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Search results for: molecular complexes
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Studies on the solid-liquid equilibria and intermolecular interactions Urea binary mixtures with Sulfanilamide and Sulfacetamide
PublicationThe binary phase diagrams of Sulfanilamide-Urea (SN-U) and Sulfacetamide-Urea (SC-U) were measured using differential scanning calorimetry technique (DSC). Both examined mixtures were found to form simple binary eutectics. The limited miscibility in the solid state observed by DSC, proving inability of co-crystallization in new multi-molecular form, was also confirmed using PXRD and FTIR-ATR measurements of solid dispersions...
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Molecular Structures of the Phospha-Wittig Reaction Intermediate: Initial Step in the Synthesis of Compounds with a C═P–P Bond as Products in the Phospha-Wittig Reaction
PublicationThe phospha-Wittig reactivity ofβ-diketiminate titanium(III) complexes with phosphanylphosphido ligands was investigated. The reactions of [MeNacNacTi(Cl){η2-P(SiMe3)-PtBu2}] and [MeNacNacTi(Cl){η2-P(SiMe3)-P(Ph)tBu}] with acetone conducted in toluene solution under mild conditions led to the phospha-Wittig intermediates [{(ArN=C(Me)CHC(Me)=NAr)(C(Me)2O}Ti(Cl){PtBu2-P(SiMe3)C(Me)2O}] (1) and [{(ArN=C(Me)CHC(Me)=NAr) (C-(Me)2O}Ti(Cl){P(Ph)tBu-P(SiMe3)C(Me)2O}]...
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How do sterols determine the antufungal activitiy of amphotericin B? Free energy of binding between the drug and its membrane targets.
PublicationAmphotericin B (AmB) is a well-known polyene antibiotic used to treat systemic fungal infections. It is commonly accepted that the presence of sterols in the membrane is essential for the AmB biological activity, that is, for the formation of transmembrane ion channels. The selective toxicity of AmB for fungal cells is attributed to the fact that it is more potent against fungal cell membranes containing ergosterol than against...
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Molecular Dynamics to Predict Cryo-EM: Capturing Transitions and Short-Lived Conformational States of Biomolecules
PublicationSingle-particle cryogenic electron microscopy (cryo-EM) has revolutionized the field of the structural biology, providing an access to the atomic resolution structures of large biomolecular complexes in their near-native environment. Today’s cryo-EM maps can frequently reach the atomic-level resolution, while often containing a range of resolutions, with conformationally variable regions obtained at 6 Å or worse. Low resolution...
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Structural, magnetic and spectral properties of tetrahedral cobalt(II) silanethiolates: a variety of structures and manifestation of field-induced slow magnetic relaxation
PublicationBlue crystals of five heteroleptic cobalt(II) silanethiolates 1–5 have been obtained by the reaction of [Co{SSi (tBuO)3}2(NH3)]2 with aminopyridines and aminomethylpyridines at an appropriate molar ratio and their structural, spectral, thermal and magnetic properties have been established and described. All complexes 1–5 contain Co(II) ions in a tetrahedral CoN2S2 environment formed by (tBuO)3SiS− residues and pyridines and present...
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The Effect of Sterols on Amphotericin B Self-Aggregation in a Lipid Bilayer as Revealed by Free Energy Simulations
PublicationAmphotericin B (AmB) is an effective but toxic antifungal drug, known to increase the permeability of the cell membrane, presumably by assembling into transmembrane pores in a sterol-dependent manner. The aggregation of AmB molecules in a phospholipid bilayer is, thus, crucial for the drug’s activity. To provide an insight into the molecular nature of this process, here, we report an atomistic molecular dynamics simulation study...
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The Product of Matrix Metalloproteinase Cleavage of Doxorubicin Conjugate for Anticancer Drug Delivery: Calorimetric, Spectroscopic, and Molecular Dynamics Studies on Peptide–Doxorubicin Binding to DNA
PublicationMatrix metalloproteinases (MMPs) are extracellular matrix degradation factors, promoting cancer progression. Hence, they could provide an enzyme-assisted delivery of doxorubicin (DOX) in cancer treatment. In the current study, the intercalation process of DOX and tetrapeptide-DOX, the product of the MMPs' cleavage of carrier-linked DOX, into dsDNA was investigated using stationary and time-resolved fluorescence spectroscopy, UV-Vis...
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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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Photophysical processes in the selected white organic light-emitting diodes
PublicationThe first part discusses history of organic emitters, the scope of the work, phenomena in molecular systems, types of architectures in OLEDs, types of OLEDs emitting white light with examples from the literaturę and a description of the parameters chcracterizing LEDs. The second part describes materials, production of the samples, the measurement systems and results. In chapter 8.1 the results for the OLEDs based on emission from...
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Rhodotorulic Acid and its Derivatives: Synthesis, Properties, and Applications
PublicationSiderophores are low molecular weight compounds produced by microorganisms to scavenge iron in iron-deficient environments. Rhodotorulic acid (RA), a natural hydroxamate siderophore, plays a vital role in iron acquisition for fungi and bacteria. As the simplest natural hydroxamate siderophore, RA exhibits a high affinity for ferric ions, enabling it to form stable complexes that facilitate iron uptake and transport within microorganisms....
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The Interaction of Heptakis (2,6-di-O-Methyl)-β-Cyclodextrin with Mianserin Hydrochloride and Its Influence on the Drug Toxicity
PublicationOne tetracyclic antidepressant, mianserin hydrochloride (MIA), has quite significant side effects on a patients’ health. Cyclodextrins, which are most commonly used to reduce the undesirable features of contained drugs within their hydrophobic interior, also have the potential to alter the toxic behavior of the drug. The present paper contains investigations and the characteristics of interaction mechanisms for MIA and the heptakis...
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Structural, spectral and magnetic properties of Ni(II), Co(II) and Cd(II) compounds with imidazole derivatives and silanethiolate ligands
PublicationA series of new metal heteroleptic complexes have been obtained in simple reactions of 1-(3-aminopropyl)-imidazole (api) and 1,4-bis(imidazol-1-yl)-butane (bbi) ligands with metal silanethiolates or acetylacetonates. The obtained complexes are the coordination polymers [Ni{SSi(tBuO)3}2(μ-api)]n1, [Co{SSi(tBuO)3}2(μ-api)]n2, [Cd{SSi(tBuO)3}2(μ-api)·2CH3OH]n3, [Cd{SSi(tBuO)3}2(μ-bbi)·CHCl3]n4 and the dimer [Co{SSi(tBuO)3}2(μ-bbi)·3CH3OH]25....
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Intermolecular Hydrogen Bonding Directed by Aryl–Perfluoroaryl π–π Stacking Interactions
PublicationThe crystal structures of five compounds capable of forming self-complementary hydrogen bonds but crystallizing as catemers or creating more complex crystal structures were compared with their complexes prepared by cocrystallization with perfluoroaryl compounds. The results of X-ray diffraction revealed that in all the cases the π–π stacking interactions caused reorganization of hydrogen bonds and induced creation of the expected...
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Rhodotorulic Acid and its Derivatives: Synthesis, Properties, and Applications
PublicationSiderophores are low molecular weight compounds produced by microorganisms to scavenge iron in iron-deficient environments. Rhodotorulic acid, a natural hydroxamate siderophore, plays a vital role in iron acquisition for fungi and bacteria. As the simplest natural hydroxamate siderophore, it exhibits a high affinity for ferric ions, enabling it to form stable complexes that facilitate iron uptake and transport within microorganisms....
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Syntheses and structures of the first terminal phosphanylphosphido complex of hafnium [cp2hf(cl){η1-(me3si)p-p(net2)2}] and the firstzirconocene-phosphanylphosphinidene dimer [cp2zr{μ2-p-p(net2)2}2zrcp2]
PublicationReactions of (Et2N)2P-P(SiMe3)Li with [Cp2MCl2] (M= Zr, Hf) in toluene or pentane yield the related terminal phosphanylphosphido complexes [Cp2M(Cl){η1-(Me3Si)P-P(NEt2)2}]. The solid statestructure of [Cp2Hf(Cl){η1-(Me3Si)P-P(NEt2)2}] was established by single crystal X-ray diffraction. The reaction of (Et2N)2P-P(SiMe3)Li with [Cp2ZrCl2] in THF or DME solutions leads to the formationof deep red crystals of the first neutral diamagnetic...
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Natural Deep Eutectic Solvents as Agents for Improving Solubility, Stability and Delivery of Curcumin
PublicationPurpose Study on curcumin dissolved in natural deep eutectic solvents (NADES) was aimed at exploiting their beneficial properties as drug carriers. Methods The concentration of dissolved curcumin in NADES was measured. Simulated gastrointestinal fluids were used to determine the concentration of curcumin and quantum chemistry computations were performed for clarifying the origin of curcumin solubility enhancement in NADES. Results NADES...
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Thermodynamics aspects of interactions between acridine derivatives and DNA
PublicationDNA is a molecular target for many anticancer and antiviral drugs. Therefore, a clear understanding of the interaction of small molecules with DNA is important in the rational design of ligands that can bind to DNA with high affinity and selectivity. There are several methods to investigate interactions between drug and DNA. Some of them measure changing into DNA structures, such as lengthening and untwisting of helix of DNA. Other...
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Active Site Architecture and Reaction Mechanism Determination of Cold Adapted beta-D-galactosidase from Arthrobacter sp. 32cB
PublicationArthbetaDG is a dimeric, cold-adapted beta-D-galactosidase that exhibits high hydrolytic and transglycosylation activity. A series of crystal structures of its wild form, as well as its ArthbetaDG_E441Q mutein complexes with ligands were obtained in order to describe the mode of its action. The ArthbetaDG_E441Q mutein is an inactive form of the enzyme designed to enable observation of enzyme interaction with its substrate. The...
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Drug-resistant and hospital-associated Enterococcus faecium from wastewater, riverine estuary and anthropogenically impacted marine catchment basin.
PublicationEnterococci, ubiquitous colonizers of humans and other animals, play an increasingly important role in health-care associated infections (HAIs). Acquisition of resistance determinants not only seriously limits available therapeutic options but also increases available gene pool for other species. It is believed that the recent evolution of two clinically relevant species, Enterococcus faecalis and Enterococcus faecium occurred...
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Mono- and polynuclear Co(II) silanethiolates with aliphatic diamines
PublicationFour Co(II) complexes, [Co{SSi(OtBu)3}2(dmpda)] 1, [Co{SSi(OtBu)3}2(bda)2]n2 [Co{SSi(OtBu)3}2(pda)2]n3 and [Co{SSi(OtBu)3}2(hda)2]n4 [dmpda = 3-(dimethylamino)-1-propylamine; bda = 1.4-butanediamine; pda = 1.5-pentanediamine; had = 1.6-hexanediamine] have been synthesized and characterized using X-ray diffraction. Complex 1 is mononuclear and contains Co(II) coordinated by dmpda molecule in chelating mode, whereas compounds 3 and...
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Interplay between Aryl···Perfluoroaryl and Hydrogen Bonding Interactions in Cocrystals of Pentafluorophenol with Molecules of Trigonal Symmetry
PublicationCocrystals of seven star-shaped triaryl compounds with pentafluorophenol (pfp) were prepared and structurally characterized by the single-crystal X-ray diffraction method. Cocrystallization of pfp with planar (or almost planar) compounds gave six 3:1 molecular complexes with well-defined layered structures. The layers are composed of alternating pfp3 trimers, linked by hydrogen bonding, and triaryl molecules held together in planes...
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Applicability of phenolic acids as effective enhancers of cocrystals solubility of methylxanthines
PublicationApplicability of phenolic acids as potential cocrystal formers for methylxanthine derivatives was analyzed both in terms of cocrystallization probabilities and solubility advantage. The cocrystal formation abilities were evaluated using mixing enthalpy estimated within the conductor like screening model for real solvents (COSMO-RS) framework. The solubility improvement of potential cocrystals was estimated by formulation of the...
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Reverse vaccinology-based prediction of a multi-epitope SARS-CoV-2 vaccine and its tailoring to new coronavirus variants
PublicationThe genome feature of SARS-CoV-2 leads the virus to mutate and creates new variants of concern. Tackling viral mutations is also an important challenge for the development of a new vaccine. Accordingly, in the present study, we undertook to identify B- and T-cell epitopes with immunogenic potential for eliciting responses to SARS-CoV-2, using computational approaches and its tailoring to coronavirus variants. A total of 47 novel...
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NMR study of the complexes of tris(oxaalkyl) borates with SbCl5
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Guanosine Dianions Hydrated by One to Four Water Molecules
PublicationIntermolecular interactions such as those present in molecule···water complexes may profoundly influence the physicochemical properties of molecules. Here, we carried out an experimental–computational study on doubly deprotonated guanosine monophosphate···water clusters, [dGMP – 2H]2–·nH2O (n = 1–4), using a combination of negative anion photoelectron spectroscopy (NIPES) with molecular dynamics (MD) and quantum chemical (QM) calculations....
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Reactivity of Phosphanylphosphinidene Complex of Tungsten(VI) toward Phosphines: A New Method of Synthesis of catena-Polyphosphorus Ligands
PublicationThe reactivity of an anionic phosphanylphosphinidene complex of tungsten(VI), [(2,6-i-Pr2C6H3N)2(Cl)- W(η2-t-Bu2P=P)]Li·3DME toward PMe3, halogenophosphines, and iodine was investigated. Reaction of the starting complex with Me3P led to formation of a new neutral phosphanylphosphinidene complex, [( 2,6-i-Pr2C6H3N)2(Me3P)W(η2-t-Bu2P=P)]. Reactions with halogenophosphines yielded new catena-phosphorus complexes. From reaction with...
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Potentiometric and AM1d studies of silicon podands—silver(I) complexes
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Damian Rosiak dr inż.
PeopleEducation 2010–2014: Gdansk University of Technology, Chemical Faculty (Eng.) field of study: biotechnology specialty: drug biotechnology 2014–2015: Gdansk University of Technology, Chemical Faculty (M.Sc.) field of study: biotechnology specialty: drug biotechnology 2015–2020: Gdansk University of Technology, Department of Inorganic Chemistry (Ph.D.) discipline: chemical sciences specialty: inorganic chemistry Scientific...
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DMSO hydration redefined: Unraveling the hydrophobic hydration of solutes with a mixed hydrophilic–hydrophobic characteristic
PublicationHydrophobic hydration of solutes with a mixed hydrophilic--hydrophobic characteristics is still poorly understood. This is because both experimental and theoretical methods find it difficult to see the ice-like water structure around the nonpolar solute groups, unlike hydrogen bonds with the hydrophilic groups. In order to unravel this problem, we have investigated DMSO hydration by means of infrared spectroscopy and theoretical...
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Utilization of oriented crystal growth for screening of aromatic carboxylic acids cocrystallization with urea
PublicationThe possibility of molecular complex formation in the solid state of urea with benzoic acid analogues was measured directly on the crystallite films deposited on the glass surface using powder X-ray diffractometry (PXRD). Obtained solid mixtures were also analyzed using Fourier transform infrared spectroscopy (FTIR). The simple droplet evaporation method was found to be efficient, robust, fast and cost-preserving approach for first...
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Telomere uncapping by common oxidative guanine lesions: Insights from atomistic models
PublicationOxidative damage to DNA is widely known to contribute to aging and disease. This relationship has been extensively studied for telomeres – structures that cap chromosome ends – due to their role in cell proliferation and senescence, and exceptional susceptibility to oxidation. Indeed, the repetitive telomeric DNA sequence contains the 5′-GGG-3′ motif that has the lowest ionization potential of all trinucleotides. Accordingly, experiments...
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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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Potentiometric and AM1d studies of silicon and phosphorous podands-silver (I) complexes
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Potentiometric and AM1d studies of silicon and boron podands—silver (I) complexes
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Targeting yeast topoisomerase II by imidazo and triazoloacridinone derivatives resulting in their antifungal activity
PublicationFungal pathogens are considered as serious factors for deadly diseases and are a case of medical concern. Invasive fungal infections also complicate the clinical course of COVID-19, leading to a significant increase in mortality. Furthermore, fungal strains' multidrug resistance has increased the demand for antifungals with a different mechanism of action. The present study aimed to identify antifungal compounds targeting yeast...
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Antibiotic-sterol interactions provide insight into the selectivity of natural aromatic analogues of amphotericin B and their photoisomers
PublicationAromatic heptaene macrolides (AHMs) belong to the group of polyene macrolide antifungal antibiotics. Members of this group were the first to be used in the treatment of systemic fungal infections. Amphotericin B (AmB), a non-aromatic representative of heptaene macrolides, is of significant clinical importance in the treatment of internal mycoses. It includes the all-trans heptaene chromophore, whereas the native AHMs contain two...
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B-podand complexes with sodium ions: the reaction heats and PM5 semiempirical calculation
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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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Preparation and characterization of dummy-template molecularly imprinted polymers as potential sorbents for the recognition of selected polybrominated diphenyl ethers
PublicationThe main aim of this work was to conduct the preliminary/basic research concerning the preparation process of a new dummy molecularly imprinted polymer (DMIP) materials. Developed DMIPs were proposed as a sorption material in solid-phase extraction (SPE) technique for recognition of selected low mass polybrominated diphenyl ethers (PBDEs) e PBDE-47 and PBDE-99. Four new DMIPs were synthesized employing bulky polymerization technique...
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New dioxomolybdenum(VI) complexes of tetradentate Schiff base as catalysts for epoxidation of olefins
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New Dinuclear Macrocyclic Copper(II) Complexes as Potentially Fluorescent and Magnetic Materials
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FTIR and NMR studies of bis(oxaalkyl) sulphates(IV) and their complexes with proton and some metal cations
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The reaction heats and PM5 semiempirical studies of complexes formed between silicon podand and monovalent cations
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The reaction heats and PM5 semiempirical studies of complexes formed between silicon podand and Li+ cations
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Density functional theory calculations on entire proteins for free energies of binding: Application to a model polar binding site
PublicationIn drug optimization calculations, the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method can be used to compute free energies of binding of ligands to proteins. The method involves the evaluation of the energy of configurations in an implicit solvent model. One source of errors is the force field used, which can potentially lead to large errors due to the restrictions in accuracy imposed by its empirical nature....
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Unraveling Energy Transfer and Fluorescence Quenching Dynamics in Biomolecular Complexes: A Comprehensive Study of Imiquimod-Rifampicin Interaction.
PublicationIn nature, numerous biomolecules are implicated in charge transfer (CT) and energy transfer (ET) mechanisms crucial for fundamental processes such as photosynthesis. Unveiling these mechanisms is pertinent to multiple disciplines including chemistry, engineering and biochemistry. This letter presents a study involving two molecules forming a model system with efficient ET properties. Specifically, their complex exhibits dark quenching...
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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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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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Solvothermal synthesis and structural characterization of three polyoxotitanium-organic acid clusters
PublicationThree new titanium oxo-clusters Ti4O2(OiPr)10(OOCPhMe)2 (I), Ti6O4(OEt)8(OOCPhMe)8 (II) and Ti6O6(OEt)6(OOCCHPh2)6 (III) were obtained by easy one-step solvothermal reactions of titanium(IV) isopropoxide, alcohols and carboxylic acids. The three compounds were characterized by single-crystal and powder X-ray diffraction, TGA/DSC, optical and electron microscopy, and FTIR and NMR spectroscopy. X-ray powder diffraction and spectroscopy...
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Physicochemical profile of Os (III) complexes with pyrazine derivatives: From solution behavior to DNA binding studies and biological assay
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