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Search results for: LiCs molecule
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Molecular characterisation of fowl adenovirus type 7 isolated from poultry associated with inclusion body hepatitis in Poland
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THE EFFECTS OF APPLYING CHITOSAN OF DIFFERENT MOLECULAR WEIGHTS ON THE QUALITY OF KAMCHATKA BERRIES (LONICERA CAERULEA L.): PART 2
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High- and low-Molecular Weight oat Beta-Glucan Reveals Antitumor Activity in Human Epithelial Lung Cancer
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Molecular organization of antifungal antibiotic amphotericin B in lipid monolayers studied by means of Fluorescence Lifetime Imaging Microscopy
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On the Possibility of the Amphotericin B-Sterol Complex Formation in Cholesterol- and Ergosterol-Containing Lipid Bilayers: A Molecular Dynamics Study
PublicationAmphotericin B (AmB) is a well-known membrane-active antibiotic that has been used to treat systemicfungal infections for more than 45 years. Therapeutic application of AmB is based on the fact that it is moreactive against ergosterol-containing membranes of fungal cells than against mammalian membranes withcholesterol. In this paper, we examine the hypothesis according to which the selectivity of the AmB's membraneaction originates...
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Transcriptomic Profile of Genes Encoding Proteins Involved in Pathogenesis of Sjögren’s Syndrome Related Xerostomia—Molecular and Clinical Trial
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Application of Multiplexed Replica Exchange Molecular Dynamics to the UNRES Force Field: Tests with α and α+β Proteins
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Interactions of vasopressin and oxytocin receptors with vasopressin analogues substituted in position 2 with 3,3′-diphenylalanine - a molecular docking study
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Micelle-bound conformations of neurohypophyseal hormone analogues modified with a Cα-disubstituted residue: NMR and molecular modelling studies
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Conformational studies of vasopressin and mesotocin using NMR spectroscopy and molecular modelling methods. Part I: studies in water
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Self-assembly and interactions of short antimicrobial cationic lipopeptides with membrane lipids: ITC, FTIR and molecular dynamics studies
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Molecular Response in Intestinal and Immune Tissues to in Ovo Administration of Inulin and the Combination of Inulin and Lactobacillus lactis Subsp. cremoris
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Electron-Induced Decomposition of Uracil-5-yl O-(N,N-dimethylsulfamate): Role of Methylation in Molecular Stability
PublicationThe incorporation of modified uracil derivatives into DNA leads to the formation of radical species that induce DNA damage. Molecules of this class have been suggested as radiosensitizers and are still under investigation. In this study, we present the results of dissociative electron attachment to uracil-5-yl O-(N,N-dimethylsulfamate) in the gas phase. We observed the formation of 10 fragment anions in the studied range of electron...
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Virulence, antifungal susceptibility and molecular mechanisms of echinocandin resistance among Candida isolates recovered from clinical specimens
PublicationFungi of the genus Candida belong to the natural microflora of healthy individuals. However, they can also be a cause of opportunistic infections especially among patients with an impaired immune system. The first line therapy of Candida infections is based on triazoles. However, in recent years there an increase of azole resistant Candida spp., in particular C. glabrata and C. krusei, has been observed. For this reason, echinocandin...
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Kinetics of molecular decomposition under irradiation of gold nanoparticles with nanosecond laser pulses—A 5-Bromouracil case study
PublicationABSTRACT Laser illuminated gold nanoparticles (AuNPs) efficiently absorb light and heat up the surrounding medium, leading to versatile applications ranging from plasmonic catalysis to cancer photothermal therapy. Therefore, an in-depth understanding of the thermal, optical, and electron induced reaction pathways is required. Here, the electrophilic DNA nucleobase analog 5-Bromouracil (BrU) has been used as a model compound to...
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The Role of Molecular Structure in Monte Carlo Simulations of the Secondary Electron Yield and Backscattering Coefficient from Methacrylic Acid
PublicationIn this paper, we show the influence of the chemical structure of four different conformers on the secondary electron emission and backscattering of an electron beam from a gel of methacrylic acid. The conformers have different permanent dipole moments, which determines the cross sections for elastic collisions with electrons. The cross sections are used in Monte Carlo simulations of an electron beam, which enters the gel of methacrylic...
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Molecular mechanism and energetics of coupling between substrate binding and product release in the F 1 -ATPase catalytic cycle
PublicationF1-ATPase is a motor protein that couples the rotation of its rotary γ subunit with ATP synthesis or hydrolysis. Single-molecule experiments indicate that nucleotide binding and release events occur almost simultaneously during the synthesis cycle, allowing the energy gain due to spontaneous binding of ADP to one catalytic β subunit to be directly harnessed for driving the release of ATP from another rather than being dissipated...
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Performance of extended Lagrangian schemes for molecular dynamics simulations with classical polarizable force fields and density functional theory
PublicationIterative energy minimization with the aim of achieving self-consistency is a common feature of Born-Oppenheimer molecular dynamics (BOMD) and classical molecular dynamics with polarizable force fields. In the former, the electronic degrees of freedom are optimized, while the latter often involves an iterative determination of induced point dipoles. The computational effort of the self-consistency procedure can be reduced by re-using...
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Quest for the Molecular Basis of Improved Selective Toxicity of All-Trans Isomers of Aromatic Heptaene Macrolide Antifungal Antibiotics
PublicationThree aromatic heptaene macrolide antifungal antibiotics, Candicidin D, Partricin A (Gedamycin) and Partricin B (Vacidin) were subjected to controlled cis-trans to all trans photochemical isomerization. The obtained all-trans isomers demonstrated substantially improved in vitro selective toxicity in the Candida albicans cells: human erythrocytes model. This effect was mainly due to the diminished hemotoxicity. The molecular modeling...
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Palladium versus Platinum: The Metal in the Catalytic Center of a Molecular Photocatalyst Determines the Mechanism of the Hydrogen Production with Visible Light
PublicationTo develop highly efficient molecular photocatalysts for visible light-driven hydrogen production, a thorough understanding of the photophysical and chemical processes in the photocatalyst is of vital importance. In this context, in situ X-ray absorption spectroscopic (XAS) investigations show that the nature of the catalytically active metal center in a (N^N)MCl2 (M=Pd or Pt) coordination sphere has a significant impact on the...
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Long range molecular dynamics study of regulation of eukaryotic glucosamine-6-phosphate synthase activity by UDP-GlcNAc
PublicationGlucosamine-6-phosphate (GlcN-6-P) synthase catalyses the first and practically irreversible step in hexosamine metabolism. The final product of this pathway, uridine 5' diphospho N-acetyl-D-glucosamine (UDPGlcNAc), is an essential substrate for assembly of bacterialand fungal cell walls. Moreover, the enzyme is involved in phenomenon of hexosamine induced insulin resistance in type II diabetes, which makes it a potential target...
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Ionic liquids: predictions of physicochemical properties with experimental and/or DFT-calculated LFER parameters to understand molecular interactions in solution
PublicationPublikacja zawiera modele pozwalające na przewidywanie współczynnika podziału oktanol-woda (log P), rozpuszczalności w wodzie oraz krytycznego stężenia micelizacji (CMC) cieczy jonowych oraz współczynników aktywności anionowej i hydrofobowości w wodzie i w mieszaninie oktanolu z wodą. Modele oparte są na liniowych zależnościach energii swobodnej (LFER) i wykorzystują parametry zmierzone i/lub wyliczone na podstawie funkcjonalnej...
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MM/PBSA analysis of molecular dynamics simulations of bovine beta-lactoglobulin: free energy gradients in conformational transitions?
PublicationPraca dotyczy pH zależnych zmian konformacyjnych EF pętli beta-laktoglobuliny. Zmiany te są śledzone za pomocą metod obliczeniowych chemii (dynamika molekularna oraz metody MM/PBSA).
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Formation, crystal and molecular structures of heteroleptic zinc(II) tri-tert-butoxysilanethiolates with ZnNO2S2 and ZnN2S2 coordination pattern.
PublicationZsyntetyzowano pięć tri-tert-butoksysilanotiolanów cynku zawierających jako dodatkowe ligandy heterocykliczne, zasady azotowe. Wzór ogólny tych kompleksów to Zn(SSi(OBut)3)2L, gdzie L=alfa-pikolina, 2,4-lutydyna, N-metyloimidazol lub Zn(SSiOBut)3)2L2, gdzie L=N-metyloimidazol lub pirydyna. Określono strukturę krystaliczną otrzymanych związków oraz zmierzono widma IR i NMR.
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Molecular modelling of transition state analogue inhibitors of glucosamine-6-P synthase and glucose-6-P isomerase.
PublicationStruktura kompleksu 2-amino-2-deoksy-D-glucitolo-6-P (ADGP) z centrum aktywnym syntazy GlcN-6-P z E. coli została wykorzystAna jako punkt wyjścia do modelowania molekularnego analogów ADGP. Używając programu GROMOS96 wygenerowano konformacje analogów o najniższych energiach wewnętrznych, które następnie ''dokowano'' w centrum aktywnym enzymu. Dokonano syntezy wybranych związków i określono parametry kinetyczne i termodynamiczne...
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Oscillating water-oil-water liquid membrane systems for molecular recognition of substances belonging to diferent taste classes
PublicationBadano oscylacje róznicy potencjału elektrochemicznego miedzy fazami wodnymi. Jedna faza wodna zawiera kationowy lub anionowy surfaktant podczas gdy w drugiej fazie wodnej znajduje sie substancja odpowiedzialna za smak. Dwie fazy wodne sa rozdzielone faza olejową. Oscylacje były analizowane poprzez konstrukcje portretów fazowych uzywając metody opoznienia czasowego. Kształt portretów fazowych jest rozny dla oscylatorów z kationowym...
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Comparative molecular dynamics study of dimeric and monomeric forms of HIV-1 protease in ligand bound and unbound state
PublicationHuman immunodeficiency virus type 1 protease (HIV-1 PR) is a viral-encoded enzyme that forms a homodimer. HIV-1 PR is essential for replication and assembly of the virus and inactivation of HIV-1 PR enzyme causes production of immature, noninfectious viral particles and thus HIV-1 PR is an attractive target in anti-AIDS drug design. In our current work, we performed molecular dynamics (MD) calculations (500 ns) for two different...
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Toward Mechanosynthesis of diamondoid structures: III. Quantum-chemical study of silylene molecule and silicon atom transfer mechanism from caped SWCNT tip to the reaction center on a hydrogenated Si(111) surface
PublicationOpublikowana wcześniej (Modelling Simul. Mater. Sci. Eng., Vol. 7, 1999, pp. 43-58) strategia mechanosyntezy struktur krzemu na uwodornionej płaszczyźnie Si(111) została poszerzona poprzez uwzględnienie ostrza w postaci zamkniętej SWCNT jako urządzenia kontrolującego położenie cząsteczki sililenu oraz atomu krzemu.
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In the search for experimental and quantumchemical evidence for zwitterionic nature of (2 E )-3-[4-(dimethylamino)phenyl]-2-nitroprop-2-enenitrile – An extreme example of donor–π–acceptor push–pull molecule
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Role of the Solvation Water in Remote Interactions of Hyperactive Antifreeze Proteins with the Surface of Ice
PublicationMost protein molecules do not adsorb onto ice, one of the exceptions being so-called antifreeze proteins. In this paper, we describe that there is a force pushing an antifreeze protein molecule away from the ice surface when it is not oriented with its ice-binding plane toward the ice and that this pushing force may be also present even when the protein is oriented with its ice-binding plane toward the ice. This force is absent...
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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
PublicationMononuclear 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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COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY A-MOLECULAR & INTEGRATIVE PHYSIOLOGY
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EUROPEAN JOURNAL OF NUCLEAR MEDICINE AND MOLECULAR IMAGING
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QUARTERLY JOURNAL OF NUCLEAR MEDICINE AND MOLECULAR IMAGING
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American Journal of Nuclear Medicine and Molecular Imaging
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Wiley Interdisciplinary Reviews-Computational Molecular Science
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Asia-Pacific Journal of Molecular Biology and Biotechnology
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Cold Spring Harbor Molecular Case Studies
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PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY
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AMERICAN JOURNAL OF RESPIRATORY CELL AND MOLECULAR BIOLOGY
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Physical Review A - Atomic, Molecular, and Optical Physics
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MUTATION RESEARCH-FUNDAMENTAL AND MOLECULAR MECHANISMS OF MUTAGENESIS
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QUARTERLY JOURNAL OF NUCLEAR MEDICINE AND MOLECULAR IMAGING
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SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
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Why is the cubic structure preferred in newly formed ice?
PublicationMolecular dynamics was employed to explain the preference for the cubic structure in newly formed crystals of ice. The results showed that in supercooled liquid water the molecules connected by hydrogen bonds are more likely to adopt relative orientations similar to the ones characteristic for cubic ice. The observed preference for certain relative orientations of molecules in the hydrogen-bonded pairs results in the higher probability...
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The Metal-Free Regioselective Deuteration of 2-Methylquinolin-8-ol and 2,5-Dimethylquinolin-8-ol, Spectroscopic and Computational Studies
PublicationAbstract: Aim and Background: Introducing deuterium to a molecule is of interest to a wide variety of research, including investigation of reaction mechanisms or kinetics, analysis of drug metabolism, structural elucidation of molecules, and syntheses of isotopically labeled materials used for NMR spectroscopy and medicinal research. Objective: The transition-metal-free regioselective deuteration of 2-methylquinolin-8-ol...
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Molecular Heteroconjugation Equilibria in (n-Butylamine + Acetic Acid) Systems in Binary (Dimethyl Sulfoxide + 1,4-Dioxane) Solvent Mixtures
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The use of fast molecular descriptors and artificial neural networks approach in organochlorine compounds electron ionization mass spectra classification
PublicationDeveloping of theoretical tools can be very helpful for supporting new pollutant detection. Nowadays, a combination of mass spectrometry and chromatographic techniques are the most basic environmental monitoring methods. In this paper, two organochlorine compound mass spectra classification systems were proposed. The classification models were developed within the framework of artificial neural networks (ANNs) and fast 1D and...
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Molecular modeling of Gram-positive bacteria peptidoglycan layer, selected glycopeptide antibiotics and vancomycin derivatives modified with sugar moieties
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Molecular dynamics study of 4-OH-phenylacetyl- D -Y(Me)FQNRPR-NH 2 selectivity to V1a receptor
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