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Search results for: MOLECULAR UMBRELLA
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Fragmentation of Tetrahydrofuran Molecules by H+, C+, and O+ Collisions at the Incident Energy Range of 25–1000 eV
PublicationWe have studied fragmentation processes of the gas-phase tetrahydrofuran (THF) molecules in collisions with the H+, C+, and O+ cations. The collision energies have been varied between 25 and 1000 eV and thus covered a velocity range from 10 to 440 km/s. The following excited neutral fragments of THF have been observed: the atomic hydrogen H(n), n = 4–9, carbon atoms in the 2p3s 1P1, 2p4p 1D2, and 2p4p 3P states and vibrationally...
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Enhancing colloidal stability of nanodiamond via surface modification with dendritic molecules for optical sensing in physiological environments
PublicationPre-treatment of diamond surface in low-temperature plasma for oxygenation and in acids for carboxylation was hypothesized to promote the branching density of the hyperbranched glycidol polymer. This was expected to increase the homogeneity of the branching level and suppress interactions with proteins. As a result, composite nanodiamonds with reduced hydrodynamic diameters that are maintained in physiological environments were...
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Rotationally inelastic collisions of electrons with H2 and N2 molecules: converged space-frame calculations at low energies.
PublicationW pracy zostały obliczone przekroje czynne na rotacyjne wzbudzenia cząsteczek H2 i N2 w wyniku zderzeń z niskoenergetycznymi elektronami. Układ silnie sprzężonych równań został rozwiązany w laboratoryjnym układzie odniesienia przy pomocy algorytmu MVPA.
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Site-to-site distance distribution in flexible molecules: theoretical evaluation of the donor and/or acceptor fluorescence decay function
PublicationPrzedstawiono wyrażenie teoretyczne opisujące zależność funkcji zaniku fluorescencji od rozkładu odległości P(r) pomiędzy donorami i akceptorami w giętkich molekułach dwuchromoforowych. Wyrażenie uwzględnia wiekoeksponencjalny zanik izolowanych donorów i akceptorów, a także możliwość niekompletnego oznakowania molekuł akceptorami. Przyjęto, że względne zmiany odległości donorów i akceptorów w czasie życia fluorescencji donora mogą...
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Targeting Spike‐ACE2 Interface of SARS‐CoV‐2 and its Omicron Variant: A Comparative Screening of Potential Inhibitors for Existing and Anticipating Variants Using Molecular Modelling Approach
PublicationThe recent COVID pandemic has shown major impact on public health and economic crisis. Despite the development of many vaccines and drugs against the severe acute respiratory syndrome (SARS) coronavirus 2, the pandemic still persists. The continued spread of the virus is largely driven by the emergence of viral variants such as α, β, γ, delta, epsilon spike, omicron and its subvariants (BA.1,2,3) which can evade the current vaccines...
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Implementation of Molecular Dynamics and Its Extensions with the Coarse-Grained UNRES Force Field on Massively Parallel Systems: Toward Millisecond-Scale Simulations of Protein Structure, Dynamics, and Thermodynamics
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Surface-enhanced Raman scattering (SERS) and tip-enhanced Raman scattering (TERS) in label-free characterization of erythrocyte membranes and extracellular vesicles at the nano-scale and molecular level
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Combined computational-experimental approach to predict blood–brain barrier (BBB) permeation based on “green” salting-out thin layer chromatography supported by simple molecular descriptors
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Effect of in vitro gastro‐pancreatic digestion on antioxidant activity of low‐molecular‐weight (<3.5 kDa) peptides from dry‐cured pork loins with probiotic strains of LAB
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Investigation of mechanism of desmopressin binding in vasopressin V2 receptor versus vasopressin V1a and oxytocin receptors: Molecular dynamics simulation of the agonist-bound state in the membrane–aqueous system
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BMC MOLECULAR BIOLOGY
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CELLULAR AND MOLECULAR NEUROBIOLOGY
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Cellular & Molecular Immunology
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EXPERIMENTAL AND MOLECULAR PATHOLOGY
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MOLECULAR AND CELLULAR NEUROSCIENCE
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MOLECULAR AND CELLULAR ENDOCRINOLOGY
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MOLECULAR BIOLOGY REPORTS
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Molecular Ecology Resources
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MOLECULAR BIOLOGY AND EVOLUTION
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Statistical Method for Analysis of Interactions Between Chosen Protein and Chondroitin Sulfate in an Aqueous Environment
PublicationWe present the statistical method to study the interaction between a chosen protein and another molecule (e.g., both being components of lubricin found in synovial fluid) in a water environment. The research is performed on the example of univariate time series of chosen features of the dynamics of mucin, which interact with chondroitin sulfate (4 and 6) in four different saline solutions. Our statistical approach is based on recurrence...
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The POCOBIO Database for Computed Scattering Cross-Sections for Positron Collisions with Biomolecular Systems
PublicationThe design of a database for positron interactions with biomolecular systems is outlined. The database contains only scattering cross sections, which are derived from theory. The data model is defined in a very flexible way, which facilitates the usage of weakly bound clusters of molecules and molecular systems with many tautomeric forms.
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Interactions of PDA tetramers with the Au surfaces
Open Research DataThis dataset contains electrostatic difference potential (EDP) maps, density of states (DOS) spectra, and adsorption geometries of cyclic tetramers on the Au surface. The real polydopamine was modelled either as the cyclic tetramers in the oxidised (indolequinone, IQ) and reduced (dihydroxyindole, DHI) chemistries with all units being the same - either...
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In silico modelling for predicting the cationic hydrophobicity and cytotoxicity of ionic liquids towards the Leukemia rat cell line, Vibrio fischeri and Scenedesmus vacuolatus based on molecular interaction potentials of ions
PublicationIn this study we present prediction models for estimating in silico the cationic hydrophobicity and the cytotoxicity (log [1/EC50]) of ionic liquids (ILs) towards the Leukemia rat cell line (IPC-81), the marine bacterium Vibrio fischeri and the limnic green algae Scenedesmus vacuolatus using linear free energy relationship (LFER) descriptors computed by COSMO calculations. The LFER descriptors used for the prediction model (i.e....
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A DFT computational study on the molecular mechanism of the nitro group migration in the product derived from 3-nitro-2-(trifluoromethyl)-2 H -chromene and 2-(1-phenylpropylidene)malononitrile
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The role of solvent solubility parameters in the formation of intermittent low and high molecular weight polystyrene rich structures in a thin film resulting from water vapor induced phase separation
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Study of New Oxytocin Antagonist Barusiban (Fe200 440) Affinity Toward Human Oxytocin Receptor Versus Vasopressin V1a and V2 Receptors - Molecular Dynamics Simulation in POPC Bilayer
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Scattering of electrons from 1-butene, H2C=CHCH2CH3, and 2-methylpropene,H2C=C(CH3)2, molecules
PublicationZmierzono, wykorzystując liniową technikę transmisyjną, całkowite absolutne przekroje czynne (TCS) na rozpraszanie elektronów na cząsteczce 1-butenu (H2C=CHCH2CH3) oraz 2-metylpropene (H2C=C(CH3)2) w zakresie energii padających elektronów, od 1 do 400 eV oraz od 1 do 350 eV. Kształt przekroju czynnego dla obu badanych izomerów butenu jest podobny. Dwie struktury w uzyskanych krzywych TCS, są wyraźnie widoczne: mały pik w okolicy...
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Preparation and characterization of dummy-template molecularly imprinted polymers as potential sorbents for the recognition of selected polybrominated diphenyl ethers
PublicationThe main aim of this work was to conduct the preliminary/basic research concerning the preparation process of a new dummy molecularly imprinted polymer (DMIP) materials. Developed DMIPs were proposed as a sorption material in solid-phase extraction (SPE) technique for recognition of selected low mass polybrominated diphenyl ethers (PBDEs) e PBDE-47 and PBDE-99. Four new DMIPs were synthesized employing bulky polymerization technique...
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The role of uropathogenic Escherichia coli adhesive molecules in inflammatory response- comparative study on immunocompetent hosts and kidney recipients
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Theoretical Studies on the Structure, Stability, Ability To Undergo Internal Transformations, and Tautomerization, as Well as Reactivity, of H2PPH2 and HPPH3 Molecules
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APPLICATION OF BINARY-ENCOUNTER-BETHE METHOD TO ELECTRON-IMPACT IONIZATION CROSS SECTION CALCULATIONS FOR BIOLOGICALLY RELEVANT MOLECULES
PublicationElectron-impact cross sections for platinum chemotherapeutic compounds, purine and pyrimidine molecules calculated using binary-encounterBethe model are presented as examples of possible applications of that method.
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Why is the cubic structure preferred in newly formed ice?
PublicationMolecular dynamics was employed to explain the preference for the cubic structure in newly formed crystals of ice. The results showed that in supercooled liquid water the molecules connected by hydrogen bonds are more likely to adopt relative orientations similar to the ones characteristic for cubic ice. The observed preference for certain relative orientations of molecules in the hydrogen-bonded pairs results in the higher probability...
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Non-ergodic fragmentation upon collision-induced activation of cysteine–water cluster cations
PublicationCysteine–water cluster cations Cys(H2O)3,6 + and Cys(H2O)3,6H+ are assembled in He droplets and probed by tandem mass spectrometry with collision-induced activation. Benchmark experimental data for this biologically important system are complemented with theory to elucidate the details of the collisioninduced activation process. Experimental energy thresholds for successive release of water are compared to water dissociation energies...
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Optical photoluminescent, and electroluminescent properties of organic solids
PublicationThis chapter discusses optical, photoluminescence and electroluminescence properties of organic materials. First, the spectral features of individual molecules and molecular solid states are analysed. Next, the excitonic processes in organic materials are discussed. The chapter reviews experimental methods leading to the determination of basic excitonic parameters. Finally, the electroluminescence phenomena in organic materials...
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Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology
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SiMiSnoRNA: Collection of siRNA, miRNA, and snoRNA database for RNA Interference
PublicationObjective:The discovery of sequence specific gene silencing which occurs due to the presence of double-stranded RNAs has considerable impact on biology, revealing an unknown level of regulation of gene expression. This process is known as RNA interference (RNAi) or RNA silencing in which RNA molecules inhibit gene expression, typically by causing the destruction of specific mRNA molecule. Two types of small RNA molecules - small...
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Interactions of protons with furan molecules studied by collision-induced emission spectroscopy at the incident energy range of 50–1000 eV
PublicationInvestigations of the ion-molecule reactions provide insight into many fields ranging from the stellar wind interaction with interstellar media, up to medicine and industrial applications. Besides the applications, the understanding of these processes is itself a problem of fundamental importance. Thus, interactions of protons with the gas-phase furan molecules have been investigated for the first time in the energy range of 50–1000...
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Understanding ion–ion and ion–solvent interactions in aqueous solutions of morpholinium ionic liquids with N-acetyl-L-alaninate anion through partial molar properties and molecular dynamics simulations
PublicationAmino acid ionic liquids (AAILs) provide a low toxicity, biodegradable alternative to conventional ionic liquids, while also maintaining solubility in water. Densities and sound velocities of aqueous solutions of four amino acid ionic liquids (AAILs), based on the N-alkyl-N-methylmorpholinium ([Mor1,R], R = 2, 3, 6, 8) cation and N-acetyl-L-alaninate ([N-Ac-L-Ala]) anion were measured at T = (293.15–313.15) K and at atmospheric...
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Toward Mechanosynthesis of Diamondoid Structures: VI. Quantum-Chemical Molecular Dynamics Comparison of Conditions for the STM Tip Driven Mechanosynthesis on Hydrogenated Si(111), Si(110) and Si(100) Surfaces.
Publicationmożliwość prototypowania przejściowych generacji nano-urządzeń otrzymanych drogą pozycjonowanej mechanosyntezy za pomocą stm wyposażonego w ostrze typu swcnt są analizowane metodą kwantowo-chemicznej dynamiki molekularnej. proponowana strategia syntezy polega na insercji atomów si oraz cząsteczek sih2 we wiązania si-h na uwodornionej powierzchni si(111), si(110) oraz si(100) kryształu krzemu. rezultaty modelowania sugerują, że...
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Synthesis and molecular structure of novel 2-(alkylthio)-4-chloro-N-(4,5-dihydro-5-oxo-1H-1,2,4-triazol-3-yl)-5-methylbenzenesulfonamideswith potential anticancer activity
PublicationOtrzymano 15 nowych związków: 2-(alkilotio)-4-chloro-N-(4,5-dihydro-5-oxo-1H-1,2,4-triazol-3-yl)-5-metylobenzenosulfonamidów, dla których opracowano nową metodę syntezy. Dla jednej pochodnej wyznaczono strukturę rentgenowską. Związek nr 36 wykazuje wysoką aktywność przeciwnowotworową w stosunku do 13 linii komórek nowotworowych o poziomie GI_50 w zakresie stężeń 1,9-3,0 μM.
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Molecular epidemiology of Serratia marcescens in two hospitals in Danzig, Poland, over a 5-year period.Molecular epidemiology of Serratia marcescens in two hospitals in Gdańsk, Poland, over a 5-year period.
PublicationW pracy badano zmiany populacji Serratia marcescens w ciągu 5 lat w dwóch szpitalach klinicznych Gdańska. Posłużono się wartościami MIC, wynikami typowania genetycznego RAPD-PCR, PFGE i nową metodą ADSRRS-fingerprinting oraz analizą beta-laktamaz o rozszerzonym spektrum substratowym (ESBL). Dzięki określeniu lekowrażliwości na najnowsze antybiotyki beta-laktamowe wykryto fenotypy wykazujące derepresję cefalosporynazy AmpC u 23%...
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Assessing ecotoxicity, synergic and antagonistic actions of commonly used components of polymerization mixture in molecularly imprinted polymers preparation process
PublicationIncreasingly, the challenge is the optimal process of developing a suitable MIP-type sorptive material (taking into account its final form and application area), which is mainly related to the efficiency/effectiveness of the polymerization process. The lack of reaction or its low efficiency generates additional waste and puts it into the environmental cycle. The main aim of the performed research was the estimation of ecotoxicity,...
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The Influence of COD Fraction Forms and Molecules Size on Hydrolysis Process Developed by Comparative OUR Studies in Activated Sludge Modelling
PublicationThe activated sludge models (ASMs) commonly used by the International Water Association (IWA) task group are based on chemical oxygen demand (COD) fractionations. However, the proper evaluation of COD fractions, which is crucial for modelling and especially oxygen uptake rate (OUR) predictions, is still under debate. The biodegradation of particulate COD is initiated by the hydrolysis process, which is an integral part of an ASM....
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Reactivity of bulky aminophosphanes towards small molecules: Activation of dihydrogen and carbon dioxide by aminophosphane/borane frustrated Lewis pairs
PublicationA series of mono- and bisaminophosphanes with formulas R2NPR’R’’ and (R2N)2PR’ (R = iPr, Cy; R’ = Ph, Cy; R’’ = iPr) were characterized by X-ray analysis, NMR spectroscopy and computational methods. The common structural futures of these species are short and polarized PAN bonds, a pyramidal geometry at the P atom and an almost planar geometry at the N atoms. According to DFT calculations, these...
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Novel molecules containing structural features of NSAIDs and 1,2,3-triazole ring: Design, synthesis and evaluation as potential cytotoxic agents
PublicationFor the first time the template containing structural features of more than one NSAIDs and the 1,2,3-triazole ring was explored for the identification of potential cytotoxic agents. These new and complex molecules were predicted to be effective inhibitors of PDE4B by molecular modelling studies in silico. The multi-step synthesis of these compounds were carried out starting from the well-known drug nimesulide and involved the use...
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Novel molecules containing structural features of NSAIDs and 1,2,3-triazole ring: Design, synthesis and evaluation as potential cytotoxic agents
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Surface Site Modulations by Conjugated Organic Molecules To Enhance Visible Light Activity of ZnO Nanostructures in Photocatalytic Water Splitting
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Structural and Evolutionary Analysis Indicate That the SARS-CoV-2 Mpro Is a Challenging Target for Small-Molecule Inhibitor Design
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Structural and Evolutionary Analysis Indicate that the SARS-CoV-2 Mpro is an Inconvenient Target for Small-Molecule Inhibitors Design
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O 1s excitation and ionization processes in the CO2 molecule studied via detection of low-energy fluorescence emission
PublicationOxygen 1s excitation and ionization processes in the CO2 molecule have been studied with dispersed and non-dispersed fluorescence spectroscopy as well as with the vacuum ultraviolet (VUV) photon-photoion coincidence technique. The intensity of the neutral O emission line at 845 nm shows particular sensitivity to core-to-Rydberg excitations and core-valence double excitations, while shape resonances are suppressed. In contrast,...