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Search results for: field-molecule interaction
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Long-range, water-mediated interaction between a moderately active antifreeze protein molecule and the surface of ice
PublicationUsing molecular dynamics simulations, we show that a molecule of moderately active antifreeze protein (type III AFP, QAE HPLC-12 isoform) is able to interact with ice in an indirect manner. This interaction occurs between the ice binding site (IBS) of the AFP III molecule and the surface of ice, and it is mediated by liquid water which separates these surfaces. As a result, the AFP III molecule positions itself at a specific orientation...
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Molecular hydrogen solvated in water – A computational study
PublicationThe aqueous hydrogen molecule is studied with molecular dynamics simulations at ambient temperature and pressure conditions, using a newly developed flexible and polarizable H2 molecule model. The design and implementation of this model, compatible with an existing flexible and polarizable force field for water, is presented in detail. The structure of the hydration layer suggests that first-shell water molecules accommodate the...
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Charge dependence of fragmentation process induced by ion collisions with furan molecule
PublicationThe goal of this work is to describe the system evolution after ion-molecule interaction. We combine different quantum chemistry and statistical mechanics approaches in order to give extended description of the process. Herein we report on a recent study of the fragmentation mechanism of neutral, singly- and doubly-ionized furan molecule in the gas phase.
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Electron collisions with cyanoacetylene HC3N : Vibrational excitation and dissociative electron attachment
PublicationWe experimentally probe electron collisions with HC3N in the energy range from 0 to 10 eV with the focus on vibrational excitation and dissociative electron attachment. The vibrational excitation cross sections show a number of resonances which are mode specific: the two dominant π∗ resonances are visible in the excitation of all the vibrational modes; however, broad σ ∗ resonances are visible only in certain bond-stretching vibrational...
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The adiabatic potentials of low-lying electronic states of the NaRb molecule
PublicationAdiabatic potential energy curves and spectroscopic constants have been calculated for the NaRb molecule. The results of ten states of the symmetry Σ+, six states of the symmetry Π, and two states of the symmetry Δ are obtained by the nonrelativistic quantum chemical method used with pseudopotentials describing the interaction of valence electrons with atomic cores. Analysis is based on a comparison with the results of other theoretical...
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Coarse-grained simulation - an efficient approach for studying motions of large proteins
PublicationOne of the most important challenges in performing Molecular Dynamics (MD) simulations of large protein complexes is to accommodate the model accuracy and the simulation timescale. Hitherto, for the most relevant dynamics of protein aggregates in an explicit aqueous environment, the timescale reachable for the all-atoms simulations is of hundreds of nanoseconds. This range is four to six orders of magnitude smaller than processes...
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Diphosphination of CO2 and CS2 mediated by frustrated Lewis pairs - catalytic route to phosphanyl derivatives of formic and dithioformic acid
PublicationThe first example of CO2 diphosphination is described. Reactions of unsymmetrical diphosphanes with CE2 (E = O, S) catalyzed by BPh3 insert a CE2 molecule into the P-P bond with formation of the products of the general formula R2P-E-C(=E)-PR2. The obtained CO2 adducts arise from synergistic interaction of diphosphane and borane with CO2 molecule.
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Yields and Time-of-Flight Spectra of Neutral High-Rydberg Fragments at the K Edges of the CO2 Molecule
PublicationWe have studied the production of neutral fragments in high-Rydberg (HR) states at the C 1s and O 1s edges of the CO2 molecule by performing two kinds of experiments. First, the yields of neutral HR fragments were measured indirectly by ionizing such fragments in a static electric field and by collecting resulting singly charged positive ions as a function of the photon energy. Such measurements reveal not only excitations below...
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Low-energy positron scattering from gas-phase pyrimidine: A quantum treatment of the dynamics and a comparison with experiments
PublicationWe are reporting detailed quantum scattering calculations that describe the diffusion of a beam of low-energy positrons interacting with the pyrimidine target as a gas-phase partner. The calculations have employed an essentially ab initio model for the short-range correlation interaction and for the electrostatic interaction of an impinging positron and the electron+nuclear structure of the target molecule at its equilibrium geometry.
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Investigation of interaction between xanthene dye rhodamine B and metagenomic-derivated methylthioadenosine phosphorylase RSFP
PublicationIn the previous study we found that the expression of the metagenomic - derived methylthioadenosine phosphorylase gene (rsfp) in E. coli cells and the presence of rhodamine B in the growth medium were crucial for the pink fluorescence of one E. coli colony from Antarctic soil metagenomic library (Cieśliński et al., 2009). In this study, rsfp gene expression was induced by an arabinose promoter in an LMG194 E. coli strain and the...
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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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Theoretical studies of fragmentation processes of neutral and ionized furan molecule
PublicationThis PhD thesis focuses on the fragmentation mechanism of the furan molecule in the gas phase. The approach taken in this work comprised of three theoretical methodologies considering the dynamical, energetical and entropic aspects of the studied process. First, molecular dynamics simulations were performed. Next, the potential energy surfaces were explored at the DFT/B3LYP level of theory. Finally, a new statistical Microcanonical...
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Water-mediated influence of a crowded environment on internal vibrations of a protein molecule
PublicationThe influence of crowding on the protein inner dynamics is examined by putting a single protein molecule close to one or two neighboring protein molecules. The presence of additional molecules influences the amplitudes of protein fluctuations. Also, a weak dynamical coupling of collective velocities of surface atoms of proteins separated by a layer of water is detected. The possible mechanisms of these phenomena are described....
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The 41Σ+ electronic state of LiCs molecule
PublicationThe 41Σ+ state of LiCs molecule is observed experimentally for the first time. The inverted perturbation approach (IPA) method is used to derive the potential energy curve of the state from the measured spectra. The experiment is accompanied by theoretical calculations of adiabatic potentials for excited states in LiCs including 41Σ+, performed with the MOLPRO program package. The irregular shape of the 41Σ+ state potential predicted...
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Modified Peptide Molecules As Potential Modulators of Shelterin Protein Functions; TRF1
PublicationIn this work, we present studies on relatively new and still not well-explored potential anticancer targets which are shelterin proteins, in particular the TRF1 protein can be blocked by in silico designed "peptidomimetic" molecules. TRF1 interacts directly with the TIN2 protein, and this protein-protein interaction is crucial for the proper functioning of telomere, which could be blocked by our novel modified peptide molecules....
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Determination of energy-transfer distributions in ionizing ion-molecule collisions
PublicationThe main objective of this study is to determine the energy transfer occuring in ion-molecule collisions. In order to solve this problem, we followed two approaches; the first one by validating a purely experimental method and the second one by testing a new theoretical model M3C (Microcanonical Metropolis Monte Carlo).
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Possible schemes of photoassociation processes in the KLi molecule with newly calculated potential energy curves
PublicationWe present four promising schemes for photoassociative formation of KLi molecule in its ground electronic state. Analysis is based on newly calculated adiabatic potentials supported by transition dipole moments and Franck-Condon factors.
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TOTAL CROSS SECTION MEASUREMENTS FOR ELECTRON SCATTERING ON METHYL FORMATE (HCOOCH3) MOLECULE: METHYLATION EFFECT
PublicationWe present the absolute total cross section (TCS) for electron scattering from the methyl formate (HCOOCH3) molecule measured in the 10-300 eV energy range, with electrostatic electron spectrometer working in the linear transmission mode. Comparison of TCS for the HCOOCH3 molecule with that measured earlier for the formic acid (HCOOH) compound manifests the methylation effect i.e. the response of the electron scattering dynamics...
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Optimization of the femtosecond laser impulse for excitation and the Spin-Orbit mediated dissociation in the NaRb Dimer
PublicationWe study the dynamics of multiple coupled states under the influence of an arbitrary time-dependent external field to investigate the femtosecond laser-driven excitation and the spin-orbit mediated dissociation in the NaRb dimer. In this process, the dimer is excited from the ground triplet state 1^3Sigma+ to the 1^3Pi state using the femtosecond laser impulse and the spin-orbit coupling between the 1^3Pi and 2^1Sigma+ states results...
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Influence of S-Oxidation on Cytotoxic Activity of Oxathiole-Fused Chalcones
PublicationSynthesis, in vitro cytotoxic activity, and interaction with tubulin of oxidized, isomeric 1-(5-alkoxybenzo[d] [1,3]oxathiol-6-yl)-3-phenylprop-2-en-1-ones and 1-(6- alkoxybenzo[d][1,3]oxathiol-5-yl)-3-phenylprop-2-en-1- ones are described. Most of the compounds demonstrated cytotoxic activity at submicromolar concentrations. It was found that oxidation of sulfur atom of the oxathiole-fused chalcones strongly influenced activity...
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Sequence-dependent structural properties of B-DNA: what have we learned in 40 years?
PublicationThe structure of B-DNA, the physiological form of the DNA molecule, has been a central topic in biology, chemistry and physics. Far from uniform and rigid, the double helix was revealed as a flexible and structurally polymorphic molecule. Conformational changes that lead to local and global changes in the helix geometry are mediated by a complex choreography of base and backbone rearrangements affecting the ability of the B-DNA...
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Low-energy positron scattering from gas-phase uracil
PublicationQuantum scattering calculations are presented for the interaction of low energy positrons with the uracil molecule, an important component of biological systems. The rotational elastic and inelastic cross sections and vibrational inelastic cross sections are reported and compared with existing experiments, indicating a general trend of the cross sections different from the experimental findings and in line with what should be expected...
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Joint experimental and theoretical study on electron scattering from titanium tetrachloride (TiCl4) molecule
PublicationAbsolute grand-total cross section for electron scattering from titanium tetrachloride, TiCl4, molecule was measured at electron-impact energies ranging from 0.3 to 300 eV, in the linear electron-transmission experiment. The elastic integral, differential, momentum transfer, and total ionization cross sections for TiCl4 molecule were also calculated for low and intermediate collisional energies at the level of various theories. The...
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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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The influence of anchoring group position in ruthenium dye molecule on performance of dye-sensitized solar cells
PublicationThe effect of anchoring group position and, in consequence, the orientation of the ruthenium dye molecule on titania surface on the performance of dye-sensitized solar cells has been studied intensively. Three model ruthenium sensitizing dyes bearing carboxylic anchoring group in ortho, meta or para position were synthesized and well characterized by spectroscopic, electrochemical, photophysical and photochemical measurements....
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Mangiferin Affects Melanin Synthesis by an Influence on Tyrosinase: Inhibition, Mechanism of Action and Molecular Docking Studies
PublicationMangiferin is a strong antioxidant that presents a wide range of biological activities. The aim of this study was to evaluate, for the first time, the influence of mangiferin on tyrosinase, an enzyme responsible for melanin synthesis and the unwanted browning process of food. The research included both the kinetics and molecular interactions between tyrosinase and mangiferin. The research proved that mangiferin inhibits tyrosinase...
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Synthesis, crystal structure and spectroscopic characterization of new anionic iridium(III) complexes and their interaction with biological targets
PublicationThe synthesis and characterisation of new anionic iridium(II) complexes (NH4)2[IrCl4(κ2N,N’-H2biim)]2 · 5H2O (1) and ((CH3)2NH2)[IrCl4(κ2N,N’-PyBIm)] · H2O (2) are presented in this article. Spectroscopic methods (1H, 13C and 15N NMR, FTIR, UV-Vis) were used to characterize these new complexes. Solid-state structural analysis (SC-XRD) of complexes 1 and 2 shows a slightly distorted octahedral geometry of Ir(III) ions, which is...
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Muramyl dipeptide-based analogs as potential anticancer compounds: Strategies to improve selectivity, biocompatibility, and efficiency
PublicationAccording to the WHO, cancer is the second leading cause of death in the world. This is an important global problem and a major challenge for researchers who have been trying to find an effective anticancer therapy. A large number of newly discovered compounds do not exert selective cytotoxic activity against tumorigenic cells and have too many side effects. Therefore, research on muramyl dipeptide (MDP) analogs has attracted interest...
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Interfacial water controls the process of adsorption of hyperactive antifreeze proteins onto the ice surface
PublicationA mechanism of interactions between the ice-binding surface of a hyperactive antifreeze protein molecule and the ice surface is proposed, involving the influence of water present between the two surfaces on the behavior of the approaching molecule. It is demonstrated that the interfacial water, even before its full solidification, can act as a factor that pushes away or pulls nearer the protein molecule to ensure its proper positioning....
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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
PublicationDespite 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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Dopants and gas modifiers in ion mobility spectrometry
PublicationThe ion mobility techniques, including the most commonly used drift-tube ion mobility spectrometry (IMS) and differential mobility spectrometry (DMS), are used successfully for the detection of a wide range of organic compounds in the gas phase. In order to improve detection quality, admixtures are added to gas streams flowing through the detector. Dopants mostly prevent the ionization of interfering chemicals however, better detection...
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H2O˙+ and OH+ reactivity versus furan: experimental low energy absolute cross sections for modeling radiation damage
PublicationRadiotherapy is one of the most widespread and efficient strategies to fight malignant tumors. Despite its broad application, the mechanisms of radiation-DNA interaction are still under investigation. Theoretical models to predict the effects of a particular delivered dose are still in their infancy due to the difficulty of simulating a real cell environment, as well as the inclusion of a large variety of secondary processes. This...
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Progress in targeting tumor cells by using drug-magnetic nanoparticles conjugate.
PublicationTo limit the cytotoxicity of anticancer drugs against healthy cells, an appropriate carrier should be synthesized to deliver the drug to the tumor tissue only. A good solution is to anchor a magnetic nanoparticle to the molecule of the drug and to use a properly directed external magnetic field. We have shown that the improved by us synthesis of the conjugate of doxorubicin with iron-oxide magnetic nanoparticles allows a substantial...
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Scattering of electrons by a 1,2-butadiene (C4H6) molecule: measurements and calculations
PublicationWe present the results of experimental and theoretical study on electron collisions with a 1,2-butadiene (H2C=C=CHCH3) molecule. Absolute grand-total cross sections (TCSs) were measured using a linear electron-transmission method for collision energies in the 0.5–300 eV range. Two distinct features in the TCS energy curve were detected: a narrow peak located at 2.3 eV and a broad enhancement centered around 9 eV. We attributed...
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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
PublicationBODIPY 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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<i>N,N</i>'-diphenylthiourea acetone monosolvate
PublicationIn the title compound, C13H12N2S·C3H6O, the phenyl rings of the thiourea molecule are in syn and anti positions in relation to the C=S bond. Two molecules are connected by N-HS=C hydrogen bonds into a centrosymmetric dimer. An additional N-HO=C hydrogen bond to the acetone solvent molecule and some weak C-H interactions reinforce the crystal structure.
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Methods for Elucidation of DNA-Anticancer Drug Interactions and Their Applications in the Development of New Drugs
PublicationDNA damaging agents including anthracyclines, camptothecins and platinum drugs are among most frequently used drugs in the chemotherapeutic routine. Due to their relatively low selectivity for cancer cells, administration is associated with adverse side effects, whereas the inherent genotoxicity of these drugs is associated with risk of developing secondary cancers. Development of new drugs, which could be spared of these drawbacks...
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Born–Oppenheimer potential energy curves of NaK from the optimised atomic basis sets
PublicationThe article presents adiabatic potential energy curves of the ground and excited electronic states for the diatomic NaK molecule. The calculations were made using the ab initio computational methods to include electron correlation. The studied molecule was calculated as the effective two-electron problem, in which only the valence electrons of the molecule are explicitly taken into account. The remaining electrons with atomic nuclei...
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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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Trichloridobis(ethyldiphenylphosphine)-(tetrahydrofuran)molybdenum(III)
PublicationIn the mononuclear title compound, [MoCl3(C4H8O)(C14H15P)2], obtained by the reaction of trichlorotris(tetrahydrofuran)molybdenum(III) and ethyldiphenylphosphine in tetrahydrofuran (THF) solution, the MoIII atom is six-coordinated by one O atom of a THF molecule, two P atoms from two ethyldiphenylphosphine ligands and three Cl atoms in a distorted octahedral geometry. The C atoms of the THF molecule are disordered over two positions...
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Morphology control via dual solvent crystallization for high-mobility functionalized pentacene-blend thin film transistors
PublicationWe present an approach to improving the performance of solution processed organic semiconductor transistors based on a dual solvent system. We here apply this to a blend containing the π-conjugated small molecule 6,13 bis(triisopropylsilylethynyl) pentacene (TIPS-pentacene) and polystyrene, which acts as an inert binder. Using a semiconductor-binder solution of two solvents, where the main solvent is a better solvent of the small...
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O 1s excitation and ionization processes in the CO2 molecule studied via detection of low-energy fluorescence emission
PublicationOxygen 1s excitation and ionization processes in the CO2 molecule have been studied with dispersed and non-dispersed fluorescence spectroscopy as well as with the vacuum ultraviolet (VUV) photon-photoion coincidence technique. The intensity of the neutral O emission line at 845 nm shows particular sensitivity to core-to-Rydberg excitations and core-valence double excitations, while shape resonances are suppressed. In contrast,...
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Corrosion Inhibition Mechanism and Efficiency Differentiation of Dihydroxybenzene Isomers Towards Aluminum Alloy 5754 in Alkaline Media
PublicationThe selection of efficient corrosion inhibitors requires detailed knowledge regarding the interaction mechanism, which depends on the type and amount of functional groups within the inhibitor molecule. The position of functional groups between different isomers is often overlooked, but is no less important, since factors like steric hinderance may significantly affect the adsorption mechanism. In this study, we have presented how...
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Correlation between partial inhibition of hydrogen evolution using thiourea and catalytic activity of AB5-type hydrogen storage alloy towards borohydride electrooxidation
PublicationDirect borohydride fuel cells (DBFCs) are devices which directly convert the chemical energy stored in the borohydride ion and oxidant into electrical energy as a result of redox reactions. Unfortunately, a significant amount of fuel is lost as a result of the undesirable hydrolysis reaction. The selection of an efficient borohydride hydrolysis inhibitor requires detailed knowledge regarding the interaction mechanism between the...
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Photoelectron and threshold photoelectron valence spectra of pyridine
Publication. The pyridine molecule has been examined by the means of photoelectron and threshold photoelectron spectroscopies. Ionization energies were determined for both outer and inner valence orbitals and new adiabatic values were also resolved. Vibronic structure associated with several states was assigned mainly to be due to C–C stretches and ring bends. Additionally a Rydberg state converging to 7b2 state was ascribed. The data shown...
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Electron scattering from 2-methyl–1,3-butadiene,C5H8, molecules: Role of methylation
PublicationWe report cross-section results from experimental and theoretical investigations into electron collisions with the 2-methyl–1,3-butadiene [C5H8] molecule. The current results are compared with our previous results for the 1,3-butadiene [C4H6] molecule, a structural homologue of 2-methyl–1,3-butadiene, to investigate how the methylation (the substitution of hydrogen atom by a methyl group) affects the shape and/or magnitude of the...
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Potential energy surfaces of the low-lying electronic states of the Li+LiCs system
PublicationAb initio quantum chemistry calculations are performed for the mixed alkali triatomic system. Global minima of the ground and first excited doublet states of the trimer are found and Born-Oppenheimer potential energy surfaces of the Li atom interacting with the LiCs molecule were calculated for these states. The lithium atom is placed at various distances and bond angles from the lithium-caesium dimer. Three-body nonadditive forces...
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Hybrid design approach in education using a progressive rule-based digital design development. Sopot College experiences.
PublicationBudynek sam w sobie może być uznany za hybrydę inżynierii i Beaux-Arts. Obecnie istnieje wiele narzędzi, które mogą pomóc architektom w opracowaniu i optymalizowu ich innowacyjnych koncepcje. Artykuł opisuje projekt hybrydowego podejścia opartego na połączeniu tradycyjnej architekturze i Komputerowego projektowania na podstawie programu studiów w Sopocie College, Wydział Architektury. Artykuł bada dziedzinie współpracy i interakcji...
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Dissociative Electron Attachment to 5-Iodo-4-thio-2′-deoxyuridine: A Potential Radiosensitizer of Hypoxic Cells
PublicationIn the search for effective radiosensitizers for tumor cells, halogenated uracils have attracted more attention due to their large cross section for dissociation upon the attachment of low-energy electrons. In this study, we investigated dissociative electron attachment (DEA) to 5-iodo-4-thio-2'-deoxyuridine, a potential radiosensitizer using a crossed electron-molecule beam experiment coupled with quadrupole mass spectrometry....
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Catena-Poly[[(tetrahydrofuran-[kappa]O)lithium(I)]-bis([mu]-trimethylsilanolato-[kappa]2O:O)-gallium(III)-bis([mu]-trimethylsilanolato-[kappa]2O:O)-[(tetrahydrofuran-[kappa]O)lithium(I)]-[mu]-bromido]
PublicationThe title chain polymer compound, [GaLi2Br(C3H9OSi)4(C4H8O)2]n, was obtained in the reaction of GaBr3 with Me3SiOLi in toluene/tetrahydrofuran. The GaIII atom, located on a twofold rotation axis, is coordinated by four trimethylsilanolate ligands and has a distorted tetrahedral geometry. The LiI atom is four coordinated by one bridging Br atom located on an inversion centre, two trimethylsilanolate ligands and one tetrahydrofurane...