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Effect of osmolytes on the thermal stability of proteins: replica exchange simulations of Trp-cage in urea and betaine solutions
PublicationAlthough osmolytes are known to modulate the folding equilibrium, the molecular mechanism of their effect on thermal denaturation of proteins is still poorly understood. Here, we simulated the thermal denaturation of a small model protein (Trp-cage) in the presence of denaturing (urea) and stabilizing (betaine) osmolytes, using the all-atom replica exchange molecular dynamics simulations. We found that urea destabilizes Trp-cage...
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Superconductivity in a new intermetallic structure type based on endohedral Ta@Ir7Ge4 clusters
PublicationWe report the observation of superconductivity at a temperature near 3.5 K for the previously unreported compound TaIr2Ge2. In addition to being a superconductor, this material displays a new crystal structure type that contains endohedral clusters, as determined by single-crystal x-ray diffraction structure refinement; the structure is more complex than those of the commonly observed tetragonal 122 intermetallic phases. Despite...
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Electron scattering from tin tetrachloride (SnCl4) molecules
PublicationAbsolute grand-total cross section (TCS) for electron scattering from a tin tetrachloride, SnCl4, molecule was measured at electron-impact energies ranging from 0.6 to 300 eV, in the linear electron-transmission experiment. The measured TCS energy dependence shows two very pronounced enhancements peaking near 1.2 eV and around 9.5 eV, separated with a deep minimum centered close to 3 eV. The low energy structure is attributed to...
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Electronic transition dipole moment functions of the first singlet Sigma gerade plus state of the Lithium dimer
Open Research DataElectronic transition dipole moment functions (ETDMF) of the first singlet Sigma gerade plus (1sSg+) state have been calculated for the Lithium dimer. ETDMFs are needed in understanding processes like photodissociation, photoassociation, cooling, and trapping of molecules. The results of the five ETDMFs have been obtained by the nonrelativistic multireference...
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Electronic transition dipole moment functions of the first triplet Sigma ungerade plus state of the Lithium dimer
Open Research DataElectronic transition dipole moment functions (ETDMF) of the first triplet Sigma ungerade plus (1tSu+) state have been calculated for the Lithium dimer. ETDMFs are needed in understanding processes like photodissociation, photoassociation, cooling, and trapping of molecules. The results of the five ETDMFs have been obtained by the nonrelativistic multireference...
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Electronic transition dipole moment functions of the first singlet Delta gerade and first triplet Delta ungerade states of the Lithium dimer
Open Research DataElectronic transition dipole moment functions (ETDMF) of the first singlet Delta gerade (1sDg) and first triplet Delta ungerade (1tDu) states have been calculated for the Lithium dimer. ETDMFs are needed in understanding processes like photodissociation, photoassociation, cooling, and trapping of molecules. The results of the four ETDMFs have been obtained...
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Electronic transition dipole moment functions of the second triplet Sigma ungerade plus state of the Lithium dimer
Open Research DataElectronic transition dipole moment functions (ETDMF) of the second triplet Sigma ungerade plus (2tSu+) state have been calculated for the Lithium dimer. ETDMFs are needed in understanding processes like photodissociation, photoassociation, cooling, and trapping of molecules. The results of the five ETDMFs have been obtained by the nonrelativistic multireference...
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Electronic transition dipole moment functions of the second singlet Sigma ungerade plus and second triplet Sigma gerade plus states of the Lithium dimer
Open Research DataElectronic transition dipole moment functions (ETDMF) of the second singlet Sigma ungerade plus (2sSu+) and second triplet Sigma gerade plus (2tSg+) states have been calculated for the Lithium dimer. ETDMFs are needed in understanding processes like photodissociation, photoassociation, cooling, and trapping of molecules. The results of the four ETDMFs...
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Electronic transition dipole moment functions of the third singlet Sigma gerade plus state of the Lithium dimer
Open Research DataElectronic transition dipole moment functions (ETDMF) of the third singlet Sigma gerade plus (3sSg+) state have been calculated for the Lithium dimer. ETDMFs are needed in understanding processes like photodissociation, photoassociation, cooling, and trapping of molecules. The results of the five ETDMFs have been obtained by the nonrelativistic multireference...
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Electronic transition dipole moment functions of the first singlet Sigma ungerade plus and first triplet Sigma gerade plus states of the Lithium dimer
Open Research DataElectronic transition dipole moment functions (ETDMF) of the first singlet Sigma ungerade plus (1sSu+) and first triplet Sigma gerade plus (1tSg+) states have been calculated for the Lithium dimer. ETDMFs are needed in understanding processes like photodissociation, photoassociation, cooling, and trapping of molecules. The results of the four ETDMFs...
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Electronic transition dipole moment functions of the third triplet Sigma ungerade plus state of the Lithium dimer
Open Research DataElectronic transition dipole moment functions (ETDMF) of the third triplet Sigma ungerade plus (3tSu+) state have been calculated for the Lithium dimer. ETDMFs are needed in understanding processes like photodissociation, photoassociation, cooling, and trapping of molecules. The results of the five ETDMFs have been obtained by the nonrelativistic multireference...
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Electronic transition dipole moment functions of the fourth triplet Sigma ungerade plus state of the Lithium dimer
Open Research DataElectronic transition dipole moment functions (ETDMF) of the fourth triplet Sigma ungerade plus (4tSu+) state have been calculated for the Lithium dimer. ETDMFs are needed in understanding processes like photodissociation, photoassociation, cooling, and trapping of molecules. The results of the five ETDMFs have been obtained by the nonrelativistic multireference...
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Electronic transition dipole moment functions of the fourth singlet Sigma gerade plus state of the Lithium dimer
Open Research DataElectronic transition dipole moment functions (ETDMF) of the fourth singlet Sigma gerade plus (4sSg+) state have been calculated for the Lithium dimer. ETDMFs are needed in understanding processes like photodissociation, photoassociation, cooling, and trapping of molecules. The results of the five ETDMFs have been obtained by the nonrelativistic multireference...
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Electronic transition dipole moment functions of the first singlet Pi gerade and first triplet Pi gerade states of the Lithium dimer
Open Research DataElectronic transition dipole moment functions (ETDMF) of the first singlet Pi gerade (1sPg) and first triplet Pi gerade (1tPg) states have been calculated for the Lithium dimer. ETDMFs are needed in understanding processes like photodissociation, photoassociation, cooling, and trapping of molecules. The results of the four ETDMFs have been obtained...
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Electronic transition dipole moment functions of the second singlet Sigma gerade plus state of the Lithium dimer
Open Research DataElectronic transition dipole moment functions (ETDMF) of the second singlet Sigma gerade plus (2sSg+) state have been calculated for the Lithium dimer. ETDMFs are needed in understanding processes like photodissociation, photoassociation, cooling, and trapping of molecules. The results of the five ETDMFs have been obtained by the nonrelativistic multireference...
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Electronic transition dipole moment functions of the fifth singlet Sigma gerade plus state of the Lithium dimer
Open Research DataElectronic transition dipole moment functions (ETDMF) of the fifth singlet Sigma gerade plus (5sSg+) state have been calculated for the Lithium dimer. ETDMFs are needed in understanding processes like photodissociation, photoassociation, cooling, and trapping of molecules. The results of the five ETDMFs have been obtained by the nonrelativistic multireference...
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Electronic transition dipole moment functions of the third singlet Sigma ungerade plus and third triplet Sigma gerade plus states of the Lithium dimer
Open Research DataElectronic transition dipole moment functions (ETDMF) of the third singlet Sigma ungerade plus (3sSu+) and third triplet Sigma gerade plus (3tSg+) states have been calculated for the Lithium dimer. ETDMFs are needed in understanding processes like photodissociation, photoassociation, cooling, and trapping of molecules. The results of the four ETDMFs...
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Electronic transition dipole moment functions of the second singlet Pi gerade and second triplet Pi gerade states of the Lithium dimer
Open Research DataElectronic transition dipole moment functions (ETDMF) of the second singlet Pi gerade (2sPg) and second triplet Pi gerade (2tPg) states have been calculated for the Lithium dimer. ETDMFs are needed in understanding processes like photodissociation, photoassociation, cooling, and trapping of molecules. The results of the four ETDMFs have been obtained...
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Electronic transition dipole moment functions of the fifth triplet Sigma ungerade plus state of the Lithium dimer
Open Research DataElectronic transition dipole moment functions (ETDMF) of the fifth triplet Sigma ungerade plus (5tSu+) state have been calculated for the Lithium dimer. ETDMFs are needed in understanding processes like photodissociation, photoassociation, cooling, and trapping of molecules. The results of the five ETDMFs have been obtained by the nonrelativistic multireference...
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Spin-Orbit Coupling Matrix Elements in the KRb Molecule
Open Research DataThe allowed 190 spin-orbit coupling (SOC) matrix elements have been calculated for the singlet (s) and triplet (t) Sigma+ (S+), Pi (P), and Delta (D) electronic states of the KRb molecule. These SOCs are needed for investigations of areas connected with classical spectroscopy, deperturbation analysis of the observed spectra, atom-molecule and molecule-molecule...
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Determinants of Directionality and Efficiency of the ATP Synthase Fo Motor at Atomic Resolution
PublicationFo subcomplex of ATP synthase is a membrane-embedded rotary motor that converts proton motive force into mechanical energy. Despite a rapid increase in the number of high-resolution structures, the mechanism of tight coupling between proton transport and motion of the rotary c-ring remains elusive. Here, using extensive all-atom free energy simulations, we show how the motor’s directionality naturally arises from the interplay...
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Nano-structured Pt embedded in acidic salts of heteropolymolybdate matrices: MS EXAFS study
PublicationA structural study of Pt nano-catalysts is presented in the paper. The innovation in the case of the considered catalytic materials resides in the use a meso-microporous inorganic matrix of heteropolyacid salt of composition X2.5H0.5YMo12O40 where X = Rb, Cs and Y = P, Si as a catalyst support. Metallic nanoparticles were created by platinum ions reduction in a hot H2/Argon stream and were mainly located into matrix pores. As the...
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Magnetic-dipole-to-electric-quadrupole cross-susceptibilities for relativistic hydrogenlike atoms in some low-lying discrete energy eigenstates
PublicationIn this paper we present tabulated data for magnetic-dipole-to-electric-quadrupole cross-susceptibilities (χ_{M1→E2}) for Dirac one-electron atoms with a pointlike, spinless and motionless nucleus of charge Ze. Numerical values of this susceptibility for the hydrogen atom (Z = 1) and for hydrogenic ions with 2 \leqslant Z \leqslant 137 are computed from the general analytical formula, recently derived by us (Stefanska, 2016), valid...
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A coarse‐grained approach to NMR ‐data‐assisted modeling of protein structures
PublicationThe ESCASA algorithm for analytical estimation of proton positions from coarse-grained geometry developed in our recent work has been implemented in modeling protein structures with the highly coarse-grained UNRES model of polypeptide chains (two sites per residue) and nuclear magnetic resonance (NMR) data. A penalty function with the shape of intersecting gorges was applied to treat ambiguous distance restraints, which automatically...
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Storing Matter’technique in SIMS depth profile analysis
PublicationSecondary ion mass spectrometry (SIMS) is a very useful technique for the analysis of layered systems. It is based on the primary ion beam sputtering of solids and mass analysis of the emitted secondary ions. A main limitation of this technique results from the direct quantitative analysis, since the ionization efficiency of a given atom is highly influenced by the neighbouring atoms at the surface. This phenomenon is known as...
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Proton transfer and hydrogen bonds in supramolecular, self-assembled structures of imidazolium silanethiolates. X-ray, spectroscopic and theoretical studies
PublicationThe reaction of 1-methylimidazole, 2-ethyl-4-methylimidazole and 2-ethylimidazole with tris(2,6- diisopropylphenoxy)silanethiol (TDST) leads to the formation of three new salts, which have been characterized by elemental analyses, thermogravimetric analyses, FTIR spectroscopy, and their structures were determined by single-crystal X-ray diffraction. Structural analyses indicate that in all three compounds a proton transfer has...
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Role of cholesterol in substrate recognition by -secretase
Publication-Secretase is an enzyme known to cleave multiple substrates within their transmembrane domains, with the amyloid precursor protein of Alzheimer’s Disease among the most prominent examples. The activity of -secretase strictly depends on the membrane cholesterol content, yet the mechanistic role of cholesterol in the substrate binding and cleavage remains unclear. In this work, we used all-atom molecular dynamics simulations to examine...
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Studies on the charge density distribution in p-substituted phenylnitrenium cation
PublicationAniline and its derivatives are known to be mutagenic. This activity is caused by the formation of phenylnitrenium cations during aniline oxidation. Reactivity of the positively charged chemical species can be measured by means of s+ substituent constant. In this paper charge density distribution in p-substituted nitrenium cations and reactivity indices such as, hardness η, electronegativity χ , and electrophilicily ω were analyzed....
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10-Methyl- and 9,10-dimethyl acridinium methyl sulfate
PublicationThe title compounds, C(14)H(12)N(+).CH(3)O(4)S(-), (I), and C(15)H(14)N(+).CH(3)O(4)S(-), (II), respectively, crystallize with the planar 10-methylacridinium or 9,10-dimethylacridinium cations arranged in layers, parallel to the twofold axis in (I) and perpendicular to the 2(1) axis in (II). Adjacent cations in both compounds are packed in a 'head-to-tail' manner. The methyl sulfate anion only exhibits planar symmetry in (II)....
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Electronic structure of TbBa2Cu3O7
PublicationW pracy wykonano obliczenia kwantowomechaniczne struktury elektronowej hipotetycznego materiału TbBa2Cu3O7 (Dy123) metodą FP-LAPW (full potential - linearized augmented plane wave) w ramach formalizmu DFT (density functional theory) stosując przybliżenie GGA (generalized gradient approximation). Ze względu na silne oddziaływania korelacyjne elektronów 4f w atomie Tb zastosowano dodatkowo poprawkę kulombowską U w ramach modelu...
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Synthesis and properties of AxV2Al20 (A = Th, U, Np, Pu) ternary actinide aluminides
PublicationPolycrystalline samples of AxV2Al20 (A = Ce, Th, U, Np, Pu; 0.7 ≤ x ≤ 1.0) actinide intermetallics were synthesized using the arc-melting method. Crystal structure studies were performed by means of powder x-ray diffraction and the Rietveld refinement method. All studied compounds crystallize in the CeCr2Al20-type structure (space group Fd-3m, no. 227) with the actinoid and Ce atom located in the oversized icosahedral cage formed...
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Copolymerization of Styrene and Pentadecylphenylmethacrylate (PDPMA): Synthesis, Characterization, Thermomechanical and Adhesion Properties
PublicationThe copolymerization of styrene (St) with a bioderived monomer, pentadecylphenylmethacrylate (PDPMA), via atom transfer radical polymerization (ATRP) was studied in this work.The copolymerization reactivity ratio was calculated using the composition data obtained from1HNMR spectroscopy, applying Kelen-Tudos and Finemann-Ross methods. The reactivity ratio of styrene (r1=0.93) and PDPMA (r2=0.05) suggested random copolymerization...
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Why Are Left-Handed G-Quadruplexes Scarce?
PublicationG-quadruplexes (G4s) are nucleic acid structures crucial for the regulation of gene expression and genome maintenance. While they hold promise as nanodevice components, achieving desired G4 folds requires understanding the interplay between stability and structural properties, like helicity. Although right-handed G4 structures dominate the experimental data, the molecular basis for this preference over left-handed helicity is unclear....
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Optimization of parallel implementation of UNRES package for coarse‐grained simulations to treat large proteins
PublicationWe report major algorithmic improvements of the UNRES package for physics-based coarse-grained simulations of proteins. These include (i) introduction of interaction lists to optimize computations, (ii) transforming the inertia matrix to a pentadiagonal form to reduce computing and memory requirements, (iii) removing explicit angles and dihedral angles from energy expressions and recoding the most time-consuming energy/force terms...
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Are the short cationic lipopeptides bacterial membrane disruptors? Structure-Activity Relationship and molecular dynamic evaluation
PublicationShort cationic lipopeptides are amphiphilic molecules that exhibit antimicrobial activity mainly against Grampositives. These compounds bind to bacterial membranes and disrupt their integrity. Here we examine the structure-activity relation (SAR) of lysine-based lipopeptides, with a prospect to rationally design more active compounds. The presented study aims to explain how antimicrobial activity of lipopeptides is affected by...
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Phosphinophosphoranes: Mixed-Valent Phosphorus Compounds with Ambiphilic Properties
PublicationHerein, we present a simple synthesis of mixed-valent phosphinophosphoranes bearing three- and five-coordinate phosphorus centers. Compounds with phosphorus–phosphorus bonds were synthesized via a reaction of lithium phosphides RR′PLi with cat2PCl (cat = catecholate), whereas derivatives with methylene-linked phosphorus centers were obtained via a reaction of phosphanylmethanides RR′CH2Li with cat2PCl. The presence of accessible...
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Deep Eutectic Solvents or Eutectic Mixtures? Characterization of Tetrabutylammonium Bromide and Nonanoic Acid Mixtures
PublicationDeep eutectic solvents have quickly attracted the attention of researchers because they better meet the requirements of green chemistry and thus have the potential to replace conventional hazardous organic solvents in some areas. To better understand the nature of these mixtures, as well as expand the possibilities of their use in different industries, a detailed examination of their physical properties, such as density, viscosity,...
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DFT study of low-energy electron interaction with pyridine, pyrazine and their halo derivatives
PublicationIn this work, the density functional theory with B3LYP hybrid functional was employed to calculate quantities useful for estimating the behavior of pyridine, pyrazine and their derivatives monosubstituted with Cl or Br atom, when exposed to low-energy electron impact. Vertical electron affinities obtained in several Pople basis sets and in aug-cc-pVTZ basis set are reported. Although some of the investigated molecules do not form...
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ESCASA : Analytical estimation of atomic coordinates from coarse‐grained geometry for nuclear‐magnetic‐resonance ‐assisted protein structure modeling. I. Backbone and Hβ protons
PublicationA method for the estimation of coordinates of atoms in proteins from coarse-grained geometry by simple analytical formulas (ESCASA), for use in nuclear-magnetic-resonance (NMR) data-assisted coarse-grained simulations of proteins is proposed. In this paper, the formulas for the backbone Hα and amide (HN) protons, and the side-chain Hβ protons, given the Cα-trace, have been derived and parameterized, by using the interproton distances...
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Unexpected Z/E isomerism of N-methyl-O-phosphothioyl benzohydroxamic acids, their oxyphilic reactivity and inertness to amines
PublicationThiophosphinoylation of N-methyl p-substituted benzohydroxamic acids using disulfanes (method A) or diphenylphosphinothioyl chloride (method B) provides only one conformer of the respective O-phosphothioyl derivative (Xray and NMR analysis). Undergoing the P-transamidoxylation reaction is an evidence of the reversibility of thiophosphinoylation. Only those products containing strong EWG substituents in the aroyl residue or bulky...
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The influence of the type of halogen substituent and its position on the molecular conformation, intermolecular interactions and crystal packing for a series of 1-benzoyl-3-(halogenophenyl)thioureas
PublicationBy the reaction of benzoyl chloride, potassium isothiocyanate and the appropriate halogenoaniline, i.e. 2/3/4-(bromo/iodo)aniline, we have obtained five new 1-benzoyl-3-(halogenophenyl)thioureas, namely, 1-benzoyl-3-(2-bromophenyl)- thiourea and 1-benzoyl-3-(3-bromophenyl)thiourea, C14H11BrN2OS, and 1-benzoyl-3-(2-iodophenyl)thiourea, 1-benzoyl-3-(3-iodophenyl)thiourea and 1-benzoyl-3-(4-iodophenyl)thiourea, C14H11IN2OS. Structural...
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Speaker Recognition Using Convolutional Neural Network with Minimal Training Data for Smart Home Solutions
PublicationWith the technology advancements in smart home sector, voice control and automation are key components that can make a real difference in people's lives. The voice recognition technology market continues to involve rapidly as almost all smart home devices are providing speaker recognition capability today. However, most of them provide cloud-based solutions or use very deep Neural Networks for speaker recognition task, which are...
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Wykorzystanie chromatografii jonowej w analityce jonów cyjankowych
PublicationNazwa cyjanki obejmuje związki, które zawierają w swojej cząsteczce grupę –C≡N, w której atom węgla i azotu są połączone wiązaniem potrójnym. Są to trujące i niebezpieczne związki, które znalazły swoje zastosowanie w różnych dziedzinach. Cyjanki wykorzystywane są w różnych strefach działalności przemysłowej, włączając w to przemysł wydobywczy i chemiczny. Naturalnym źródłem cyjanków są rośliny m.in. maniok, migdały, fasola, siemię...
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Molecular dynamics simulations reveal the balance of forces governing the formation of a guanine tetrad—a common structural unit of G-quadruplex DNA
PublicationG-quadruplexes (G4) are nucleic acid conformations of guanine-rich sequences, in which guanines are arranged in the square-planar G-tetrads, stacked on one another. G4 motifs form in vivo and are implicated in regulation of such processes as gene expression and chromosome maintenance. The structure and stability of various G4 topologies were determined experimentally; however, the driving forces for their formation are not fully...
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Cooperativity of Halogen- and Chalcogen-Bonding Interactions in the Self-Assembly of 4‑Iodoethynyl- and 4,7-Bis(iodoethynyl)benzo-2,1,3-chalcogenadiazoles: Crystal Structures, Hirshfeld Surface Analyses, and Crystal Lattice Energy Calculations
PublicationSeveral new 4-iodoethynyl- and 4,7-bis- (iodoethynyl)benzo-2,1,3-chalcogenadiazoles were prepared, and a comprehensive analysis of the most prominent secondary bonding interactions responsible for the crystal self-assembly was performed using X-ray diffraction. The presence of both the iodoethynyl and chalcogenadiazole moieties allows an evaluation of the preference of these molecules to aggregate through either chalcogen- or halogen-bonding...
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Distinguishing of cocrystals from simple eutectic mixtures: phenolic acids as potential pharmaceutical coformers
PublicationThe multiparameter model comprising 1D and 2D QSPR/QSAR descriptors was proposed and validated for phenolic acid binary systems. This approach is based on the optimization of regression coefficients for maximization of the percentage of true positives in the pool of systems comprising either simple binary eutectics or cocrystals. The training set consisted of 58 eutectics and 168 cocrystals. The solid dispersions collection used...
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Synthesis, Molecular Structure, Metabolic Stability and QSAR Studies of a Novel Series of Anticancer N-Acylbenzenesulfonamides
PublicationA series of novel N-acyl-4-chloro-5-methyl-2-(R1-methylthio)benzenesulfonamides 18–47 have been synthesized by the reaction of N-[4-chloro-5-methyl-2-(R1-methylthio) benzenesulfonyl]cyanamide potassium salts with appropriate carboxylic acids. Some of them showed anticancer activity toward the human cancer cell lines MCF-7, HCT-116 and HeLa, with the growth percentages (GPs) in the range from 7% to 46%. Quantitative structure-activity relationship...
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Structure and properties of the exopolysaccharides produced by Pseudomonas mutabilis T6 and P. mutabilis ATCC 31014
PublicationThis paper presents a study on the purification, primary structure, and rheological properties of exopolysaccharides isolated from cultures of Pseudomonas mutabilis T6 and P. mutabilis ATCC 31014. Both polymers are exopolysaccharides of D-mannose. The mannan isolated from P. mutabilis T6 contains on average about 5% of residual b-D-glucose, in contrast to the mannan from P. mutabilis ATCC 31014, which contained only trace amounts...
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Atmospheric degradation mechanism of anthracene initiated by OH•: A DFT prediction
PublicationDensity functional theory (DFT) calculations at the M06-2X/def2-TZVP level have been employed to investigate the atmospheric oxidation mechanism of anthracene (ANT) initiated by HO•. Direct hydrogen atom abstraction from the ANT using HO• takes place hardly at ambient conditions while the addition of HO• to the C1, C2, and C4 sites are thermodynamically and kinetically more advantageous. The addition reactions are controlled by...
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Synchrotron radiation photoemission spectroscopy of the oxygen modified CrCl3 surface
PublicationWe investigate the experimentally challenging CrCl3 surface by photon energy dependent photoemission (PE). The core and valence electrons after cleavage of a single crystal, either in a ultrahigh vacuum (UHV) or in air, are studied by keeping the samples at 150 1C, aiming at confirming the atomic composition with respect to the expected bulk atomic structure. A common spectroscopic denominator revealed by data is the presence of...