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Optical Spectroscopic Studies of Tetrahydrofuran Fragmentation Induced by Collisions with Dihydrogen Cations
PublikacjaCollisions of dihydrogen cations with tetrahydrofuran molecules have been studied. Luminescence spectra and the emission functions of the excited products at projectile energies ranging from 8 to 1000 eV have been measured using collision-induced emission spectroscopy. The recorded spectra are dominated by the atomic lines of the hydrogen Balmer series, whose intensities decrease more quickly than derived by the quantum-theoretical...
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Low-energy interactions related to atmospheric and extreme conditions
PublikacjaThis Topical Issue, entitled “Low-Energy Interactions Related to Atmospheric and Extreme Conditions”, showcases a collection of eighteen articles that reported recent theoretical and experimental findings pertaining to the following topics: – low-energy interactions of charged particles (electrons [1–7], protons [8], positrons [9]), and photons [10] with atoms and molecules of biological [1–4,7,8], astrochemical [10], industrial,...
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Carbonic anhydrase inhibitors. Synthesis, and molecular structure of novel series N-substituted N'-(2-arylmethylthio-4-chloro-5- methylbenzenesulfonyl)guanidines and their inhibition of human cytosolic isozymes I and II and the transmembrane tumor-associated isozymes IX and XII
PublikacjaA series of novel N-substituted N'-(2-arylmethylthio-4-chloro-5-methylbenzenesulfonyl)guanidines 9 e41 have been synthesized and investigated as inhibitors of four isoforms of zinc enzyme carbonic anhydrase (CA.EC 4.2.1.1), that is the cytosolic CA I and II, and cancer-associated isozymes CA IX and XII. Against the human CA I investigated compounds showed KI in the range of 87e6506 nM, toward hCA II ranging from 7.8 to 4500 nM,...
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Discovery of small-molecule regenerative drugs using a model of complex tissue injury in mice. Transcriptomic responses of neurodevelopmental genes during pharmacologically induced regeneration
PublikacjaDespite significant development in regenerative medicine, there is a deficit of effective therapies for wound healing and tissue regeneration. Research performed using animal wound models allows for a better understanding of this complex process, searching for compounds with pro-regenerative properties, and assessing their efficacy and safety. Unfortunately, the lack of adequate preclinical models proves to be an issue as no animal...
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Optoelectronic system for monitoring of thin diamond layers growth
PublikacjaDevelopment of the optoelectronic system for monitoring of diamond/DLC (Diamond-Like-Carbon) thin films growth during mu PA ECR CVD (Microwave Plasma Assisted Electron Cyclotron Resonance Chemical Vapour Deposition) process is described. The multi-point Optical Emission Spectroscopy (OES) and Raman spectroscopy were employed as non-invasive optoelectronic tools. Dissociation of H-2 molecules, excitation and ionization of hydrogen...
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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
PublikacjaA 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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Self-assembly of secondary aryl amides in cocrystals with perfluoroaryl coformers: structural analysis and synthon preferences
PublikacjaCooperation of aryl⋯perfluoroaryl stacking interactions and hydrogen bonds was utilized in the construction of six novel cocrystals of aromatic cis-amides with pentafluorobenzoic acid (pfba) and pentafluorophenol (pfp). They were obtained by crystallization from solution and structurally characterized. In four instances, the components form heterotetrameric motifs, in which amide:amide homodimer interacts symmetrically on two sides...
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Hydration of Simple Model Peptides in Aqueous Osmolyte Solutions
PublikacjaThe biology and chemistry of proteins and peptides are inextricably linked with water as the solvent. The reason for the high stability of some proteins or uncontrolled aggregation of others may be hidden in the properties of their hydration water. In this study, we investigated the effect of stabilizing osmolyte–TMAO (trimethylamine N-oxide) and destabilizing osmolyte–urea on hydration shells of two short peptides, NAGMA (N-acetyl-glycine-methylamide)...
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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
PublikacjaSingle 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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Direct human contact with siloxanes (silicones): safety or risk. Part 1: characteristics of siloxanes (silicones
PublikacjaSiloxanes are commonly known as silicones. They belong to the organosiliconcompounds and are exclusively obtained by synthesis. Their chemical structuredetermines a range of physicochemical properties which were recognized as unique.Due to the susceptibility to chemical modifications, ability to create short, long orcomplex polymer particles, siloxanes found an application in many areas of human life.
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Synthesis and characterization of novel renewable polyesters based on 2,5-furandicarboxylic acid and 2,3-butanediol
PublikacjaNovel polyesters from 2,5-furandicarboxylic acid or 2,5-dimethyl-furandicarboxylate and 2,3-butanediol have been synthesized via bulk polycondensation catalyzed by titanium (IV) n-butoxide, tin (IV) ethylhexanoate, or zirconium (IV) butoxide. The polymers were analyzed by size exclusion chromatography, nuclear magnetic resonance spectroscopy, Fourier transform infrared spectroscopy (FTIR), matrix-assisted laser ionization-desorption...
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Mechanism of antifreeze protein functioning and the “anchored clathrate water” concept
PublikacjaIn 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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Diaryl Sulfide Derivatives as Potential Iron Corrosion Inhibitors: A Computational Study
PublikacjaThe present work aimed to assess six diaryl sulfide derivatives as potential corrosion inhibitors. These derivatives were compared with dapsone (4,4′-diaminodiphenyl sulfone), a common leprosy antibiotic that has been shown to resist the corrosion of mild steel in acidic media with a corrosion efficiency exceeding 90%. Since all the studied compounds possess a common molecular backbone (diphenyl sulfide), dapsone was taken as the...
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Mechanochemical Energy Transduction during the Main Rotary Step in the Synthesis Cycle of F1-ATPase
PublikacjaF1-ATPase is a highly efficient molecular motor that can synthesize ATP driven by a mechanical torque. Its ability to function reversibly in either direction requires tight mechanochemical coupling between the catalytic domain and the rotating central shaft, as well as temporal control of substrate binding and product release. Despite great efforts and significant progress, the molecular details of this synchronized and fine-tuned...
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Nanofiltration-Assisted Concentration Processes of Phenolic Fractions and Carotenoids from Natural Food Matrices
PublikacjaIn new food formulations, carotenoids and phenolic compounds are likely to be the most sought after food ingredients according to their bioactivity, nutraceutical, nutritional value, and compatibility properties once incorporated into food formulations. Such solutes are naturally present in many plant-based sources, and some portions are directly consumed when enriching food products and formulations; however, some portions, which...
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Potential energy curves, transition and permanent dipole moments of KRb
PublikacjaWe present extensive calculations of 48 adiabatic potential energy curves of the KRb molecule. Efforts have been focused on preparing the appropriate basis sets. Compared to previous approaches, the set of new potential energy curves is extended to higher excitations, including the single-excited K(4s2S)+Rb(5d2D) and double-excited K(4p2P)+Rb(5p2P) atomic limits. Larger distances between nuclei are also taken into account. New...
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Właściwości mechaniczne tworzywa PET - przegląd literatury
PublikacjaThe article describes the influance of the microstructure and environment conditions on the mechanical properties of PET material. From the microskopic point of view, mechanical and thermal properties of PET material have the biggest influance on orientation and crystallization processes of material. From the macroskopic point of view mechanical properties can be described by parameters derived from strees-strain mechanical answers...
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OBTAINING OF COUMARONE-INDENE RESINS BASED ON LIGHT FRACTION OF COAL TAR 3. COUMARONE-INDENE RESINS WITH METHACRYLIC FRAGMENTS
PublikacjaThe method for obtaining coumarone-indene resins with methacrylic fragments (CIRM) was developed with the addition of methyl ethacrylate, using a light fraction of coal tar and its fraction boiling within 423–463 К. CIRM was obtained via radical cooligomerization using 2,2'-azobis (2-methyl-propionitrile) as the initiator. The effect of the initiator amount, temperature and reaction time on the yield, softening temperature and...
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Are stabilizing osmolytes preferentially excluded from the protein surface? FTIR and MD studies
PublikacjaInteractions between osmolytes and hen egg white lysozyme in aqueous solutions were studied by means of FTIR spectroscopy and molecular dynamics. A combination of difference spectra method and chemometric analysis of spectroscopic data was used to determine the number of osmolyte molecules interacting with the protein, and the preferential interaction coefficient in presented systems. Both osmolytes – L-proline and trimethylamine-N-oxide...
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Novel, Fully Biobased Semicrystalline Polyamides
PublikacjaNovel, semicrystalline polyamides and co(polyamides) were synthesized from biobased sebacic acid (SA), 2,5-diamino-2,5-dideoxy-1,4;3,6-dianhydroiditol (diaminoisoidide, DAII) as well as from 1,4-diaminobutane (DAB), also known as putrescine in nature. Low molecular weight polyamides were obtained by melt polycondensation of the salts based on these monomers or by interfacial polycondensation. In order to increase their molecular...
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Solvation of ionic liquids based on N-methyl-N-alkyl morpholinium cations in dimethylsulfoxide – volumetric and compressibility studies
PublikacjaThe 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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Ceragenin CSA-13 as free molecules and attached to magnetic nanoparticle surfaces induce caspase-dependent apoptosis in human breast cancer cells via disruption of cell oxidative balance
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Threshold photoelectron studies of isoxazole over the energy range 9.9-30 eV
PublikacjaThe threshold photoelectron spectrum of the isoxazole molecule, C3H3NO has been measured over the photon energy range 9.9-30 eV with the use of synchrotron radiation. In the 9.9-10.8 eV range, corresponding to photoionization from the highest occupied molecular orbital 3a"(π3), seven well resolved vibrational series have been observed and their modes are tentatively assigned. A strong adiabatic ionization, with an energy of 11.132...
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Nonconventional 1,8-Diazafluoren-9-One Aggregates for Green Light Enhancement in Hybrid Biocompatible Media
PublikacjaOrganic aggregates currently play a prominent role, mainly for their unique optoelectronic properties in the aggregated state. Such properties can be related to the aggregates’ structure and the molecular packing mode. In the literature, we have well-established models of H and J aggregates defined based on the molecular exciton model. However, unconventional aggregates, the most unrecognized forms, have been generating interest...
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Stability and phase transition investigation of olanzapine polymorphs
PublikacjaWe use electrical embedded-fragment QM method with both DFT/ωB97XD/6-31G* and MP2/6-31G* to investigate the phase transformations of olanzapine. Gibbs free energy calculations predict that form I is always the most stable structure and form II is the least stable one, while form IV is more stable than form III below about 200 K but less stable above this temperature, implying a polymorphic phase transformation. This may account...
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Membrane Sterols Modulate the Binding Mode of Amphotericin B without Affecting Its Affinity for a Lipid Bilayer
PublikacjaMembrane-active antibiotics are known to selectively target certain pathogens based on cell membrane properties, such as fluidity, lipid ordering, and phase behavior. These are in turn modulated by the composition of a lipid bilayer and in particular by the presence and type of membrane sterols. Amphotericin B (AmB), the golden standard of antifungal treatment, exhibits higher activity toward ergosterol-rich fungal membranes, which...
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A Cu/Zn heterometallic complex with solvent-binding cavity, catalytic activity for the oxidation of 1-phenylethanol and unusual magnetic properties
PublikacjaMononuclear and polymeric complexes of zinc(II) and copper(II) have been synthesized using two isomers of the hemi-salen ligand with a different mutual orientation of donor atoms. The heterometallic Cu/Zn metallocycle features a catalytic niche filled with the molecule of water and molecules of methanol. This unusual compound exhibits both pronounced catalytic activity in the reaction of oxidation of a secondary alcohol to ketone...
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Cobalt(II) and Cobalt(III) Tri‐tert‐butoxysilanethiolates. Synthesis, Properties, Crystal and Molecular Structures of [Co{μ‐SSi(OBut)3}{SSi(OBut)3}(NH3)]2 and [Co{SSi(OBut)3}2(NH3)4][SSi(OBut)3] Complexes
PublikacjaThe heteroleptic neutral tri‐tert‐butoxysilanethiolate of cobalt(II) incorporating ammonia as additional ligand (1) has been prepared by the reaction of a cobalt(II) ammine complex with tri‐tert‐butoxysilanethiol in water. Complex 1, dissolved in hexane, undergoes oxidation in an ammonia saturated atmosphere to the ionic cobalt(III) compound 2. Molecular and...
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Effect of hydroxylated soybean oil and bio-based propanediol on the structure and thermal properties of synthesized bio-polyurethanes
PublikacjaThe aim of this work was to obtain bio-polyurethanes using synthetic compounds and bio-components, i.e. bio-glycols. Bio-polyurethanes were prepared by means of the prepolymer method. Prepolymers were synthesized from 4,4′-diphenylmethane diisocyanate (MDI) and a polyol mixture containing 75% by weight of commercial polyether and 25% by weight of hydroxylated soybean oils (H2 or H3), the latter being obtained in the reaction with...
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Novel Biomass-Based Polymers: Synthesis, Characterization, and Application
PublikacjaA wide range of polymers were prepared from biomass-derivatives, using different polymerization mechanisms. Well-defined, fully hydroxy-functional polyesters based on aliphatic diols were synthesized, using either conventional metal-based catalysts or the organic superbase 1,5,7-triazabicyclododecene (TBD). Unsaturated polyesters were also made, offering additional functionality to these biobased resins. Metal-catalyzed or enzymatic...
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How Chain Transfer Leads to a Uniform Polymer Particle Morphology and Prevents Reactor Fouling
PublikacjaABSTRACT: The effect of adding diethyl zinc as a chain transfer agent during the polymerization of propylene in heptane performed at 80 °C was studied. Although it was expected that the chain transfer would stop after precipitation of the polymer, the polymer molecular weight continued to increase throughout the whole of the polymerization. The presence of diethyl zinc had an additional effect that the polymerizations were devoid...
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Renewable natural resources as green alternative substrates to obtain bio-based non-isocyanate polyurethanes-review
PublikacjaCommercially available polyurethanes are synthesized by the polyaddition of diisocyanates with polyols and low molecular weight chain extenders. A new approach to polyurethanes synthesis is realized via non-isocyanate routes. Negative impacts of petroleum-based chemicals on the environment and human health as well as gradual reduction of fuel-based resources, which leads to an increase in their prices, are an incentive to looking...
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The structure of novel polyurethanes containing synthetic poly[(R,S)-3-hydroxybutyrate]
PublikacjaThe aim of this study was to estimate the structure of new polyurethanes with the potential to be used in medicine. Atactic poly[(R,S)-3-hydroxybutyrate], obtained via a ring-opening polymerization, and polycaprolactonediol or polyoxytetramethylenediol were used to built the soft segments. 4,4'-methylene dicyclohexyl diisocyanate and 1,4-butanediol were the components to form hard segments. Polyurethanes with low-molecular weight...
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Investigation of rotational state-changing collisions of C2N− ions with helium
PublikacjaThe cross sections for rotational inelastic collisions between atoms and a molecular anion can be very large, if the anion has a dipole moment. This makes molecular anions very efficient in cooling atomic gases. We address rotational inelastic collisions of Helium atoms with the molecular anion C2N–. Here we present preliminary calculations of the potential energy surface.
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Application of Box-Behnken design in response surface methodology for the molecularly imprinted polymer pipette-tip solid phase extraction of methyl red from seawater samples and its determination by spectrophotometery
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Separation and determination of ciprofloxacin in seawater, human blood plasma and tablet samples using molecularly imprinted polymer pipette‐tip solid phase extraction and its optimization by response surface methodology
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Peptide dendrimers as antifungal agents and carriers for potential antifungal agent—N3‐(4‐methoxyfumaroyl)‐(S)‐2,3‐ diaminopropanoic acid—synthesis and antimicrobial activity
PublikacjaA series of peptide dendrimers and their conjugates with antimicrobial agent FMDP (N3‐(4‐methoxyfumaroyl)‐(S)‐2,3‐diamino‐propanoic acid) were synthesized. The obtained compounds were tested for the antibacterial and antifungal activity. All novel dendrimers displayed much better activity against the tested strains than FMDP itself. Moreover, their conjugates with FMDP also exhibited antimicrobial activity. The most promising molecules...
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Novel 2-(2-arylmethylthio-4-chloro-5-methylbenzenesulfonyl)-1-(1,3,5-triazin-2-ylamino)guanidine derivatives: Inhibition of human carbonic anhydrase cytosolic isozymes I and II and the transmembrane tumor-associated isozymes IX and XII, anticancer activity, and molecular modeling studies
PublikacjaA series of novel 2-(2-arylmethylthio-4-chloro-5-methylbenzenesulfonyl)-1-(6-substituted-4-chloro-1,3,5-triazin-2-ylamino)guanidine derivatives 9–20 have been synthesized by substitution of chlorine atom at the 1,3,5-triazine ring in compounds 5–8 with 3- or 4-aminobenzenesulfonamide and 4-(aminomethyl)benzenesulfonamide hydrochloride. All the synthesized compounds were evaluated for their inhibitory activity toward hCA I, II,...
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A spectroscopic study of the cis/trans-isomers of penta-2,4-dienoic acid attached to gold nanoclusters
PublikacjaIn this theoretical work, we present a spectroscopic analysis of the cis/trans-isomers of a molecular switch, penta-2,4-dienoic acid, attached to gold clusters of different size (1, 2 and 20 gold atoms). We have simulated 4 different spectroscopic techniques: Infrared spectroscopy, normal Raman scattering, absorption spectra and resonance Raman scattering. We discuss how the position and the conformation of the molecule determine...
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Highly Conserved Homotrimer Cavity Formed by the SARS-CoV-2 Spike Glycoprotein: A Novel Binding Site
PublikacjaAn important stage in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) life cycle is the binding of the spike (S) protein to the angiotensin converting enzyme-2 (ACE2) host cell receptor. Therefore, to explore conserved features in spike protein dynamics and to identify potentially novel regions for drugging, we measured spike protein variability derived from 791 viral genomes and studied its properties by molecular...
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Role of the Solvation Water in Remote Interactions of Hyperactive Antifreeze Proteins with the Surface of Ice
PublikacjaMost 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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A highly thermostable, homodimeric single-stranded DNA-binding protein from Deinococcus radiopugnans
PublikacjaWe report the identification and characterization of the single-stranded DNA-binding protein (SSB) from the mesophile and highly radiation-resistant Deinococcus radiopugnans (DrpSSB). PCR-derived DNA fragment containing the complete structural gene for DrpSSB protein was cloned and expressed in Escherichia coli. The gene consisting of an open reading frame of 900 nucleotides encodes a protein of 300 amino acids with a calculated...
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Thermodynamics aspects of interactions between acridine derivatives and DNA
PublikacjaDNA is a molecular target for many anticancer and antiviral drugs. Therefore, a clear understanding of the interaction of small molecules with DNA is important in the rational design of ligands that can bind to DNA with high affinity and selectivity. There are several methods to investigate interactions between drug and DNA. Some of them measure changing into DNA structures, such as lengthening and untwisting of helix of DNA. Other...
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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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Valence and ionic lowest-lying electronic states of small esters studied by high resolution vacuum ultraviolet photoabsorption, photoelectron spectroscopy and ab initio calculations
PublikacjaEsters are an important class of oxygenated volatile organic compounds used in food flavorings, perfumes and other cosmetic products. They are present in fruits and pheromones and are emitted to the atmosphere naturally. Esters are also formed in the atmosphere as a product of the oxidation of ethers. Some of them form poly-molecule chains and are used in plastics. Phosphoesters form DNA backbone, while nitroesters are known for...
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Rhodotorulic Acid and its Derivatives: Synthesis, Properties, and Applications
PublikacjaSiderophores are low molecular weight compounds produced by microorganisms to scavenge iron in iron-deficient environments. Rhodotorulic acid, a natural hydroxamate siderophore, plays a vital role in iron acquisition for fungi and bacteria. As the simplest natural hydroxamate siderophore, it exhibits a high affinity for ferric ions, enabling it to form stable complexes that facilitate iron uptake and transport within microorganisms....
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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....
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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,...
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Unique agreement of experimental and computational infrared spectroscopy: a case study of lithium bromide solvation in an important electrochemical solvent
PublikacjaInfrared (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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Retention modeling of some saccharides separated on an amino column.
PublikacjaUsing an amino column (Supelcosil LC-NH2) and different mixtures of acetonitrile-water, quantitative structure-retention relationship models are discussed. These models are based on computed molecular descriptors representing numerically structured features of some saccharides. The obtained results are underlining the lipophilicity/hydrophilicity balance, and how this is controlling the separation of the saccharides. The resulting...