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Wyniki wyszukiwania dla: BINDING ENERGY
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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
PublikacjaHerein, 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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Recycling of Industrial Waste as Soil Binding Additives—Effects on Soil Mechanical and Hydraulic Properties during Its Stabilisation before Road Construction
PublikacjaTo improve the in situ soil stabilization, different chemical additives are used (ion exchange compounds, additives based on H2SO4 or vinyl polymers, and organic additives using lignosul- fonates). One interesting alternative is the production of additives from various waste materials. The extensive testing of waste-based blends with soil was performed; the mechanical (unconfined compressive strength (UCS)) and hydraulic (capillary...
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Studies of the Interaction Dynamics in Albumin-Chondroitin Sulfate Systems by Recurrence Method
PublikacjaThe physicochemical basis of lubrication of articular cartilage is still not fully understood. However, the synergy between components of the synovial fluid can be a crucial factor that could explain this phenomenon. This work presents a nonlinear data analysis technique named the recurrence method, applied to the system involving two components of synovial fluid: albumin and chondroitin sulfate (CS) immersed in a water environment....
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Molecular dynamics study on the role of solvation water in the adsorption of hyperactive AFP to the ice surface
PublikacjaUsing computer simulations, the early stages of the adsorption of the CfAFP molecule to the ice surface were analyzed. We found that the ice and the protein interact at least as early as when the protein is about 1 nm away from the ice surface. These interactions are mediated by interfacial solvation water and are possible thanks to the structural ordering of the solvent. This ordering leads to positional preference of the protein...
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Lower rim substituted p-tert-butylcalix[4]arene; Part 14. Synthesis, structures and binding studies of calix[4]arene thioamides
PublikacjaA number of p-tert-butylcalix[4]arene thioamides were synthesized and characterized by 1H-NMR and elemental analysis. Compounds 1-5 are O-substituted derivatives with -CH2-C(=S)-N-X groups, where NX = morpholidyl, NEt2, NHC2H4Ph, NHCH2Ph and NHEt,respectively. The X-ray structures of the ligands 1, 3, 5 and of the complex 3Pb(ClO4)2, (compound 6), are presented and their slightly distorted cone conformation is established. The...
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Dynamics of changes in iron concentration and total iron binding capacity in blood plasma of goat kids during their first month of life (Short Communication)
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Design, Chemical Synthesis and Kinetic Studies of Trypsin Chromogenic Substrates Based on the Proteinase Binding Loop of Cucurbita maxima Trypsin Inhibitor (CMTI-III)
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Inhibition of inflammatory response in human keratinocytes by magnetic nanoparticles functionalized with PBP10 peptide derived from the PIP2-binding site of human plasma gelsolin
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Conformational latitude – activity relationship of KPPR tetrapeptide analogues toward their ability to inhibit binding of vascular endothelial growth factor 165 to neuropilin‐1
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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
PublikacjaMatrix 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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Review—Advances in Rechargeable Lithium-Ion Batteries Utilizing Polyoxometalate-Functionalized Nanocarbon Materials
PublikacjaPolyoxometalates (POMs) are inorganic nanoclusters that consist of oxygen and transition metals. These nanoclusters serve as excellent precursors for creating electrode materials that contain transition metals. Additionally, the interaction between POMs and carbon substrates produces positive synergistic effects. There has been considerable attention on employing POMs and carbon nanostructures (for example carbon nanotubes, graphene,...
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Problem of aggregation in dye-DNA interaction, calorimetry studies
PublikacjaNucleic acids are the biological target for many antimicrobial, antitumor and antiviral drugs. Ligand-DNA interactions can be classified into two major categories: 1. covalent binding, which can provide to intermolecular adducts, 2. physico-chemical interactions, which can be divided into intercalation (e.g. adriamycin) or groove binding (e.g. dystamycin). There are several methods to investigate interactions between drug and DNA....
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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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Synchrotron radiation photoemission spectroscopy of the oxygen modified CrCl3 surface
PublikacjaWe investigate the experimentally challenging CrCl3 surface by photon energy dependent photoemission (PE). The core and valence electrons after cleavage of a single crystal, either in a ultrahigh vacuum (UHV) or in air, are studied by keeping the samples at 150 1C, aiming at confirming the atomic composition with respect to the expected bulk atomic structure. A common spectroscopic denominator revealed by data is the presence of...
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Characterization of single-stranded DNA-binding proteins from the psychrophilic bacteria Desulfotalea psychrophila, Flavobacterium psychrophilum, Psychrobacter arcticus, Psychrobacter cryohalolentis, Psychromonas ingrahamii, Psychroflexus torquis, and Photobacterium profundum
PublikacjaBackground: Single-stranded DNA-binding proteins (SSBs) play essential roles in DNA replication, recombination and repair in Bacteria, Archaea and Eukarya. In recent years, there has been an increasing interest in SSBs, since they find numerous applications in diverse molecular biology and analytical methods. Results: We report the characterization of single-stranded DNA-binding proteins from the psychrophilic bacteria Desulfotalea...
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The Efficacious Benefit of 25-Hydroxy Vitamin D to Prevent COVID-19: An In-Silico Study Targeting SARS-CoV-2 Spike Protein
PublikacjaThe environment has rapidly looked at proven specialist task forces in the aftermath of the COVID-19 pandemic to build public health policies and measures to mitigate the effects of emerging coronaviruses. According to the researchers, taking 10 μg of 25-hydroxy vitamin D daily is recommended to keep us safe. There have been several studies recently indicating that there is a reduced risk of contracting Coronavirus by 25-hydroxy...
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Temperature-dependent structure-property modeling of viscosity for ionic liquids
PublikacjaIn this paper we present the methodology for assessing the ionic liquids' viscosity at six temperature points (25, 35, 45, 50, 60 and 70 [C]), which utilizes only the in silico approach. The main idea of such assessment is based on the "correction equation" describing the correlation between experimentally measured viscosity and theoretically derived density (calculated with use of molecular mechanics), given at 6 different temperature...
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Towards the Application of Structure-Property Relationship Modeling in Materials Science: Predicting the Seebeck Coefficient for Ionic Liquid/Redox Couple Systems
PublikacjaThis work focuses on determining the influence of both ionic liquid (IL) type and redox couple concentration on Seebeck coefficient values of such a system. The quantitative structure property relationship (QSPR) and read-across techniques are proposed as methods to identify structural features of ILs (mixed with LiI/I2 redox couple), which have the most influence on the Seebeck coefficient (Se) values of the system. ILs consisting...
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Investigation of mechanism of desmopressin binding in vasopressin V2 receptor versus vasopressin V1a and oxytocin receptors: Molecular dynamics simulation of the agonist-bound state in the membrane–aqueous system
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Fatty Acid-Binding Protein 7 (FABP-7), Glutamic Acid and Neurofilament Light Chain (NFL) as Potential Markers of Neurodegenerative Disorders in Psoriatic Patients—A Pilot Study
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Correlation between the Reactivity and Spectroscopic Properties of N-Substituted Secondary Thioamides. New Intramolecular N• •H+• •N Binding Approach and Proton Complexes Based on Thioamide Ligation
PublikacjaFrom a comparison of chem. shifts and wavenumbers of several secondary thioamides and amides having monocationic substituents attached to thiocarbamoyl or carbamoyl groups by a polymethylene chain, new intramol. unconventional N···H+···N H bonding effects were discovered. It is argued that the CH2-N rotation is hindered and two +H···NHMe nonequiv. protons occur in a proton spectrum of hydrochloride RCH2C(S)NH(CH2)3NHMe-HCl...
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Study of Icosahedral Clusters in Close-packed Simple Liquids
PublikacjaThe local structure of liquid copper was determined using Steinhardt order parameters, with particular attention paid to icosahedral clusters. The positions of atoms were obtained from three sets of molecular dynamics simulations, with the forces obtained from: the Sutton-Chen (SC) potential, the Naval Research Laboratory total energy tight-binding (NRL-TB) method and the divide-and-conquer learn-on-the-fly (DCLOTF) method, respectively....
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Collagen Type II—Chitosan Interactions as Dependent on Hydroxylation and Acetylation Inferred from Molecular Dynamics Simulations
PublikacjaChitosan–collagen blends have been widely applied in tissue engineering, joints diseases treatment, and many other biomedical fields. Understanding the affinity between chitosan and collagen type II is particularly relevant in the context of mechanical properties modulation, which is closely associated with designing biomaterials suitable for cartilage and synovial fluid regeneration. However, many structural features influence...
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The Ellenbogen's “Matter as Software” Concept for Quantum Computer Implementation. C60 and X@C60 Molecules as Available Molecular Building Blocks (MBBs) for Tip-Based Nanofabrication (TBN) of Quantum Computing Devices
PublikacjaThe TBN bottom-up strategy of building quantum devices from C60 and X@C60 MBBs is proposed as an extension of the Ellenbogen's “Matter as Software” idea to quantum information processing. The capped SW or DW CNT STM tip is considered as device for manipulating C60 and X@C60 molecules. In this article, the possibility of using easily available on the market C60 Fullerene and endohedral X@C60 molecules together with commercial CNT...
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Application of Alanine Scanning to Determination of Amino Acids Essential for Peptide Adsorption at the Solid/Solution Interface and Binding to the Receptor: Surface-Enhanced Raman/Infrared Spectroscopy versus Bioactivity Assays
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Electron attachment to representative cations composing ionic liquids
PublikacjaUsing ab initio electronic structure methods with flexible atomic orbital basis sets, we investigated the electronic structure and stability of reduction products of selected representative cations (C+) constituting ionic liquids. We found that an electron attachment to such cations leads to the neutral radicals, whereas a subsequent attachment of another (i.e., excess) electron leads to adiabatically stable anions only in two...
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Cement kiln dust
PublikacjaThe volume of cement production in the world has remained at the level of approxi mately 4.1 billion tons/year. The cement production process is energy intensive and is the world’s leading emitter of carbon dioxide. Therefore, the main activities cement plants are aimed at introducing technologies changes in production of clinkier.The construction industry is responsible for the majority of CO2 emissions to the atmosphere: the...
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Molecular dynamics simulations of the affinity of chitin and chitosan for collagen: the effect of pH and the presence of sodium and calcium cations
PublikacjaChitosan and chitin are promising biopolymers used in many areas including biomedical applications, such as tissue engineering and viscosupplementation. Chitosan shares similar properties with hyaluronan, a natural component of synovial fluid, making it a good candidate for joint disease treatment. The structural and energetic consequences of intermolecular interactions are crucial for understanding the biolubrication phenomenon...
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Optoelectronic properties of curved carbon systems
PublikacjaSystematic investigation of optoelectronic properties of curved carbon systems has been performed and the results have been compared with the representatives of flat carbon systems. Moreover, the application of third order dispersion corrected density functional tight binding method (with third order corrections of self-consistent charges) including Becke-Johnson dumping (DFTB3-D3(BJ)) has been validated in order to obtain reliable...
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Rare A360T Mutation Alters GSK3β(Ser9) Binding in the Cytosolic Loop of Presenilin 1, Influencing β-Catenin Nuclear Localization and Pro-Death Gene Expression in Alzheimer’s Disease Case
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Rotation Triggers Nucleotide-Independent Conformational Transition of the Empty β Subunit of F1-ATPase
PublikacjaF1-ATPase (F1) is the catalytic portion of ATP synthase, a rotary motor protein that couples proton gradients to ATP synthesis. Driven by a proton flux, the F1 asymmetric γ subunit undergoes a stepwise rotation inside the α3β3 headpiece and causes the β subunits’ binding sites to cycle between states of different affinity for nucleotides. These concerted transitions drive the synthesis of ATP from ADP and phosphate. Here, we study...
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Diagnostyka eksploatacyjna okrętowych silników spalinowych - tłokowych i turbinowych
PublikacjaW monografii przedstawiono wybrane zagadnienia diagnostyki technicznej silników spalinowych dużej mocy, zarówno tłokowych, jak i turbinowych, ukierunkowane na eksploatację okrętowych (i nie tylko) systemów energetycznych, w których występują tego typu silniki. W początkowej części opracowania zaproponowano koncepcję systemowego ujęcia diagnostyki eksploatacyjnej silników okrętowych w aspekcie obowiązujących standardów światowych...
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Sex hormone-binding globulin (SHBG) mitigates ER stress and improves viability and insulin sensitivity in adipose-derived mesenchymal stem cells (ASC) of equine metabolic syndrome (EMS)-affected horses
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Modeling of the alcohol dehydrogenase active site. Two different modes of alcohol binding in crystals of zinc and cadmium tri-tert-butoxysilanethiolates evidenced by X-ray diffraction and solid state vibrational spectroscopy
PublikacjaOpisano syntezę, struktury cząsteczkowe oraz widma FT-IR, 1H. 13C, 29Si, 113Cd NMR dziesięciu nowych, mieszanoligandowych kompleksów cynku i kadmu z ligandem tri-tert-butoksysilanotiolanowym i pochodnymi imidazolu. Za pomocą rentgenowskiej analizy strukturalnej i spektroskopii w podczerwieni udokumentowano dwa różne sposoby wiązania etanolu i metanolu w kryształach tych związków. Opisane kompleksy stanowią modele miejsca aktywnego...
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Modeling of the Alcohol Dehydrogenase Active Site: Two Different Modes of Alcohol Binding in Crystals of Zinc and Cadmium Tri‐tert‐butoxysilanethiolates Evidenced by X‐ray Diffraction and Solid‐State Vibrational Spectroscopy
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Fabrication and Significant Photoelectrochemical Activity of Titania Nanotubes Modified with Thin Indium Tin Oxide Film
PublikacjaOrdered titanium dioxide nanotubes (TiO2NTs) modified with indium tin oxide (ITO) films were obtained via magnetron sputtering, in which ITO plate was used as a target, onto the as-anodized titania support followed by the calcination process. The morphology of fabricated material with deposited oxide was investigated using scanning electron microscopy. Raman and UV–Vis spectroscopies were utilized to characterize crystalline phase...
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Multi-GPU-powered UNRES package for physics-based coarse-grained simulations of structure, dynamics, and thermodynamics of protein systems at biological size- and timescales
PublikacjaCoarse-grained models are nowadays extensively used in biomolecular simulations owing to the tremendous extension of size- and time-scale of simulations. The physics-based UNRES (UNited RESidue) model of proteins developed in our laboratory has only two interaction sites per amino-acid residue (united peptide groups and united side chains) and implicit solvent. However, owing to rigorous physics-based derivation, which enabled...
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Effect of Nanohydroxyapatite on Silk Fibroin–Chitosan Interactions—Molecular Dynamics Study
PublikacjaFibroin–chitosan composites, especially those containing nanohydroxyapatite, show potential for bone tissue regeneration. The physicochemical properties of these biocomposites depend on the compatibility between their components. In this study, the intermolecular interactions of fibroin and chitosan were analyzed using a molecular dynamics approach. Two types of systems were investigated: one containing acetic acid and the other...
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Occurrence and properties of sulphate reducing bacteria in groundwater in Gdańsk region; Selected methods of elimination.Bakterie redukujące siarczany na ujęciach wód podziemnych w regionie gdańskim.
PublikacjaGdańsk region is situated in the area with good hydrogeological conditions. The ground-water designed for drinking purposes is taken mainly from the Quaternary and addition-ally from Cretaceous aquifers. The urban development and intensive take off have caused the increase of water exploitation and as a consequence of the changes of hydrogeological conditions the deterioration of chemical and bacteriological quality of water has...
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The potential of raw sewage sludge in construction industry – A review
PublikacjaExcess sewage sludge produced in any municipal or industrial wastewater treatment plant becomes a serious problem due to its increasing amount. This increase is related to the improvement of treatment technologies, expansion of sewage systems and the development of new industrial plants. The implementation and development of new technologies related to the utilization of sewage sludge is currently based on treating it as a substrate....
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Organic-inorganic composites consisted of poly(3,4-ethylenedioxythiophene)and Prussian Blue analogues
PublikacjaThe organic-inorganic material consisted of poly(3,4-ethylenedioxythiophene) (pEDOT) and copper hexacyanoferrate (Cuhcf) was synthesized. The pEDOT film with Fe(CN)63−/4− as counter-ions potentiodynamically polarized in aqueous CuCl2 electrolyte brings about stable hybrid material (pEDOT/Cuhcf) performing single redox activity of FeII/III at a formal potential Ef = 0.61 V (vs. Ag/AgCl/0.1 M KCl) and less clearly shaped two redox...
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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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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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Biochemical, Structural Analysis, and Docking Studies of Spiropyrazoline Derivatives
PublikacjaIn this study, we evaluated the antiproliferative potential, DNA damage, crystal struc‐ tures, and docking calculation of two spiropyrazoline derivatives. The main focus of the research was to evaluate the antiproliferative potential of synthesized compounds towards eight cancer cell lines. Compound I demonstrated promising antiproliferative properties, especially toward the HL60 cell line, for which IC50 was equal to 9.4 μM/L....
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Hydration of N-Hydroxyurea from Ab Initio Molecular Dynamics Simulations
PublikacjaN-Hydroxyurea (HU) is an important chemotherapeutic agent used as a first-line treatment in conditions such as sickle cell disease and β-thalassemia, among others. To date, its properties as a hydrated molecule in the blood plasma or cytoplasm are dramatically understudied, although they may be crucial to the binding of HU to the radical catalytic site of ribonucleotide reductase, its molecular target. The purpose of this work...
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Antitumor Activity of Triazine Mimic Antibiotics for DNA-binding Implications (Impressive Activity in Vitro Against a Variety of Tumor Types in the NCI-60 Screen): NSC 710607 To Fight HCT-116 Human Colon Carcinoma Cell Lines in Vivo Using the Hollow Fiber Assay and Xenograft Mouse Models
PublikacjaPurpose Successful clinical applications of DNA-directed selective cytotoxic agents disrupt the vital replication/transcription processes and ultimately lead to cancer cell death. This study aimed to examine the growth screen of two lead triazine compounds in a number of cell lines and xenografts and to develop anticancer agents with noncovalent binding affinity bringing fewer side effects. Methods The NCI initial hollow...
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Exploring the cocrystallization potential of urea and benzamide
PublikacjaThe cocrystallization landscape of benzamide and urea interacting with aliphatic and aromatic carboxylic acids was studied both experimentally and theoretically. Ten new cocrystals of benzamide were synthesized using an oriented samples approach via a fast dropped evaporation technique. Information about types of known bi-component cocrystals augmented with knowledge of simple binary eutectic mixtures was used for the analysis...
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Stable nanoconjugates of transferrin with alloyed quaternary nanocrystals Ag–In–Zn–S as a biological entity for tumor recognition
PublikacjaOne way to limit the negative effects of anti-tumor drugs on healthy cells is targeted therapy employing functionalized drug carriers. Here we present a biocompatible and stable nanoconjugate of transferrin anchored to Ag-In-Zn-S quantum dots modified with 11-mercaptoundecanoic acid (Tf-QD) as a drug carrier versus typical anticancer drug, doxorubicin. Detailed investigations of Tf-QD nanoconjugates without and with doxorubicin...
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Cold recycled mixtures for binder courses - laboratory evaluation of mechanical properties
PublikacjaCold recycled mixtures composed with cement and bituminous emulsion are nowadays commonly used material for base layer. Typical pavement with cold recycled mixtures usually consists of two asphalt courses (wearing and binding course) constructed over cold recycled base. Therefore the next step in cold recycling is possibility of design of binding courses with recycled materials, but with potential to obtain high quality mixtures...
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Quantitative fluorescent determination of DNA – Ochratoxin a interactions supported by nitrogen-vacancy rich nanodiamonds
PublikacjaOchratoxin A (OTA) is a hazardous contaminant of a large variety of plant and animal originated food. Herein, we report an interaction of OTA with calf thymus DNA (ct DNA) on the nanodiamond surface. We employed multispectroscopic techniques to elucidate the binding mechanism of OTA with ct DNA. The fluorescence and UV–Vis spectroscopy results show that OTA binds to ds ct DNA and forms complexes. We obtained the binding constants...