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Screening of potential inhibitors for COVID-19 main protease from phytoconstituents of Tectona grandis Linn: application of molecular modeling studies
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Sulfanyl porphyrazines: Molecular barrel-like self-assembly in crystals, optical properties and in vitro photodynamic activity towards cancer cells
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Imidazolidine-4-one derivatives in the search for novel chemosensitizers of Staphylococcus aureus MRSA: Synthesis, biological evaluation and molecular modeling studies
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Differential cross section for electron impact excitation of the a1 δ g state of molecular oxygen in the 15-180° angular range.
PublicationZmierzono absolutne różniczkowe przekroje czynne na wzbudzeniu drobin tlenu do poziomu oscylacyjnego v=0 stanu a1 δ g. Pomiary wykonano dla energii elektronów równej 10eV w zakresie kątów rozproszenia od 15° do 180°.
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A BODIPY‐Molecular Rotor in Giant Unilamellar Vesicles: A Case Study by Polarization‐Resolved Time‐resolved Emission and Transient Absorption Spectroscopy
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Molecular Heterogeneity of Papillary Thyroid Cancer: Comparison of Primary Tumors and Synchronous Metastases in Regional Lymph Nodes by Mass Spectrometry Imaging
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Molecular docking studies towards development of novel Gly-Phe analogs for potential inhibition of Cathepsin C (dipeptidyl peptidase I).
PublicationCathepsin C is a cysteine protease required for activation of various pro-inflammatory serine proteases and, essentially, is of interest as a therapeutic target. Cathepsin C coordinate system was employed as a model to study the interaction of some already available inhibitors of Cathepsin C. Compounds containing Gly-Phe fragment with functional groups at its ends were designed by knowledge based approach. Using AutoDock and...
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Molecular geometry and optical activity of helically chiral N-nitrosamines derived from 1,2,3,4-tetrahydro- and 1,2,3,4,7,8,9,10-octahydro-1,10-phenanthroline
PublicationX-ray crystallographic analysis of the title N-nitrosamines revealed that they assume helical conformations in the solid state. Nitrosamines 1b and 2b were resolved by inclusion crystallization with optically active diols (TADDOLs). The absolute configuration of the guest molecules in the complexes 1b·3b and 2b·3b was assigned as M. The optical activity of the resolved compounds is manifested by their solid state CD spectra, which...
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The extended version of restriction analysis approach for the examination of the ability of low-molecular-weight compounds to modify DNA in a cell-free system
PublicationOne of the primary requirements in toxicology is the assessment of ability of chemicals to induce DNA covalent modification. There are several well-established methods used for this purpose such as 32P-Postlabeling or HPLC-MS. However, all of these approaches have difficult to overcome limitations, which prevents their use in genotoxin screening. Here, we describe the simple protocol exploiting specificity of restriction enzymes...
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KRAS mutation testing in borderline ovarian tumors and low-grade ovarian carcinomas with a rapid, fully integrated molecular diagnostic system
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Pharmacological Classification and Activity Evaluation of Furan and Thiophene Amide Derivatives Applying Semi-Empirical ab initio Molecular Modeling Methods
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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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Time-of-flight electron scattering from molecular hydrogen: Benchmark cross sections for excitation of the X1Σ+g→b3Σ+u transition
PublicationThe electron impact X1Σ+g to b3Σ+u transition in molecular hydrogen is one of the most important dissociation pathways to forming atomic hydrogen atoms, and is of great importance in modeling astrophysical and industrial plasmas where molecular hydrogen is a substantial constituent. Recently it has been found that the convergent close-coupling (CCC) cross sections of Zammit et al. [Phys. Rev. A 95, 022708 (2017)] are up to a factor...
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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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Encapsulation of Amikacin into Microparticles Based on Low-Molecular-Weight Poly(lactic acid) and Poly(lactic acid-co-polyethylene glycol)
PublicationThe aim of this study was to fabricate novel microparticles (MPs) for efficient and long-term delivery of amikacin (AMI). The emulsification method proposed for encapsulating AMI employed low-molecular-weight poly(lactic acid) (PLA) and poly(lactic acid-co-polyethylene glycol) (PLA−PEG), both supplemented with poly(vinyl alcohol) (PVA). The diameters of the particles obtained were determined as less than 30 μm. Based on an in-vitro...
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Novel 1,2,3-Triazole Derivatives as Mimics of Steroidal System—Synthesis, Crystal Structures Determination, Hirshfeld Surfaces Analysis and Molecular Docking
PublicationHerein, we present the synthesis and crystal structures determination of five 4-(1-phenyl-1H-1,2,3-triazol-4-yl)phenol derivatives containing halogen atoms, 6a–e, which may be used as an excellent mimic of steroids in the drug development process. Good quality crystals obtained for all of the synthesized compounds allowed the analysis of their molecular structures. Subsequently, the determined crystal structures were used to calculate...
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Effect of heat treatment on the diffusion intermixing and structure of the Cu thin film on Si (111) substrate: a molecular dynamics simulation study
PublicationThis work is devoted to the study of the diffusion process at the interface between copper films with a thickness of 2, 3, 4, 7 and 10 atomic monolayers and silicon substrate by molecular dynamics simulation method. For this purpose, the variation of the concentration of copper and silicon along the perpendicular direction to the interface was investigated. An analysis of the density profile along this direction made it possible...
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Long range molecular dynamics study of interactions of the eukaryotic glucosamine-6-phosphate synthase with fructose-6-phosphate and UDP-GlcNAc
PublicationGlucosamine-6-phosphate synthase (EC 2.6.1.16) is responsible for catalysis of the first and practically irreversible step in hexosamine metabolism. The final product of this pathway, uridine 5 diphospho Nacetyl- d-glucosamine (UDP-GlcNAc), is an essential substrate for assembly of bacterial and fungal cell walls. Moreover, the enzyme is involved in phenomenon of hexosamine induced insulin resistance in type II diabetes, which...
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Optical investigation of molecular structure of sophisticated materials forphotonics. Photonics Applications in Astronomy, Communications, Industry and High Energy Physics Experiments.
PublicationZastosowano komplementarne metody optyczne: spektroskopię ramanowską oraz spektroskopię w podczerwieni do badania reakcji zachodzących w czasie wytwarzania polimerów hybrydowych metodą zol-żel. Otrzymane rezultaty umożliwiły uszczegółowienie opisu reakcji hydrolizy monomerów w trakcie żelowania.
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The chaperone-usher pathway of bacterial adhesin biogenesis - from molecular mechanism to strategies of anti-bacterial prevention and modern vaccine design
PublicationSystem chaperone-usher (białko opiekuńcze-białko kanałotwórcze) warunkuje biogenezę powierzchniowych struktur adhezyjnych, odpowiedzialnych za wirulencję wielu bakterii gram-ujemnych. Powyższy mechanizm został zbadany na poziomie strukturalnym w przypadku różnych gatunków bakterii patogennych. Celem powyższej pracy było przedstawienie molekularnego mechanizmu biogenezy struktur adhezyjnych na bazie systemu chaperone-usher. Otrzymane...
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ORGANIC PREPARATIONS AND PROCEDURES INTERNATIONAL
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Mollecular mechanism and chemicl kinetic description of nitrobenzene liquid membrane oscillator containing benzyldimethyltetradecylammonium chloride surfactant
PublicationBadano oscylacje róznicy potencjału między fazami wodnymi oscylatora z nitrobenzenową membraną ciekłą zawierającego chlorek benzylodimetylotetradecyloamoniowy. Opisano chemię fizyczną tego oscylatora oraz omówiono rolę efektów hydrodynamicznych w powstawaniu oscylacji. Zaproponowano nowy mechanizm oparty na transferze masy par jonowych. Oscylacje są generowane na granicy faza akceptowa/ membrana ciekła i są spowodowane autokatalityczną...
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Evaluation of the suitability of low hazard surfactants for the separation of phenols and carotenoids from red-flesh orange juice and olive mill wastewater using cloud point extraction
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Configurations of H 3 + (H2)n clusters and their energies
PublicationThe H-3(+) ion plays an important role in low temperature astrophysical and laboratory plasmas. It is considered as the initiator of many ion-molecule chemistries. Also its clusters with H-2 are quite interesting. We study configurations of the H-3(+)(H-2)(n) clusters for n = 1 up to n = 12 as a simple test system. Total energies for these structures, with zero point vibration corrections have been calculated. Stabilization energies...
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Weakly Hydrated Solute of Mixed Hydrophobic–Hydrophilic Nature
PublicationInfrared (IR) spectroscopy is a commonly used and invaluable tool in studies of solvation phenomena in aqueous solutions. Concurrently, density functional theory calculations and ab initio molecular dynamics simulations deliver the solvation shell picture at the molecular detail level. The mentioned techniques allowed us to gain insights into the structure and energy of the hydrogen bonding network of water molecules around methylsulfonylmethane...
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BLOOD CELLS MOLECULES AND DISEASES
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Structural and Dynamic Properties of Water within the Solvation Layer around Various Conformations of the Glycine-based Polypeptide
PublicationSeveral conformations of the solvated glycine-based polypeptides were investigated using molecular dynamics simulations. Some properties of water in the neighboring space around these molecules were investigated. It was found that water forms a well-defined layer—the first solvation shell—around the peptide molecule, and thickness of this layer is independent of the peptide structure and is equal to approximately 0.28 nm. Within...
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Novel analogues of bradykinin conformationally restricted in the C-terminal part of the molecule
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Double amino acid – A novel molecule enabling peptide interpenetrating structures
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Evidence for solid state electrochemical degradation within a small molecule OLED
PublicationAcridone 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...
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Water-mediated influence of a crowded environment on internal vibrations of a protein molecule
PublicationThe influence of crowding on the protein inner dynamics is examined by putting a single protein molecule close to one or two neighboring protein molecules. The presence of additional molecules influences the amplitudes of protein fluctuations. Also, a weak dynamical coupling of collective velocities of surface atoms of proteins separated by a layer of water is detected. The possible mechanisms of these phenomena are described....
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Charge dependence of fragmentation process induced by ion collisions with furan molecule
PublicationThe goal of this work is to describe the system evolution after ion-molecule interaction. We combine different quantum chemistry and statistical mechanics approaches in order to give extended description of the process. Herein we report on a recent study of the fragmentation mechanism of neutral, singly- and doubly-ionized furan molecule in the gas phase.
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Molecular Omics
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MOLECULAR IMMUNOLOGY
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MOLECULAR SIMULATION
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MOLECULAR MICROBIOLOGY
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MOLECULAR ECOLOGY
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MOLECULAR MEDICINE
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Fragmentation of isoxazole molecules by electron impact in the energy range 10-85 eV
PublicationBadano fragmentację cząsteczek isoxazolu w zderzeniach z elektronami metodą wzbudzenia optycznego. Obserwowano linie wzbudzonego wodoru z serii Balmera oraz pasma emisyjne fragmentów CH oraz CN. Zmierzono bezwzględne wartości emisyjnych przekrojów czynnych.
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Electron-scattering total cross sections for complex molecules: group additivity rule
PublicationZaprezentowano całkowite przekroje czynne na rozpraszanie elektronów na dwóch rodzinach drobin: pierwszej - zawierającej azot jako atom centralny [N(CH3)3, NH2CH3, NH3]oraz drugiej - rodzinę eterów cyklicznych [c-(CH2)nO, gdzie n=2-5]. Zostało pokazane, że TCS dla niektórych drobin wieloatomowych można wyznaczyć na podstawie wyników TCS dla drobin o prostszej budowie lub ich fragmentów.
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Formation of CN (B2Σ+) radicals in the vacuum-ultraviolet photodissociation of pyridine and pyrimidine molecules
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Magnetic Molecularly Imprinted Polymer Particles Synthesized by Suspension Polymerization in Silicone Oil
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Molecularly Imprinted Polymers for Stir Bar Sorptive Extraction: Synthesis, Characterization, and Application
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In-Tube Molecularly Imprinted Polymer Solid-Phase Microextraction for the Selective Determination of Propranolol
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Non-parametric application of Tsallis statistics to systems consisting of M hydrogen molecules
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Exploring Solanum tuberosum Epoxide Hydrolase Internal Architecture by Water Molecules Tracking
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Review of the applicability of ionic liquid matrices for the quantification of small molecules by MALDI MS
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Formation of CN (B2∑+) radicals in the vacuum-ultraviolet photodissociation of pyridine and pyrimidine molecules
PublicationFormation of the excited CN(B2∑+) free radicals in the photodissociation of pyridine (C5H5N) and pyrimidine (C4H4N2) molecules was investigated over the energy ranges 16–27 and 14.7–25 eV, respectively. Photon-induced fluorescence spectroscopy was applied to detect the vibrationally and rotationally excited CN radicals by recording the B2∑+→X2∑+ emission bands (violet system). The measured dissociation yield curves demonstrate...
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Hydrogen migration in formation of NH(A3Π) radicals in photodissociations of isoxazole and pyridine molecules
PublicationIn the present study, the H atom migration was observed in the photodissociation processes of the isoxazole and pyridine molecules in the gas-phase, applying the photon-induced fluorescence spectroscopy (PIFS).
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How water mediates the long-range interactions between remote protein molecules
PublicationThe 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...