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Search results for: MOLECULAR UMBRELLAS
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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.
PublicationMass 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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Optoelectronic system for investigation of cvd diamond/DLC layers growth
PublicationDevelopment 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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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
PublicationThe 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
PublicationtCross-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
PublicationSamples 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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New Molecular Markers Involved in Regulation of Ovarian Granulosa Cell Morphogenesis, Development and Differentiation during Short-Term Primary In Vitro Culture—Transcriptomic and Histochemical Study Based on Ovaries and Individual Separated Follicles
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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
PublicationThe 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...
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Novel 5-Substituted 2-(Aylmethylthio)-4-chloro-N-(5-aryl-1,2,4-triazin-3-yl)benzenesulfonamides: Synthesis, Molecular Structure, Anticancer Activity, Apoptosis-Inducing Activity and Metabolic Stability
PublicationA series of novel 5-substituted 2-(arylmethylthio)-4-chloro-N-(5-aryl-1,2,4-triazin-3-yl) benzenesulfonamide derivatives 27–60 have been synthesized by the reaction of aminoguanidines with an appropriate phenylglyoxal hydrate in glacial acetic acid. A majority of the compounds showed cytotoxic activity toward the human cancer cell lines HCT-116, HeLa and MCF-7, with IC50 values below 100 M. It was found that for the analogues 36–38...
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L1 Cell Adhesion Molecule Overexpression Down Regulates Phosphacan and Up Regulates Structural Plasticity-Related Genes Rostral and Caudal to the Complete Spinal Cord Transection
PublicationL1 cell adhesion molecule (L1CAM) supports spinal cord cellular milieu after contusion and compression lesions, contributing to neuroprotection, promoting axonal outgrowth, and reducing outgrowth-inhibitory molecules in lesion proximity. We extended investigations into L1CAM molecular targets and explored long-distance effects of L1CAM rostral and caudal to complete spinal cord transection (SCT) in...
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Mapping the Structural and Dynamic Determinants of pH-Sensitive Heparin Binding to Granulocyte Macrophage Colony Stimulating Factor
PublicationGranulocyte macrophage colony stimulating factor (GMCSF) is an immunomodulatory cytokine that is harnessed as a therapeutic. GMCSF is known to interact with other clinically important molecules, such as heparin, suggesting that endogenous and administered GMCSF has the potential to modulate orthogonal treatment outcomes. Thus, molecular level characterization of GMCSF and its interactions with biologically active compounds is critical...
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Collagen and hyaluronic acid hydrogel in water-in-oil microemulsion delivery systems
PublicationThe efficacy of microemul-sion in dermal and transdermal delivery of active ingredients. Here, we assessed the water-in-oilmicroemulsion capacity to incorporate two natural polymers, i.e. collagen and hyaluronic acid withlow and high molecular weight. Systems were extensively characterized in terms of conductivity, phaseinversion studies, droplet diameter, polydispersity index and rheological properties. The results of thisresearch...
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EASY ACCESS TOOL FOR SMALL INTERFERING RNA (siRNA) DATA
PublicationFor many decades it was an accepted dogma of molecular genetics that the expression of genes is a “one-way-road” leading only in one direction from DNA to RNA to proteins. Recent discoveries in modern molecular genetics have challenged this dogma showing that specific RNA molecules play a central role in controlling the activity of genes by changing the structure of DNA sequences, targeting other RNAs for degradation or blocking...
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An effective method for studying intermolecular interactions in binary liquids with hydrogen bonds: FTIR spectra and ab initio calculations in the N-methylformamide - methanol system
PublicationMolecular complexes in methanol (MeOH)−N-methylformamide (NMF) mixtures were studied based on their FTIR-ATR spectra, to which two methods of analysis were applied: factor analysis and a quantitative version of the difference-spectra method. The mean composition of a complex between NMF and MeOH molecules over the whole range of mixture compositions was determined. Absorbing species differentiated with regard to the interaction...
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Magnetic Molecularly Imprinted Polymer Nanoparticles for Selective Extraction of Copper from Aqueous Solutions Prior to Its Flame Atomic Absorption Determination
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Magnetic molecularly imprinted polymer nanoparticles for selective extraction of copper from aqueous solutions prior to its flame atomic absorption determination
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Ionization and fragmentation of the six-membered heterocycles containing oxygen – Comparative studies of electron and photon impact on the 3,4-dihydro-2H-pyran molecules
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Multi-step functionalization procedure for fabrication of vertically aligned mesoporous silica thin films with metal-containing molecules localized at the pores bottom
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Elastic cross-section calculations for electron collisions with XY4 (X=Si,Ge; Y=H, F, Cl, Br, I) molecules
PublicationObliczano elastyczne przekroje czynne dla tetraedrycznych związków krzemu i germanu. Otrzymane wyniki porównano z innymi dostępnymi wynikami obliczeń oraz z danymi doświadczalnymi; dla energii powyżej 100 eV uzyskano zadowalającą zgodność.
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Molecularly targeted nanoparticles: an emerging tool for evaluation of expression of the receptor for advanced glycation end products in a murine model of peripheral artery disease
PublicationAbstract Background: Molecular imaging with molecularly targeted probes is a powerful tool for studying the spatio-temporal interactions between complex biological processes. The pivotal role of the receptor for advanced glycation end products (RAGE) in numerous pathological processes, aroused the demand for RAGE targeted imaging in various diseases. In the study, we evaluated the use of a diagnostic imaging agent for RAGE quantification...
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Inner-shell fragmentation of molecules into neutral fragments in high-Rydberg states induced by soft X-ray excitation with pulsed-field ionization
PublicationIn the present communication, we will show the results of measurements probing the production of neutral high-Rydberg fragments at the K edges of the molecules containing oxygen and nitrogen atoms. The experiments were performed at the Gas Phase beamline of the Elettra synchrotron radiation laboratory (Trieste, Italy), exploiting a combined soft X-ray excitation with pulsed-field ionization and ion time-of-flight (TOF) spectrometry...
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Designing efficient A-D-A1-D-A type fullerene free acceptor molecules with enhanced power conversion efficiency for solar cell applications
PublicationThe achievement of highly efficient power conversion efficiency (PCE) is a big concern for non-fullerene organic solar cells (NF-OSCs) because PCE can depend on numerous variables. Here, new five novel acceptor molecules without fullerenes were developed and investigated using DFT (density functional theory) and TD-DFT (time dependent-density functional theory). Compared to the recently synthesized molecule (PZ-dIDTC6), the developed...
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Soft X-ray Induced Production of Neutral Fragments in High-Rydberg States at the O 1s Ionization Threshold of the Water Molecule
PublicationDissociation of water molecules after soft X-ray absorption can yield neutral fragments in high-Rydberg (HR) states. We have studied the production of such fragments by field ionization and ion time-of-flight (TOF) spectrometry. Neutral HR fragments are created at all resonances below the O 1s ionization potential (IP) and particularly within 1 eV above the O 1s IP. The latter effect is due to the recapture of the O 1s photoelectrons...
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Electron-impact ionization of fluoromethanes – Review of experiments and binary-encounter models
PublicationExperiments 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...
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Isocyanate-Free Polyurethanes
PublicationIsocyanate-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...
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Correlated Particle Motion and THz Spectral Response of Supercritical Water
PublicationMolecular dynamics simulations of supercritical water reveal distinctly different distance-dependent modulations of dipolar response and correlations in particle motion compared to ambient conditions. The strongly perturbed H-bond network of water at supercritical conditions allows for considerable translationaland rotational freedom of individual molecules. These changes give rise to substantially different infrared spectra and...
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Geometry optimization of steroid sulfatase inhibitors - the influence on the free binding energy with STS
PublicationIn the paper we review the application of two techniques (molecular mechanics and quantum mechanics) to study the influence of geometry optimization of the steroid sulfatase inhibitors on the values of descriptors coded their chemical structure and their free binding energy with the STS protein. We selected 22 STS-inhibitors and compared their structures optimized with MM+, PM7 and DFT B3LYP/6–31++G* approaches considering separately...
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Introduction to MIP synthesis, characteristics and analytical application
PublicationOne of the trends in analytical chemistry is associated with designing and developing new types of sample preparation techniques, which might significantly increase the efficiency and selectivity of the analytes isolation or/and preconcentration process. One of the most widely employed solutions are selective sorption materials, defined as molecularly imprinted polymers (MIPs), as well as the sorbents with the molecular fingerprint....
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Anharmonic Infrared Spectroscopy through the Fourier Transform of Time Correlation Function Formalism in ONETEP
PublicationDensity functional theory molecular dynamics (DFT-MD) provides an efficient framework for accurately computing several types of spectra. The major benefit of DFTMD approaches lies in the ability to naturally take into account the effects of temperature and anharmonicity, without having to introduce any ad hoc or a posteriori corrections. Consequently, computational spectroscopy based on DFT-MD approaches plays a pivotal role in...
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Potassium Tri-tert-butoxysilanethiolates: Synthesis, Properties, and Crystal and Molecular Structures of [(tBuO)3SiSK]6[THF]2·2THF, {[(tBuO)3SiS]2K2}n, and [(tBuO)3SiSK]4[H2O]4·C6H6
PublicationW reakcji tri-tert-butoksysilanotiolu z potasem otrzymano trzy nowe związki:[(tBuO)3SiSK]6[THF]2·2THF, {[(tBuO)3SiS]2K2}n, i[(tBuO)3SiSK]4[H2O]4·C6H6. Stanowią one dogodne substraty w syntezach kompleksów silanotiolanowych metali przejściowych. Charakteryzują się one również różnorodnością tworzonych układów. Rentgenowska analiza strukturalna wykazała, iż tworzą one trzy typy makrocząsteczkowych układów, w których...
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Cobalt(II) tri-tert-butoxysialanethiolates.Synthesis, properties, crystal and molecular structures of [Co{SSi(OtBu)3}2(L)] and[Co{SSi(OtBu)3}2(L)2] type complexes with monodentate nitrogen ligands.
PublicationThe title heteroleptic neutral cobalt(II) tri-tert-butoxysilanethiolate complexes with monodentate nitrogen bases (L) as additional ligands have been prepared by the reactions of [Co{μ-SSi(OtBu)3}{SSi(OtBu)3}(NH3)]2 (1) with respective bases. For pyridine both types have been prepared...
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Zakażenia bakteryjne w przewlekłym zapaleniu ucha środkowego - ocena przydatności diagnostyki molekularnej opartej o technikę PCR. Bacterial infection in chronic otitis media - assessment of usefulness of molecular diagnostic based in PCR method.
PublicationIdentyfikacja zakażeń w przewlekłym zapaleniu ucha środkowego jest trudna, o czym świadczą wysokie odsetki ujemnych wyników badań bakteriologicznych. Przyczyną tego jest trudność w uzyskiwaniu wiarygodnego materiału do badań oraz stosunkowo niska czułość klasycznych metod diagnostycznych. Amplifikacja bakteryjnego DNA techniką PCR jest badaniem, które może przyczynić się do zwiększenia efektywności i czułości badań bakteriologicznych....
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Synthesis, molecular structure, and metabolic stability of new series of N' -(2-alkylthio-4-chloro-5-methylbenzenesulfonyl)-1-(5-phenyl-1 H -pyrazol-1-yl)amidine as potential anti-cancer agents
PublicationA series of new N'-(2-alkylthio-4-chloro-5-methylbenzenesulfonyl)-1-(5-phenyl-1H-pyrazol-1-yl)amidine derivatives have been synthesized and evaluated in vitro by MTT assays for their antiproliferative activity against cell lines of colon cancer HCT-116, cervical cancer HeLa and breast cancer MCF-7. The studied compounds display selective activity mainly against HCT-116 and HeLa cells. Thus, five compounds show selective cytotoxic...
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Properties of water in the region between a tubulin dimer and a single motor head of kinesin
PublicationA kinesin is a molecular motor that can perform movement on a microtubule track in a stepping-like manner. This motion is connected with processes of association and dissociation of kinesin and tubulin. Water is an important participant in these kinds of molecular interactions. This is why we have decided to investigate the dynamical and structural properties of water in the region between the kinesin catalytic domain and the tubulin...
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Modification of gradient HPLC method for determination of small molecules' affinity to human serum albumin under column safety conditions: Robustness and chemometrics study
PublicationIn the early stages of drug discovery, beyond the biological activity screening, determining the physicochemical properties that affect the distribution of molecules in the human body is an essential step. Plasma protein binding (PPB) is one of the most important investigated endpoints. Nevertheless, the methodology for measuring %PPB is significantly less popular and standardized than other physicochemical properties, like lipophilicity....
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Application potential of dummy molecularly imprinted polymers as solidphase extraction sorbents for determination of low-mass polybrominated diphenyl ethers in soil and sediment samples
PublicationDespite the introduction of restrictive regulations in the USA and the European Union, polybrominated diphenyl ethers (PBDEs) are still found in various types of environmental and biological samples at significant concentration levels. The presence of these persistent organic pollutants in the environment raises important issues because of their negative impact on immunological and neurological systems, and on the hormonal balances...
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A competition between two- and three-body dissociation channels in photo-double-ionization of tetrahydro-2H-pyran and 3,4-dihydro-2H-pyran molecules
PublicationVarious molecules possess structures consisting of the heterocyclic rings containing oxygen atoms. These substances often play a significant role in many different fields of chemistry, medicine, and biology. Due to a specific atomic composition and bond arrangement, many of these molecules retain unique electronic properties, which may be probed by diverse spectroscopic techniques, including those utilizing synchrotron radiation....
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The Effect of Sterols on Amphotericin B Self-Aggregation in a Lipid Bilayer as Revealed by Free Energy Simulations
PublicationAmphotericin 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...
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Synthetic strategies in construction of organic macromolecular carrier–drug conjugates
PublicationMany 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...
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Physical crosslinking of hyaluronic acid in the presence of phospholipids in an aqueous nano-environment
PublicationHyaluronic acid and phospholipids are two components in the synovial joint cavity that contribute to joint lubrication synergistically. Molecular dynamics simulations were performed and hydrogen bonds in hyaluronic acid were analyzed to identify specific sites that are responsible for its physical cross-linking. Two molecular masses of hyaluronic acid, 10 kDa and 160 kDa, were considered. We use molecular dynamics simulations and...
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The Metal-Free Regioselective Deuteration of 2-Methylquinolin-8-ol and 2,5-Dimethylquinolin-8-ol, Spectroscopic and Computational Studies
PublicationAbstract: Aim and Background: Introducing deuterium to a molecule is of interest to a wide variety of research, including investigation of reaction mechanisms or kinetics, analysis of drug metabolism, structural elucidation of molecules, and syntheses of isotopically labeled materials used for NMR spectroscopy and medicinal research. Objective: The transition-metal-free regioselective deuteration of 2-methylquinolin-8-ol...
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Quasirelativistic potential energy curves and transition dipole moments of NaRb
PublicationWe report on extensive calculations of quasi-relativistic potential energy curves and, for the first time, transition dipole moments including spin-orbit and scalar-relativistic effects of the NaRb molecule. The calculated curves of the 0+, 0-, 1, 2 and 3 molecular states correlate for large internuclear separation with the fourteen lowest atomic energies up to the Na(3s ^2S_{1/2}) + Rb(7s ^2S_{1/2}) atomic limit. Several new features...
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In silico assessment and sonochemical synthesis of 2-alkynyl 3-chloropyrazines as prospective ligands for SARS-CoV-2
PublicationThe recent global pandemic caused by COVID-19 has triggered an intense effort worldwide towards the development of an effective cure for this disease. In our effort we have explored the 2-alkynyl substituted 3-chloropyrazine framework as a potential template for the design of molecules for this purpose. Our strategy was supported by the in silico studies of representative compounds to assess their binding affinities via docking...
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Toward Mechanosynthesis of Diamondoid Structures: IX Commercial Capped CNT Scanning Probe Microscopy Tip as Nowadays Available Tool for Silylene Molecule and Silicon Atom Transfer
PublicationAccording to K. E. Drexler, advanced mechanosynthesis will employ advanced nanomachines, but advanced nanomachines will themselves be product of advanced mechanosynthesis. This circular relationship must be broken in SPM technology development. In the article, the possibility of use easy available commercial CNT tips to assembly silicon-based intermediate generations of nano-devices is considered. Mechanosynthesis of a target class...
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Interfacial water controls the process of adsorption of hyperactive antifreeze proteins onto the ice surface
PublicationA mechanism of interactions between the ice-binding surface of a hyperactive antifreeze protein molecule and the ice surface is proposed, involving the influence of water present between the two surfaces on the behavior of the approaching molecule. It is demonstrated that the interfacial water, even before its full solidification, can act as a factor that pushes away or pulls nearer the protein molecule to ensure its proper positioning....
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Application of molecularly imprinted polymer pipette tip micro-solid phase extraction of nalidixic acid and acetaminophen from pills and seawater samples and their determination by spectrophotometry
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