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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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Chemically Bonded Silica Stationary Phases: Synthesis, Physicochemical Characterization, and Molecular Mechanism of Reversed-Phase HPLC Retention
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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
PublikacjaTo 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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On the Possibility of the Amphotericin B-Sterol Complex Formation in Cholesterol- and Ergosterol-Containing Lipid Bilayers: A Molecular Dynamics Study
PublikacjaAmphotericin 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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MM/PBSA analysis of molecular dynamics simulations of bovine beta-lactoglobulin: free energy gradients in conformational transitions?
PublikacjaPraca 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.
PublikacjaZsyntetyzowano 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.
PublikacjaStruktura 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
PublikacjaBadano 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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THE EFFECTS OF APPLYING CHITOSAN OF DIFFERENT MOLECULAR WEIGHTS ON THE QUALITY OF KAMCHATKA BERRIES (LONICERA CAERULEA L.): PART 2
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Comparative molecular dynamics study of dimeric and monomeric forms of HIV-1 protease in ligand bound and unbound state
PublikacjaHuman 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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Quest for the Molecular Basis of Improved Selective Toxicity of All-Trans Isomers of Aromatic Heptaene Macrolide Antifungal Antibiotics
PublikacjaThree 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
PublikacjaF1-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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The Role of Molecular Structure in Monte Carlo Simulations of the Secondary Electron Yield and Backscattering Coefficient from Methacrylic Acid
PublikacjaIn 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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Theoretical study of highly-excited states of KRb molecule
PublikacjaSemi-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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Cross sections for electron collision with pyridine [C5H5N] molecule
PublikacjaThe 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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Polarisation effects in low-energy positron–molecule scattering
PublikacjaThe 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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Dehydrogenation in electron-induced dissociative ionization of pyridine molecule
PublikacjaThe 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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Progress in development of molecularly imprinted polymers as sorbents for sample preparation
PublikacjaSample 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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The electronic structure of p-xylylene and its reactivity with vinyl molecules
PublikacjaThe 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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Moderately Reactive Molecules Forming Stable Ionic Compounds with Superhalogens
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Nonlinear Influence of Sound on the Vibrational Energy of Molecules in a Relaxing Gas
PublikacjaDynamics 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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VUV photofragmentation of the six-membered heterocyclic molecules containing oxygen
PublikacjaCancer 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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Molecularly imprinted polymers applied in capillary electrochromatography and electrophoresis techniques
PublikacjaMolecularly 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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Proton affinity and proton transfer energy for selected organic molecules
PublikacjaThe 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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Application of molecularly imprinted polymers in analytical chiral separations and analysis
PublikacjaOver 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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Charge transfer and formation of complexes in the He+ collisions with the furan molecules
PublikacjaCharge 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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Observation of the Hydrogen Migration in the Cation-Induced Fragmentation of the Pyridine Molecules
PublikacjaThe 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
PublikacjaElectron 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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Electron scattering by trimethylene oxide, c-(CH2)3O, molecules
PublikacjaZmierzono 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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ThDione: A Powerful Electron‐Withdrawing Moiety for Push–Pull Molecules
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Dependence of bimolecular recombination rate constant on different experimental parameters
PublikacjaZ 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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Elimination and migration of hydrogen in the vacuum-ultraviolet photodissociation of pyridine molecules
PublikacjaElimination 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
PublikacjaWe 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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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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Molecular Heteroconjugation Equilibria in (n-Butylamine + Acetic Acid) Systems in Binary (Dimethyl Sulfoxide + 1,4-Dioxane) Solvent Mixtures
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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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Molecular heteroconjugation equilibria in (n-butylamine + acetic acid) systems in binary (dimethyl sulfoxide + 1,4-dioxane) solvent mixtures
PublikacjaWyznaczono 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
PublikacjaWspółkrystalizacja 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.