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Wyniki wyszukiwania dla: DIATOMIC MOLECULES
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Influence of bulky 3,3′-diphenylalanine enantiomers replacing position 2 of AVP analogues on their conformations: NMR and molecular modeling studies
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Hopping or Tunneling? Tailoring the Electron Transport Mechanisms through Hydrogen Bonding Geometry in the Boron-Doped Diamond Molecular Junctions
PublikacjaMechanisms of charge transport in molecular junctions involving hydrogen bonds are complex and remain mostly unclear. This study is focused on the elucidation of the electron transfer in a molecular device consisting of two boron-doped diamond interfaces bound with an aromatic linker and a hydrogen bonding surrogating molecule. The projected local density of states (PLODS) analysis coupled with transmission spectra and current−voltage...
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Molecular and structural basis of inner core lipopolysaccharide alterations in Escherichia coli: incorporation of glucuronic acid and phosphoethanolamine in the heptose region.
PublikacjaIt is well established that lipopolysaccharide (LPS) often carries nonstoichiometric substitutions in lipid A and in the inner core. In this work, the molecular basis of inner core alterations and their physiological significance are addressed. A new inner core modification of LPS is described, which arises due to the addition of glucuronic acid on the third heptose with a concomitant loss of phosphate on the second heptose. This...
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Nickel(II) tri-tert-butoxysilanethiolates with N-heterocyclic bases as additional ligands: Synthesis, molecular structure and spectral studies
PublikacjaW publikacji przedstawiono metodę syntezy trzech kompleksów silanotiolanowych z takimi N-heterocyklicznymi zasadami jak: pirydyna, 2-metylopirydyna i 3,5-dimetylopirydyna. Dla tych kompleksów przeprowadzono badania X-Ray, analizy elementarnej. Przy pomocy rentgenowskiej analizy strukturalnej wykazano różną koordynację atomu centralnego - niklu.
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Intramolecular transformation of an antifungal antibiotic nystatin A1 into its isomer, iso-nystatin A1 - structural and molecular modeling studies
PublikacjaNystatin A1, a polyene macrolide antifungal antibiotic, in a slightly basic or acidic solution undergoes an intramolecular transformation, yielding a structural isomer, the translactonization product, iso-nystatin A1 with lactone ring diminished by two carbon atoms. Structural evidence is provided by advanced NMR and Mass Spectrometry (MS) studies. Molecular dynamics simulations and quantum mechanics calculations gave the insight...
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Molecular structures and supramolecular architectures of two chromogenic 13-membered azobenzocrown ethers with a peripheral hydroxyl group in the benzene ring.
PublikacjaOkreślono strukturę krystaliczną dwóch pochodnych 13-członowego eteru azobenzokoronowego z peryferyjną grupą hydroksylową, metodą analizy rentgenostrukturalnej monokryształów. W stanie stałym 13-członowy eter azobenzokoronowy zawierający grupę OH jako podstawnik w pierścieniu aromatycznym w pozycji para do grupy azowej występuje w formie chinono-hydrazonu. Forma ta stabilizowana jest przez silne wewnątrzcząsteczkowe wiązanie wodorowe....
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ESCASA : Analytical estimation of atomic coordinates from coarse‐grained geometry for nuclear‐magnetic‐resonance ‐assisted protein structure modeling. I. Backbone and Hβ protons
PublikacjaA method for the estimation of coordinates of atoms in proteins from coarse-grained geometry by simple analytical formulas (ESCASA), for use in nuclear-magnetic-resonance (NMR) data-assisted coarse-grained simulations of proteins is proposed. In this paper, the formulas for the backbone Hα and amide (HN) protons, and the side-chain Hβ protons, given the Cα-trace, have been derived and parameterized, by using the interproton distances...
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Molecular biology
Kursy Online -
Molecular biology
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Discovery of small-molecule regenerative drugs using a model of complex tissue injury in mice. Transcriptomic responses of neurodevelopmental genes during pharmacologically induced regeneration
PublikacjaDespite significant development in regenerative medicine, there is a deficit of effective therapies for wound healing and tissue regeneration. Research performed using animal wound models allows for a better understanding of this complex process, searching for compounds with pro-regenerative properties, and assessing their efficacy and safety. Unfortunately, the lack of adequate preclinical models proves to be an issue as no animal...
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A Cu/Zn heterometallic complex with solvent-binding cavity, catalytic activity for the oxidation of 1-phenylethanol and unusual magnetic properties
PublikacjaMononuclear and polymeric complexes of zinc(II) and copper(II) have been synthesized using two isomers of the hemi-salen ligand with a different mutual orientation of donor atoms. The heterometallic Cu/Zn metallocycle features a catalytic niche filled with the molecule of water and molecules of methanol. This unusual compound exhibits both pronounced catalytic activity in the reaction of oxidation of a secondary alcohol to ketone...
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AFM images of the platinum (111) single crystal surface as delivered, without the polishing treatment
Dane BadawczePlatinum (111) single crystal surface images as delivered, without polishing treatment. Topographic measurements in contact mode. NTEGRA Prima (NT-MDT) device. CSG probe 10.
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Interference-Free Determination of Trace Copper in Freshly Ripened Honeys by Flame Atomic Absorption Spectrometry Following a Preconcentration by Solid-Phase Extraction and a Two-Step Elution Process
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Surface characteristics of glass fibres covered with an aluminum layer after a chemical modification process using secondary ion mass spectrometry (SIMS) and atomic force microscopy (AFM)
PublikacjaPrzedstawiono wyniki z badań powierzchni modyfikowanych włókien szklanych (przed i po procesie chemicznej modyfikacji ich powierzchni), które są kandydatem na przyszły oryginalny bezmatrycowy materiał odniesienia lotnych analitów etenu (C2H4) metodami spektrometrii mas jonów wtórnych oraz mikroskopii sił atomowych. Badania miały na celu obserwację zmian oraz procesów, jakie zaszły na powierzchni włókien szklanych pokrytych...
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Anharmonic Infrared Spectroscopy through the Fourier Transform of Time Correlation Function Formalism in ONETEP
PublikacjaDensity 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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Peptide dendrimers as antifungal agents and carriers for potential antifungal agent—N3‐(4‐methoxyfumaroyl)‐(S)‐2,3‐ diaminopropanoic acid—synthesis and antimicrobial activity
PublikacjaA series of peptide dendrimers and their conjugates with antimicrobial agent FMDP (N3‐(4‐methoxyfumaroyl)‐(S)‐2,3‐diamino‐propanoic acid) were synthesized. The obtained compounds were tested for the antibacterial and antifungal activity. All novel dendrimers displayed much better activity against the tested strains than FMDP itself. Moreover, their conjugates with FMDP also exhibited antimicrobial activity. The most promising molecules...
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AFM (atomic force microscopy) images of borophene flakes obtained during ball milling at different operating parameters
Dane BadawczeThis dataset contains atomic force microscopy (AFM) images of representative borophene flakes obtained during ball milling. The operational parameters of the ball-milling process included rotation speed (250, 450, and 650 rpm), time of ball-milling (1, 3, 6, and 12 h), and the mass loading of starting bulk boron (1, 2, 3 g).
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Application of Multivariate Adaptive Regression Splines (MARSplines) Methodology for Screening of Dicarboxylic Acids Cocrystal Using 1D and 2D Molecular Descriptors
PublikacjaDicarboxylic acids (DiAs) are probably one of the most popular cocrystals formers. Due to the high hydrophilicity and non-toxicity, they are promising solubilizes of active pharmaceutical ingredients (APIs). Although DiAs appear to be highly capable of forming multicomponent crystals with various compounds, some systems reported in the literature are physical mixtures the solid state without forming stable intermolecular complex....
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Novel 1,2,3-Triazole Derivatives as Mimics of Steroidal System—Synthesis, Crystal Structures Determination, Hirshfeld Surfaces Analysis and Molecular Docking
PublikacjaHerein, we present the synthesis and crystal structures determination of five 4-(1-phenyl-1H-1,2,3-triazol-4-yl)phenol derivatives containing halogen atoms, 6a–e, which may be used as an excellent mimic of steroids in the drug development process. Good quality crystals obtained for all of the synthesized compounds allowed the analysis of their molecular structures. Subsequently, the determined crystal structures were used to calculate...
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Molecular Heterogeneity of Papillary Thyroid Cancer: Comparison of Primary Tumors and Synchronous Metastases in Regional Lymph Nodes by Mass Spectrometry Imaging
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Encapsulation of Amikacin into Microparticles Based on Low-Molecular-Weight Poly(lactic acid) and Poly(lactic acid-co-polyethylene glycol)
PublikacjaThe aim of this study was to fabricate novel microparticles (MPs) for efficient and long-term delivery of amikacin (AMI). The emulsification method proposed for encapsulating AMI employed low-molecular-weight poly(lactic acid) (PLA) and poly(lactic acid-co-polyethylene glycol) (PLA−PEG), both supplemented with poly(vinyl alcohol) (PVA). The diameters of the particles obtained were determined as less than 30 μm. Based on an in-vitro...
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Time-of-flight electron scattering from molecular hydrogen: Benchmark cross sections for excitation of the X1Σ+g→b3Σ+u transition
PublikacjaThe electron impact X1Σ+g to b3Σ+u transition in molecular hydrogen is one of the most important dissociation pathways to forming atomic hydrogen atoms, and is of great importance in modeling astrophysical and industrial plasmas where molecular hydrogen is a substantial constituent. Recently it has been found that the convergent close-coupling (CCC) cross sections of Zammit et al. [Phys. Rev. A 95, 022708 (2017)] are up to a factor...
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Molecular typing of Staphylococcus aureus isolated from cows with mastitis in the east of Poland on the basis of polymorphism of genes coding protein A and coagulase
PublikacjaPolimorfizm genów kodujących białko A i koagulazę wykorzystano do badania zmienności genetycznej bakterii Staphylococcus aureus wyizolowanych z gruczołów mlekowych krów u których stwierdzono stan zapalny. W badanej grupie 82 szczepów wyróżniono 24 genotypy.
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Rozdział 6. Epidemiologia molekularna - nowe metody typowania diagnostycznego mikroorganizmów = Molecular epidemiology new methods for diagnostic typing of microorganismus
PublikacjaMolekularne metody diagnostyczne oparte o analizę kwasów nukleinowych dają nowe możliwości laboratoriom w szybkim wykrywaniu i różnicowaniu mikroorganizmów patogennych. W pracy przedstawiono panujące tendencje w zastosowaniach metod typowania genetycznego znaczących klinicznie mikroorganizmów w Europie, a także omówiono niektóre techniki stosowane w laboratoriach mikrobiologicznych, z uwzględnieniem ich zdolności aplikacyjnych,...
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Molecular geometry and optical activity of N-nitroso-2,2,6,6-tetramethylpiperidines generated by spontaneous crystallization and inclusion complexation with optically active diols
PublikacjaTrzy N-nitrozo-2,2,6,6-tetrametylopiperydyny, których chiralność wynika z utrudnionej rotacji wokół wiązania N-N posiadającego częściowy charakter wiązania podwójnego poddano badaniom stereochemicznym i spektroskopowym. Badane związki tworzą kompleksy inkluzyjne z optycznie czynnymi gospodarzami - Taddolami, w których N-nitrozo-2,2,6,6-tetrametylopiperydyny przyjmują chiralną konformację co dowodzą ich widma CD wykonane w ciele...
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Differential cross section for electron impact excitation of the a1 δ g state of molecular oxygen in the 15-180° angular range.
PublikacjaZmierzono absolutne różniczkowe przekroje czynne na wzbudzeniu drobin tlenu do poziomu oscylacyjnego v=0 stanu a1 δ g. Pomiary wykonano dla energii elektronów równej 10eV w zakresie kątów rozproszenia od 15° do 180°.
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Arginine-, d-arginine-vasopressin, and their inverso analogues in micellar and liposomic models of cell membrane: CD, NMR, and molecular dynamics studies
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Ergodicity and model quality in template-restrained canonical and temperature/Hamiltonian replica exchange coarse-grained molecular dynamics simulations of proteins
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KRAS mutation testing in borderline ovarian tumors and low-grade ovarian carcinomas with a rapid, fully integrated molecular diagnostic system
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Pharmacological Classification and Activity Evaluation of Furan and Thiophene Amide Derivatives Applying Semi-Empirical ab initio Molecular Modeling Methods
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A BODIPY‐Molecular Rotor in Giant Unilamellar Vesicles: A Case Study by Polarization‐Resolved Time‐resolved Emission and Transient Absorption Spectroscopy
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Sulfanyl porphyrazines: Molecular barrel-like self-assembly in crystals, optical properties and in vitro photodynamic activity towards cancer cells
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Imidazolidine-4-one derivatives in the search for novel chemosensitizers of Staphylococcus aureus MRSA: Synthesis, biological evaluation and molecular modeling studies
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Structural elucidation of transmembrane transporter protein bilitranslocase: Conformational analysis of the second transmembrane region TM2 by molecular dynamics and NMR spectroscopy
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Screening of potential inhibitors for COVID-19 main protease from phytoconstituents of Tectona grandis Linn: application of molecular modeling studies
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Molecular dynamics simulations reveal the balance of forces governing the formation of a guanine tetrad—a common structural unit of G-quadruplex DNA
PublikacjaG-quadruplexes (G4) are nucleic acid conformations of guanine-rich sequences, in which guanines are arranged in the square-planar G-tetrads, stacked on one another. G4 motifs form in vivo and are implicated in regulation of such processes as gene expression and chromosome maintenance. The structure and stability of various G4 topologies were determined experimentally; however, the driving forces for their formation are not fully...
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Effect of heat treatment on the diffusion intermixing and structure of the Cu thin film on Si (111) substrate: a molecular dynamics simulation study
PublikacjaThis work is devoted to the study of the diffusion process at the interface between copper films with a thickness of 2, 3, 4, 7 and 10 atomic monolayers and silicon substrate by molecular dynamics simulation method. For this purpose, the variation of the concentration of copper and silicon along the perpendicular direction to the interface was investigated. An analysis of the density profile along this direction made it possible...
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Molecular docking studies towards development of novel Gly-Phe analogs for potential inhibition of Cathepsin C (dipeptidyl peptidase I).
PublikacjaCathepsin C is a cysteine protease required for activation of various pro-inflammatory serine proteases and, essentially, is of interest as a therapeutic target. Cathepsin C coordinate system was employed as a model to study the interaction of some already available inhibitors of Cathepsin C. Compounds containing Gly-Phe fragment with functional groups at its ends were designed by knowledge based approach. Using AutoDock and...
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The extended version of restriction analysis approach for the examination of the ability of low-molecular-weight compounds to modify DNA in a cell-free system
PublikacjaOne of the primary requirements in toxicology is the assessment of ability of chemicals to induce DNA covalent modification. There are several well-established methods used for this purpose such as 32P-Postlabeling or HPLC-MS. However, all of these approaches have difficult to overcome limitations, which prevents their use in genotoxin screening. Here, we describe the simple protocol exploiting specificity of restriction enzymes...
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Characteristics of hydration water around hen egg lysozyme as the protein model in aqueous solution. FTIR spectroscopy and molecular dynamics simulation
PublikacjaW niniejszej pracy przedstawiono wyniki badań dotyczące hydratacji białka modelowego - lizozymu z jaja kurzego w roztworze wodnym. Wiodącą techniką stosowaną w badaniach była spektroskopia oscylacyjna FTIR z zastosowaniem techniki rozcieńczenia izotopowego wody półciężkiej HDO w roztworze wody zwykłej. Analiza widma HDO przy pomocy "metody widm zaburzonych" pozwoliła na wyizolowanie widma wody zaburzonej przez lizozym, a tym samym...
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Molecular geometry and optical activity of helically chiral N-nitrosamines derived from 1,2,3,4-tetrahydro- and 1,2,3,4,7,8,9,10-octahydro-1,10-phenanthroline
PublikacjaX-ray crystallographic analysis of the title N-nitrosamines revealed that they assume helical conformations in the solid state. Nitrosamines 1b and 2b were resolved by inclusion crystallization with optically active diols (TADDOLs). The absolute configuration of the guest molecules in the complexes 1b·3b and 2b·3b was assigned as M. The optical activity of the resolved compounds is manifested by their solid state CD spectra, which...
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Toward mechanosynthesis of diamondoid sructures: viii. quantum-chemical molecular dynamics simulations of hexagonal silicon-iv structure synthesis with stm
Publikacjaw tej publikacji badano metodami kwantowo-chemicznymi różne strategie mechanosyntezy heksagonalnego krzemu iv. określono przybliżone warunki mechanosyntezy krzemu w formie lonsdaleitu za pomocą uhv-spm.
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Long range molecular dynamics study of interactions of the eukaryotic glucosamine-6-phosphate synthase with fructose-6-phosphate and UDP-GlcNAc
PublikacjaGlucosamine-6-phosphate synthase (EC 2.6.1.16) is responsible for catalysis of the first and practically irreversible step in hexosamine metabolism. The final product of this pathway, uridine 5 diphospho Nacetyl- d-glucosamine (UDP-GlcNAc), is an essential substrate for assembly of bacterial and fungal cell walls. Moreover, the enzyme is involved in phenomenon of hexosamine induced insulin resistance in type II diabetes, which...
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Optical investigation of molecular structure of sophisticated materials forphotonics. Photonics Applications in Astronomy, Communications, Industry and High Energy Physics Experiments.
PublikacjaZastosowano komplementarne metody optyczne: spektroskopię ramanowską oraz spektroskopię w podczerwieni do badania reakcji zachodzących w czasie wytwarzania polimerów hybrydowych metodą zol-żel. Otrzymane rezultaty umożliwiły uszczegółowienie opisu reakcji hydrolizy monomerów w trakcie żelowania.
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The chaperone-usher pathway of bacterial adhesin biogenesis - from molecular mechanism to strategies of anti-bacterial prevention and modern vaccine design
PublikacjaSystem chaperone-usher (białko opiekuńcze-białko kanałotwórcze) warunkuje biogenezę powierzchniowych struktur adhezyjnych, odpowiedzialnych za wirulencję wielu bakterii gram-ujemnych. Powyższy mechanizm został zbadany na poziomie strukturalnym w przypadku różnych gatunków bakterii patogennych. Celem powyższej pracy było przedstawienie molekularnego mechanizmu biogenezy struktur adhezyjnych na bazie systemu chaperone-usher. Otrzymane...
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A BODIPY‐Based Molecular Rotor in Giant Unilamellar Vesicles: A Case Study by Polarization‐Resolved Time‐Resolved Emission and Transient Absorption Spectroscopy
PublikacjaBODIPY and BODIPY-derived systems are widely applied as fluorophores and as probes for viscosity detection in solvents and biological media. Their orientational and rotational dynamics in biological media are thus of vital mechanistic importance and extensively investigated. In this contribution, polarization-resolved confocal microscopy is used to determine the orientation of an amphiphilic BODIPY-cholesterol derivative in homogeneous...
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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
PublikacjaMolecular 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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L1 Cell Adhesion Molecule Overexpression Down Regulates Phosphacan and Up Regulates Structural Plasticity-Related Genes Rostral and Caudal to the Complete Spinal Cord Transection
PublikacjaL1 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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Toward Mechanosynthesis of Diamondoid Structures: IX Commercial Capped CNT Scanning Probe Microscopy Tip as Nowadays Available Tool for Silylene Molecule and Silicon Atom Transfer
PublikacjaAccording 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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The Metal-Free Regioselective Deuteration of 2-Methylquinolin-8-ol and 2,5-Dimethylquinolin-8-ol, Spectroscopic and Computational Studies
PublikacjaAbstract: 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...