therapy. Photoinduced electron transfer (ET) in BrU labeled duplexes comprising the 50 -GBrU or 50 -ABrU sequence showed that a much lower reactivity was found for the 50 -GBrU pattern. Since the ionization potential of G is lower than that of A, this sequence selectivity...
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Spectroscopic and photophysical properties of ZNTPP in a room temperature ionic liquid
PublikacjaThe steady-state absorption and emission spectra and the time-resolved Soret- and Q-band excited fluorescence profiles of the model metalloporphyrin, ZnTPP, have been measured in a highly purified sample of the common room temperature ionic liquid, [bmim][PF(6)]. S(2)-S(0) emission resulting from Soret-band excitation behaves in a manner completely consistent with that of molecular solvents of the same polarizability. The ionic...
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Calculating the Partition Coefficients of Organic Solvents in Octanol/Water and Octanol/Air
PublikacjaPartition 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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Self-assembly, stability and conductance of amphotericin B channels: bridging the gap between structure and function
PublikacjaAmphotericin B (AmB), one of the most powerful but also toxic drugs used to treat systemic mycoses, is believed to selectively permeabilize fungal cell membranes to ions in a sterol-dependent manner. Unfortunately, the structure of the biologically active AmB channels has long eluded researchers, obstructing the design of safer alternatives. Here, we investigate the structural and thermodynamic aspects of channel formation, stability,...
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Radiative lifetime of a BODIPY dye as calculated by TDDFT and EOM-CCSD methods: solvent and vibronic effects
PublikacjaThe radiative emission lifetime and associated S1 excited state properties of a BODIPY dye are investigated with TDDFT and EOM-CCSD calculations. The effects of a solvent are described with the polarizable continuum model using the linear response (LR) approach as well as state-specific methods. The Franck–Condon (FC), Herzberg–Teller (HT) and Duschinsky vibronic effects are evaluated for the absorption and emission spectra, and...
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Effect of osmolytes of different type on DNA behavior in aqueous solution. Experimental and theoretical studies
PublikacjaOsmolytes, 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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Albumin–Hyaluronan Interactions: Influence of Ionic Composition Probed by Molecular Dynamics
PublikacjaThe 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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Manifestation of Intermolecular Interactions in the IR Spectra of 2- and 4-Methylmethcathinones Hydrochlorides: DFT Study and Hirshfeld Surfaces Analysis
PublikacjaThis paper reports a Hirshfeld surfaces analysis of crystalline 2- and 4-methylmethcathinone (2-MMC and 4-MMC) hydrochlorides to analyze NH∙Cl and CH∙∙∙Cl intermolecular interactions and approve the formation of the NН2+–Cl– salt fragment in both 2-MMC∙HCl and 4-MMC∙HCl crystals. Two isomeric dimers were separated from the corresponding crystal packing to model IR spectra of the crystalline 2-MMC∙HCl...
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Solvent dependency of carbon dioxide Henry's constant in aqueous solutions of choline chloride-ethylene glycol based deep eutectic solvent
PublikacjaThe 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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Ionic liquids for nano- and microstructures preparation. Part 1: Properties and multifunctional role
PublikacjaIonic liquids (ILs) are a broad group of organic salts of varying structure and properties, used in energy conversion and storage, chemical analysis, separation processes, as well as in the preparation of particles in nano- and microscale. In material engineering, ionic liquids are applied to synthesize mainly metal nanoparticles and 3D semiconductor microparticles. They could generally serve as a structuring agent or as a reaction...
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Multicomponent ionic liquid CMC prediction
PublikacjaWe created a model to predict CMC of ILs based on 704 experimental values published in 43 publications since 2000. Our model was able to predict CMC of variety of ILs in binary or ternary system in a presence of salt or alcohol. The molecular volume of IL (Vm), solvent-accessible surface (Sˆ), solvation enthalpy (DsolvGN), concentration of salt (Cs) or alcohol (Ca) and their molecular volumes (Vms and Vma, respectively) were chosen...
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Thermodynamics and Intermolecular Interactions of Nicotinamide in Neat and Binary Solutions: Experimental Measurements and COSMO-RS Concentration Dependent Reactions Investigations
PublikacjaIn this study, the temperature-dependent solubility of nicotinamide (niacin) was measured in six neat solvents and five aqueous-organic binary mixtures (methanol, 1,4-dioxane, acetonitrile, DMSO and DMF). It was discovered that the selected set of organic solvents offer all sorts of solvent effects, including co-solvent, synergistic, and anti-solvent features, enabling flexible tuning of niacin solubility. In addition, differential...
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Collagen type II–hyaluronan interactions – the effect of proline hydroxylation: a molecular dynamics study
PublikacjaHyaluronan–collagen composites have been employed in numerous biomedical applications. Understanding the interactions between hyaluronan and collagen is particularly important in the context of joint cartilage function and the treatment of joint diseases. Many factors affect the affinity of collagen for hyaluronan. One of the important factors is the ratio of 3- or 4-hydroxy proline to proline residues. This article presents...
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Molecular basis of the osmolyte effect on protein stability: a lesson from the mechanical unfolding of lysozyme
PublikacjaOsmolytes are a class of small organic molecules that shift the protein folding equilibrium. For this reason, they are accumulated by organisms under environmental stress, and find applications in biotechnology where proteins need to be stabilized or dissolved. However, despite years of research, debate continues over the exact mechanisms underpinning the stabilizing and denaturing effect of osmolytes. Here, we simulated the mechanical...
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Experimental and theoretical studies on the Sulfamethazine-Urea and Sulfamethizole-Urea solid-liquid equilibria
PublikacjaThe miscibility of active pharmaceutical ingredients with excipients is an important aspect in pharmaceutical technology protocols. In this study, the differential scanning calorimetry (DSC) was used for Sulfamethazine-Urea (SI–U) and Sulfamethizole-Urea (SO–U) solid-liquid phase diagrams determination. Both sulfonamides form simple binary eutectics with Urea. The lack of new co-crystal phase formation was confirmed by inspection...
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The ONETEP linear-scaling density functional theory program
PublikacjaWe present an overview of the ONETEP program for linear-scaling density functional theory (DFT) calculations with large basis set (planewave) accuracy on parallel computers. The DFT energy is computed from the density matrix, which is constructed from spatially localized orbitals we call Non-orthogonal Generalized Wannier Functions (NGWFs), expressed in terms of periodic sinc (psinc) functions. During the calculation, both the...
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Mutually polarizable QM/MM model with in situ optimized localized basis functions
PublikacjaWe 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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Practical Approach to Large-Scale Electronic Structure Calculations in Electrolyte Solutions via Continuum-Embedded Linear-Scaling Density Functional Theory
PublikacjaWe present the implementation of a hybrid continuum-atomistic model for including the effects of a surrounding electrolyte in large-scale density functional theory (DFT) calculations within the Order-N Electronic Total Energy Package (ONETEP) linear-scaling DFT code, which allows the simulation of large complex systems such as electrochemical interfaces. The model represents the electrolyte ions as a scalar field and the solvent...
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Performance of the AMOEBA Water Model in the Vicinity of QM Solutes: A Diagnosis Using Energy Decomposition Analysis
PublikacjaThe 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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Understanding ion–ion and ion–solvent interactions in aqueous solutions of morpholinium ionic liquids with N-acetyl-L-alaninate anion through partial molar properties and molecular dynamics simulations
PublikacjaAmino acid ionic liquids (AAILs) provide a low toxicity, biodegradable alternative to conventional ionic liquids, while also maintaining solubility in water. Densities and sound velocities of aqueous solutions of four amino acid ionic liquids (AAILs), based on the N-alkyl-N-methylmorpholinium ([Mor1,R], R = 2, 3, 6, 8) cation and N-acetyl-L-alaninate ([N-Ac-L-Ala]) anion were measured at T = (293.15–313.15) K and at atmospheric...
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Adiabatic Compressibilities of Divalent Transition-Metal Perchlorates and Chlorides in N,N-Dimethylacetamide and Dimethylsulfoxide
PublikacjaZmierzono prędkości rozchodzenia się dźwięku roztworów nadchloranów i chlorków manganu(II), kobaltu(II), niklu(II), miedzi(II) i cynku(II) w N,N-dimetyloacetamidzie i dimetylosulfotlenku w temperaturze 298.15 K. Obliczono ściśliwości adiabatyczne i pozorne ściśliwości adiabatyczne badanych roztworów. Przedyskutowano wpływ anionu i rodzaju rozpuszczalnika na uzyskane graniczne wartości pozornych ściśliwości adiabatycznych soli.
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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
PublikacjaApparent 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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Excited-state proton transfer and geminate recombination in the molecular cage of β-cyclodextrin
PublikacjaExcited-state proton transfer and geminate recombination in aqueous heptakis(2,6-di-O-methyl)-β-cyclodextrin have been compared with those in water by monitoring the photoinduced prototropic tautomerization of 6-hydroxyquinoline, which occurs via forming anionic intermediate. Enol deprotonation decelerates by 18 times whereas its reverse process accelerates slightly with encapsulation. The imine protonation of the intermediate...
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How water mediates the long-range interactions between remote protein molecules
PublikacjaThe 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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The significance of the properties of water for the working cycle of the kinesin molecular motor
PublikacjaExplicit 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...