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Electron-impact ionization of fluoromethanes – Review of experiments and binary-encounter models
PublicationExperiments and recommended data on electron-impact ionization of methane and fluoromethanes (CH3F, CH2F2, CHF3, CF4) are reviewed and compared with binary-encounter models (Gryzinski’s, ´ Deutsch and Märk’s, and Kim and Rudd’s). A good agreement between recent experiments and the two latter classical-like models is shown. Kim and Rudd’s model (calculated presently in the restricted HartreeFock 6-31**G orbital basis) predicts well...
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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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Geometry optimization of steroid sulfatase inhibitors - the influence on the free binding energy with STS
PublicationIn the paper we review the application of two techniques (molecular mechanics and quantum mechanics) to study the influence of geometry optimization of the steroid sulfatase inhibitors on the values of descriptors coded their chemical structure and their free binding energy with the STS protein. We selected 22 STS-inhibitors and compared their structures optimized with MM+, PM7 and DFT B3LYP/6–31++G* approaches considering separately...
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Introduction to MIP synthesis, characteristics and analytical application
PublicationOne of the trends in analytical chemistry is associated with designing and developing new types of sample preparation techniques, which might significantly increase the efficiency and selectivity of the analytes isolation or/and preconcentration process. One of the most widely employed solutions are selective sorption materials, defined as molecularly imprinted polymers (MIPs), as well as the sorbents with the molecular fingerprint....
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Cobalt(II) tri-tert-butoxysialanethiolates.Synthesis, properties, crystal and molecular structures of [Co{SSi(OtBu)3}2(L)] and[Co{SSi(OtBu)3}2(L)2] type complexes with monodentate nitrogen ligands.
PublicationThe title heteroleptic neutral cobalt(II) tri-tert-butoxysilanethiolate complexes with monodentate nitrogen bases (L) as additional ligands have been prepared by the reactions of [Co{μ-SSi(OtBu)3}{SSi(OtBu)3}(NH3)]2 (1) with respective bases. For pyridine both types have been prepared...
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Synthesis, molecular structure, and metabolic stability of new series of N' -(2-alkylthio-4-chloro-5-methylbenzenesulfonyl)-1-(5-phenyl-1 H -pyrazol-1-yl)amidine as potential anti-cancer agents
PublicationA series of new N'-(2-alkylthio-4-chloro-5-methylbenzenesulfonyl)-1-(5-phenyl-1H-pyrazol-1-yl)amidine derivatives have been synthesized and evaluated in vitro by MTT assays for their antiproliferative activity against cell lines of colon cancer HCT-116, cervical cancer HeLa and breast cancer MCF-7. The studied compounds display selective activity mainly against HCT-116 and HeLa cells. Thus, five compounds show selective cytotoxic...
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Potassium Tri-tert-butoxysilanethiolates: Synthesis, Properties, and Crystal and Molecular Structures of [(tBuO)3SiSK]6[THF]2·2THF, {[(tBuO)3SiS]2K2}n, and [(tBuO)3SiSK]4[H2O]4·C6H6
PublicationW reakcji tri-tert-butoksysilanotiolu z potasem otrzymano trzy nowe związki:[(tBuO)3SiSK]6[THF]2·2THF, {[(tBuO)3SiS]2K2}n, i[(tBuO)3SiSK]4[H2O]4·C6H6. Stanowią one dogodne substraty w syntezach kompleksów silanotiolanowych metali przejściowych. Charakteryzują się one również różnorodnością tworzonych układów. Rentgenowska analiza strukturalna wykazała, iż tworzą one trzy typy makrocząsteczkowych układów, w których...
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Zakażenia bakteryjne w przewlekłym zapaleniu ucha środkowego - ocena przydatności diagnostyki molekularnej opartej o technikę PCR. Bacterial infection in chronic otitis media - assessment of usefulness of molecular diagnostic based in PCR method.
PublicationIdentyfikacja zakażeń w przewlekłym zapaleniu ucha środkowego jest trudna, o czym świadczą wysokie odsetki ujemnych wyników badań bakteriologicznych. Przyczyną tego jest trudność w uzyskiwaniu wiarygodnego materiału do badań oraz stosunkowo niska czułość klasycznych metod diagnostycznych. Amplifikacja bakteryjnego DNA techniką PCR jest badaniem, które może przyczynić się do zwiększenia efektywności i czułości badań bakteriologicznych....
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Anharmonic Infrared Spectroscopy through the Fourier Transform of Time Correlation Function Formalism in ONETEP
PublicationDensity 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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A competition between two- and three-body dissociation channels in photo-double-ionization of tetrahydro-2H-pyran and 3,4-dihydro-2H-pyran molecules
PublicationVarious molecules possess structures consisting of the heterocyclic rings containing oxygen atoms. These substances often play a significant role in many different fields of chemistry, medicine, and biology. Due to a specific atomic composition and bond arrangement, many of these molecules retain unique electronic properties, which may be probed by diverse spectroscopic techniques, including those utilizing synchrotron radiation....
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Application potential of dummy molecularly imprinted polymers as solidphase extraction sorbents for determination of low-mass polybrominated diphenyl ethers in soil and sediment samples
PublicationDespite the introduction of restrictive regulations in the USA and the European Union, polybrominated diphenyl ethers (PBDEs) are still found in various types of environmental and biological samples at significant concentration levels. The presence of these persistent organic pollutants in the environment raises important issues because of their negative impact on immunological and neurological systems, and on the hormonal balances...
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Modification of gradient HPLC method for determination of small molecules' affinity to human serum albumin under column safety conditions: Robustness and chemometrics study
PublicationIn the early stages of drug discovery, beyond the biological activity screening, determining the physicochemical properties that affect the distribution of molecules in the human body is an essential step. Plasma protein binding (PPB) is one of the most important investigated endpoints. Nevertheless, the methodology for measuring %PPB is significantly less popular and standardized than other physicochemical properties, like lipophilicity....
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Properties of water in the region between a tubulin dimer and a single motor head of kinesin
PublicationA kinesin is a molecular motor that can perform movement on a microtubule track in a stepping-like manner. This motion is connected with processes of association and dissociation of kinesin and tubulin. Water is an important participant in these kinds of molecular interactions. This is why we have decided to investigate the dynamical and structural properties of water in the region between the kinesin catalytic domain and the tubulin...
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Synthetic strategies in construction of organic macromolecular carrier–drug conjugates
PublicationMany metabolic inhibitors, considered potential antimicrobial or anticancer drug candidates, exhibit verylimited ability to cross the biological membranes of target cells. The restricted cellular penetration ofthose molecules is often due to their highhydrophilicity. One of the possible solutions to this problem is aconjugation of an inhibitor with a molecular organic nanocarrier. The conjugate thus formed should beable to penetrate...
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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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Physical crosslinking of hyaluronic acid in the presence of phospholipids in an aqueous nano-environment
PublicationHyaluronic acid and phospholipids are two components in the synovial joint cavity that contribute to joint lubrication synergistically. Molecular dynamics simulations were performed and hydrogen bonds in hyaluronic acid were analyzed to identify specific sites that are responsible for its physical cross-linking. Two molecular masses of hyaluronic acid, 10 kDa and 160 kDa, were considered. We use molecular dynamics simulations and...
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The Metal-Free Regioselective Deuteration of 2-Methylquinolin-8-ol and 2,5-Dimethylquinolin-8-ol, Spectroscopic and Computational Studies
PublicationAbstract: Aim and Background: Introducing deuterium to a molecule is of interest to a wide variety of research, including investigation of reaction mechanisms or kinetics, analysis of drug metabolism, structural elucidation of molecules, and syntheses of isotopically labeled materials used for NMR spectroscopy and medicinal research. Objective: The transition-metal-free regioselective deuteration of 2-methylquinolin-8-ol...
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Quasirelativistic potential energy curves and transition dipole moments of NaRb
PublicationWe report on extensive calculations of quasi-relativistic potential energy curves and, for the first time, transition dipole moments including spin-orbit and scalar-relativistic effects of the NaRb molecule. The calculated curves of the 0+, 0-, 1, 2 and 3 molecular states correlate for large internuclear separation with the fourteen lowest atomic energies up to the Na(3s ^2S_{1/2}) + Rb(7s ^2S_{1/2}) atomic limit. Several new features...
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Toward Mechanosynthesis of Diamondoid Structures: IX Commercial Capped CNT Scanning Probe Microscopy Tip as Nowadays Available Tool for Silylene Molecule and Silicon Atom Transfer
PublicationAccording to K. E. Drexler, advanced mechanosynthesis will employ advanced nanomachines, but advanced nanomachines will themselves be product of advanced mechanosynthesis. This circular relationship must be broken in SPM technology development. In the article, the possibility of use easy available commercial CNT tips to assembly silicon-based intermediate generations of nano-devices is considered. Mechanosynthesis of a target class...
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In silico assessment and sonochemical synthesis of 2-alkynyl 3-chloropyrazines as prospective ligands for SARS-CoV-2
PublicationThe 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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Interfacial water controls the process of adsorption of hyperactive antifreeze proteins onto the ice surface
PublicationA mechanism of interactions between the ice-binding surface of a hyperactive antifreeze protein molecule and the ice surface is proposed, involving the influence of water present between the two surfaces on the behavior of the approaching molecule. It is demonstrated that the interfacial water, even before its full solidification, can act as a factor that pushes away or pulls nearer the protein molecule to ensure its proper positioning....
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Fabrication of a Molecularly Imprinted Polymer Adsorbent for Pipette Tip Micro Solid-phase Extraction of Levofloxacin from Aqueous Samples Prior to its Spectrophotometric Determination
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Application of molecularly imprinted polymer pipette tip micro-solid phase extraction of nalidixic acid and acetaminophen from pills and seawater samples and their determination by spectrophotometry
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Application of response surface methodology to optimize pipette tip micro-solid phase extraction of dyes from seawater by molecularly imprinted polymer and their determination by HPLC
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Localization and Orientation of Xanthophylls in a Lipid Bilayer
PublicationXanthophylls (polar carotenoids) play diverse biological roles, among which are modulation of the physical properties of lipid membranes and protection of biomembranes against oxidative damage. Molecular mechanisms underlying these functions are intimately related to the localization and orientation of xanthophyll molecules in lipid membranes. In the present work, we address the problem of localization and orientation of two xanthophylls...
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Theoretical estimation of acid–base properties of Lewis and Brønsted centres at the V-W-O catalyst surface: water molecule as the probe in DFT calculations
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Synthesis and structural, electrochemical and photophysical studies of triferrocenyl-substituted 1,3,5-triphenylbenzene: a cyan-light emitting molecule showing aggregation-induced enhanced emission
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Influence of pH and low-molecular weight organic compounds in solution on selected spectroscopic and analytical parameters of flowing liquid anode atmospheric pressure glow discharge (FLA-APGD) for the optical emission spectrometric (OES) determination of Ag, Cd, and Pb
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A. Computational analysis by molecular docking of thirty alkaloid compounds from medicinal plants as potent inhibitors of SARS-CoV-2 main protease(2020). Focused on analysis of the Medicinal plants that have potential therapeutic ability against COVID-19.
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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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Effect of Aromatic System Expansion on Crystal Structures of 1,2,5-Thia- and 1,2,5-Selenadiazoles and Their Quaternary Salts: Synthesis, Structure, and Spectroscopic Properties
PublicationRational manipulation of secondary bonding interactions is a crucial factor in the construction of new chalcogenadiazole-based materials. This article reports detailed experimental studies on phenanthro[9,10-c][1,2,5]chalcogenadiazolium and 2,1,3-benzochalcogenadiazolium salts and their precursors. The compounds were synthesized, characterized employing NMR and UV-Vis spectroscopy. TD-DFT calculations were also performed. The influence...
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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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The preparation and evaluation of core-shell magnetic dummy-template molecularly imprinted polymers for preliminary recognition of the low-mass polybrominated diphenyl ethers from aqueous solutions
PublicationThe design, preparation process, binding abilities, morphological characteristic and prospective field of application of dummy-template magnetic molecularly imprinted polymer (DMMIP) for preliminary recognition of the selected low-mass polybrominated diphenyl ethers (PBDE-47 and PBDE-99) from aquatic environment were investigated. The surface of iron oxide (Fe3O4) nanopowder (50-100 nm particles size) was modified with tetraethoxysilane...
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Determination of profenofos in seawater and foodstuff samples after its molecularly imprinted polymer pipette-tip micro solid phase extraction optimized by response surface methodology
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Development of Safirinium dyes for new applications: fluorescent staining of bacteria, human kidney cells, and the horny layer of the epidermis
PublicationLow-molecular synthetic fluorophores are convenient tools in bioimaging applications. Several derivatives of Safirinium dyes as well as their reactive N-hydroxysuccinimide (NHS) esters bearing diverse substituents were synthesized and evaluated experimentally in terms of their lipophilicity by means of reverse-phase and immobilized artificial membrane high-performance liquid chromatography. Subsequently, the selected compounds...
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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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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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Carbonic anhydrase inhibitors. Synthesis, and molecular structure of novel series N-substituted N'-(2-arylmethylthio-4-chloro-5- methylbenzenesulfonyl)guanidines and their inhibition of human cytosolic isozymes I and II and the transmembrane tumor-associated isozymes IX and XII
PublicationA series of novel N-substituted N'-(2-arylmethylthio-4-chloro-5-methylbenzenesulfonyl)guanidines 9 e41 have been synthesized and investigated as inhibitors of four isoforms of zinc enzyme carbonic anhydrase (CA.EC 4.2.1.1), that is the cytosolic CA I and II, and cancer-associated isozymes CA IX and XII. Against the human CA I investigated compounds showed KI in the range of 87e6506 nM, toward hCA II ranging from 7.8 to 4500 nM,...
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Discovery of small-molecule regenerative drugs using a model of complex tissue injury in mice. Transcriptomic responses of neurodevelopmental genes during pharmacologically induced regeneration
PublicationDespite significant development in regenerative medicine, there is a deficit of effective therapies for wound healing and tissue regeneration. Research performed using animal wound models allows for a better understanding of this complex process, searching for compounds with pro-regenerative properties, and assessing their efficacy and safety. Unfortunately, the lack of adequate preclinical models proves to be an issue as no animal...
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Self-assembly of secondary aryl amides in cocrystals with perfluoroaryl coformers: structural analysis and synthon preferences
PublicationCooperation of aryl⋯perfluoroaryl stacking interactions and hydrogen bonds was utilized in the construction of six novel cocrystals of aromatic cis-amides with pentafluorobenzoic acid (pfba) and pentafluorophenol (pfp). They were obtained by crystallization from solution and structurally characterized. In four instances, the components form heterotetrameric motifs, in which amide:amide homodimer interacts symmetrically on two sides...
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The importance of the shape of the protein-water interface of a kinesin motor domain for dynamics of the surface atoms of the protein
PublicationSingle kinesin motor domain immersed in water has been investigated using molecular dynamics. It has been found that local properties of water in solvation shell change along with the nature of neighboring protein surface. However, a detailed analysis leads to the conclusion that the geometrical features of hydrogen bonds and overall structure of kinesin hydration water is not very different from bulk water. The local values of...
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Hydration of Simple Model Peptides in Aqueous Osmolyte Solutions
PublicationThe biology and chemistry of proteins and peptides are inextricably linked with water as the solvent. The reason for the high stability of some proteins or uncontrolled aggregation of others may be hidden in the properties of their hydration water. In this study, we investigated the effect of stabilizing osmolyte–TMAO (trimethylamine N-oxide) and destabilizing osmolyte–urea on hydration shells of two short peptides, NAGMA (N-acetyl-glycine-methylamide)...
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Optoelectronic system for monitoring of thin diamond layers growth
PublicationDevelopment of the optoelectronic system for monitoring of diamond/DLC (Diamond-Like-Carbon) thin films growth during mu PA ECR CVD (Microwave Plasma Assisted Electron Cyclotron Resonance Chemical Vapour Deposition) process is described. The multi-point Optical Emission Spectroscopy (OES) and Raman spectroscopy were employed as non-invasive optoelectronic tools. Dissociation of H-2 molecules, excitation and ionization of hydrogen...
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The importance of the shape of the protein–water interface of a kinesin motor domain for dynamics of the surface atoms of the protein
PublicationA single kinesin motor domain immersed in water has been investigated using molecular dynamics. It has been found that local properties of water in the solvation shell change along with the nature of the neighboring protein surface. However, a detailed analysis leads to the conclusion that the geometrical features of hydrogen bonds and overall structure of kinesin hydration water are not very different from bulk water. The local...
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Topical delivery of pharmaceutical and cosmetic macromolecules using microemulsion systems
PublicationMicroemulsions are transparent, thermodynamically stable colloidal systems. Over the recent years, they have been increasingly investigated due to their potential as skin delivery vehicles for a wide range of drug molecules. The nanoscale particle size and the specificity of microemulsion components are the main features determining the skin permeation process. However, in order to effectively cross the skin barrier, the active...
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Unveiling the electron-induced ionization cross sections and fragmentation mechanisms of 3,4-dihydro-2H-pyran
PublicationThe interactions of electrons with molecular systems under various conditions are essential to interdisciplinary research fields extending over the fundamental and applied sciences. In particular, investigating electron-induced ionization and dissociation of molecules may shed light on the radiation damage to living cells, the physicochemical processes in interstellar environments, and reaction mechanisms occurring in combustion...
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Mechanism of antifreeze protein functioning and the “anchored clathrate water” concept
PublicationIn 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
PublicationThe 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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Mechanochemical Energy Transduction during the Main Rotary Step in the Synthesis Cycle of F1-ATPase
PublicationF1-ATPase is a highly efficient molecular motor that can synthesize ATP driven by a mechanical torque. Its ability to function reversibly in either direction requires tight mechanochemical coupling between the catalytic domain and the rotating central shaft, as well as temporal control of substrate binding and product release. Despite great efforts and significant progress, the molecular details of this synchronized and fine-tuned...
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Potential energy curves, transition and permanent dipole moments of KRb
PublicationWe present extensive calculations of 48 adiabatic potential energy curves of the KRb molecule. Efforts have been focused on preparing the appropriate basis sets. Compared to previous approaches, the set of new potential energy curves is extended to higher excitations, including the single-excited K(4s2S)+Rb(5d2D) and double-excited K(4p2P)+Rb(5p2P) atomic limits. Larger distances between nuclei are also taken into account. New...