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Search results for: APPARENT MOLAR VOLUME APPARENT MOLAR COMPRESSIBILITY MOLECULAR DYNAMICS AMINO ACID IONIC LIQUIDS MORPHOLINIUM IONIC LIQUIDS WATER
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Ionic hydration behavior derived from infrared spectra in HDO
PublicationNa podstawie widm HDO w zakresie podczerwieni scharakteryzowano hydratacjejonów o różnym charakterze. Zastosowana analiza danych widmowych opierała się na metodzie widm różnicowych. Wyniki prowadzą do wniosku, że kationy i aniony wywierają jakościowo bardzo różny wpływ na strukturę wody. Energia wiązań wodorowych cząsteczek wody oddziaływającej z anionem zmienia się proporcjonalnie z siłą polaryzującą anionów. W przeciwieństwie...
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Ionic transport in silica xerogels investigated by dynamic current voltagecharacteristics.
PublicationPodano wstępne rezultaty badania transportu ujemnych jonów w kserożelach Si02 w warunkach wysokiego gradientu temperatury w próbce, wywołanego jej ekstremalnie niską przewodnością cieplną. Uzyskane charakterystyki pozostają w zgodzie z przewidywaniami teoretycznymi. Na ich podstawie określono znak jonów, ich ruchliwość i energię aktywacji.
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Simulation of solid state ionic conductors I-V characteristics
PublicationW pracy przedstawiono sumulacje charakterystyk prądowo-napięciowych czujników elktrokatalitycznych. Zastosowano metode różnić skończonych.
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Molecular dynamics simulations of the affinity of chitin and chitosan for collagen: the effect of pH and the presence of sodium and calcium cations
PublicationChitosan and chitin are promising biopolymers used in many areas including biomedical applications, such as tissue engineering and viscosupplementation. Chitosan shares similar properties with hyaluronan, a natural component of synovial fluid, making it a good candidate for joint disease treatment. The structural and energetic consequences of intermolecular interactions are crucial for understanding the biolubrication phenomenon...
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Fabrication of ILs-Assisted AgTaO3 Nanoparticles for the Water Splitting Reaction: The Effect of ILs on Morphology and Photoactivity
PublicationThe design of an active, stable and ecient photocatalyst that is able to be used for hydrogen production is of great interest nowadays. Therefore, four methods of AgTaO3 perovskite synthesis, such as hydrothermal, solvothermal, sol-gel and solid state reactions, were proposed in this study to identify the one with the highest hydrogen generation eciency by the water splitting reaction. The comprehensive results clearly show that...
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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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Catalytic Mechanism of Non-Target DNA Cleavage in CRISPR-Cas9 Revealed by Ab Initio Molecular Dynamics
PublicationCRISPR-Cas9 is a cutting-edge genome editing technology, which uses the endonuclease Cas9 to introduce mutations at desired sites of the genome. This revolutionary tool is promising to treat a myriad of human genetic diseases. Nevertheless, the molecular basis of DNA cleavage, which is a fundamental step for genome editing, has not been established. Here, quantum–classical molecular dynamics (MD) and free energy methods are used...
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“Dilute & Shoot” approach for rapid determination of trace amounts of nicotine in zero-level e-liquids by reversed phase liquid chromatography and hydrophilic interactions liquid chromatography coupled with tandem mass spectrometry-electrospray ionization
PublicationTwo analytical procedures are proposed where HILIC and RPLC techniques are coupled with tandem mass spectrometry detection for rapid determination of trace amounts of nicotine in zero-level liquids for electronic cigarettes. Samples are prepared on the basis of the approach “dilute & shoot” which makes this important step quick and not complicated. The chromatographic separation was carried out on a Zorbax XDB column (RPLC method)...
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Molecular dynamics-based model of VEGF-A and its heparin interactions
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The Impact of Sloshing Liquids on Ship Stability for Various Dimensions of Partly Filled Tanks
PublicationLiquid sloshing phenomenon taking place in partly filled ships' tanks directly affects the stability of a vessel. However, only static calculations are carried out onboard ships nowadays and static transfer of liquid weight is taken into account in the course of routine stability calculation. The paper is focused on a dynamic heeling moment due to liquid sloshing in tanks onboard ships. A number of numerical simulations of liquid...
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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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Effect of Cl/Ni molar ratio on the catalytic conversion of polypropylene into Cu–Ni/C composites and their application in catalyzing “Click” reaction
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Molecular dynamics simulation of polymerization of p-xylylene
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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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Water and chemical properties of hydrometeors over central european mountains
PublicationAtmospheric pollutants are transferred to the groundby the contribution of various types of hydrometeors. Because ofthe different techniques of measurement, comparative analysesbetween them are often neglected. Hence, the main goal is tocompare water volume and chemistry of different types ofhydrometeors and their role in both: water balance and pollutantsdeposition. The results of water input and atmospheric depositschemistry...
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Determination of methylcyclopentadienyl-manganese tricarbonyl in gasoline and water via ionic-liquid headspace single drop microextraction and electrothermal atomic absorption spectrometry
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Pre‐exascale HPC approaches for molecular dynamics simulations. Covid‐19 research: A use case
PublicationExascale computing has been a dream for ages and is close to becoming a reality that will impact how molecular simulations are being performed, as well as the quantity and quality of the information derived for them. We review how the biomolecular simulations field is anticipating these new architectures, making emphasis on recent work from groups in the BioExcel Center of Excellence for High Performance Computing. We exemplified...
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Identification of 1H‐indene‐(1, 3, 5, 6)‐tetrol derivatives as potent pancreatic lipase inhibitors using molecular docking and molecular dynamics approach
PublicationPancreatic lipase is a potential therapeutic target to treat diet-induced obesity in humans, as obesity-related diseases continue to be a global problem. Despite intensive research on finding potential inhibitors, very few compounds have been introduced to clinical studies. In this work, new chemical scaffold 1H-indene-(1,3,5,6)-tetrol was proposed using knowledge-based approach, and 36 inhibitors were derived by modifying its...
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Molecular dynamics simulations of the growth of poly(chloro-para-xylylene) films
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Facile formation of self-organized TiO2 nanotubes in electrolyte containing ionic liquid - ethylammonium nitrate and their remarkable photocatalytic properties
PublicationThe oriented TiO2 nanotube arrays (NTs) are identified as a stable, active and recyclable photocatalytic surface. However, their photoactivity is strictly depended on morphology (especially length), which could be controlled by anodic oxidation parameters, including electrolyte properties. To control the morphology, were successfully synthesized a series of NTs by a novel approach where ionic liquid (IL), ethylammonium nitrate...
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Measurements of photoionization of mercury atoms into the 6s 2S1/2, 5d96s2 2D5/2 and 5d96s2 2D3/2 ionic states over the energy range from 10.5 eV to 18.7 eV
PublicationPhotoionization of mercury atoms into the three lowest ionic states, 5d106s 2S1/2, 5d96s2 2D5/2 and 5d96s2 2D3/2 has been studied in the photon energy ranges from their respective thresholds to 18.7 eV. The photoionization spectra were obtained with high energy resolution at an angle of 0° with respect to the polarization vector of the photon beam. The high energy resolution and sensitivity achieved in the measurements permitted...
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Double amino acid – A novel molecule enabling peptide interpenetrating structures
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Experimental and predicted physicochemical properties of monopropanolamine-based deep eutectic solvents
PublicationIn this work, the novel deep eutectic solvents (DESs) based on 3-amino-1-propanol (AP) as hydrogen bond donor (HBD) and tetrabutylammonium bromide (TBAB) or tetrabutylammonium chloride (TBAC) or tetraethylammonium chloride (TEAC) as hydrogen bond acceptors (HBAs) were synthesized with different molar ratios of 1: 4, 1: 6 and 1: 8 salt to AP. Fourier Transform Infrared Spectroscopy measurements were performed to provide an evidence...
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Experimental and predicted physicochemical properties of monopropanolamine-based deep eutectic solvents
PublicationIn this work, the novel deep eutectic solvents (DESs) based on 3-amino-1-propanol (AP) as hydrogen bond donor (HBD) and tetrabutylammonium bromide (TBAB) or tetrabutylammonium chloride (TBAC) or tetraethylammonium chloride (TEAC) as hydrogen bond acceptors (HBAs) were synthesized with different molar ratios of 1:4, 1:6 and 1:8 salt to AP. Fourier Transform Infrared Spectroscopy measurements were performed to provide an evidence...
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Numerical Modeling of Water and Ice Dynamics for Analysis of Flow Around the Kiezmark Bridge Piers
PublicationThis paper presents the results of a numerical model study on the effect of ice on the proposed bridge piers in the Vistula River outlet and its effect on flow conditions in the river. The model DynaRICE is used in this study, which is a two-dimensional hydro-ice dynamic numerical model developed for dynamic ice transport and jamming in rivers. To simulate river hydrodynamics in the vicinity of the bridge piers, 2-dimensional numerical...
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Non-ionic and zwitterionic forms of neutral arginine – an ab initio study
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Non-Destructive Testing for the In Situ Assessment of the Ionic Flux in Cementitious Materials
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Amine-Based Ionic Liquid for CO2 Capture and Electrochemical or Thermal Regeneration
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Cytotoxicity, acute and subchronic toxicity of ionic liquid, didecyldimethylammonium saccharinate, in rats
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Epoxy/Ionic Liquid-Modified Mica Nanocomposites: Network Formation–Network Degradation Correlation
PublicationWe synthesized pristine mica (Mica) and N-octadecyl-N’-octadecyl imidazolium iodide (IM) modified mica (Mica-IM), characterized it, and applied it at 0.1–5.0 wt.% loading to prepare epoxy nanocomposites. Dynamic differential scanning calorimetry (DSC) was carried out for the analysis of the cure potential and kinetics of epoxy/Mica and epoxy/Mica-IM curing reaction with amine curing agents at low loading of 0.1 wt.% to avoid particle...
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Novel “acid tuned” deep eutectic solvents based on protonated L-proline
PublicationThe paper presents new types of deep eutectic solvents (DESs) based on L-proline protonated using three different acids (hydrochloric, sulfuric and phosphoric)and playing the role of a hydrogen bond acceptor(HBA). Glucose and xylitol were used as hydrogen bond donors (HBD). A series of deep eutectic solvents with various mole ratios were obtained for the systems L-proline: glucose and L-proline: xylitol. Density, melting point,...
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Chromogenic amides of pyridine-2,6-dicarboxylic acid as anion receptors
PublicationThe synthesis of simple, chromogenic pyridine-2,6-dicarboxylic acid amides, derivates of isomeric nitroanilines and aminonitrophenols, and their ion binding properties are described. The ligands' response to ionic species was examined by naked eye and was studied with the use of UV-Vis spectroscopy in DMSO and its mixture with water. The effect of the localisation and the type of the substituents in aromatic rings were discussed....
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Structure and Molecular Dynamics in Renewable Polyamides from Dideoxy-Diamino Isohexide
PublicationThe chemical structure, the conformation, andthe flexibility of the polymer chain fragments present in thepolyamides synthesized from 2,5-diamino-2,5-dideoxy-1,4;3,6-dianhydrosorbitol, 1,4-diaminobutane, and either sebacic orbrassylic acid have been studied by liquid-state 2D NMRspectroscopy viz. correlation spectra (COSY) and heteronuclearmultiple-bond correlation spectra (gHMBC), by 13Ccross-polarization/magic-angle spinning...
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Computational fluid dynamics - lustres and shadows.
PublicationThe paper is devoted to the different aspects of CFD. The advantages of this concept are evident and obvious; powerfuk and effective tools bring this technology closer to the quantifiable world. However, certain weaknesses in this structure are apparent. Sometimes, a simplistic tendency towards simplifications and facilitations may degenerate and lead to negative behaviours and signs. These have not been serious up to date, but...
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Ultrashort Cationic Lipopeptides–Effect of N-Terminal Amino Acid and Fatty Acid Type on Antimicrobial Activity and Hemolysis
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Influence of a lipid bilayer on the conformational behavior of amphotericin B derivatives - A molecular dynamics study.
PublicationAmphotericin B (AmB) is an effective but very toxic antifungal antibiotic. In our laboratory a series of AmB derivatives of improved selectivity of action was synthesized and tested. To understand molecular basis of this improvement, comparative conformational studies of amphotericin B and its two more selectivederivatives were carried out in an aqueous solution and in a lipid membrane. These molecular simulation studies revealed...
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Mechanism of recognition of parallel G-quadruplexes by DEAH/RHAU helicase DHX36 explored by molecular dynamics simulations
PublicationBecause of high stability and slow unfolding rates of G-quadruplexes (G4), cells have evolved specialized helicases that disrupt these non-canonical DNA and RNA structures in an ATP-dependent manner. One example is DHX36, a DEAH-box helicase, which participates in gene expression and replication by recognizing and unwinding parallel G4s. Here, we studied the molecular basis for the high affinity and specificity of DHX36 for parallel-type...
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Lubricant property and rolling contact fatigue test of oil-in-water emulsion type HFA-E and oil Total Azolla 46 as working liquids in hydraulic systems
PublicationW artykule scharakteryzowano i opisano wyniki badań własności smarnych wody destylowanej, emulsji wodno-olejowej typu HFA-E (1% oleju w wodzie) sporządzonej na bazie koncentratu Isosynth VX110BF, oleju Total Azolla 46 i samego koncentratu Isosynth VX110BF (tylko dla porównania z olejem, emulsją i wodą). W artykule pokazano wyniki badań pittingu z użyciem wody, emulsji i oleju jako środków smarnych. Ponadto w artykule przedstawiono...
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Anisotropic mechanical behavior and auxeticity of penta-graphene: Molecular statics/molecular dynamics studies
PublicationWe investigate the mechanical properties of penta-graphene (PG), a recently proposed two-dimensional carbon allotrope using atomistic simulation techniques combined with the empirical description of interatomic interactions. We report on the dependence of its three in-plane mechanical moduli (i.e. Young's modulus, Poisson's ratio and shear modulus) on the deformation direction, strain and temperature. We show that PG displays a...
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Molecular aspects of the interaction between amphotericin B and a phospholipid bilayer: molecular dynamics studies.
PublicationAmfoterycyna B jest antybiotykiem z grupy polienów makrolidowych. Stosowany jest on w leczeniu układowych infekcji grzybowych. Wiadomo że związek ten oddziałuje ze składnikami błon lipidowych i tworzy kanały. W przedstawianej pracy prezentowane są wyniki symulacji przeprowadzonej dynamiką molekularną układu składającego się z 200 cząsteczek lipidów DMPC i jednej cząsteczki amfoterycyny ułożonej na powierzchni błony. Z przeprowadzonej...
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Molecular dynamics simulations of ultraprecision machining of fcc monocrystals
PublicationArtykuł zawiera wyniki wielkoskalowych symulacji dynamiczno-molekularnych ultraprecyzyjnego skrawania monokryształów metali niedeformowalnym narzędziem. Zmiennymi parametrami symulacji były: szybkość i głębokość skrawania, temperatura, orientacja krystalograficzna skrawanego kryształu oraz kształt narzędzia.Analizie poddano zmiany strukturalne w obrabianym materiale.
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Study of the Interactions between Neurophysin II and Dipeptide Ligand by Means of Molecular Dynamics
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Investigation of vortex assisted magnetic deep eutectic solvent based dispersive liquid–liquid microextraction for separation and determination of vanadium from water and food matrices: Multivariate analysis
PublicationA new and simple vortex assisted magnetic deep eutectic solvent dispersive liquid–liquid microextraction procedure (VA-MDES-DLLME) was developed for the determination of vanadium (V) in food and water samples by flame atomic absorption spectrometry (FAAS). In the extraction medium, a bis(acetylpivalylmethane) ethylenediimine (H2APM2en) was used for the complexation of V(V) in sample solution at pH 6. The VA-MDES-DLLME was optimized...
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Characteristics of hydration water around hen egg lysozyme as the protein model in aqueous solution. FTIR spectroscopy and molecular dynamics simulation
PublicationW niniejszej pracy przedstawiono wyniki badań dotyczące hydratacji białka modelowego - lizozymu z jaja kurzego w roztworze wodnym. Wiodącą techniką stosowaną w badaniach była spektroskopia oscylacyjna FTIR z zastosowaniem techniki rozcieńczenia izotopowego wody półciężkiej HDO w roztworze wody zwykłej. Analiza widma HDO przy pomocy "metody widm zaburzonych" pozwoliła na wyizolowanie widma wody zaburzonej przez lizozym, a tym samym...
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α-Amino Acids In Water: A Review Of VCD And ROA Spectra
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Calix[4]arene phosphonates - recognition of amino alcohols in water.
PublicationOpracowano syntezę nowych rozpuszczalnych w wodzie pochodnych kaliks[4]arenów posiadających grupy fosfonowe w górnej części pierścieni aromatycznych. Zaprezentowano wyniki kompleksowania tych gospodarzy aminoalkoholi takich jak efedryna, norefedryna i noradrenalina.
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β2-Homo-Amino Acid Scan of µ-Selective Opioid Tetrapeptide TAPP
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Thermal properties of lanthanide(III) complexes with 5-amino-1,3-benzenedicarboxylic acid
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Deep Eutectic Solvents or Eutectic Mixtures? Characterization of Tetrabutylammonium Bromide and Nonanoic Acid Mixtures
PublicationDeep eutectic solvents have quickly attracted the attention of researchers because they better meet the requirements of green chemistry and thus have the potential to replace conventional hazardous organic solvents in some areas. To better understand the nature of these mixtures, as well as expand the possibilities of their use in different industries, a detailed examination of their physical properties, such as density, viscosity,...
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Molecular dynamics study of the influence of calcium ions on the conformation of gelsolin S2 domain
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