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Electron Scattering on X(CH3)4 Molecules: Applicability of Simple Additivity Rule and Role of Methylation
PublicationTo investigate influence of target methylation (substitution of a hydrogen atom by methyl group) on electron-collision processes we compare absolute total cross sections for XH4 and X(CH3)4 molecules, where X is Si and Ge, respectively. We also compare experimental TCSs energy dependencies with estimated data obtained using simple formula and TCSs for methyl group and those for SiH4 and GeH4. Electron-scattering TCSs for mentioned...
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Bis(diethylamido-[kappa]N)(diethylamine-[kappa]N)bis(2,6-diisopropylphenylamido-[kappa]N)zirconium(IV)
PublicationIn the title compound, [Zr(C12H18N)2(C4H10N)2(C4H11N)] or [Zr(HNC6H3iPr2)2(NEt2)2(HNEt2)], which was obtained by the reaction of Zr(NEt)4 with iPr2C6H3NH2, the Zr IV atom is in a trigonal–bipiramidal geometry in which the N atoms from two iPr2C6H3NH and one NEt2 ligand occupy the equatorial positions, and the N atoms of an NEt2 and an Et2NH ligand occupy the apical positions. An intramolecular N—HN contact occurs. There are two...
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Correlated Particle Motion and THz Spectral Response of Supercritical Water
PublicationMolecular dynamics simulations of supercritical water reveal distinctly different distance-dependent modulations of dipolar response and correlations in particle motion compared to ambient conditions. The strongly perturbed H-bond network of water at supercritical conditions allows for considerable translationaland rotational freedom of individual molecules. These changes give rise to substantially different infrared spectra and...
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Hydration of amino acids: FTIR spectra and molecular dynamics studies
PublicationThe hydration of selected amino acids, alanine, glycine, proline, valine, isoleucine and phenylalanine, has been studied in aqueous solutions by means of FTIR spectra of HDO isotopically diluted in H2O. The difference spectra procedure and the chemometric method have been applied to remove the contribution of bulk water and thus to separate the spectra of solute-affected HDO. To support interpretation of obtained spectral results,...
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SiMiSnoRNA: Collection of siRNA, miRNA, and snoRNA database for RNA Interference
PublicationObjective:The discovery of sequence specific gene silencing which occurs due to the presence of double-stranded RNAs has considerable impact on biology, revealing an unknown level of regulation of gene expression. This process is known as RNA interference (RNAi) or RNA silencing in which RNA molecules inhibit gene expression, typically by causing the destruction of specific mRNA molecule. Two types of small RNA molecules - small...
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Interactions of protons with furan molecules studied by collision-induced emission spectroscopy at the incident energy range of 50–1000 eV
PublicationInvestigations of the ion-molecule reactions provide insight into many fields ranging from the stellar wind interaction with interstellar media, up to medicine and industrial applications. Besides the applications, the understanding of these processes is itself a problem of fundamental importance. Thus, interactions of protons with the gas-phase furan molecules have been investigated for the first time in the energy range of 50–1000...
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Unique agreement of experimental and computational infrared spectroscopy: a case study of lithium bromide solvation in an important electrochemical solvent
PublicationInfrared (IR) spectroscopy is a widely used and invaluable tool in the studies of solvation phenomena in electrolyte solutions. Using state-of-the-art chemometric analysis of a spectral series measured in a concentration-dependent manner, the spectrum of the solute-affected solvent can be extracted, providing a detailed view of the structural and energetic states of the solvent molecules influenced by the solute. Concurrently,...
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The hydrogen bond network structure within the hydration shell around simple osmolytes: Urea, tetramethylurea, and trimethylamine-N-oxide, investigated using both a fixed charge and a polarizable water model
PublicationDespite numerous experimental and computer simulation studies, a controversy still exists regarding the effect of osmolytes on the structure of surrounding water. There is a question, to what extent some of the contradictory results may arise from differences in potential models used to simulate the system or parameters employed to describe physical properties of the mixture and interpretation of the results. Bearing this in mind,...
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The hydrogen bond network structure within the hydration shell around simple osmolytes: Urea, tetramethylurea, and trimethylamine-N-oxide, investigated using both a fixed charge and a polarizable water model
PublicationDespite numerous experimental and computer simulation studies, a controversy still exists regarding the effect of osmolytes on the structure of surrounding water. There is a question, to what extent some of the contradictory results may arise from differences in potential models used to simulate the system or parameters employed to describe physical properties of the mixture and interpretation of the results. Bearing this in mind,...
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4-[(tert-Butyldimethylsilyl)oxy]-6-methoxy-7-methyl-5-(oxiran-2-ylmethyl)-2-benzofuran-3(1H)-one
PublicationThe title compound, C19H28O5Si, was obtained in the reaction of 1,3-dihydro-4-[(tert-butyldimethylsilyl)oxy]-6-methoxy-7-methyl-3-oxo-5-(prop-2-enyl)isobenzofuran with meta-chloroperbenzoic acid. This reaction is one of the stages of the total synthesis of mycophenolic acid, which we attempted to modify. The title compound forms crystals with only weak intermolecular interactions. The strongest stacking interaction is found between...
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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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How water mediates the long-range interactions between remote protein molecules
PublicationThe high crowding of macromolecules in the cytoplasm affects the processes that occur inside a living cell. It can, for example, promote the forming of various loosely connected structures of proteins. It also means that bulk water is, essentially, not present there. The relatively thin layer of solvent that separates macromolecules may be able to participate in the long-range interactions between them and make them respond to...
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Telomerase inhibition - unfulfilled hopes in the perfect molecular target
PublicationTelomerase plays a pivotal role in cell proliferation, homeostasis, and neoplastic transformation, making it a promising molecular target for cancer chemotherapy. Of note, although hTERT has been explored thoroughly as a target, none of the promising molecules has been approved as a drug until now. The subject of research conducted as part of my doctoral dissertation is explaining the cellular and molecular mechanism of action...
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Computational analysis of substituent effects on proton affinity and gas-phase basicity of TEMPO derivatives and their hydrogen bonding interactions with water molecules
PublicationThe study investigates the molecular structure of 2,2,6,6-tetramethylpiperidine-1-oxyl (TEMPO) and its derivatives in the gas phase using B3LYP and M06-2X functional methods. Intermolecular interactions are analyzed using natural bond orbital (NBO) and atoms in molecules (AIM) techniques. NO2-substituted TEMPO displays high reactivity, less stability, and softer properties. The study reveals that the stability of TEMPO derivatives...
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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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Recent advancements in molecularly imprinted polymers for the removal of heavy metal ions and dyes
PublicationContamination set off by highly toxic metal ions and dyes is a big threat to the environment and living beings. Various industries like metal plating, mining, pesticides, battery manufacturing, and dyeing release metal ions and toxic dyes directly into the water. It is necessary to remove these toxic substances from the environment. Molecular imprinting technology (MIT) got a lot of attention in the last two decades because of...
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Compatibility of Crude Oil Blends─Processing Issues Related to Asphaltene Precipitation, Methods of Instability Prediction─A Review
PublicationProcessing crude oil of variable composition, especially due to the need to process crude oil blends obtained from various sources, presents a tremendous process challenge. This is mainly due to the destabilization of the colloidal system manifested mostly by the precipitation of the asphaltene fraction. The precipitation of asphaltenes from crude oil is a serious problem during extraction, transport, and processing. In the latter...
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Valence and ionic lowest-lying electronic states of small esters studied by high resolution vacuum ultraviolet photoabsorption, photoelectron spectroscopy and ab initio calculations
PublicationEsters are an important class of oxygenated volatile organic compounds used in food flavorings, perfumes and other cosmetic products. They are present in fruits and pheromones and are emitted to the atmosphere naturally. Esters are also formed in the atmosphere as a product of the oxidation of ethers. Some of them form poly-molecule chains and are used in plastics. Phosphoesters form DNA backbone, while nitroesters are known for...
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Formation of OH Radicals as Evidence of Intramolecular Hydrogen Migration in Cation-Induced Dissociation of Furan Molecules
PublicationWe present the experimental results on a hydrogen atom migration preceding fragmentation of the furan molecules induced by the H3+ and C+ impact. The excited OH(A2Σ+) radical has been detected among the furan decomposition products using collision-induced emission spectroscopy. However, the OH moiety is absent in the furan ring skeleton, so detecting the OH(A2Σ+→X2Π) luminescence indicates the intramolecular H atom relocation prior...
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Vibrational excitation of acetylene by positron impact
PublicationVibrationally inelastic quantum calculations are carried out at low collision energies for the scattering of a beam of positrons off acetylene gaseous molecules. The normal mode analysis is assumed to be valid and the relative fluxes into the C–C and C–H symmetric vibrational modes are computed within a Body-Fixed (BF) formulation of the dynamics by solving the relevant vibrational Coupled Channels (VCC) equations. The clear dominance...
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Excited-state proton transfer and geminate recombination in the molecular cage of β-cyclodextrin
PublicationExcited-state proton transfer and geminate recombination in aqueous heptakis(2,6-di-O-methyl)-β-cyclodextrin have been compared with those in water by monitoring the photoinduced prototropic tautomerization of 6-hydroxyquinoline, which occurs via forming anionic intermediate. Enol deprotonation decelerates by 18 times whereas its reverse process accelerates slightly with encapsulation. The imine protonation of the intermediate...
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Ionization and fragmentation of furan molecules by electron collisions
PublicationCation mass spectra obtained by electron impact were measured to investigate the ionization and ionic fragmentation of furan, C4H4O, molecules in the gas phase. The most abundant cations, with comparable intensities in the mass spectra, were the parent, C4H4O+, cation (68 amu) and the C3H3+ fragment (39 amu). The appearance energies of most of the observed ionic fragments were determined and the possible fragmentation processes...
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Thermal self-action effects of acoustic beam in a vibrationally relaxing gas
PublicationThermal self-action of acoustic beam in a molecular gas with excited internal degrees of molecules’ freedom, is studied. This kind of thermal self-action differs from that in a Newtonian fluid. Heating or cooling of a medium takes place due to transfer of internal vibrational energy. Equilibrium and non-equilibrium gases, which may be acoustically active, are considered. A beam in an acoustically active gas is self-focusing unlike...
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Ionization and ionic fragmentation of tetrahydrofuran molecules by electron collisions
PublicationElectron impact ionization and ionic fragmentation of tetrahydrofuran molecules in the gas phase were studied in the energy range from ionization threshold up to 150 eV using the technique of mass spectrometry. The cation mass spectra, ionization and ionic fragmentation efficiencies were measured over this energy range. Well-resolved mass peaks were detected in the mass range 10-72 amu and assigned to corresponding ionic molecular...
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1,3-Di-<i>n</i>-butylthiourea
PublicationIn the title compound, C9H20N2S, the n-butyl groups are in syn and anti positions in relation to the C=S bond. In the crystal, two molecules are connected by two N-H···S=C hydrogen bonds into a centrosymmetric dimer. Another N-H···S=C hydrogen bond links the dimers, forming layers with a hydrophilic interior and a hydrophobic exterior, which spread across the (100) plane. Interlacing of the...
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Proton transfer reactions for ionized water clusters
PublicationCalculations of formation energies of the ionized water clusters and energies of reactions between small (including less than eight water molecules) neutral and positively ionized water clusters are presented. Moreover, we discuss some reaction paths between neutral and positively charged dimers, trimers and tetramers and proton transfer reactions (PTR) between cyclic clusters and H3O+ ions which can appear in beam experiments...
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Charge Transfer, Complexes Formation and Furan Fragmentation Induced by Collisions with Low-Energy Helium Cations
PublicationThe present work focuses on unraveling the collisional processes leading to the fragmentation of the gas-phase furan molecules under the He+ and He2+ cations impact in the energy range 5–2000 eV. The presence of different mechanisms was identified by the analysis of the optical fragmentation spectra measured using the collision-induced emission spectroscopy (CIES) in conjunction with the ab initio calculations. The measurements of...
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Synthesis, structural characterization and reactivity of new trisubstituted N1-acylamidrazones: solid state and solution studies
PublicationA series of new linear trisubstituted N1-acylamidrazones have been investigated using a variety of analytical techniques and theoretical calculations to check the influence of the type of N1-acyl substituent on the resonance forms and conformational behavior in the solid state and in solution. The 1D- and 2D-NMR experiments, supported by computational studies, revealed that in solution all amidrazones exhibit conformational syn/anti...
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Crystal and electronic structures of Ni(II) silanethiolates containing flexible diamine ligands
PublicationFive nickel(II) complexes containing aliphatic diamines and tri-tert-butoxysilanethiolate ligand have been synthesized for the purpose of studying their structural, spectral (IR, UV–Vis, HF EPR) and thermal properties. Complexes (1)–(5) have been prepared in high yield by reactions of [Ni{SSi(OtBu)3}2(NH3)(H2O)] with 1.3-propanediamine (L1), 1,6-hexanediamine (L2), or 1,7-heptanediamine (L3). The X-ray structures were determined...
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Taurine as a water structure breaker and protein stabilizer
PublicationThe enhancing effect on the water structure has been confirmed for most of the osmolytes exhibiting both stabilizing and destabilizing properties in regard to proteins. The presented work concerns osmolytes, which should be classified as “structure breaking” solutes: taurine and N,N,N-trimethyltaurine (TMT). Here, we combine FTIR spectroscopy, DSC calorimetry and DFT calculations to gain an insight into the interactions between...
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Elastic scattering of electrons by water: An ab initio study
PublicationIn this work we devise a theoretical and computational method to compute the elastic scattering of electrons from a non-spherical potential, such as in the case of molecules and molecular aggregates. Its main feature is represented by the ability of calculating accurate wave functions for continuum states of polycentric systems via the solution of the Lippmann-Schwinger equation, including both the correlation effects and multi-scattering...
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A Series of Novel 3D Coordination Polymers Based on the Quinoline-2,4-dicarboxylate Building Block and Lanthanide(III) Ions—Temperature Dependence Investigations
PublicationA series of novel 3D coordination polymers [Ln2(Qdca)3(H2O)x]yH2O (x = 3 or 4, y = 0–4) assembled from selected lanthanide ions (Ln(III) = Nd, Eu, Tb, and Er) and a non-explored quinoline- 2,4-dicarboxylate building block (Qdca2 = C11H5NO4 2) were prepared under hydrothermal conditions at temperatures of 100, 120, and 150 C. Generally, an increase in synthesis temperature resulted in structural transformations and the formation...
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Study of the Effect of Filling Thermoplastic Medical Polyurethane with PVA, PLA or Diatomite on the Relaxation Times Distributions of 1H NMR
PublicationIn this work, to characterize the mobility of diferent sections of the macromole‑ cules of polyurethane (PUR), polyvinyl alcohol (PVA), and polylactic acid (PLA), as well as the density of crosslinks of the polymer chains when using fllers, we used the distributions of spin–lattice and spin–spin relaxation times for the protons. It is shown that the rigidity of the thermoplastic polymers depends on the sizes of the granules of...
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Electrochemically Induced Synthesis of Triphenylamine-based Polyhydrazones
PublicationTriphenylamine-based hydrazones were subjected to electropolymerization process that gave well conductive hydrazone based polymers. The first example of polyhydrazone formation during the electrochemical process was shown. The estimation of polymer structure was demonstrated using IR spectroelectrochemistry. The EPR spectroelectrochemistry allowed to explain why in some cases dimer couldn’t be formed. The results of electrochemical,...
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On thio‐substituted N‐heterocyclic arsines
PublicationMetathesis of N-heterocyclic chloroarsines with sulfur-based nucleophiles furnished thio-substituted 1,3,2-diazarsolidines and 1,3,2-diazarsolenes. Crystallographic and NMR spectroscopic studies revealed that a thiocyanato-diazarsolene exhibits a salt-like structure composed of weakly interacting thiocyanate and arsenium ions, while the remaining products formed neutral molecules. The structural data indicate that the heterocyclic...
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Turmeric nanofiber-encapsulated natural product formulation act as a phytogenic feed additive—A study in broilers on growth performance, biochemical indices of blood, and E. coli in cecum
PublicationA phytogenic feed additive (PFA) formulation was prepared with bioactive molecules—curcuminoids, gingerol, and carvacrol by encapsulating in nanofiber isolated from turmeric spent (turmeric nanofiber, TNF). This formulation was completely characterized by scanning electron microscope, ultra performance liquid chromatography, and gas chromatography and evaluated for its efficacy. PFA-encapsulated TNF (PFA@TNF) considerably increased...
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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
PublicationX-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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Dipole-driven dynamics for near-threshold electron/positron interactions with pyrimidinic DNA bases: a path to compound formations
PublicationCalculations are reported for electron and positron scattering from isolated cytosine and thymine, where the two pyrimidinic single-ring DNA bases, in the gas-phase at energies near the elastic threshold, they reveal the special features of the dipole-driven scattering states. All molecules examined exhibit, in fact, supercritical (>1.67 D) permanent dipoles which can therefore also support, below threshold, excited bound compound...
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Low-energy interactions related to atmospheric and extreme conditions
PublicationThis Topical Issue, entitled “Low-Energy Interactions Related to Atmospheric and Extreme Conditions”, showcases a collection of eighteen articles that reported recent theoretical and experimental findings pertaining to the following topics: – low-energy interactions of charged particles (electrons [1–7], protons [8], positrons [9]), and photons [10] with atoms and molecules of biological [1–4,7,8], astrochemical [10], industrial,...
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Dissociative electron attachment and anion-induced dimerization in pyruvic acid
PublicationWe report partial cross sections for the dissociative electron attachment to pyruvic acid. A rich fragmentation dynamics is observed. Electronic structure calculations facilitate the identification of complex rearrangement reactions that occur during the dissociation. Furthermore, a number of fragment anions produced at electron energies close to 0 eV are observed, that cannot originate from single electron-molecule collisions....
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Elastic electron scattering and vibrational excitation of isoxazole molecules in the energy range from 2 to 20 eV
PublicationDifferential cross sections for elastic electron scattering and the excitation of the C-H vibrational modes of isoxazole molecules were measured in the energy range from 2 to 20 eV and over the scattering angle range from 10◦ to 180◦. The cross sections at the scattering angles of and above 90◦ were accessible with the use of a magnetic angle changer. The differential cross sections were integrated to yield integral and momentum...
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Optical Spectroscopic Studies of Tetrahydrofuran Fragmentation Induced by Collisions with Dihydrogen Cations
PublicationCollisions of dihydrogen cations with tetrahydrofuran molecules have been studied. Luminescence spectra and the emission functions of the excited products at projectile energies ranging from 8 to 1000 eV have been measured using collision-induced emission spectroscopy. The recorded spectra are dominated by the atomic lines of the hydrogen Balmer series, whose intensities decrease more quickly than derived by the quantum-theoretical...
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Dissociative photo-double-ionization of the isoxazole molecules
PublicationThe five-membered heterocyclic rings are incorporated into a wide variety of structures that play a vital role in many biochemical processes. In particular, the isoxazole molecule appears in many bioactive compounds due to its unique ring structure that consists of one oxygen atom and one nitrogen atom at adjacent positions. The unique atomic composition and bond arrangement of isoxazole imply its specific electronic properties...
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Electron impact ionization and cationic fragmentation of the pyridazine molecules
PublicationElectron impact mass spectroscopy was used to investigate ionization and cationic fragmentation of the pyridazine (1,2 diazine), C4H4N2, molecules in the gas phase. The mass spectra were measured and the observed mass peaks assigned to the corresponding cations. The appearance energies of most of the cationic fragments were determined and the possible fragmentation processes are discussed. The total cross section for electron...
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Low-energy positron scattering from gas-phase tetrahydrofuran: A quantum treatment of the dynamics and a comparison with experiments
PublicationIn this paper we report new quantum calculations of the dynamics for low-energy positrons interacting with gaseous molecules of tetrahydrofuran. The new quantum scattering cross sections are differential and integral cross sections at collision energies between 1.0 and 25.0 eV and include a careful treatment of the additional effects on the scattering process brought about by the permanent dipole moment of the target molecule....
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Synthesis and characterization of mononuclear Zn(II), Co(II) and Ni(II) complexes containing a sterically demanding silanethiolate ligand derived from tris(2,6-diisopropylphenoxy)silanethiol
PublicationFour heteroleptic complexes of zinc(II), cobalt(II) and nickel(II) containing a monodentate silanethiolate ligand derived from tris(2,6-diisopropylphenoxy)silanethiol (TDST), were prepared and characterized. The geometries of ligands in the complexes are typical: distorted tetrahedral in zinc and cobalt(II) complexes and square planar in nickel(II) compound. Magnetic studies performed for Ni(II) and Co(II) compounds confirm the...
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Stimulated by cyclodextrins high yield synthesis of azocrown analogues comprising pyrrole or imidazole residues
PublicationThe influence of cyclodextrins (CDs) on the formation of azocrown ethers comprising pyrrole, imidazole and substituted imidazole has been studied. Pyrrole, imidazole, 2-methyl-, 4-methyl- and 4-phenylimidazole were coupled with bisdiazonium salts derived from bis-1,5-(2-aminophenoxy)-3-oxapentane or bis-1,8-(2-aminophenoxy)-3,6-dioxaoctane to form macrocyclic compounds with two azo units. The syntheses were performed under standard...
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Synthesis and characterisation of starch cuprate
PublicationThe cupration of granular potato starch with ammonium tetrachlorocuprate(II) was performed by a 20 min lasting microwave-assisted process and by 40 min convectional heating. In both cases the degree of esterification (DE) did not exceed 0.0064. A higher dose of cuprate had a positive effect on DE, regardless of whether the microwave irradiation or the convectional heating was applied, and on the thermal stability of the starch...
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Cross sections for ionization and ionic fragmentation of pyrimidine molecules by electron collisions
PublicationThe electron impact mass spectroscopy and the total ion collection measurements were used to investigate the ionization and ionic fragmentation of the pyrimidine, C4H4N2, molecules in the gasphase. The cation mass spectra were measured in the 10−85 amu range and the observed mass peaks assigned to corresponding ionic fragments. The most abundant cation in the mass spectra is the parent cation, C4H4N+2, at 80 amu. The appearance...
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Inner-shell fragmentation of molecules into neutral fragments in high-Rydberg states induced by soft X-ray excitation with pulsed-field ionization
PublicationIn the present communication, we will show the results of measurements probing the production of neutral high-Rydberg fragments at the K edges of the molecules containing oxygen and nitrogen atoms. The experiments were performed at the Gas Phase beamline of the Elettra synchrotron radiation laboratory (Trieste, Italy), exploiting a combined soft X-ray excitation with pulsed-field ionization and ion time-of-flight (TOF) spectrometry...