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Electron interactions with Bis(pentamethylcyclopentadienyl) titanium(IV) dichloride and difluoride
PublikacjaWe present a combined experimental and theoretical study of the interaction of electrons with Bis(pentamethylcyclopentadienyl)titanium(IV) dichloride (Cp∗2TiCl2) and difluoride (Cp∗2TiF2). We report the experimental measurements of partial cross sections for the dissociative electron attachment (DEA) and the electron ionization (EI) mass spectra of isolated molecules. Estimates of the absolute cross sections are done on the basis...
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Induction of chirality in 4,4'-azopyridine by halogen-bonding interaction with optically active ditopic donors
PublikacjaOptically active ditopic halogen bond donors bearing two 4-iodotetrafluorophenyl groups were obtained by reaction of chiral diols with iodopentafluorobenzene. Co-crystallization of these donors with anti-4,4′-azopyridine afforded binary complexes containing infinite chains of the alternating component molecules connected by halogen bonds. The solid state CD measurements confirmed that complexation induces optical activity of the...
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Enzymatic cross-linking of β-lactoglobulin in solution and at air–water interface: Structural constraints
PublikacjaEffective and controlled use of cross-linking enzymes in structure engineering of food systems depends on characterization of the favorable conditions for enzyme-substrate complex and the limiting factors for the desired modification. In this respect, we analyzed the susceptibility of bovine β-lactoglobulin (BLG) to enzymatic cross-linking by Trichoderma reesei tyrosinase (TrTyr) and transglutaminase (TG). Changes in BLG molecular...
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Conformation analysis and semiclassical dynamics study of charge exchange process induced by collision of C2+ ions with tetrahydrofuran
PublikacjaWe present the results of recent investigations of charge transfer processes in the collisions of C²⁺ ions with heterocyclic molecules of tetrahydrofuran.
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Effect of ectoine on hydration spheres of peptides–spectroscopic studies
PublikacjaIn this paper, we use FTIR spectroscopy to characterize the hydration water of ectoine, its interactions with two peptides–diglycine and NAGMA, and the properties of water molecules in the hydration spheres of both peptides changed by the presence of the osmolyte. We found that the interaction of ectoine with the peptide hydration shells had no effect on its own hydration sphere. However, the enhanced hydration layer of the osmolyte...
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Cross section calculations for electron scattering from platinum chemotherapeutic compounds
PublikacjaCross section for electron impact ionization of carboplatin, C6H12N2O4Pt, and oxaliplatin, C8H14N2O4Pt, have been calculated within binary-encounter-Bethe model for energies from the ionization threshold up to 5000 eV. Cross section for elastic electron scattering from carboplatin and oxaliplatin molecules have also been derived using independent atom method (IAM) and additivity rule for collision energies ranging from 50 eV to...
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Electron impact fragmentation of pyrrole molecules studied by fluorescence emission spectroscopy
PublikacjaThe fluorescence emission spectroscopy using electron impact excitation technique was employed to study fragmentation processes of the gas phase pyrrole molecules. The following excited fragmentation species were observed by detection of their fluorescence decay: the atomic hydrogen H(n), n = 4-7 and the diatomic CH(A2Δ), CN(B2Σ+), NH(A3Π) and C2(d3Πg) fragments. These atomic and molecular products differ from those previously...
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Why is the cubic structure preferred in newly formed ice?
PublikacjaMolecular dynamics was employed to explain the preference for the cubic structure in newly formed crystals of ice. The results showed that in supercooled liquid water the molecules connected by hydrogen bonds are more likely to adopt relative orientations similar to the ones characteristic for cubic ice. The observed preference for certain relative orientations of molecules in the hydrogen-bonded pairs results in the higher probability...
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An examination of an Antarctic soil metagenomic-derivate putative methylthioadenosine phosphorylase gene as a novel reporter gene for promoter trapping
PublikacjaThe rsfp gene was discovered during examination ofan Antarctic soil-derived metagenome library and encodesa bacterial methylthioadenosine phosphorylase (GenBank accession number GQ202582). In a previous study, we found that E. coli colonies expressing the rsfp gene reveal strong pink fluorescence after exposure to UV light when grown on culture medium supplemented with rhodamine B (Cieśliński et al., 2009). In contrast to that,...
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Novel molecules containing structural features of NSAIDs and 1,2,3-triazole ring: Design, synthesis and evaluation as potential cytotoxic agents
PublikacjaFor the first time the template containing structural features of more than one NSAIDs and the 1,2,3-triazole ring was explored for the identification of potential cytotoxic agents. These new and complex molecules were predicted to be effective inhibitors of PDE4B by molecular modelling studies in silico. The multi-step synthesis of these compounds were carried out starting from the well-known drug nimesulide and involved the use...
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Electron energy-loss spectroscopy of excited states of the diazine molecules: Pyridazine
PublikacjaExcitation of the valence electronic states of the pyridazine molecules in the gas phase have been studied using the technique of electron energy-loss spectroscopy. Varying the electron scattering conditions, the residual electron energy and scattering angle, enabled the optically-allowed and -forbidden excitations to be differentiated. The measured energy-loss spectra enabled the vertical excitation energies of the observed states...
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Simplified AutoDock force field for hydrated binding sites
Publikacjahas been extracted from the Protein Data Bank and used to test and recalibrate AutoDock force field. Since for some binding sites water molecules are crucial for bridging the receptor-ligand interactions, they have to be included in the analysis. To simplify the process of incorporating water molecules into the binding sites and make it less ambiguous, new simple water model was created. After recalibration of the force field on...
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Ultrasound assisted synthesis of 3-alkynyl substituted 2-chloroquinoxaline derivatives: Their in silico assessment as potential ligands for N-protein of SARS-CoV-2
PublikacjaIn view of recent global pandemic the 3-alkynyl substituted 2-chloroquinoxaline framework has been explored as a potential template for the design of molecules targeting COVID-19. Initial in silico studies of representative compounds to assess their binding affinities via docking into the N-terminal RNA-binding domain (NTD) of N-protein of SARS-CoV-2 prompted further study of these molecules. Thus building of a small library of...
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Anharmonic Infrared Spectroscopy through the Fourier Transform of Time Correlation Function Formalism in ONETEP
PublikacjaDensity functional theory molecular dynamics (DFT-MD) provides an efficient framework for accurately computing several types of spectra. The major benefit of DFTMD approaches lies in the ability to naturally take into account the effects of temperature and anharmonicity, without having to introduce any ad hoc or a posteriori corrections. Consequently, computational spectroscopy based on DFT-MD approaches plays a pivotal role in...
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Hydrogen migration in formation of NH(A3Π) radicals in photodissociations of isoxazole and pyridine molecules
PublikacjaIn the present study, the H atom migration was observed in the photodissociation processes of the isoxazole and pyridine molecules in the gas-phase, applying the photon-induced fluorescence spectroscopy (PIFS).
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Positron binding to alkali-metal hydrides: The role of molecular vibrations
PublikacjaThe bound vibrational levels for J=0 have been computed for the series of alkali-metal hydride molecules from LiH to RbH, including NaH and KH. For all four molecules the corresponding potential-energy curves have been obtained for each isolated species and for its positron-bound complex (e+XH). It is found that the calculated positron affinity values strongly depend on the molecular vibrational state for which they are obtained...
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Roadmap on dynamics of molecules and clusters in the gas phase
PublikacjaThis roadmap article highlights recent advances, challenges and future prospects in studies of the dynamics of molecules and clusters in the gas phase. It comprises nineteen contributions by scientists with leading expertise in complementary experimental and theoretical techniques to probe the dynamics on timescales spanning twenty orders of magnitudes, from attoseconds to minutes and beyond, and for systems ranging in complexity...
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Tuning Ferulic Acid Solubility in Choline-Chloride- and Betaine-Based Deep Eutectic Solvents: Experimental Determination and Machine Learning Modeling
PublikacjaDeep eutectic solvents (DES) represent a promising class of green solvents, offering particular utility in the extraction and development of new formulations of natural compounds such as ferulic acid (FA). The experimental phase of the study undertook a systematic investigation of the solubility of FA in DES, comprising choline chloride or betaine as hydrogen bond acceptors and six different polyols as hydrogen bond donors....
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APPLICATION OF BINARY-ENCOUNTER-BETHE METHOD TO ELECTRON-IMPACT IONIZATION CROSS SECTION CALCULATIONS FOR BIOLOGICALLY RELEVANT MOLECULES
PublikacjaElectron-impact cross sections for platinum chemotherapeutic compounds, purine and pyrimidine molecules calculated using binary-encounterBethe model are presented as examples of possible applications of that method.
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Electronically Excited States in Solution via a Smooth Dielectric Model Combined with Equation-of-Motion Coupled Cluster Theory
PublikacjaWe present a method for computing excitation energies for molecules in solvent, based on the combination of a minimal parameter implicit solvent model and the equation-of-motion coupled-cluster singles and doubles method (EOM-CCSD). In this method, the solvent medium is represented by a smoothly varying dielectric function, constructed directly from the quantum mechanical electronic density using only two tunable parameters. The...
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Influence of rhamnolipids and ionic cross-linking conditions on the mechanical properties of alginate hydrogels as a model bacterial biofilm
PublikacjaThe literature indicates the existence of a relationship between rhamnolipids and bacterial biofilm, as well as the ability of selected bacteria to produce rhamnolipids and alginate. However, the influence of biosurfactant molecules on the mechanical properties of biofilms are still not fully understood. The aim of this research is to determine the effect of rhamnolipids concentration, CaCl2 concentration, and ionic cross-linking...
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In silico assessment and sonochemical synthesis of 2-alkynyl 3-chloropyrazines as prospective ligands for SARS-CoV-2
PublikacjaThe recent global pandemic caused by COVID-19 has triggered an intense effort worldwide towards the development of an effective cure for this disease. In our effort we have explored the 2-alkynyl substituted 3-chloropyrazine framework as a potential template for the design of molecules for this purpose. Our strategy was supported by the in silico studies of representative compounds to assess their binding affinities via docking...
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The hydration of selected biologically relevant molecules – the temperature effect on apparent molar volume and compression
PublikacjaThe densities and sound velocities at T = (288.15, 293.15, 298.15, 303.15 and 308.15) K were measured for aqueous solutions of glycine, trimethylamine-N-oxide, taurine and N-methylacetamide. From these data, the apparent molar volumes, V the apparent molar isentropic compressions, KS,, and the Passynski hydration numbers of solutes were determined. The concentration dependencies of the calculated quantities, their limiting values...
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Optoelectronic system for investigation of cvd diamond/DLC layers growth
PublikacjaDevelopment of the optoelectronic system for non-invasive monitoring of diamond/DLC (Diamond-Like-Carbon) thin films growth during μPA ECR CVD (Microwave Plasma Assisted Electron Cyclotron Resonance Chemical Vapour Deposition) process is described. The system uses multi-point Optical Emission Spectroscopy (OES) and long-working-distance Raman spectroscopy. Dissociation of H2 molecules, excitation and ionization of hydrogen atoms...
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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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Water-mediated influence of a crowded environment on internal vibrations of a protein molecule
PublikacjaThe 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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Hydrogen migration in formation of NH(A3Π) radicals via superexcited states in photodissociation of isoxazole molecules
PublikacjaFormation of the excited NH(A 3Π) free radicals in the photodissociation of isoxazole (C3H3NO) molecules has been studied over the 14-22 eV energy range using photon-induced fluorescence spectroscopy. The NH(A 3Π) is produced through excitation of the isoxazole molecules into higher-lying superexcited states. Observation of the NH radical, which is not a structural unit of the isoxazole molecule, corroborates the hydrogen atom...
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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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Hydration of Oxometallate Ions in Aqueous Solution
PublikacjaThe strength of hydrogen bonding to and structure of hydrated oxometallate ions in aqueous solution have been studied by double difference infrared (DDIR) spectroscopy and large-angle X-ray scattering (LAXS), respectively. Anions are hydrated by accepting hydrogen bonds from the hydrating water molecules. The oxygen atom of the permanganate and perrhenate ions form weaker and longer hydrogen bonds to water than the hydrogen bonds...
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Studies of the Interaction Dynamics in Albumin-Chondroitin Sulfate Systems by Recurrence Method
PublikacjaThe physicochemical basis of lubrication of articular cartilage is still not fully understood. However, the synergy between components of the synovial fluid can be a crucial factor that could explain this phenomenon. This work presents a nonlinear data analysis technique named the recurrence method, applied to the system involving two components of synovial fluid: albumin and chondroitin sulfate (CS) immersed in a water environment....
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Methylation effect in e−— scattering on methyl-substituted ethylenes
PublikacjaMethylation effect has been observed and studied in electron-scattering from selected hydrocarbon molecules. In measured total cross section (TCS) functions we have noticed energy shifts and changes in the intensity of observed structures.
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Mechanism of antifreeze protein functioning and the “anchored clathrate water” concept
PublikacjaIn liquid water, there is a natural tendency to form aggregates that consist of water molecules linked by hydrogen bonds. Such spontaneously formed aggregates are surrounded by a "sea" of disordered water molecules, with both forms remaining in equilibrium. The process of creating water aggregates also takes place in the solvation water of proteins, but in this case the interactions of water molecules with the protein surface shift...
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Diaryl Sulfide Derivatives as Potential Iron Corrosion Inhibitors: A Computational Study
PublikacjaThe present work aimed to assess six diaryl sulfide derivatives as potential corrosion inhibitors. These derivatives were compared with dapsone (4,4′-diaminodiphenyl sulfone), a common leprosy antibiotic that has been shown to resist the corrosion of mild steel in acidic media with a corrosion efficiency exceeding 90%. Since all the studied compounds possess a common molecular backbone (diphenyl sulfide), dapsone was taken as the...
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Recent total cross section measurements in electron scattering from molecules
PublikacjaThe grand-total cross sections (TCSs) for electron scattering from a range of molecules, measured over the period 2009-2019 in various laboratories, with the use of different electron transmission systems, are reviewed. Where necessary, the presented TCS data are also compared to earlier results. Collection of investigated molecular targets (biomolecules, biofuels, molecules of technological application,hydrocarbons) reflects their...
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Role of methylation in electron scattering on X(CH3)4 (X= C, Si, Ge) molecules (2)
PublikacjaTo investigate how replacement of H atom with methyl group (CH3) – in tetrahedral compounds of carbon, silicon and germanium – affects electron scattering process, total cross sections (TCS) for electron scattering from C(CH3)4, Si(CH3)4 and Ge(CH3)4 molecules have been compared with data for CH4, SiH4 and GeH4 molecules. All examined data have been obtained with the same experimental setup. The shape of all discussed TCS energy...
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Amides as models to study the hydration of proteins and peptides — spectroscopic and theoretical approach on hydration in various temperatures
PublikacjaInteractions with water are one of the key factors which determine protein stability and activity in aqueous solutions. However, the protein hydration is still insufficiently understood. N-methylacetamide (NMA) is regarded as a minimal part of the peptide backbone and the relative simplicity of its structure makes it a good model for studies on protein–water interactions. In this paper, the influence of NMA and N,N-dimethylacetamide...
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Electron collisions with X(CH3)4 molecules (X = C, Si, Ge)
PublikacjaAbsolute grand-total cross sections (TCSs) for electron scattering from tetramethylmethane [C(CH3)4], tetramethylsilane [Si(CH3)4], and tetramethylgermane [Ge(CH3)4] molecules have been measured at electron-impact energies extending from around 0.5 to 300 eV in the linear electron-transmission experiment. The measured TCS energy dependences show very pronounced broad enhancement, peaking near 5.5 eV for Si(CH3)4 and Ge(CH3)4 molecules...
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Crystallographic study of self-organization in the solid state including quasi-aromatic pseudo-ring stacking interactions in 1-benzoyl-3-(3,4-dimethoxyphenyl)thiourea and 1-benzoyl-3-(2-hydroxypropyl)thiourea
Publikacja1-Benzoylthioureas contain both carbonyl and thiocarbonyl functional groups and are of interest for their biological activity, metal coordination ability and involvement in hydrogen-bond formation. Two novel 1-benzoylthiourea derivatives, namely 1-benzoyl-3-(3,4-dimethoxyphenyl)thiourea, C₁₆H₁₆N₂O₃S, (I), and 1-benzoyl-3-(2-hydroxypropyl)thiourea, C₁₁H₁₄N₂O₂S, (II), have been synthesized and characterized. Compound (I) crystallizes...
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Encapsulation of an anticancer drug Isatin inside a host nano-vehicle SWCNT: a molecular dynamics simulation
PublikacjaThe use of carbon nanotubes as anticancer drug delivery cargo systems is a promising modality as they are able to perforate cellular membranes and transport the carried therapeutic molecules into the cellular components. Our work describes the encapsulation process of a common anticancer drug, Isatin (1H-indole-2,3-dione) as a guest molecule, in a capped single-walled carbon nanotube (SWCNT) host with chirality of (10,10). The...
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Electron-impact ionization cross section calculations for 5-chloropyridine and 5-bromopyridine molecules
PublikacjaThe total cross sections for the single electron-impact ionization of 5-chloropyridine (5-C5H4ClN) and 5-bromopyridine (5-C5H4BrN) molecules have been calculated using binary-encounter-Bethe method for electron energies ranging from the ionization threshold up to 5 keV.
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SYNTHESIS AND PROPERTIES OF OLIGOMERS WITH HYDROXY END-GROUPS
PublikacjaMethods of oligomers (polymers) with hydroxy end-groups obtaining are examined. The synthesis of hydroxy-containing oligomers based on epoxy resins is of special attention. The molecules of mentioned oligomers apart from free primary and secondary hydroxy groups contain epoxy, peroxy, carboxy or acrylic groups.
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Hunting for the Magnesium(I) Species: Formation, Structure, andReactivity of some Donor-Free Grignard Compounds
PublikacjaMagnesium bromide radicals have to be prepared as high-temperature molecules and trapped as a metastable solution because a seemingly simple reduction of donor-free Grignard compounds failed. However, the essential role of magnesium(I) species during the formation of Grignard compounds could be demonstrated experimentally.
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ELECTRON ATTACHMENT TO HETEROGENEOUS MOLECULAR CLUSTERS
PublikacjaHeterogeneous clusters are unique model species enabling studies of bulk and surface processes by vacuum restricted methods. This is of particular importance for the reactions of low-energy electrons which have extremely short penetration depth in bulk environments. This contribution overviews our recent experiments with low-energy electrons and clusters prepared by different techniques. First, the deposition of molecules on argon...
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Topochemical, Single‐Crystal‐to‐Single‐Crystal [2+2] Photocycloadditions Driven by Chalcogen‐Bonding Interactions
PublikacjaThe face-to-face association of (E)-1,2-di(4-pyridyl)ethylene (bpen) molecules into rectangular motifs stabilized for the first time by chalcogen bonding (ChB) interactions is shown to provide photoreactive systems leading to cyclobutane formation through single-crystal-to-single-crystal [2+2] photodimerizations. The chelating chalcogen bond donors are based on original aromatic, ortho-substituted bis(selenocyanato)benzene derivatives...
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Peptide dendrimers as antifungal agents and carriers for potential antifungal agent—N3‐(4‐methoxyfumaroyl)‐(S)‐2,3‐ diaminopropanoic acid—synthesis and antimicrobial activity
PublikacjaA series of peptide dendrimers and their conjugates with antimicrobial agent FMDP (N3‐(4‐methoxyfumaroyl)‐(S)‐2,3‐diamino‐propanoic acid) were synthesized. The obtained compounds were tested for the antibacterial and antifungal activity. All novel dendrimers displayed much better activity against the tested strains than FMDP itself. Moreover, their conjugates with FMDP also exhibited antimicrobial activity. The most promising molecules...
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Redox property switching in MOFs with open metal sites for improved catalytic hydrogenation performance
PublikacjaIn this study, a decompression-thermalization strategy was utilized for a Cu-containing metal-organic framework (MOF) to tune its redox and catalytic hydrogenation properties. Remarkably, at just 120 °C, open metal sites (OMSs) were successfully constructed by removing coordinated solvent molecules to generate the daughter MOF-120. The tailored redox property of MOF-120 is correlated with the presence of OMSs. Compared with the...
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The POCOBIO Database for Computed Scattering Cross-Sections for Positron Collisions with Biomolecular Systems
PublikacjaThe design of a database for positron interactions with biomolecular systems is outlined. The database contains only scattering cross sections, which are derived from theory. The data model is defined in a very flexible way, which facilitates the usage of weakly bound clusters of molecules and molecular systems with many tautomeric forms.
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Structural and dynamic properties of water within the solvation layer around various conformations of the glycine-based polypeptide
PublikacjaSeveral conformations of the solvated glycine-based polypeptides were investigated using molecular dynamics simulations. Some properties of water in the neighbouring space around these molecules were investigated. It was found, that water forms a well-defined layer - the first solvation shell - around the peptide molecule, and thickness of this layer is independent of the peptide structure, and it equals to approximately 0.28 nm....
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An effective method for studying intermolecular interactions in binary liquids with hydrogen bonds: FTIR spectra and ab initio calculations in the N-methylformamide - methanol system
PublikacjaMolecular complexes in methanol (MeOH)−N-methylformamide (NMF) mixtures were studied based on their FTIR-ATR spectra, to which two methods of analysis were applied: factor analysis and a quantitative version of the difference-spectra method. The mean composition of a complex between NMF and MeOH molecules over the whole range of mixture compositions was determined. Absorbing species differentiated with regard to the interaction...
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Molecular basis of the osmolyte effect on protein stability: a lesson from the mechanical unfolding of lysozyme
PublikacjaOsmolytes are a class of small organic molecules that shift the protein folding equilibrium. For this reason, they are accumulated by organisms under environmental stress, and find applications in biotechnology where proteins need to be stabilized or dissolved. However, despite years of research, debate continues over the exact mechanisms underpinning the stabilizing and denaturing effect of osmolytes. Here, we simulated the mechanical...