Wyszukiwarka
Wyniki wyszukiwania dla: MOLECULES
-
Why the Solvation Water around Proteins Is More Dense than Bulk Water
PublikacjaThe 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...
-
Structure of solvation water around the active and inactive regions of a type III antifreeze protein and its mutants of lowered activity
PublikacjaWater 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...
-
Two-body dissociation of isoxazole following double photoionization – an experimental PEPIPICO and theoretical DFT and MP2 study
PublikacjaThe dissociative double photoionization of isoxazole molecules has been investigated experimentally and theoretically. The experiment has been carried out in the 27.5–36 eV photon energy range using vacuum ultraviolet (VUV) synchrotron radiation excitation combined with ion time-of-flight (TOF) spectrometry and photoelectron–photoion–photoion coincidence (PEPIPICO) technique. Five wellresolved two-body dissociation channels have...
-
Reviewing the recent developments of using graphene-based nanosized materials in membrane separations
PublikacjaAccording to the potentialities of graphene-based materials and their unique physicochemical properties. Such 2D nanomaterials are likely to be the most implemented within the improvement of the selective separations of polymer membranes, together with enhanced physicochemical properties (such as hydrophilicity/hydrophobicity, transport of molecules, mechanical and thermal features, among others). Hence, this review compiles and...
-
Heteroleptic tri-tert-butoxysilanethiolate complexes of manganese(II) - thermal studies
PublikacjaThe thermal behavior of Mn(II) silanethiolate series [Mn(SR)2L(MeOH)n], where R=SSi(OBut)3, L=heterocyclic nitrogen base and n=0, 1 or 2 has been comparatively investigated using differential scanning calorimetry (DSC), thermogravimetry (TG) and TG-infrared spectoscopy (IR) techniques. The TG curves indicate the differences in the thermal decomposition due to presence of distinct N-donor ligands and labile MeOH molecules coordinated...
-
Cloning, expression, purification and characterization of recombinant trehalose synthase from Deinococcus radiodurans.
PublikacjaTrehalose (α-D-glucopyranosyl-1,1-α-D-glucopyranoside) is a nonreducing disacharide in which the two glucose molecules are linked trough a α-1,1-glycosidic bond. Trehalose is readily hydrolyzed to glucose and can be used as a reserve of that sugar in the cell. The presence of trehalose was found in the cells of fungi and yeasts, bacteria, nematodes, insects, eggs, pupae and some plants. The characteristics of trehalose make it...
-
Beneficial effects and potential risks of tomato consumption for human health: An overview
PublikacjaTomato and its derived products have a very interesting nutritional value in addition to prominent antioxidant,anti-inflammatory, and anticancer activities. In terms of tomatoes are generally quite safe to eat. However,overall consumption varies from individual to individual. Indeed, either beneficial or harmful effects of plantsor their derived products are closely related to quality, including the presence of biologically active...
-
Distillation cleanup preceded gc determination of short-chain monocarboxylic acids in aqueous and solid samples of wastewater origin = Oznaczanie krótkołańcuchowych kwasów monokarboksylowych w próbkach wodnych i stałych pochodzących z oczyszczalni ścieków z wykorzystaniem chromatografii gazowej poprzedzonej destylacją
PublikacjaShort-chain monocarboxylic acids (SCMAs) (C2-C5) formed in the process of aerobic biodegradation of larger organic molecules should often be monitored to optimize wastewater biological treatment and study the processes of converting organic waste matter into methane, etc. Gas chromatography (GC) seems a method of choice for such a task. Majority of samples require clean up before they can be injected into GC system. In this work...
-
ortho-Fluorobenzanilides and ortho-fluorothiobenzanilides: Molecular conformations and crystal packing
PublikacjaSeries of 2-fluoro and 2,6-difluorobenzanilides and their thiobenzanilide analogs have been synthesized to investigate the influence of the fluorine atom on their crystal structures and self-assembly in the crystal lattice. The X-ray analysis of the single crystal revealed that the synthesized molecules adopt a geometry being deflected from planarity. The deflection was investigated by analysis of dihedral angles between mean planes...
-
Protein thermal stabilization in aqueous solutions of osmolytes
PublikacjaProteins’ 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...
-
Benzene-induced hydro(solvo)thermal synthesis of Cu2+ and Zn2+ coordination polymers based on 1,3-benzenedicarboxylate
PublikacjaHydro(solvo)thermal reactions of Cu(NO3)2·2.5H2O or Zn(NO3)2·6H2O with 1,3-H2bdc provided two structurally different coordination polymers; a 2D network “metallacalixarene” based on the paddlewheel-type cluster with the formula [Cu(1,3-bdc)·H2O]·H2O (1) and a 3D framework [Zn(1,3-bdc)] (2), respectively. The use of a base was unnecessary in this synthesis; however, the presence of benzene played a crucial role in the crystallization...
-
Evidence for solid state electrochemical degradation within a small molecule OLED
PublikacjaAcridone derivative have been synthesised and used as OLED (Organic Light Emitting Diode) emitters which were found to be electroactive. Electrochemical investigations showed a side reaction takes place inside an active layer which diminished the overall device efficiency. By using a dopant and host active layer architecture, the formation of the by product was removed. The by-product was identified as a σ-dimer formed inside an...
-
Comparative molecular modelling of biologically active sterols
PublikacjaMembrane sterols are targets for a clinically important antifungal agent – amphotericin B. The relatively specific antifungal action of the drug is based on a stronger interaction of amphotericin B with fungal ergosterol than with mammalian cholesterol. Conformational space occupied by six sterols has been defined using the molecular dynamics method to establish if the conformational features correspond to the preferential interaction...
-
Interaction of Novel Ionic Liquids with Soils
PublikacjaWith the constant development of new ionic liquids, the understanding of the chemical fate of these compounds also needs to be updated. To this effect, in this contribution, the interaction of a number of novel ionic liquids with soils was determined. Therefore, three novel headgroups (ammonium, phosphonium or pyrrolidinium) with single or quaternary substitution were tested on a variety of soils with high to low organic matter...
-
Targeting shelterin proteins for cancer therapy.
PublikacjaAs a global health challenge, cancer prompts continuous exploration for innovative therapies that are also based on new targets. One promising avenue is targeting the shelterin protein complex, a safeguard for telomeres crucial in preventing DNA damage. The role of shelterin in modulating ataxia- telangiectasia mutated (ATM) and ataxia-telangiectasia and Rad3-related (ATR) kinases, key players in the DNA damage response (DDR),...
-
Excess molar volume and viscosity deviation for binary mixtures of gamma-butyrolactone with dimethyl sulfoxide
PublikacjaThe densities of binary liquid mixtures of dimethyl sulfoxide and gamma-butyrolactone at (293.15, 298.15, 303.15 and 313.15) K and viscosity at T=298.15 K have been measured at atmospheric pressure over theentire range of concentration. From these data the excess molar volumes VE at (293.15, 298.15, 303.15 and 313.15) K and the viscosity deviation, the excess entropy, and the excess Gibbs energy of activation for viscous flow at...
-
Application of multicriteria decision analysis to assess the greenness of molecularly imprinted polymers synthesis components
PublikacjaThe study applies multicriteria decision analysis (MCDA) to rank the components of molecularly imprinted polymers (MIPs) synthesis according to their greenness. The components are taken from papers that are describing synthesis of MIPs for persistent organic pollutants (POPs) sorbents. Functional monomers (n = 14), target/surrogate molecules (n = 10), porogens (n = 8), cross-linking agents (n = 8) and initiators (n = 4) are described...
-
Wykorzystanie wiązań niekowalencyjnych do otrzymywania jedno- i dwuskładnikowych struktur supramolekularnych
PublikacjaPrzedstawiona rozprawa doktorska dotyczy badań nad wykorzystaniem oddziaływań międzycząsteczkowych do projektowania i syntezy uporządkowanych struktur krystalicznych, ze szczególnym uwzględnieniem wiązań halogenowych i chalkogenowych jako stosunkowo nowych i bardzo atrakcyjnych z punktu widzenia inżynierii kryształu. Praca podzielona jest na kilka części. Pierwsza z nich stanowi wstęp teoretyczny obejmujący opis, założenia oraz...
-
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...
-
Synthesis of compounds with C-P-P and C=P-P bond systems based on the phospha-Wittig reaction
PublikacjaA reactivity study of a β-diketiminate titanium(III) phosphanylphosphido complex [MeNacNacTi(Cl){η2-P(SiMe3)-PtBu2}] (1) towards ketones such as benzophenone, 9-fluorenone, acetophenone, cyclopentanone, cyclohexanone and cycloheptanone is reported. The reactions of 1 with aromatic ketones (without α-protons) directly lead to the Ti(III) complex [MeNacNacTi(μ2-Cl)(OSiMe3)] (5) as well as Ti(IV) complexes with the pinacol condensation...
-
Minimal parameter implicit solvent model for ab initioelectronic-structure calculations
PublikacjaAbstract - We present an implicit solvent model for ab initio electronic-structure calculations which is fully self-consistent and is based on direct solution of the nonhomogeneous Poisson equation. The solute cavity is naturally defined in terms of an isosurface of the electronic density according to the formula of Fattebert and Gygi (J. Comput. Chem., 23 (2002) 662). While this model depends on only two parameters, we demonstrate...
-
Isocyanate-Free Polyurethanes
PublikacjaIsocyanate-free polyurethanes (also called non-isocyanate polyurethanes, or NIPUs) are alternatives to the conventional (commercially used) polyurethanes synthesized using di- or polyisocyanates, polyols, and chain extenders with low molecular weight. The major routes of NIPUs’ synthesis involve polyaddition of cyclic carbonates and di- or polyamines, polycondensation of carbamates, and diols. The most important intermediates are...
-
Spontaneous electron emission vs dissociation in internally hot silver dimer anions
PublikacjaReferring to a recent experiment, we theoretically study the process of a two-channel decay of the diatomic silver anion (Ag2-), namely the spontaneous electron ejection giving Ag2 + e- and the dissociation leading to Ag- + Ag. The ground state potential energy curves of the silver molecules of diatomic neutral and negative ion were calculated using proper pseudo-potentials and atomic basis sets. We also estimated the non-adiabatic...
-
Ligand-Modified Boron-Doped Diamond Surface: DFT Insights into the Electronic Properties of Biofunctionalization
PublikacjaWith the increasing power of computation systems, theoretical calculations provide a means for quick determination of material properties, laying out a research plan, and lowering material development costs. One of the most common is Density Functional Theory (DFT), which allows us to simulate the structure of chemical molecules or crystals and their interaction. In developing a new generation of biosensors, understanding the nature...
-
Selective adsorption of BTEX on calixarene-based molecular coordination network determined by 13C NMR spectroscopy
PublikacjaBenzene, toluene, ethylbenzene, and xylenes (BTEX), a class of volatile organic compounds, are harmful pollutants but also very important precursors in organic industrial chemistry. Among different approaches used for the BTEX treatment, the adsorption technology has been recognized as an efficient approach because it allows to recover and reuse both adsorbent and adsorbate. However, the selective adsorption of the components is...
-
Adsorption-assisted transport of water vapour in super-hydrophobic membranes filled with multilayer graphene platelets
PublikacjaThe effects of confinement of multilayer graphene platelets in hydrophobic microporous polymeric membranes are here examined. Intermolecular interactions between water vapour molecules and nanocomposite membranes are envisaged to originate assisted transport of water vapour in membrane distillation processes when a suitable filler-polymer ratio is reached. Mass transport coefficients are estimated under different working conditions,...
-
Proton Transfer Reaction Mass Spectrometry for Plant Metabolomics
PublikacjaVolatile organic compounds (VOCs) emitted by plants are a valuable source of information on their growth, theirresponse to stress, and the condition of their habitat. The recent trend in the analysis of low-mass molecules ofplant origin is metabolomics, which in the context of volatiles is often referred to as volatolomics. It requires theuse of modern analytical instrumentation...
-
The Ellenbogen's "Matter as Software" Concept for Quantum Computer Implementation: III. Selection of X@C60 Molecular Building Blocks (MBBs) for Tip-Based Nanofabrication (TBN) of Trapped Neutral Atom Quantum Computing Devices
PublikacjaThe selection of guest atoms X of X@C60 MBBs for TBN of trapped neutral atom quantum computing devices is reported. Assuming the all-optical quantum computing as a final target stage, the two criteria are most important: the charge q accumulated on the C60 host must be as low as possible, and the atom X must have one or more available excited states within the band falling into the low energy window of neutral C60 molecule electronic...
-
Water-mediated long-range interactions between the internal vibrations of remote proteins
PublikacjaIt 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....
-
Electron-impact ionization of fluoromethanes – Review of experiments and binary-encounter models
PublikacjaExperiments and recommended data on electron-impact ionization of methane and fluoromethanes (CH3F, CH2F2, CHF3, CF4) are reviewed and compared with binary-encounter models (Gryzinski’s, ´ Deutsch and Märk’s, and Kim and Rudd’s). A good agreement between recent experiments and the two latter classical-like models is shown. Kim and Rudd’s model (calculated presently in the restricted HartreeFock 6-31**G orbital basis) predicts well...
-
Inhibition of amyloid fibril formation of hen egg white lysozyme by trimethylamine N-oxide at low pH
PublikacjaIn vitro inhibition of the formation of fibrous aggregates of proteins (amyloids) has gained increasing attention due to the number of diseases associated with protein misfolding and fibrillation. An interesting group of compounds for which pronounced activity against this phenomenon can be expected consists of low molecular weight substances (osmolytes) which have the ability to change protein stability. Here we investigate the...
-
<i>N,N,N</i>-Trimethyl-N-(methyl 5-deoxy-2,3-<i>O</i>-isopropylidene-β-D-ribofuranosid-5- yl)ammonium 4-methylbenzenesulfonate sesquihydrate.
PublikacjaThe structure of the title compound, [C12H24NO4][C7H7O3S]·1.5H2O, contains alternating layers parallel to (001) of hydrophobic and polar character, stabilized by C-H...O hydrogen bonding. The furan ring adopts an envelope conformation with the C(OMe) atom as the flap, and the dioxolane ring is twisted about one of the O-C(methine) bonds. A comparison to related compounds is presented. The tosylate-O atoms were disordered over two...
-
On the electronic structure of methyl butyrate and methyl valerate
PublikacjaWe present novel results of the analysis of the electronic structure of two aliphatic esters: methyl butyrate and methyl valerate. High-resolution photoabsorption spectra were collected and analyzed over the energy range 4.0–10.8 eV and showed for both the molecules not only a clear band of the HOMO to LUMO transition, but also vibronic structure associated with the first Rydberg-valence transition. Photoelectron spectra recorded...
-
Adsorption behavior and corrosion inhibitive characteristics of newly synthesized cyano-benzylidene xanthenes on copper/sodium hydroxide interface: Electrochemical, X-ray photoelectron spectroscopy and theoretical studies
PublikacjaElegant process for synthesis of 3-(7H-dibenzo[c,h]xanthen-7-yl)benzaldehyde (3), as new starting material to create a set of novel xanthene analogues, 2-(3-(7H-dibenzo[c,h]xanthen-7-yl)benzylidene)malononitrile (4), 3-(3-(7H-dibenzo[c,h]xanthen-7-yl)phenyl)-2-cyanoacrylic acid (5), and Ethyl-3-(3-(7H-dibenzo[c,h]xanthen-7-yl)phenyl)-2-cyanoacrylate (6), was achieved starting with available materials under mild conditions. Various...
-
Bile salts in digestion and transport of lipids
PublikacjaBecause of their unusual chemical structure, bile salts (BS) play a fundamental role in intestinal lipid digestion and transport. BS have a planar arrangement of hydrophobic and hydrophilic moieties, which enables the BS molecules to form peculiar self-assembled structures in aqueous solutions. This molecular arrangement also has an influence on specific interactions of BS with lipid molecules and other compounds of ingested food...
-
Light-Modulated Sunscreen Mechanism in the Retina of the Human Eye
PublikacjaThe functioning of the human eye in the extreme range of light intensity requires a combination of the high sensitivity of photoreceptors with their photostability. Here, we identify a regulatory mechanism based on dynamic modulation of light absorption by xanthophylls in the retina, realized by reorientation of pigment molecules induced by trans–cis photoisomerization. We explore this photochemically switchable system using chromatographic...
-
Synthetic strategies in construction of organic macromolecular carrier–drug conjugates
PublikacjaMany metabolic inhibitors, considered potential antimicrobial or anticancer drug candidates, exhibit verylimited ability to cross the biological membranes of target cells. The restricted cellular penetration ofthose molecules is often due to their highhydrophilicity. One of the possible solutions to this problem is aconjugation of an inhibitor with a molecular organic nanocarrier. The conjugate thus formed should beable to penetrate...
-
Explicit solvent repulsive scaling replica exchange molecular dynamics ( RS‐REMD ) in molecular modeling of protein‐glycosaminoglycan complexes
PublikacjaGlycosaminoglcyans (GAGs), linear anionic periodic polysaccharides, are crucial for many biologically relevant functions in the extracellular matrix. By interacting with proteins GAGs mediate processes such as cancer development, cell proliferation and the onset of neurodegenerative diseases. Despite this eminent importance of GAGs, they still represent a limited focus for the computational community in comparison to other classes...
-
LattE- first-principles lattice energy calculations
PublikacjaCrystal engineering is currently attracting much interest. Its aim is to create materials of predefined properties fulfilling the requirements imposed by the applications. There are several parameters describing crystal structures, but the most important one is probably the energy of a crystal lattice. It is the energy released by the system when crystalline solid is formed out of molecules or ions in gaseous phase. Approximate...
-
Low-energy positron scattering from gas-phase benzene
PublikacjaIn this paper we are presenting calculations of the elastic cross section of positrons with gas-phase benzene for the energy range from 0.25 eV to 9.0 eV. The calculations are done with the molecular R-matrix method for positron-scattering from poly-atomic molecules using a scaling factor to scale the electron-positron interaction. The scaling factor influences the position of the poles of the R-matrix. We adjust the scaling factor...
-
Evaluating experimental molecular physics studies of radiation damage in DNA*
PublikacjaThe field of Atomic and Molecular Physics (AMP) is a mature field exploring the spectroscopy, excitation, ionisation of atoms and molecules in all three phases. Understanding of the spectroscopy and collisional dynamics of AMP has been fundamental to the development and application of quantum mechanics and is applied across a broad range of disparate disciplines including atmospheric sciences, astrochemistry, combustion and environmental...
-
Selected anionic and cationic surface active agents determined in river sediments – the Klodnica catchment
PublikacjaSurface active agents (SAAs) are specific compounds that contain hydrophilic/ hydrophobic group in their molecules named as amphiphilic structures. According to charge on the hydrophilic part of surfactants they can be classified into three main groups: anionic, cationic and non-ionic compounds. Due to the amphiphilic structure of SAAs they have specific properties (e.g. ability to adsorption at different surfaces, reduction of...
-
Aqueous solutions of NMA, Na2HPO4 , and NaH2PO4 as models for interaction studies in phosphate–protein systems
PublikacjaPhosphate buffers are essential for many areas of studies. However, their influence on buffered systems is often ignored. The phosphate salts can interact with biologically important macromolecules (e.g. proteins) and stabilize or destabilize them. With our research, we want to answer question what kind of interactions, if any, occur between phosphate ions and a protein backbone model — N-methylacetamide (NMA). ATR-FTIR spectroscopy...
-
Supramolecular Synthesis Based on a Combination of Se···N Secondary Bonding Interactions with Hydrogen and Halogen Bonds
PublikacjaExamination of the solid state structures of 2,1,3-benzoselenadiazole complexes with hydrogen or halogen bond donors has demonstrated that the 2,1,3-benzoselenadiazole molecules preferably form centrosymmetric dimers with use of [Se–N]2 supramolecular synthon, whereas the two remaining nitrogen atoms not involved in the [Se–N]2 supramolecular interactions can act as acceptors of hydrogen or halogen bonds. Cocrystallization of selenadiazoles...
-
Anatomy of noise in quantitative biological Raman spectroscopy
PublikacjaRaman spectroscopy is a fundamental form of molecular spectroscopy that is widely used to investigate structures and properties of molecules using their vibrational transitions. It relies on inelastic scattering of monochromatic laser light irradiating the specimen. After appropriate filtering the scattered light is dispersed onto a detector to determine the shift from the excitation wavelength, which appears in the form of...
-
The Effect of Sterols on Amphotericin B Self-Aggregation in a Lipid Bilayer as Revealed by Free Energy Simulations
PublikacjaAmphotericin B (AmB) is an effective but toxic antifungal drug, known to increase the permeability of the cell membrane, presumably by assembling into transmembrane pores in a sterol-dependent manner. The aggregation of AmB molecules in a phospholipid bilayer is, thus, crucial for the drug’s activity. To provide an insight into the molecular nature of this process, here, we report an atomistic molecular dynamics simulation study...
-
Self-Association of Amphotericin B: Spontaneous Formation of Molecular Structures Responsible for the Toxic Side Effects of the Antibiotic
PublikacjaAmphotericin B (AmB) is a lifesaving antibiotic used to treat deep-seated mycotic infections. Both the pharmaceutical activity and highly toxic side effects of the drug rely on its interaction with biomembranes, which is governed by the molecular organization of AmB. In the present work we present detailed analysis of self-assembly of AmB molecules in different environments, interesting from the physiological standpoint, based...
-
Ruch wirowy wywoływany przez ultradźwięk w płynach z relaksacją
PublikacjaRozprawa doktorska poświęcona jest badaniu ruchu wirowego wywoływanego przez ultradźwięk w różnych modelach płynów z relaksacją. Ma ona charakter teoretyczny, jednak wykorzystanie uzyskanych dzięki niej wyników może przynieść lepsze zrozumienie ruchu wirowego wywoływanego przez siłę akustyczną. W I rozdziale rozprawy przedstawione zostały ogólne rozważania dotyczące akustyki nieliniowej. Rozdział II dotyczy ruchu wirowego wywoływanego...
-
Mono- and bimetallic nanoparticles decorated KTaO 3 photocatalysts with improved Vis and UV–Vis light activity
PublikacjaNew mono- and bimetallic nanoparticle-decorated perovskite-type KTaO3 photocatalysts were successfully synthesized by hydrothermal reaction followed by photodeposition of MNPs/BNPs. The effect of noble metal type, amount of metal precursor as well as photoreduction method on the physicochemical and photocatalytic properties of MNPs- and BNPs-KTaO3 have been investigated. Photocatalytic activity under Vis light irradiation was estimated...
-
Electron-Induced Decomposition of Uracil-5-yl O-(N,N-dimethylsulfamate): Role of Methylation in Molecular Stability
PublikacjaThe incorporation of modified uracil derivatives into DNA leads to the formation of radical species that induce DNA damage. Molecules of this class have been suggested as radiosensitizers and are still under investigation. In this study, we present the results of dissociative electron attachment to uracil-5-yl O-(N,N-dimethylsulfamate) in the gas phase. We observed the formation of 10 fragment anions in the studied range of electron...