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Search results for: molecular microbiology
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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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Formation, crystal and molecular structures of heteroleptic zinc(II) tri-tert-butoxysilanethiolates with ZnNO2S2 and ZnN2S2 coordination pattern
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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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Design of a D3h-symmetry prismatic tris-(ferrocene-1,1′-diyl) molecular cage bearing boronate ester linkages
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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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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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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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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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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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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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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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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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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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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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Theoretical study of highly-excited states of KRb molecule
PublicationSemi-empirical adiabatic potential energy curves of highly excited states of the KRb molecule are calculated as a function of the internuclear distance R over a wide range from 3 to 150 a0. The diatomic molecule is treated as an effective two-electron system by using the large core pseudopotentials and core polarization potentials. All calculations are performed by using the nonrelativistic CASSCF/MRCI method with accurate basis...
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Dehydrogenation in electron-induced dissociative ionization of pyridine molecule
PublicationThe electron-impact dissociative ionization of pyridine has been investigated using mass spectrometry. Thirty-two well-resolved mass peaks have been identified in the cation mass spectra and assigned to the most likely ionic molecular fragments. The new sixteen ionic fragments' appearance energies have been determined, and sixteen others remeasured. The total cross-section for electron-impact ionization of pyridine has been measured...
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Polarisation effects in low-energy positron–molecule scattering
PublicationThe UK molecular R-matrix method has been adapted to treat positron collisions from polyatomic targets. A simple empirical enhancement factor which corrects for the underestimation of electron–positron polarisation and correlation effects in the calculations performed with the static-plus-polarization model at low scattering energies is presented. Application of this model to positron scattering from carbon dioxide at energies...
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Cross sections for electron collision with pyridine [C5H5N] molecule
PublicationThe absolute grand -total cross section (TCS) for electron scattering from pyridine, C5H5N, molecules has been measured at impact energies from 0.6 to 300 eV in the linear electron-transmission experiment. The obtained TCS energy dependence appears to be typical for targets of high electric-dipole moment; the cross section generally decreases with rising energy, except for the 3–20 eV range, where a broad enhancement peaked near...
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Molecularly imprinted polymers applied in capillary electrochromatography and electrophoresis techniques
PublicationMolecularly imprinted polymers (MIPs) are synthetic materials with predetermined selectivity for a particular analyte or group of structure-linked chemicals which make them an ideal separation component. The process of developing and applying new types of MIPs in the field of environmental analytical chemistry has been broadly discussedi n many scientific studies in recent years. The use of new types of MIP sorbents as unique sorption...
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Moderately Reactive Molecules Forming Stable Ionic Compounds with Superhalogens
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The electronic structure of p-xylylene and its reactivity with vinyl molecules
PublicationThe electronic states of p-xylylene molecule were described at the multi-configurational CASSCF/MRMP2 level of theory. The closed-shell singlet state representing the quinoidal p-xylylene molecule was pre-dicted to be the ground electronic state whereas the triplet (benzoidal) and the singlet open-shell states were found to be much higher in energy (by 159 and 423 kJ/mol, respectively, as found at the CASSCF(8,8)/6-31+G(d) level)....
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Electron scattering by trimethylene oxide, c-(CH2)3O, molecules
PublicationZmierzono całkowity przekrój czynny na rozproszenie elektronów na drobinach c-(CH2)3O w zakresie energii 1 - 400 eV. Wyniki porównano z elastycznymi i jonizacyjnymi przekrojami czynnymi obliczonymi dla tej drobiny. Przedyskutowano energetyczną zależność całkowitego przekroju czynnego na rozproszenie dla rodziny eterów cyklicznych (CH2)nO, n=2-4.
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Progress in development of molecularly imprinted polymers as sorbents for sample preparation
PublicationSample preparation has been one of the most often investigated steps in analytical procedures.These investigations are focused on problems such as isolation of analytes from the sample matrix, matrix implification, analyte enrichment to the level above the detection limit of the instrumentation used, and the removal of interfering species to improve the final determination. Techniques based on solid (adsorption) and pseudo liquid...
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Dependence of bimolecular recombination rate constant on different experimental parameters
PublicationZ otrzymanych wzorów analitycznych oraz przeprowadzonych obliczeń numerycznych wynika, że dla wysokich natężeń pola elektrycznego stała szybkości rekombinacji bimolekularnej jest funkcją zewnętrznego pola elektrycznego oraz koncentracji nośników ładunku. Szczególnie interesujący jest wynik dotyczący obniżania się stałej szybkości rekombinacji wraz ze wzrostem natężenia pola elektrycznego, który różni się zupełnie od przewidywań...
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ThDione: A Powerful Electron‐Withdrawing Moiety for Push–Pull Molecules
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Observation of the Hydrogen Migration in the Cation-Induced Fragmentation of the Pyridine Molecules
PublicationThe ability to selectively control chemical reactions related to biology, combustion, and catalysis has recently attracted much attention. In particular, the hydrogen atom relocation may be used to manipulate bond-breaking and new bond-forming processes and may hold promise for far-reaching applications. Thus, the hydrogen atom migration preceding fragmentation of the gas-phase pyridine molecules by the H+, H2+, He+, He2+, and...
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Electron energy-loss spectroscopy of excited states of the pyridine molecules
PublicationElectron energy-loss spectra of the pyridine, C5H5N, molecules in the gas phase have been measured to investigate electronic excitation in the energy range 3.5–10 eV. The applied wide range of residual electron energy and the scattering angle range from 10 ◦ to 180 ◦ enabled to differentiate between optically-allowed and -forbidden transitions. These measurements have allowed vertical excitation energies of the triplet excited...
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Charge transfer and formation of complexes in the He+ collisions with the furan molecules
PublicationCharge transfer and formation of the collision complexes have been studied experimentally in fragmentation of the furan molecules in collisions with He+ cations. The excited atomic and diatomic fragments of furan have been identified using collision-induced luminescence spectroscopy. Charge transfer ionization of the furan molecules has been observed in production of helium atoms in the excited 1s4d 1D2, 3D1,2,3 states. The fragmentation...
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Elimination and migration of hydrogen in the vacuum-ultraviolet photodissociation of pyridine molecules
PublicationElimination of the excited hydrogen atoms H(n), n = 4–7, and hydrogen migration in formation of the excited NH(A 3Π) free radicals in the photodissociation of pyridine, C5H5N, molecules have been studied over the 17.5–70 eV photon energy range. In the measurements the photon-induced fluorescence spectroscopy technique has been applied. Both fragments are produced through excitation of pyridine molecules into higher-lying superexcited...
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Binary-Encounter Model for Direct Ionization of Molecules by Positron-Impact
PublicationWe introduce two models for the computation of direct ionization cross sections by positron impact over a wide range of collision energies. The models are based on the binary-encounter-Bethe model and take into account an extension of the Wannier theory. The cross sections computed with these models show good agreement with experimental data. The extensions improve the agreement between theory and experiment for collision energies...
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Application of molecularly imprinted polymers in analytical chiral separations and analysis
PublicationOver the last two decades the process of development and application of a new types of molecular imprinted polymer (MIP) sorbents in the field of analytical chemistry have been widely described in the literature. One of the new trends in analytical chemistry practice is the use of new types of MIP sorbents as specific sorption materials constituting the stationary phase in advanced separation techniques. The following review paper...
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VUV photofragmentation of the six-membered heterocyclic molecules containing oxygen
PublicationCancer is a significant public health concern worldwide, which results in millions of deaths each year. The standard cure routine for cancer is surgery, and nowadays, radiotherapy or a hadrontherapy. Depending on the type of cancer, patients may undergo additional treatment, including targeted therapy. A combination of radio- or hadron-therapy with proper drug treatment can inhibit the proliferation of cancer cells and thus can...
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Proton affinity and proton transfer energy for selected organic molecules
PublicationThe Hartree-Fock method in 6-311G** molecular orbitals basis set has been applied to calculations of proton affinities and proton transfer reaction energies for water, methanol, acetaldehyde, ethanol, acetone, acetic acid, methyl acetate and ethyl acetate.
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Nonlinear Influence of Sound on the Vibrational Energy of Molecules in a Relaxing Gas
PublicationDynamics of a weakly nonlinear and weakly dispersive flow of a gas where molecular vibrational relaxation takes place is studied. Variations in the vibrational energy in the field of intense sound is considered. These variations are caused by a nonlinear transfer of the acoustic energy into energy of vibrational degrees of freedom in a relaxing gas. The final dynamic equation which describes this is instantaneous, it includes a...
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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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Molecular heteroconjugation equilibria in (n-butylamine + acetic acid) systems in binary (dimethyl sulfoxide + 1,4-dioxane) solvent mixtures
PublicationWyznaczono stałe kwasowe Ka(HA), Ka(BH+) oraz stałe równowagi KAHA-, KBHE+ i KAHB, w układach (n-butyloamina + kwas octowy) bez przeniesienia protonu w binarnych mieszaninach rozpuszczalników (DMSO + 1,4-dioksan). Wartości stałych wyznaczono z wykorzystaniem metody miareczkowania potencjometrycznego przy stałej sile jonowej. Stwierdzono, iż stałe heterokoniugacji molekularnej w badanych mieszaninach rozpuszczalników są liniowo...
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Co-crystals of iodopentafluorobenzene with nitrogen donors: 2-D molecular assemblies through halogen bonding and aryl-perfluoroaryl interactions
PublicationWspółkrystalizacja pentafluorojodobenzenu z metylowymi pochodnymi pirydyny prowadzi do powstania heterodimerów stabilizowanych wiązaniem halogenowym C-I...N, które organizują się w dwuwymiarowe struktury typu brick-wall, utrzymywane oddziaływaniami pi-pi pomiędzy jednostkami arylowymi i perfluoroarylowymi.
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Synthesis and reactivity of 2,2,4,4-Tetrakis(tri-tertbutoxysilane-thiolato)-1,3,2,4-dithiadistannetane - crystal and molecular structures of two polymorphic forms
PublicationTytułowy związek [Sn(μ-S){SSi(OtBu)3}2]2 (1), zawierający dwa, 4-koordynacyjne atomy cyny, krystalizuje w dwóch odmianach polimorficznych. Forma ortorombowa-1a, została otrzymana w reakcji (tBuO)3SiSH i Et3N z SnCl2, podczas gdy forma trójskośna-1b, w reakcji z SnCl4 jako substratem. Struktura krystaliczna i cząsteczkowa obydwu odmian polimorficznych została wyznaczona przez badania metodą Rentgenowskiej Analizy Strukturalnej,...
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The impact of training and neurotrophins on functional recovery after spinal cord transection: cellular and molecular mechanisms contributing to motor improvement
PublicationBeneficial effects of locomotor training on the functional recovery after complete transection of the spinal cord indicate that in chronic spinal animals spontaneous recovery processes are enhanced and shaped by the training. The mechanisms of that use-dependent improvement are still not fully understood. This review tackles three aspects of this issue: (1) neurochemical attributes of functional improvement...
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Conformational studies of vasopressin and mesotocin using NMR spectroscopy and molecular modelling methods. Part II: studies in the SDS micelle
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THE EFFECTS OF APPLYING CHITOSAN OF DIFFERENT MOLECULAR WEIGHTS ON THE GROWTH AND QUALITY OF KAMCHATKA BERRIES (LONICERA CAERULEA L.): PART 1
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