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Search results for: PHOSPHODIESTER BOND CLEAVAGE
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Low-energy (0.1 eV) electron attachment S?S bond cleavage assisted by Coulomb stabilization
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Catalytic Mechanism of Non-Target DNA Cleavage in CRISPR-Cas9 Revealed by Ab Initio Molecular Dynamics
PublicationCRISPR-Cas9 is a cutting-edge genome editing technology, which uses the endonuclease Cas9 to introduce mutations at desired sites of the genome. This revolutionary tool is promising to treat a myriad of human genetic diseases. Nevertheless, the molecular basis of DNA cleavage, which is a fundamental step for genome editing, has not been established. Here, quantum–classical molecular dynamics (MD) and free energy methods are used...
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Phosphinoborinium cation: a synthon for cationic B-P bond systems
PublicationHerein, we report access to phosphinoborinium cations via heterolytic cleavage of the boron-bromide bond in bromophosphinoborane. The product of the reaction was isolated as a dimeric dication possessing a planar P2B2 core. Activation of C-H and C-P bonds in the dication led to formation of the borinium-phosphaborene adduct. Reactivity studies revealed that title cation exhibits ambiphilic properties and intramolecular frustrated...
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5-Thiocyanato-2′-deoxyuridine as a possible radiosensitizer: electron-induced formation of uracil-C5-thiyl radical and its dimerization
PublicationIn this work, we have synthesized 5-thiocyanato-2′-deoxyuridine (SCNdU) along with the C6-deuterated nucleobase 5-thiocyanatouracil (6-D-SCNU) and studied their reactions with radiation-produced electrons. ESR spectra in γ-irradiated nitrogen-saturated frozen homogeneous solutions (7.5 M LiCl in H2O or D2O) of these compounds show that electron-induced S–CN bond cleavage occurs to form a thiyl radical (dU-5-S˙ or 6-D-U-5-S˙) and...
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N-phosphonomethylglycine utilization by the psychrotolerant yeast Solicoccozyma terricola M 3.1.4.
PublicationSolicoccozymaterricolaM 3.1.4., the yeast strain isolated from soil sample from blueberry cultivation in MiedzyrzecPodlaski in Poland, is capable to split of phosphorus to nitrogen and nitrogen to carbon bonds inN-phosphono-methylglycine (PMG, glyphosate). The biodegradation process proceeds in the phosphate-independent manner. Itis the first example of a psychrotolerant yeast strain able to degrade PMGviaCeN bond cleavage accompanied...
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General, Mild, and Metal-Free Functionalization of Indole and Its Derivatives Through Direct C3-Selenylation
PublicationA very mild method for the introduction of functionalized alkylselenyl group at C-3 position of the indole ring was developed. The proposed procedure consists of an electrophilic substitution of indole and its derivatives with bis(O,O-diisopropoxyphosphorothioyl) diselenide and subsequent cleavage of the P–Se bond with tetrabutylammonium fluoride in the presence of various electrophilic reagents. This method can be successfully...
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The Product of Matrix Metalloproteinase Cleavage of Doxorubicin Conjugate for Anticancer Drug Delivery: Calorimetric, Spectroscopic, and Molecular Dynamics Studies on Peptide–Doxorubicin Binding to DNA
PublicationMatrix metalloproteinases (MMPs) are extracellular matrix degradation factors, promoting cancer progression. Hence, they could provide an enzyme-assisted delivery of doxorubicin (DOX) in cancer treatment. In the current study, the intercalation process of DOX and tetrapeptide-DOX, the product of the MMPs' cleavage of carrier-linked DOX, into dsDNA was investigated using stationary and time-resolved fluorescence spectroscopy, UV-Vis...
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Phosphinoborenium cations stabilized by N-heterocyclic carbenes: synthesis, structure, and reactivity
PublicationPhosphinoborenium cations stabilized by N-heterocyclic carbenes (NHCs) were synthesized via the reaction of bromo(phosphino)boranes with NHCs. Their structures were investigated by heteronuclear magnetic resonance spectroscopy, X-ray diffraction, and density functional theory calculations. They possess a planar trigonal boron center directly bonded with the pyramidal phosphanyl group (PR2) and can be treated as cationic phosphinoboranes....
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Design, Synthesis, and Enzymatic Evaluation of Novel ZnO Quantum Dot-Based Assay for Detection of Proteinase 3 Activity
PublicationHerein, the synthesis and application of functionalized quantum dot-based protease probes is described. Such probes are composed of nontoxic ZnO nanocrystals decorated by amino groups followed by linker and labeled peptide attachment. Spherical NH2-terminated ZnO quantum dots (QDs) with the average size ranging from 4 to 8 nm and strong emission centered at 530 nm were prepared using the sol−gel method. The fluorescence of ZnO...
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Syntheses and Structures of Transition Metal Complexes with Phosphanylphosphinidene Chalcogenide Ligands
PublicationThe reactivity of the phosphanylphosphinidene complex [(DippN)2W(Cl)(η2-P-PtBu2)]− (1) toward chalcogens (Ch = Se, S) was studied. Reactions of stoichiometric amounts of 1 with chalcogens in DME yielded monomeric tungsten complexes with phosphanylphosphinidene chalcogenide ligands of the formula tBu2P−P−Ch (Ch = Se (in 2) and S (in 5)), which can be regarded as products of the addition of a chalcogen atom to a P=W bond in starting...
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Dissociative Electron Attachment to 5-Iodo-4-thio-2′-deoxyuridine: A Potential Radiosensitizer of Hypoxic Cells
PublicationIn the search for effective radiosensitizers for tumor cells, halogenated uracils have attracted more attention due to their large cross section for dissociation upon the attachment of low-energy electrons. In this study, we investigated dissociative electron attachment (DEA) to 5-iodo-4-thio-2'-deoxyuridine, a potential radiosensitizer using a crossed electron-molecule beam experiment coupled with quadrupole mass spectrometry....
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Theoretical studies of fragmentation processes of neutral and ionized furan molecule
PublicationThis PhD thesis focuses on the fragmentation mechanism of the furan molecule in the gas phase. The approach taken in this work comprised of three theoretical methodologies considering the dynamical, energetical and entropic aspects of the studied process. First, molecular dynamics simulations were performed. Next, the potential energy surfaces were explored at the DFT/B3LYP level of theory. Finally, a new statistical Microcanonical...
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Adhesive Monitoring with Instrumented Wedge Test
PublicationThe wedge test (sometimes called the Boeing wedge test) is amongst the most readily exploitable techniques for assessment of the rate-dependent fracture energy of adhesive materials when used to bond relatively rigid substrates. With its siblings: the double cantilever beam (DCB), and the tapered double cantilever beam (TDCB), a force is applied, essentially in cleavage, to provoke substrate separation perpendicularly to the bondline...
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Decomposition of halogenated nucleobases by surface plasmon resonance excitation of gold nanoparticles
PublicationHalogenated uracil derivatives are of great interest in modern cancer therapy, either as chemotherapeutics or radiosensitisers depending on their halogen atom. This work applies UV-Vis spectroscopy to study the radiation damage of uracil, 5-bromouracil and 5- uorouracil dissolved in water in the presence of gold nanoparticles upon irradiation with an Nd:YAG ns-pulsed laser operating at 532nm at dierent uences. Gold nanoparticles...
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H2O˙+ and OH+ reactivity versus furan: experimental low energy absolute cross sections for modeling radiation damage
PublicationRadiotherapy is one of the most widespread and efficient strategies to fight malignant tumors. Despite its broad application, the mechanisms of radiation-DNA interaction are still under investigation. Theoretical models to predict the effects of a particular delivered dose are still in their infancy due to the difficulty of simulating a real cell environment, as well as the inclusion of a large variety of secondary processes. This...
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Redox State Sensitive Spectroscopy of the Model Compound [(H-dcbpy)(2)Ru-II(NCS)(2)](2-) (dcbpy=2,2 '-Bipyridine-4,4 '-dicarboxylato)
PublicationThe charge transfer reaction mechanism in a ruthenium polypyridine model complex with isothiocyanato ligands, i.e., [(H-dcbpy)(2)Ru(NCS)(2)](2-) 2Bu(4)N(+) (Ru2H) (dcbpy = 2,2'-bipyridine-4,4'-dicarboxylato), has been investigated by combining UV-vis absorption, resonance Raman spectroscopy, and electrochemical methods. Understanding the photophysics of light-harvesting complexes of this class is an indispensable prerequisite to...
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The Mechanism of a Retro-Diels–Alder Fragmentation of Luteolin: Theoretical Studies Supported by Electrospray Ionization Tandem Mass Spectrometry Results
PublicationThe mechanisms of retro-Diels–Alder fragmentation of luteolin are studied theoretically using the Density Functional Theory method (B3LYP hybrid functional) together with the 6-311++G(d,p) basis set and supported by electrospray ionization tandem mass spectrometry (ESI-MS) results. The reaction paths leading to the formation of 1,3A and 1,3B fragment ions observed as the main spectral features in the ESI-MS spectrum are described...
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Formation of chlorinated breakdown products during degradation of sunscreen agent, 2-ethylhexyl-4-methoxycinnamate in the presence of sodium hypochlorite
PublicationIn this study, a new degradation path of sunscreen active ingredient, 2-ethylhexyl-4-methoxycinnamate (EHMC) and 4-methoxycinnamic acid (MCA) in the presence of sodium hypochlorite (NaOCl), was discussed. The reaction products were detected using gas chromatography–mass spectrometry (GC-MS). Since HOCl treatment leads to more polar products than EHMC, application of polar extracting agents, dichloromethane and ethyl acetate/n-hexane...
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Intramolecular Proton Transfer in the Radical Anion of Cytidine Monophosphate Sheds Light on the Sensitivities of Dry vs Wet DNA to Electron Attachment-Induced Damage
PublicationSingle-strand breaks (SSBs) induced via electron attachment were previously observed in dry DNA under ultrahigh vacuum (UHV), while hydrated electrons were found not able to induce this DNA damage in an aqueous solution. To explain these findings, crossed electron-molecular beam (CEMB) and anion photoelectron spectroscopy (aPES) experiments coupled to density functional theory (DFT) modeling were used to demonstrate the fundamental...
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Principles of target DNA cleavage and the role of Mg2+ in the catalysis of CRISPR–Cas9
PublicationAt the core of the CRISPR–Cas9 genome-editing technology, the endonuclease Cas9 introduces site-specific breaks in DNA. However, precise mechanistic information to ameliorate Cas9 function is still missing. Here, multimicrosecond molecular dynamics, free energy and multiscale simulations are combined with solution NMR and DNA cleavage experiments to resolve the catalytic mechanism of target DNA cleavage. We show that the conformation...
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Recent developments in disulfide bond formation
PublicationThis review summarizes the recent developments of disulfide bond formation with variety of reagents. The scope and limitation of the presented methods is discussed. The syntheses of unsymmetrical disulfides are highlighted in order to present the most versatile achievements.
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The cement-bone bond is weaker than cement-cement bond in cement-in-cement revision arthroplasty. A comparative biomechanical study
PublicationThis study compares the strength of the native bone-cement bond and the old-new cement bond under cyclic loading, using third generation cementing technique, rasping and contamination of the surface of the old cement with biological tissue. The possible advantages of additional drilling of the cement surface is also taken into account. Femoral heads from 21 patients who underwent a total hip arthroplasty performed for hip arthritis...
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Activation of the C=P bond in phosphanylphosphaalkenes C=P–P bond system) in the reaction with nucleophilic reagents: MeLi, nBuLi and tBuLi
PublicationThree reactions of phosphanylphosphaalkene (1) with nucleophiles were performed to activate the diphosphorus monomer. We observed similar results in the reactions with MeLi and nBuLi, in which the P–P bond is cleavaged and triphosphorus systems [P(Me)2–CH(biph)–CH(biph)–P–(PtBu 2)]- (1a'') and [P(nBu)2–CH(biph)–CH(biph)–P–(PtBu 2)]- (1b''), respectively, are formed depending on the nucleophilic reagent (biph ¼ biphenyl). In the...
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A review of amide bond formation in microwave organic synthesis
PublicationMicrowave-Assisted Organic Synthesis (MAOS) is one of the most current trends in organic chemistry. Herein, both the most popular and new approaches in microwave-syntheses of very important linkage in Nature - amide bond - are overviewed and compared with conventional synthetic routes.
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Experimental-Numerical Analysis of the Effect of Bar Diameter on Bond in Pull-Out Test
PublicationBar diameter is one of the basic factors affecting bond behavior, which is still of interest due to opposing opinions regarding its effect on bond behavior in the pull-out test. This paper presents an experimental and numerical bond analysis of ribbed reinforcing bar in concrete. The aim was to experimentally evaluate the effect of bar diameter on the bond behavior in the pull-out test and to perform numerical simulations of the...
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Modelling and analysis of beam/bar structure by application of bond graphs
PublicationThe paper presents an uniform, port-based approach to modelling of beam/bar systems (trusses). Port-based model of such distributed parameter system has been defined by application of the bond graph methodology and the distributed transfer function method (DTFM). The proposed method of modelling enables to formulate input data for computer analysis by application of the DTFM. The constructed computational package enables the frequency...
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Optimisation and field assessment of poroelastic wearing course bond quality
PublicationCompared to typical asphalt mixtures, poroelastic mixtures are characterised by high porosity and high flexibility, which are desirable for traffic noise reduction. However, the same properties increase the risk of debonding from the lower layer, which is a significant source of premature damage. The study investigates which of the factors – tack coat agent, type and texture of the lower layer – have the greatest impact on interlayer...
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Tests of bond between concrete and steel bars – literature background and program of own research
PublicationThis article deals with the issue of the bond between concrete and reinforcement. The bond is crucial for reinforced concrete elements because it is possible to transfer forces (stresses) from concrete to the reinforcement. Basic information related to the cooperation of concrete and rebars was recalled in the article. Selected issues concerning theoretical and numerical analysis as well as experiments of the bond phenomenon were...
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Role of the disulfide bond in stabilizing and folding of the fimbrial protein DraE from uropathogenic Escherichia coli
PublicationDr fimbriae are homopolymeric adhesive organelles of uropathogenic Escherichia coli composed of DraE subunits, responsible for the attachment to host cells. These structures are characterized by enormously high stability resulting from the structural properties of an Ig-like fold of DraE. One feature of DraE and other fimbrial subunits that makes them peculiar among Ig-like domain-containing proteins is a conserved disulfide bond...
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Reductive cleavage of the halogen-phosphorus and sulfur-phosphorus bonds with alkali metals
PublicationBadano redukcję chlorków kwasów tiofosforowych za pomocą: sodu lub potasu w ciekłym amoniaku i za pomocą antracenidku oraz naftalenidku potasu. Związki te ulegają, co wykazano, szybkiej redukcji do anionów >P-S- a te mogą być efektywnie utleniane siarką elementarną w ciekłym amoniaku.
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A highly-efficient technique for evaluating bond-orientational order parameters
PublicationWe propose a novel, highly-efficient approach for the evaluation of bond-orientational order parameters (BOPs). Our approach exploits the properties of spherical harmonics and Wigner 3jj-symbols to reduce the number of terms in the expressions for BOPs, and employs simultaneous interpolation of normalised associated Legendre polynomials and trigonometric functions to dramatically reduce the total number of arithmetic operations....
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A Model of Thermal Energy Storage According to the Convention of Bond Graphs (BG) and State Equations (SE)
PublicationThe main advantage of the use of the Bond Graphs method and State Equations for modeling energy systems with a complex structure (marine power plants, hybrid vehicles, etc.) is the ability to model the system components of different physical nature using identical theoretical basis. The paper presents a method of modeling thermal energy storage, which is in line with basic BG theory. Critical comments have been put forward concerning...
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Experiments and calibration of a bond-slip relation and efficiency factors for textile reinforcement in concrete
PublicationTextile reinforcement yarns consist of many filaments, which can slip relative each other. At modelling of the global structural behaviour, interfilament slip in the yarns, and slip between the yarns and the concrete can be considered by efficiency factors for the stiffness and strength of the yarns, and by applying a bond-slip relation between yarns and concrete. In this work, an effective and robust method for calibration of...
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Low-Barrier Hydrogen Bond Determines Target-Binding Affinity and Specificity of the Antitubercular Drug Bedaquiline
PublicationThe role of short strong hydrogen bonds (SSHB) in ligand-target binding remains largely unexplored, thereby hin- dering a potentially important avenue in the rational drug de- sign. Here, we investigate the interaction between bedaquiline (Bq), a potent anti-tuberculosis drug, and the mycobacterial ATP synthase, to unravel the role of a specific hydrogen bond to a conserved acidic residue in the target affinity and specificity....
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Activation of N2O and SO2 by the P–B Bond System. Reversible Binding of SO2 by the P–O–B Geminal Frustrated Lewis Pair
PublicationHerein, we present the first transformation of borylphosphine into borylphosphinite using nitrous oxide. Borylphosphine reacts with N2O via insertion of a single oxygen atom into the P−B bond and formation of a P−O−B bond system. Borylphosphine and borylphosphinite capture SO2 and activate it in an irreversible and reversible manner, respectively.
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Structural, spectroscopic, and computational characterization of the cleavage product of dimolybdenum(II) core under aerobic conditions
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CAUSALITY IN MODELS OF THERMAL PROCESSES IN SHIP ENGINE ROOMS WITH THE USE OF BOND GRAPH (BG) METHOD
PublicationWith a single approach to modeling elements of different physical nature, the method of Bond Graph (BG) is particularly well suited for modeling energy systems consisting of mechanical, thermal, electrical and hydraulic elements that operate in the power system engine room. The paper refers to the earlier presented new concept of thermal process modeling using the BG method. The authors own suggestions for determining causality...
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Chiral and achiral crystals, charge-assisted hydrogen-bond patterns and self-organization of selected solid diaminium thiosulfates
PublicationAbstract 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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Functionalization of cysteine derivatives by unsymmetrical disulfide bond formation
PublicationOpracowano metodę funkcjonalizacji pochodnych cysteiny przy pomocy tworzenia niesymetrycznego wiązania disulfidowego. Opracowana metoda okazała się bardzo łagodna, wydajna, i niewrażliwa na obecność dodatkowych grup funkcyjnych.
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Wave propagation in a sensor/actuator diffusion bond model
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The motif EXEXXXL in the cytosolic tail of the secretory human proprotein convertase PC7 regulates its trafficking and cleavage activity
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Modelling of energy flow in mechatronic systems. A bond graph approach
PublicationW referacie przedstawiono w sposób jednoliy modelowanie systemów mechatroniki metodą grafów wiązań (GW) w aspekcie symulacji przepływu energii. Omówiono ogólne założenia modelowania w ujęciu GW. Modelowanie przepływu energii rozważano na przykładzie napędu pojazdu hybrydowego PH-MAK.
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Modelling of energy flow in electrical machines. A bond graph approach
PublicationPrzedstawiono w ujęcia grafów wiązań model przepływu energii/mocy w maszynach elektrycznych pracujących w hybrydowych systemach przetwarzania energii. Jako przykład do rozważań przyjęto system napędu trakcyjnego pojazdów hybrydowych.
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Estimation of the Ultimate Strength of FRP Strips-to-Masonry Substrates Bond
PublicationFiber-Reinforced Polymers (FRP) were developed as a new method over the past decades due to their many beneficial mechanical properties, and they are commonly applied to strengthen masonry structures. In this paper, the Artificial Neural Network (ANN), K-fold Cross-Validation (KFCV) technique, Multivariate Adaptive Regression Spline (MARS) method, and M5 Model Tree (M5MT) method were utilized to predict the ultimate strength of...
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The Reactivity of the Imine Bond within Polynuclear Nickel(II) Complexes
PublicationThree novel Ni complexes with the Schiff base ligand 2-methoxy-6-(E-2-pyridyliminomethyl)-phenol (L1) are described. In comparison with the similar 2-(pyridine-2-ylimino-methyl)phenol (pymp), the mode of coordination of L1 is altered due to the presence of methoxy substituent introducing the sterical hindrance. During the synthesis of the complexes, partial hydrolysis of the ligand was observed. Since such immediate hydrolysis...
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Understanding the interactions between protein stabilizers and the peptide bond through the analysis of the volumetric and compressibility properties for the model systems
PublicationThis work confirms our earlier supposition, that volumetric and acoustic parameters for simple model proposed by us are directly related to stabilizing/destabilizing effect of osmolytes on proteins structure. The apparent molar volumes, V and the apparent molar isentropic compressions, KS,, of glycine and N,N,N –trimethylglycine (betaine) were determined from densities and speed of sound measurements in aqueous solution of N-methylacetamide...
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Reactive imines: Addition of 2-aminopyrimidine to the imine bond and isolation of the aminal from the equilibrium mixture aminal/imine
PublicationThe reaction between o-vanillin and 2-aminopyrimidine leads to the formation of a single crystalline product: aminal, 1, which results from the reaction of the initially formed imine with 2-aminopyrimidine. The reaction was followed by the NMR spectroscopy. VT NMR studies prove that in solution two major species are observed: aminal and imine and their ratio depends on the time or/and temperature with the imine content increasing...
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Modelling electrical machines using bond graphs for mechatronics system applications.
PublicationW artykule przedstawiono modelowanie maszyn elektrycznych metodą grafów wiązań dla potrzeb mechatroniki. Omówiono ogólne założenia modelowania maszyn elektrycznych w ujęciu grafów wiązań, bazującego na modelach wzorcowego sprzężenia transformatorowego i elektromechanicznego. Wykorzystując modele tych sprzężeń przedstawiono w ujęciu grafów wiązań model maszyny indukcyjnej w układzie współrzędnych naturalnych stojana. Model opracowano...
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Modelling of distributed-lumped parameter systems by application of modal bond graphs.
PublicationZastosowano metodę transmitancji układów o parametrach rozłożonych oraz dekompozycję modalną do modelowania wybranych układów dynamicznych. Zaproponowane podejście pozwala otrzymać dokładne modele niskiego rzędu w postaci grafów wiązań.
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Diphosphinoboranes as Intramolecular Frustrated Lewis Pairs: P–B–P Bond Systems for the Activation of Dihydrogen, Carbon Dioxide, and Phenyl Isocyanate
PublicationHerein, we present the first example of the activation of small molecules by P-B-P bond systems. The reactivity study involves reactions of two selected diphosphinoboranes, (tBu2P)2BPh (1’) and (Cy2P)2BNiPr2 (2), that differ in terms of their structural and electronic properties for the activation of dihydrogen, carbon dioxide, and phenyl isocyanate. Diphosphinoborane 1’ activates H2 under very mild conditions in the absence of...