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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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The POCOBIO Database for Computed Scattering Cross-Sections for Positron Collisions with Biomolecular Systems
PublikacjaThe 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
Dane BadawczeThis 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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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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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
PublikacjaIn 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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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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The role of uropathogenic Escherichia coli adhesive molecules in inflammatory response- comparative study on immunocompetent hosts and kidney recipients
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APPLICATION OF BINARY-ENCOUNTER-BETHE METHOD TO ELECTRON-IMPACT IONIZATION CROSS SECTION CALCULATIONS FOR BIOLOGICALLY RELEVANT MOLECULES
PublikacjaElectron-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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Scattering of electrons from 1-butene, H2C=CHCH2CH3, and 2-methylpropene,H2C=C(CH3)2, molecules
PublikacjaZmierzono, 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
PublikacjaThe 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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Why is the cubic structure preferred in newly formed ice?
PublikacjaMolecular 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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Optical photoluminescent, and electroluminescent properties of organic solids
PublikacjaThis 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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Non-ergodic fragmentation upon collision-induced activation of cysteine–water cluster cations
PublikacjaCysteine–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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SiMiSnoRNA: Collection of siRNA, miRNA, and snoRNA database for RNA Interference
PublikacjaObjective: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
PublikacjaInvestigations 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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Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology
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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.
Publikacjamożliwość 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
PublikacjaOtrzymano 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.
PublikacjaW 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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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
PublikacjaAmino 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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Surface Site Modulations by Conjugated Organic Molecules To Enhance Visible Light Activity of ZnO Nanostructures in Photocatalytic Water Splitting
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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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The Influence of COD Fraction Forms and Molecules Size on Hydrolysis Process Developed by Comparative OUR Studies in Activated Sludge Modelling
PublikacjaThe 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
PublikacjaA 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
PublikacjaFor 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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Assessing ecotoxicity, synergic and antagonistic actions of commonly used components of polymerization mixture in molecularly imprinted polymers preparation process
PublikacjaIncreasingly, 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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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
PublikacjaOxygen 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,...
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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...
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Toward Mechanosynthesis of Diamondoid Structures: X. Commercial Capped CNT SPM Tip as Nowadays Available C2 Dimer Placement Tool for Tip-Based Nanofabrication
PublikacjaAccording to Drexler, advanced mechanosynthesis will employ advanced nano-machines, but advanced nano-machines will themselves be products of advanced mechanosynthesis. This circular relationship must be broken via TBN technology development. In this article, the possibility of using easily available commercial CNT tips to assemble carbon-based intermediate generations of nano-devices is considered. Mechanosynthesis of a target...
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Low-energy positron scattering from DNA nucleobases: the effects from permanent dipoles
PublikacjaAb initio quantum calculations for low-energy positron scattering from gas-phase isolated molecular nucleobases which are part of the DNA structure are presented and discussed over the range of 1 eV to 25 eV. The calculations report the integral cross sections (ICSs) and the momentum-transfer cross sections (MTCSs) for Adenine, Guanine, Thymine and Cytosine. The calculations show very clearly the important role of the dominant...
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<i>N,N</i>'-diphenylthiourea acetone monosolvate
PublikacjaIn the title compound, C13H12N2S·C3H6O, the phenyl rings of the thiourea molecule are in syn and anti positions in relation to the C=S bond. Two molecules are connected by N-HS=C hydrogen bonds into a centrosymmetric dimer. An additional N-HO=C hydrogen bond to the acetone solvent molecule and some weak C-H interactions reinforce the crystal structure.
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Molecular basis of lipopolysaccharide heterogeneity in Escherichia coli: envelope stress-responsive regulators control the incorporation of glycoforms with a third 3-deoxy-α-D-manno-oct-2-ulosonic acid and rhamnose.
PublikacjaMass spectrometric analyses of lipopolysaccharide (LPS) from isogenic Escherichia coli strains with nonpolar mutations in the waa locus or overexpression of their cognate genes revealed that waaZ and waaS are the structural genes required for the incorporation of the third 3-deoxy-α-D-manno-oct-2-ulosonic acid (Kdo) linked to Kdo disaccharide and rhamnose, respectively. The incorporation of rhamnose requires prior sequential incorporation...
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Golden artefacts, resin figurines, body adhesives and tomb sediments from the pre-Columbian burial site El Caño (Gran Coclé, Panamá): tracing organic contents using molecular archaeometry
PublikacjaThis research aimed to determine the origin of organic residues from funerary contexts in the El Ca~no settlement (Gran Cocl�e area, Panam�a, Central America) by means of multiple molecular probing techniques (GC-MS of organic solvent extracts and pyrolysis-GC-MS, THM-GC-MS and FTIR of solid samples). The samples include particles of precious resin figurines, fillings of golden objects, tomb sediments, plant exudates from extant...
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The effect of high molecular weight bio-based diamine derivative of dimerized fatty acids obtained from vegetable oils on the structure, morphology and selected properties of poly(ether-urethane-urea)s
PublikacjaIn this work, the effect of the high molecular weight bio-based diamine on the chemical structure and selected properties of poly(ether-urethane-urea)s has been investigated. The ether-urethane prepolymer was cured using 1,4-butanediol and/or bio-based diamine. Mentioned chain extenders were used separately or in the mixture, and their different molecular weight and chemical structure resulted in obtaining materials with diversified...
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Optoelectronic system for investigation of cvd diamond/DLC layers growth
PublikacjaDevelopment of the optoelectronic system for non-invasive monitoring of diamond/DLC (Diamond-Like-Carbon) thin films growth during μPA ECR CVD (Microwave Plasma Assisted Electron Cyclotron Resonance Chemical Vapour Deposition) process is described. The system uses multi-point Optical Emission Spectroscopy (OES) and long-working-distance Raman spectroscopy. Dissociation of H2 molecules, excitation and ionization of hydrogen atoms...
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Krzysztof Piotr Bielawski Prof. dr hab.
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Molecularly imprinted stir bar sorptive extraction coupled with atomic absorption spectrometry for trace analysis of copper in drinking water samples
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Determination of (S)-warfarin using an activated screen printed gold electrode modified with gold nanoparticles and an enantioselective molecularly imprinted polymer
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Molecularly imprinted stir bar sorptive extraction coupled with high-performance liquid chromatography for trace analysis of naphthalene sulfonates in seawater
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Proteomic Profiling of Ectosomes Derived from Paired Urothelial Bladder Cancer and Normal Cells Reveals the Presence of Biologically-Relevant Molecules
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Computational analysis of substituent effects on proton affinity and gas-phase basicity of TEMPO derivatives and their hydrogen bonding interactions with water molecules
PublikacjaThe study investigates the molecular structure of 2,2,6,6-tetramethylpiperidine-1-oxyl (TEMPO) and its derivatives in the gas phase using B3LYP and M06-2X functional methods. Intermolecular interactions are analyzed using natural bond orbital (NBO) and atoms in molecules (AIM) techniques. NO2-substituted TEMPO displays high reactivity, less stability, and softer properties. The study reveals that the stability of TEMPO derivatives...
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Cross-sections for electron-scattering from 2-methyl-1-buten-3-yne, C 5 H 6 , molecules
PublikacjatCross-sections for electron collisions with the 2-methyl-1-buten-3-yne [H2C C(CH3)C CH] moleculewere measured and calculated. Absolute grand-total electron-scattering cross-section (TCS) was takenat impact energies from 0.6 to 300 eV in the linear electron-transmission experiment. The TCS energydependence for the electron–C5H6collision has two prominent enhancements separated with a deepminimum located near 1.8 eV. In addition,...
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Quantum and carbon dots conjugated molecularly imprinted polymers as advanced nanomaterials for selective recognition of analytes in environmental, food and biomedical applications
PublikacjaSamples with complex matrix analyzed during explanation of pathogenesis of various diseases and food or environmental monitoring request advanced analytical and instrumental devices. Among the materials used for described purposes, quantum (QDs) or carbon dots (CDs) layered by molecularly imprinted polymer (MIP) shells have gained widespread attention. Unique optical and physicochemical properties of QDs/CDs together with high...
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Urinary Kidney Injury Molecule-1 but Not Urinary Neutrophil Gelatinase Associated Lipocalin Is Increased after Short Maximal Exercise
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