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Wyniki wyszukiwania dla: CONFORMATIONAL ENTROPY
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Shear-Jamming in Two-Dimensional Granular Materials with Power-Law Grain-Size Distribution
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Effect of osmolytes on the thermal stability of proteins: replica exchange simulations of Trp-cage in urea and betaine solutions
PublikacjaAlthough osmolytes are known to modulate the folding equilibrium, the molecular mechanism of their effect on thermal denaturation of proteins is still poorly understood. Here, we simulated the thermal denaturation of a small model protein (Trp-cage) in the presence of denaturing (urea) and stabilizing (betaine) osmolytes, using the all-atom replica exchange molecular dynamics simulations. We found that urea destabilizes Trp-cage...
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Effect of pH on optical sensing with poly-L-lysine-modified nanodiamonds
PublikacjaNitrogen-vacancy (NV) centers are crystallographic defects which provide diamonds with unique physical properties. The centers are known for their intensive, time-stable fluorescence, and an electron spin, which exhibits long coherence time and may be manipulated using external stimuli. Nanodiamonds containing the NV centers are promising tools in biolabeling, biosensing, and drug delivery due to the aforementioned properties of...
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Chiral and achiral crystals, charge-assisted hydrogen-bond patterns and self-organization of selected solid diaminium thiosulfates
PublikacjaAbstract A series of diaminium thiosulfates, derivatives of diamines: NH2CH2CH(CH3)NH2 (1) and NH2(CH2)nNH2, n = 3-6 (2-5 respectively)and thiosulfuric acid were prepared and their structures determined by crystal X-ray diffraction analysis. Compounds 1, 2 and 4 turned out to be hydrates. The crystal structure of 1,2-proylenediaminium thiosulfate is chiral and exhibits spontaneous resolution. Crystals for both enantiomers...
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Thermodynamic interpretation and prediction of CO2 solubility in imidazolium ionic liquids based on regular solution theory
PublikacjaRegular solution theory (RST) is the most popular model for the interpretation of the interaction between CO2 and ionic liquids. In the present work, the parameters of this model were determined for the CO2 absorption in eleven imidazolium ionic liquids. The y-intercept (A) of the RST model for the investigated imidazolium liquids increases with increasing temperature whereas the slope (B) remains constant. The values of RST parameters...
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A coarse‐grained approach to NMR ‐data‐assisted modeling of protein structures
PublikacjaThe ESCASA algorithm for analytical estimation of proton positions from coarse-grained geometry developed in our recent work has been implemented in modeling protein structures with the highly coarse-grained UNRES model of polypeptide chains (two sites per residue) and nuclear magnetic resonance (NMR) data. A penalty function with the shape of intersecting gorges was applied to treat ambiguous distance restraints, which automatically...
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Dynamic Bayesian Networks for Symbolic Polyphonic Pitch Modeling
PublikacjaSymbolic pitch modeling is a way of incorporating knowledge about relations between pitches into the process of an- alyzing musical information or signals. In this paper, we propose a family of probabilistic symbolic polyphonic pitch models, which account for both the “horizontal” and the “vertical” pitch struc- ture. These models are formulated as linear or log-linear interpo- lations of up to fi ve sub-models, each of which is...
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Dynamics of quantum entanglement
PublikacjaA model of discrete dynamics of entanglement of a bipartite quantum state is considered. It involves a global unitary dynamics of the system and periodic actions of local bistochastic or decaying channel. For initially pure states the decay of entanglement is accompanied by an increase of von Neumann entropy of the system. We observe and discuss revivals of entanglement due to unitary interaction of subsystems. For some mixed states...
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Enzymatic cross-linking of β-lactoglobulin in solution and at air–water interface: Structural constraints
PublikacjaEffective and controlled use of cross-linking enzymes in structure engineering of food systems depends on characterization of the favorable conditions for enzyme-substrate complex and the limiting factors for the desired modification. In this respect, we analyzed the susceptibility of bovine β-lactoglobulin (BLG) to enzymatic cross-linking by Trichoderma reesei tyrosinase (TrTyr) and transglutaminase (TG). Changes in BLG molecular...
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Nonlinear resultant theory of shells accounting for thermodiffusion
PublikacjaThe complete nonlinear resultant 2D model of shell thermodiffusion is developed. All 2D balance laws and the entropy imbalance are formulated by direct through-the-thickness integration of respective 3D laws of continuum thermodiffusion. This leads to a more rich thermodynamic structure of our 2D model with several additional 2D fields not present in the 3D parent model. Constitutive equations of elastic thermodiffusive shells...
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Impact of Boundary Conditions on Acoustic Excitation of EntropyPerturbations in a Bounded Volume of Newtonian Gas
PublikacjaExcitation of the entropy mode in the field of intense sound, that is, acoustic heating, is theoreticallyconsidered in this work. The dynamic equation for an excess density which specifies the entropy mode,has been obtained by means of the method of projections. It takes the form of the diffusion equation withan acoustic driving force which is quadratically nonlinear in the leading order. The diffusion coefficient isproportional...
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Standing Waves in One-Dimensional Resonator Contaning an Ideal Isothermal Gas Affected by the Constant Mass Force
PublikacjaThe study is devoted to standing acoustic waves in one-dimensional planar resonator which containing an ideal gas. A gas is affected by the constant mass force. Two types of physically justified boundary conditions are considered: zero velocity or zero excess pressure at both boundaries. The variety of nodal and antinodal points is determined. The conclusion is that the nodes of pressure and antinodes of velocity do not longer...
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Book Chapter in the Prime Archives in Chemistry: 2nd Edition (dissemination of knowledge)
PublikacjaTo cite a chapter in a book include: Jaroslaw Spychala. The CON−H….+NH2 Blue-Shifting H-Bond Stabilizing Effect on Z Secondary Amides and Cyclic System Conformational Rearrangement through an Alkylamine-Chain Migration Pathway. In: VSR Rajasekhar Pullabhotla, editor. Prime Archives in Chemistry: 2nd Edition. Hyderabad, India: Vide Leaf. 2022. https://doi.org/10.1155/2022/1707245
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The synthesis and structure of a potential immunosuppressant: N-mycophenoyl malonic acid dimethyl ester
PublikacjaThe synthesis of a potential immunosuppressant, i.e. dimethyl ester of N-mycophenoyl malonic acid was optimized in the reaction of mycophenolic acid (MPA) with amino malonic dimethyl ester in the presence of propanephosphonic anhydride (T3P) as a coupling reagent. The structural properties of the obtained MPA derivative were investigated by NMR, MS and single crystal X-ray diffraction methods. Theoretical considerations of conformational...
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Anion recognition by phosphonium calix[4]arens: synthesis and physico-chemical studies
Publikacjap-tert-butylcalix[4]arenes in the cone conformation, di-and tetra substituted at the narrow rim with charged phosphonium groups have been synthesies and characterised.
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Detecting coupling directions with transcript mutual information: A comparative study
PublikacjaCausal relationships are important to understand the dynamics of coupled processes and, moreover, to influence or control the effects by acting on the causes. Among the different approaches to determine cause-effect relationships and, in particular, coupling directions in interacting random or deterministic processes, we focus in this paper on information-theoretic measures. So, we study in the theoretical part the difference between...
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Dispiro[cyclopropane-1,50-endo-tricyclo-[5.2.1.02,6]deca-3,8-diene-100,100-cyclopropane]
PublikacjaThe title compound, C14H16, is built up from three fivememberedrings. Two of the five-membered rings display anenvelope conformation and the third one is almost planar(r.m.s. deviation = 0.014 A ° ).
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Analiza i ocena poprawności działania węzła tarcia w aspekcie II zasady termodynamiki
PublikacjaW artykule przedstawiono autorską metodę sprawdzania poprawności działania węzła tarcia traktowanego jako układ tribologiczny w aspekcie II zasady termo-dynamiki na podstawie analizy i oceny wyników badań laboratoryjnych wykonanych na stanowisku badawczym. Jako stanowisko wykorzystany został zmodyfikowany węzeł tarcia aparatu czterokulowego T-02. Zaprezentowano algorytm, według którego zostały wykonane badania empiryczne. Wykazano,...
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Molecular mechanism of proton-coupled ligand translocation by the bacterial efflux pump EmrE
PublikacjaThe current surge in bacterial multi-drug resistance (MDR) is one of the largest challenges to public health, threatening to render ineffective many therapies we rely on for treatment of serious infections. Understanding different factors that contribute to MDR is hence crucial from the global “one health” perspective. In this contribution, we focus on the prototypical broad-selectivity proton-coupled antiporter EmrE, one of the...
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THREE-DIMENSIONAL numerical investigation of MHD nanofluid convective heat transfer inside a CUBIC porous container with corrugated bottom wall
PublikacjaSimultaneous use of porous media and nanofluid as a heat transfer improvement method has recently captivated a great deal of attention. The heat transfer and entropy production of the Cu-water nanofluid inside a cubic container with a heated bottom wavy wall and an elliptic inner cylinder were numerically analyzed in this study. The container is partitioned into two sections: the left side is filled with permeable media and...
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Experimental certification of more than one bit of quantum randomness in the two inputs and two outputs scenario
PublikacjaOne of the striking properties of quantum mechanics is the occurrence of the Bell-type non-locality. They are a fundamental feature of the theory that allows two parties that share an entangled quantum system to observe correlations stronger than possible in classical physics. In addition to their theoretical significance, non-local correlations have practical applications, such as device-independent randomness generation, providing...
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Thermodynamic Studies of Interactions between Sertraline Hydrochloride and Randomly Methylated β-Cyclodextrin Molecules Supported by Circular Dichroism Spectroscopy and Molecular Docking Results
PublikacjaThe interaction between sertraline hydrochloride (SRT) and randomly methylated β-cyclodextrin (RM β CD) molecules have been investigated at 298.15 K under atmospheric pressure. The method used—Isothermal Titration Calorimetry (ITC) enabled to determine values of the thermodynamic functions like the enthalpy (DH), the entropy (DS) and the Gibbs free energy (DG) of binding for the examined system. Moreover, the stoichiometry coefficient...
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The Boltzmann sequence-structure channel
PublikacjaWe rigorously study a channel that maps binary sequences to self-avoiding walks in the two-dimensional grid, inspired by a model of protein statistics. This channel, which we also call the Boltzmann sequence-structure channel, is characterized by a Boltzmann/Gibbs distribution with a free parameter corresponding to temperature. In our previous work, we verified experimentally that the channel capacity has a phase transition for...
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Complexation of amino acids derivatives in water by calix[4]arene phosphonic acids
PublikacjaSeries of the calix[4]arene phosphonic acids with various substituents at the lower rim was synthesized. Complexing properties of these receptors towards methyl esters of six amino acids strongly depended on the calix[4]arene conformation flexibility. The complex formation processes were monitored using 1H NMR spectroscopy (deuterated phosphate buffer at pD 7.3, 22 oC) and association constant values were evaluated. Inherently...
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Molecular basis and potential activity of HIV-1 reverse transcriptase toward trimethylamine-based compounds
PublikacjaReverse transcriptase (RT) inhibitors are currently used to treat human immunodeficiency virus (HIV)-1 infections. In this work, novel triethylamine derivatives were designed and studied by rigid and flexible docking and molecular dynamics (MD) approaches. An apo form of HIV-1 RT was also studied by MD simulation to analyze comparative response of protein in ligand-bound and ligand-unbound forms. Among newly designed HIV-1 RT inhibitors,...
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Unraveling the Interplay between DNA and Proteins: A Computational Exploration of Sequence and Structure-Specific Recognition Mechanisms
PublikacjaMy PhD dissertation focused on DNA-protein interactions and the recognition of specific DNA sequences and structures. I discovered that acidic amino acid residues (Asp/Glu) play a crucial role by exhibiting a preference for cytosine. Their contribution to binding affinity depends on nearby cytosines, balancing electrostatic repulsion with specific interactions. Acidic residues act as negative selectors, discouraging non-cytosine...
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The efficiency of turbomachinery in the zero-and three-dimensional approaches
PublikacjaEfficiency of turbomachinery is usually defined using an isentropic process. This approach provides a reliable reference point only when pressure and temperature measurements are available, e.g. at the casing inlet and outlet. In the case of a single stage internal efficiency determination the reference point is difficult. Computational fluid dynamics allows for an exact calculation of values of losses occurring in a turbine...
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Evaluation of structural and electrical properties of multicomponent spinel oxide thin films deposited via spray pyrolysis technique
PublikacjaThis work reports the preparation of (Mn,Co,Fe,Ni,Cr)3O4 high-entropy spinel oxide in the form of a ~ 500 nm thin film utilising a facile spray pyrolysis technique. The structural and electrical properties of the layers were characterised after exposure to temperatures in the range of 400–900 ◦C. The as-deposited layers were amorphous, and crystallised upon heat treatment at 500 ◦C. Microstructural analyses proved a homogeneous...
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About definition of modes and magnetosonic heating in a plasma’s flow: Especial cases of perpendicular and nearly perpendicular wave vector and magnetic field
PublikacjaDynamics of hydrodynamic perturbations in a plasma depend strongly on an angle between the wave vector and equilibrium straight magnetic field. The case of perpendicular propagation is especial. There are only two (fast) magnetosonic modes since two (slow) ones degenerate into the stationary one with zero speed of propagation. This demands individual definition of wave modes by the links of hydrodynamic relations. These links are...
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Synthesis, structural characterization and reactivity of new trisubstituted N1-acylamidrazones: solid state and solution studies
PublikacjaA series of new linear trisubstituted N1-acylamidrazones have been investigated using a variety of analytical techniques and theoretical calculations to check the influence of the type of N1-acyl substituent on the resonance forms and conformational behavior in the solid state and in solution. The 1D- and 2D-NMR experiments, supported by computational studies, revealed that in solution all amidrazones exhibit conformational syn/anti...
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Quantifying Contextuality
PublikacjaContextuality is central to both the foundations of quantum theory and to the novel information processing tasks. Despite some recent proposals, it still faces a fundamental problem: how to quantify its presence? In this work, we provide a universal framework for quantifying contextuality. We conduct two complementary approaches: (i) the bottom-up approach, where we introduce a communication game, which grasps the phenomenon of...
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Magnetoacoustic heating in a quasi-isentropic magnetic gas
PublikacjaThe nonlinear heating of a plasma which associates with the transfer of energy of magnetoacoustic waves into that of the entropy mode, is analytically studied. A plasma is uniform and motionless at equilibrium. Perturbations in a plasma are described by a system of ideal magnetohydrodynamic equations. The equilibrium straight magnetic strength and the wave vector form a constant angle which varies from 0 to π/2. There exist four...
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Hysteresis curves for some periodic and aperiodic perturbations in magnetosonic flow
PublikacjaA thermodynamic relation between perturbations of pressure and mass density in the magnetohydrodynamic flow is theoretically studied. Planar magnetohydrodynamic perturbations with the wave vector, which forms a constant angle with the equilibrium magnetic field, are under study. The theory considers thermal conduction of a plasma and the deviation from adiabaticity of a flow due to some kind of heating–cooling function. It also...
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Statistical Method for Analysis of Interactions Between Chosen Protein and Chondroitin Sulfate in an Aqueous Environment
PublikacjaWe 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 nonlinear effects of sound in a liquid with relaxation losses
PublikacjaThe nonlinear effects of sound in electrolyte with a chemical reaction are examined. The dynamic equations that govern non-wave modes in the field of intense sound are derived, and acoustic forces of vortex, entropy, and relaxation modes are determined in the cases of low-frequency sound and high-frequency sound. The difference in the nonlinear effects of sound in electrolyte and in a gas with excited vibrational degrees of molecules,...
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Wnikanie wodoru z paliwa i oleju do stali stopowych 26h2mf i 34hnm oraz jego oddziaływanie z defektami struktury = The hydrogen entry from fuel and oil to the 26h2mf and 34hnm alloy steels, and its interaction with structure defects
PublikacjaWykonano badania skłonności do korozji naprężeniowej przy rozciąganiu próbek ze stałą małą prędkością 10-6s-1, przy obciążeniu cyklicznie zmiennym w środowisku gorącego paliwa kotłowego i gliceryny oraz badania absorpcji wodoru dla stali stopowych 26H2MF i 34HNM w paliwie kotłowym, przepracowanym oleju mineralnym oraz glicerynie jako środowisku referencyjnym. Wykazano największą wrażliwość stali przy obciążeniach zmiennych oraz...
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Heat Transfer of the Multicolor-Laser-Sources-Irradiated Nanoparticles in Reference to Thermal Processes
PublikacjaUnlike the standard materials, metallic nanoparticles offer enhancing the heat convertion rate which implies the maximum and average temperature boost significantly in the considered system. The work’s purpose is to examine heat transfer in the metallic nanoparticles which have been deposited on a glassy substrate, enabling the nanostructures thermoablation. Furthermore, the functionalized substrate is irradiated with multicolor-laser-sources,...
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Medium-sized cyclic bis(anisylphosphonothioyl)- disulfanes and their corresponding cyclic sulfane-structures and most characteristic reactions
PublikacjaCyclic 8-, 9-, 10-, and 12-membered bis(anisylphosphonothioyl)disulfanes were synthesized. Next, structurally related 7 to 9-membered cis and trans sulfanes were isolated as a result of sulfur atom extrusion from the parent cyclic disulfanes. The results of the desulfurization of the disulfanes were compared to the results obtained for desulfurization of the respective bis(anisylphosphodithioates). Cyclic disulfanes predominantly...
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Why Are Left-Handed G-Quadruplexes Scarce?
PublikacjaG-quadruplexes (G4s) are nucleic acid structures crucial for the regulation of gene expression and genome maintenance. While they hold promise as nanodevice components, achieving desired G4 folds requires understanding the interplay between stability and structural properties, like helicity. Although right-handed G4 structures dominate the experimental data, the molecular basis for this preference over left-handed helicity is unclear....
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THE INFLUENCE OF INTERPERSONAL MOTIVATION ON POLISH CONSUMERS’ ONLINE BRAND-RELATED ACTIVITY
PublikacjaThe development of social media has a substantial impact on the surge of social engagement of Internet users. It is particularly prominent in the domain of content creation and content sharing. Such communication may contain various references to different products brands and companies. Internet users may refer to them explicitly or brands may be present in the background only. Therefore, it is pivotal for managers and researchers...
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Nonlinear increase in bubbles radii caused by sound in a bubbly liquid
PublikacjaThe nonlinear interaction of acoustic and entropy modes in a bubbly liquid is considered. The reasons for interaction are both nonlinearity and dispersion. In the field of intense sound, a decrease in the mixture density is predicted. That corresponds to the well-established growth of bubbles volumes due to rectified diffusion. The nonlinear interaction of modes as a reason for a bubble to grow due to sound, is discovered. The...
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Phase Transition in a Sequence-Structure Channel
PublikacjaWe study an interesting channel which maps binary sequences to self-avoiding walks in the two-dimensional grid, inspired by a model of protein folding from statistical physics. The channel is characterized by a Boltzmann/Gibbs distribution with a free parameter corresponding to temperature. We estimate the conditional entropy between the input sequence and the output fold, giving an upper bound which exhibits an unusual phase transition...
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The description of non-linear interactions of wave and non-wave modes in a non-adiabatic plasma flow
PublikacjaThe method of derivation of non-linear equations for interacting modes is explained and applied to a plasma's flow affected by a magnetic field. It is based on the linear projecting of the total perturbation field into specific variations of variables in individual modes of a flow. The method may be applied in many examples of fluid flows with different mechanisms of non-adiabaticity. It is of special importance in complex flows...
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Effect of Cyclodextrins on Coupling of o-Ethoxybenzenediazonium Salt with Pyrrole, Imidazole and 2-Methylimidazole
PublikacjaThe effect of b-cyclodextrin on o-ethoxybenzenediazonium salt coupling with pyrrole, imidazole and 2-methylimidazole has been studied. The differences in the reaction course, the overall yield and products distribution have been analyzed. Experiments without cyclodextrins and selected reactions with a- and c-cyclodextrins have been performed for comparison. The results are discussed in terms of co-conformation of azole molecules...
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Application of the 2-deoxyglucose scaffold as a new chiral probe for elucidation of the absolute configuration of secondary alcohols
PublikacjaHerein, we present the application of 2-deoxy-D-glucose derivatives as chiral probes for elucidation of the absolute configuration of chiral secondary alcohols. The probes are attached to the studied molecules via glycosylation reaction and the resulting products are examined by a set of standard 2D NMR experiments. The absolute configuration of an oxymethine carbon atom binding the probe is established on a basis of a set of diagnostic...
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Selective Cytostatic and Cytotoxic Anticancer Effects of Bisfunctional Agents: A Strategy for the Design of DNA Binding Agents
PublikacjaVarious agents have been synthesized and proved useful for the National Cancer Institute's anticancer testing as potential new drugs, but most agents suffer side effects from their limited selectivity against cancer cells over healthy ones. Therefore, this paper attempts to describe drugs in terms of the level of tumor cell selectivity which they possess to define the features of mols. that are essential for useful cytotoxicity....
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Unexpected Z/E isomerism of N-methyl-O-phosphothioyl benzohydroxamic acids, their oxyphilic reactivity and inertness to amines
PublikacjaThiophosphinoylation of N-methyl p-substituted benzohydroxamic acids using disulfanes (method A) or diphenylphosphinothioyl chloride (method B) provides only one conformer of the respective O-phosphothioyl derivative (Xray and NMR analysis). Undergoing the P-transamidoxylation reaction is an evidence of the reversibility of thiophosphinoylation. Only those products containing strong EWG substituents in the aroyl residue or bulky...
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A new synthetic entry to phosphinophosphinidene complexes. Synthesis and structural characterisation of the first side-on bonded and the first terminally bonded phosphinophosphinidene zirconium complexes[mu-(1,2:2-eta-tBu2PLP){Zr(Cl)Cp2}2] and [{Zr(PPhMe2)Cp2}(eta^1^-P-P-tBu2)].
PublikacjaPodano nową metodę syntezy kompleksów fosfinofosfinidenowych polegającą na reakcji dichlorku cyrkonocenu z solą litową difosfanu t-Bu2P-P(SiMe3)Li. Otrzymano pierwsze kompleksy fosfanofosfinidenowe cyrkonu z ligandem związanym w sposób boczny i ligandem związanym terminalnie.
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Singular curves in the resultant thermomechanics of shells
PublikacjaSome geometric and kinematic relations associated with the curve moving on the shell base surface are discussed. The extended surface transport relation and the extended surface divergence theorems are proposed for the piecewise smooth tensor fields acting on the regular and piecewise regular surfaces. The recently formulated resultant, two-dimensionally exact, thermodynamic shell relations - the balances of mass, linear and angular...
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Ocena efektywności monitoringu obiektów inżynierskich za pomocą sieci Bayesa
PublikacjaW swojej pracy autorzy zaproponowali zastosowanie sieci Bayesa do projektowania monitoringu i podejmowania decyzji w działaniach eksploatacyjnych. Ponadto pokazano dwie metody oceny wartości informacji diagnostycznych. Pierwszą z nich jest wartość oczekiwana EVSI (ang. Expected Value of Sample Information), która stanowi podstawę do wyboru spośród alternatywnych obserwacji symptomów zmiennej diagnostycznej. Natomiast drugą metodą...