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Search results for: chemical structure
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The synthesis and structure of a potential immunosuppressant: N-mycophenoyl malonic acid dimethyl ester
PublicationThe synthesis of a potential immunosuppressant, i.e. dimethyl ester of N-mycophenoyl malonic acid was optimized in the reaction of mycophenolic acid (MPA) with amino malonic dimethyl ester in the presence of propanephosphonic anhydride (T3P) as a coupling reagent. The structural properties of the obtained MPA derivative were investigated by NMR, MS and single crystal X-ray diffraction methods. Theoretical considerations of conformational...
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Copper-based 2D-coordination polymer as catalyst for allylation of aldehydes
PublicationA copper-tartrate, [Cu2(Tart)2(H2O)2]·4H2O, was synthesized at room temperature in aqueous media using copper chloride and D-tartaric acid. The compound crystallizes in the monoclinic system P21 space group and was characterized by infrared spectroscopy, thermogravimetry, X-ray powder diffraction and the results are in good agreement with the single crystal...
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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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Structural, physicochemical and anticancer study of Zn complexes with pyridyl-based thiazolyl-hydrazones
PublicationThiazolyl-hydrazones (THs) exhibit a wide spectrum of biological activity that can be enhanced by complexation with various metal ions. Zn(II) complexes with α-pyridine-1,3-TH ligands may represent an alternative to the standard platinum-based chemotherapeutics. In addition, they show photoluminescence properties and thus can be regarded as multifunctional materials. In this study, we synthesized and characterized three neutral...
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Reactive imines: Addition of 2-aminopyrimidine to the imine bond and isolation of the aminal from the equilibrium mixture aminal/imine
PublicationThe reaction between o-vanillin and 2-aminopyrimidine leads to the formation of a single crystalline product: aminal, 1, which results from the reaction of the initially formed imine with 2-aminopyrimidine. The reaction was followed by the NMR spectroscopy. VT NMR studies prove that in solution two major species are observed: aminal and imine and their ratio depends on the time or/and temperature with the imine content increasing...
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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
PublicationFor 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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Rotation Triggers Nucleotide-Independent Conformational Transition of the Empty β Subunit of F1-ATPase
PublicationF1-ATPase (F1) is the catalytic portion of ATP synthase, a rotary motor protein that couples proton gradients to ATP synthesis. Driven by a proton flux, the F1 asymmetric γ subunit undergoes a stepwise rotation inside the α3β3 headpiece and causes the β subunits’ binding sites to cycle between states of different affinity for nucleotides. These concerted transitions drive the synthesis of ATP from ADP and phosphate. Here, we study...
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A spectroscopic study of the cis/trans-isomers of penta-2,4-dienoic acid attached to gold nanoclusters
PublicationIn this theoretical work, we present a spectroscopic analysis of the cis/trans-isomers of a molecular switch, penta-2,4-dienoic acid, attached to gold clusters of different size (1, 2 and 20 gold atoms). We have simulated 4 different spectroscopic techniques: Infrared spectroscopy, normal Raman scattering, absorption spectra and resonance Raman scattering. We discuss how the position and the conformation of the molecule determine...
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Comparison of simplified sum-over-state expressions to calculate resonance Raman intensities including Franck-Condon and Herzberg-Teller effects
PublicationSum-over-state (SOS) expressions to simulate absorption spectroscopy and resonance Raman (RR) scattering including Franck-Condon (FC) and Herzberg-Teller (HT) effects are described. Starting from the general SOS method, several simplified SOS formulae are derived. In particular, within the so-called independent mode displaced harmonic oscillator model, it is shown that including the vibronic structure in the absorption and RR spectra...
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A review on electrospun membranes for potential air filtration application
PublicationAir pollution is one of the major environmental concerns in most highly populated cities, which is typically caused by particulate (PM2.5 and PM0.1) or gaseous pollutants that can be removed using electrospun membranes. These membranes are characterized by different features in terms of uniform and controllable structure, tuneable porosity, and high surface area, where their separation efficiency strongly depends on their properties....
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Volumes of N,N-dimethylacetamide solvated metal cations. Variation within the manganese(II) to zinc(II) series
PublicationDensities and apparent molar volumes for Mn(ClO4)2,Co(ClO4)2 , Ni(ClO4)2,Cu(ClO4)2 , and Zn(ClO4)2 in N, N -dimethylacetamide (DMA) solutions at T = 298.15 K are reported. Densities and apparent molar volumes of tetrabutylammonium tetraphenylborate...
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Molecular hydrogen solvated in water – A computational study
PublicationThe aqueous hydrogen molecule is studied with molecular dynamics simulations at ambient temperature and pressure conditions, using a newly developed flexible and polarizable H2 molecule model. The design and implementation of this model, compatible with an existing flexible and polarizable force field for water, is presented in detail. The structure of the hydration layer suggests that first-shell water molecules accommodate the...
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Performance of extended Lagrangian schemes for molecular dynamics simulations with classical polarizable force fields and density functional theory
PublicationIterative energy minimization with the aim of achieving self-consistency is a common feature of Born-Oppenheimer molecular dynamics (BOMD) and classical molecular dynamics with polarizable force fields. In the former, the electronic degrees of freedom are optimized, while the latter often involves an iterative determination of induced point dipoles. The computational effort of the self-consistency procedure can be reduced by re-using...
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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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Advances in olfaction-inspired biomaterials applied to bioelectronic noses
PublicationAmong all the senses, olfactory system of mammals is the least characterised as far as the mechanisms of odour identification are concerned. The results of recent investigations allow better understanding of the operation mechanism of the sense of smell. Progress in this field is crucial for the development of sensor technology based on olfaction-inspired biomaterials, which simulate the olfactory system of the biological counterparts....
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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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Fluctuation-enhanced and conductometric gas sensing with nanocrystalline NiO thin films: A comparison
PublicationNanocrystalline thin films of NiO were prepared by advanced reactive gas deposition, and their responses to formaldehyde, ethanol and methane gases were studied via fluctuation-enhanced and conductometric methods Thin films with thicknesses in the 200–1700-nm range were investigated in as-deposited form and after annealing at 400 and 500 °C. Morphological and structural analyses showed porous deposits with NiO nanocrystals having...
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Green engineered biomaterials for bone repair and regeneration: Printing technologies and fracture analysis
PublicationDespite the exceptional self-regeneration properties of bone, severe injuries often require additional surgical intervention such as using artificial bone constructs. These structures need to meet a number of criteria regarding their structure, performance, alongside the rate and the mechanism of erosion and fracture when implanted, for stimulating the regeneration of defected bone and, more critically providing support in the...
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sp2-rich dendrite-like carbon nanowalls as effective electrode for environmental monitoring of explosive nitroaromatic
PublicationNitroaromatic compounds are commonly used explosive materials that pose a risk to human health and ecosystems due to their acute toxicity and carcinogenicity. Nitroaromatics have numerous pathways into the environment via discarded munitions (e.g. into the Baltic Sea after World War II), after use in mining operations, and in industrial run-off from factories producing these compounds (which are produced across the world to date)....
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Long-range, water-mediated interaction between a moderately active antifreeze protein molecule and the surface of ice
PublicationUsing molecular dynamics simulations, we show that a molecule of moderately active antifreeze protein (type III AFP, QAE HPLC-12 isoform) is able to interact with ice in an indirect manner. This interaction occurs between the ice binding site (IBS) of the AFP III molecule and the surface of ice, and it is mediated by liquid water which separates these surfaces. As a result, the AFP III molecule positions itself at a specific orientation...
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Electron collisions with methyl-substituted ethylenes: Cross section measurements and calculations for 2-methyl–2-butene and 2,3-dimethyl–2-butene
PublicationWe report electron-scattering cross sections determined for 2-methyl–2-butene [(H3C)HC==C(CH3)2] and 2,3-dimethyl–2-butene [(H3C)2C=C(CH3)2] molecules. Absolute grand-total cross sections (TCSs) were measured for incident electron energies in the 0.5–300 eV range, using a linear electron-transmission technique. The experimental TCS energy dependences for the both targets appear to be very similar with respect to the shape. In each...
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3D mesoporous α-Co(OH)2 nanosheets electrodeposited on nickel foam: A new generation of macroscopic cobalt-based hybrid for peroxymonosulfate activation
PublicationCobalt-based catalysts with high stability and facile recovery for heterogeneous peroxymonosulfate (PMS) activation are still rather sparse and therefore highly desirable. Herein, 3D mesoporous α-Co(OH)2 nanosheets was created on robust nickel foam (NF) via facile electrodeposition approach at 6 mA/cm2 for only 400 s. Almost complete removal of phenol can be achieved within 7 min with a degradation rate of 0.39 min−1, 2 times higher...
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Reverse vaccinology-based prediction of a multi-epitope SARS-CoV-2 vaccine and its tailoring to new coronavirus variants
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Molecular simulations study of ligand-release mechanism in an odorant-binding protein from the southern house mosquito
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Relationship between electronic structure and geometry of silanethiols and their derivatives. Elucidation of copper group silanethiolates
PublicationWyznaczono strukturę elektronową wybranych silanotioli X3SiSH (dla X=H, C2H5, OCH3, F, Cl i Br) oraz powstalych z nich anionów. Geometrię i funkcje falowe wyznaczono przy użyciu teorii funcjonałów gęstości elektronowej DFT. Przeanalizowano wpływ efektów anomerycznych oraz wielkości calki nakładania sigma(Si-S) na obserwowane skrócenie wiązania Si-S przy deprotonowaniu silanotioli. Podano nowe wyjaśnienie wyjątkowo niskiej kwasowości...
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Conformational Studies of Two Bradykinin Antagonists by Using Two-dimensional NMR Techniques and Molecular Dynamics Simulations
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Excited electronic states of the anion of 7,7,8,8-tetracyanoquinodimethane (TCNQ)
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Novel 2019 coronavirus structure, mechanism of action, antiviral drug promises and rule out against its treatment
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Molecular Modelling of the Neurophysin II/Vasopressin Complex
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Role of the sulfur to α-carbon thioether bridges in thurincin H
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Molecular dynamics study of the influence of calcium ions on the conformation of gelsolin S2 domain
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Common functionally important motions of the nucleotide‐binding domain of H sp70
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Prediction of protein structure with the coarse-grained UNRES force field assisted by small X-ray scattering data and knowledge-based information
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Blind prediction of homo‐ and hetero‐protein complexes: The CASP13‐CAPRI experiment
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Molecular modeling study of tectoquinone and acteoside from Tectona grandis linn: a new SARS-CoV-2 main protease inhibitor against COVID-19
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Micelle-bound conformations of neurohypophyseal hormone analogues modified with a Cα-disubstituted residue: NMR and molecular modelling studies
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Atomic resolution crystal structure of HV-BBI protease inhibitor from amphibian skin in complex with bovine trypsin
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Impact of AlphaFold on structure prediction of protein complexes: The CASP15‐CAPRI experiment
PublicationWe present the results for CAPRI Round 54, the 5th joint CASP-CAPRI protein assembly prediction challenge. The Round offered 37 targets, including 14 homodimers, 3 homo-trimers, 13 heterodimers including 3 antibody–antigen complexes, and 7 large assemblies. On average 70 CASP and CAPRI predictor groups, including more than 20 automatics servers, submitted models for each target. A total of 21 941 models submitted by these groups...
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Intercalation complex of imidazoacridinone C-1311, a potential anticancer drug, with DNA helix d(CGATCG)2: stereostructural studies by 2D NMR spectroscopy.
PublicationImidazoacridinone C-1311 (Symadex®) is a powerful antitumor agent, which successfully made its way through the Phase I clinical trials and has been recommended for Phase II few a years ago. It has been shown experimentally that during the initial stage of its action C-1311 forms a relatively stable intercalation complex with DNA, yet it has shown no base-sequence specificity while binding to DNA. In this paper, the d(CGATCG)2:C-1311...
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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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Jahn-Teller and related conical intersections in the benzene radical cation and the monofluoro derivate
PublicationThe multi-state multi-mode vibronic interactions in the benzene radical cation and its monofluoro derivative have been investigated theoretically, based on high-level electronic structure calculations for the system parameters and a quantum treatment of the nuclear motion. The available experimental data are well reproduced. The interplay of different vibronic coupling mechanisms is pointed out leading to multiple nonadiabatic...
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Prediction of protein assemblies, the next frontier: The CASP14‐CAPRI experiment
PublicationWe present the results for CAPRI Round 50, the 4th joint CASP-CAPRI protein assembly prediction challenge. The Round comprised a total of 12 targets, including 6 dimers, 3 trimers, and 3 higher-order oligomers. Four of these were easy targets, for which good structural templates were available either for the full assembly, or for the main interfaces (of the higher-order oligomers). Eight were difficult targets for which only distantly...
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Influence of stabilizing osmolytes on hen egg white lysozyme fibrillation
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Modeling SARS‐CoV‐2 proteins in the CASP‐commons experiment
PublicationCritical Assessment of Structure Prediction (CASP) is an organization aimed at advancing the state of the art in computing protein structure from sequence. In the spring of 2020, CASP launched a community project to compute the structures of the most structurally challenging proteins coded for in the SARS-CoV-2 genome. Forty-seven research groups submitted over 3000 three-dimensional models and 700 sets of accuracy estimates on...
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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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Core–shell excitation of isoxazole at the C, N, and O K-edges – an experimental NEXAFS and theoretical TD-DFT study
PublicationThe near-edge X-ray absorption fine structure (NEXAFS) spectra of the gas-phase isoxazole molecule have been measured by collecting total ion yields at the C, N, and O K-edges. The spectral structures have been interpreted using time-dependent density functional theory (TD-DFT) with the short-range corrected SRC2-BLYP exchange–correlation functional. Experimental and calculated energies of core excitations are generally in good...
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The effects of gas exposure on the graphene/AlGaN/GaN heterostructure under UV irradiation
PublicationThis work demonstrates a graphene/AlGaN/GaN sensing device with two-dimensional electron gas (2DEG) toward nitrogen dioxide (NO2), tetrahydrofuran, and acetone detection under UV light irradiation. We propose combining measurements of the DC characteristics with a fluctuation-enhanced sensing method to provide insight into the gas detection mechanisms in the synergistic structure of highly stable GaN and gas-sensitive graphene....
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Tailoring properties of indium tin oxide thin films for their work in both electrochemical and optical label-free sensing systems
PublicationThis work is devoted to the identification properties of indium tin oxide (ITO) thin films responsible for their possible application in combined optical and electrochemical label-free sensing systems offering enhanced functionalities. Since any post-processing would make it difficult to identify direct relation between deposition parameters and properties of the ITO films, especially when deposition on temperature-sensitive substrates...
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Anionic states of C6Cl6 probed in electron transfer experiments
PublicationThis is the first comprehensive investigation on the anionic species formed in collisions of fast neutral potassium (K) atoms with neutral hexachlorobenzene (C6Cl6) molecules in the laboratory frame range from 10 up to 100 eV. In such ion-pair formation experiments, we also report a novel K+ energy loss spectrum obtained in the forward scattering giving evidence of the most accessible electronic states. The vertical electron affinity...
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Molecular dynamics study on the role of solvation water in the adsorption of hyperactive AFP to the ice surface
PublicationUsing computer simulations, the early stages of the adsorption of the CfAFP molecule to the ice surface were analyzed. We found that the ice and the protein interact at least as early as when the protein is about 1 nm away from the ice surface. These interactions are mediated by interfacial solvation water and are possible thanks to the structural ordering of the solvent. This ordering leads to positional preference of the protein...