1,721,198 research outputs found
Atomistic molecular dynamics simulations reveal insights into adsorption, packing, and fluxes of molecules with carbon nanotubes
No full textThis feature article discusses the current progress and the problems of applications of atomistic simulations to the understanding of the basic phenomena that govern molecule–carbon nanotube (CNT) interactions that have relevance for gas storage, sustainability and living. Molecular adsorption is assessed in the light of molecular dynamics, MD, simulations that reveal the most favourable adsorption sites of molecules and allow the interpretation of experimental data and the determination of the energy contributions to the binding. Packing is examined in view of calculations for the application of CNTs for gas storage and CO2 capture and removal. Fluxes are discussed for the separation of different types of ions in water, seawater desalination, removal of drinking water contaminants, and gas separation. Difficulties related to the modelling and to possible improvement and upscaling of the calculations are also addressed
The molecular organization of the beta-sheet region in Corneous beta-proteins (beta-keratins) of sauropsids explains its stability and polymerization into filaments
No full textThe hard corneous material of avian and reptilian scales, claws, beak and feathers is mainly derived from the presence of proteins formerly known as beta-keratins but now termed Corneous beta-proteins of sauropsids to distinguish them from keratins, which are members of the intermediate filament protein family. The modeling of the conserved 34 amino acid residues long central beta-sheet region of Corneous beta-proteins using an ab initio protein folding and structure prediction algorithm indicates that this region is formed by four antiparallel beta-sheets. Molecular dynamic simulations and Molecular Mechanics/Poisson Boltzmann Surface Area (MM-PBSA) analysis showed that the disposition of polar and apolar amino acids within the beta-region gives rise to an amphipathic core whose stability is further increased, especially in an aqueous environment, by the association into a dimer due to apolar interactions and specific amino-acid interactions. The dimers in turn polymerize into a 3 nm thick linear beta-filament due to van der Waals and hydrogen-bond interactions. It is suggested that once this nuclear core of anti-parallel sheets evolved in the genome of a reptilian ancestor of the extant reptiles and birds about 300 millions years ago, new properties emerged in the corneous material forming scales, claws, beaks and feathers in these amniotes based on the tendency of these unique corneous proteins to form stable filaments different from keratin intermediate filaments or sterical structures formed by other corneous proteins so far known
Blocking the passage: C60 geometrically clogs K+ channels
Full text linkClassical molecular dynamics (MD) simulations combined with docking calculations, potential of mean force estimates with the umbrella sampling method, and molecular mechanic/Poisson–Boltzmann surface area (MM-PBSA) energy calculations reveal that C60 may block K+ channels with two mechanisms: a low affinity blockage from the extracellular side, and an open-channel block from the intracellular side. The presence of a low affinity binding-site at the extracellular entrance of the channel is in agreement with the experimental results showing a fast and reversible block without use-dependence, from the extracellular compartment. Our simulation protocol suggests the existence of another binding site for C60 located in the channel cavity at the intracellular entrance of the selectivity filter. The escape barrier from this binding site is ∼21 kcal/mol making the corresponding kinetic rate of the order of minutes. The analysis of the change in solvent accessible surface area upon C60 binding shows that binding at this site is governed purely by shape complementarity, and that the molecular determinants of binding are conserved in the entire family of K+ channels. The presence of this high-affinity binding site conserved among different K+ channels may have serious implications for the toxicity of carbon nanomaterials
Blocking the passage: C<inf>60</inf> geometrically clogs K<sup>+</sup> channels
Full text linkClassical molecular dynamics (MD) simulations combined with docking calculations, potential of mean force estimates with the umbrella sampling method, and molecular mechanic/Poisson-Boltzmann surface area (MM-PBSA) energy calculations reveal that C60 may block K(+) channels with two mechanisms: a low affinity blockage from the extracellular side, and an open-channel block from the intracellular side. The presence of a low affinity binding-site at the extracellular entrance of the channel is in agreement with the experimental results showing a fast and reversible block without use-dependence, from the extracellular compartment. Our simulation protocol suggests the existence of another binding site for C60 located in the channel cavity at the intracellular entrance of the selectivity filter. The escape barrier from this binding site is ∼21 kcal/mol making the corresponding kinetic rate of the order of minutes. The analysis of the change in solvent accessible surface area upon C60 binding shows that binding at this site is governed purely by shape complementarity, and that the molecular determinants of binding are conserved in the entire family of K(+) channels. The presence of this high-affinity binding site conserved among different K(+) channels may have serious implications for the toxicity of carbon nanomaterials
Thermodynamics of Binding Between Proteins and Carbon Nanoparticles: The Case of C<sub>60</sub>@Lysozyme
Full text linkThe
analysis of the interaction between C<sub>60</sub> and lysozyme
provides general rules to identify the forces that govern the thermodynamics
of binding between proteins and carbon nanoparticles. The main driving
force of the binding are van der Waals interactions. Polar solvation
and entropy, contributions that are often neglected, are strongly
detrimental to the binding. These energetically relevant terms must
be taken into account when protein/CNP hybrids are designed
CNT-Confinement Effects on the Menshutkin SN2 Reaction: The Role of Nonbonded Interactions
No full textWe investigated the effects of CNT confinement ((6,6) tube) on the model Menshutkin reaction H3N + H3CCl = H3NCH3(+) + Cl(-), which is representative of chemical processes involving developing of charge separation along the reaction pathway. We used either a full QM approach or a hybrid QM/MM approach. We found that the CNT significantly lowers the activation barrier with respect to the hypothetical gas-phase reaction: The activation barrier Ea varies from 34.6 to 25.7 kcal mol-1 (a value similar to that found in a nonpolar solvent) and the endothermicity ΔE from 31.2 to 13.5 kcal mol-1. A complex interplay between C-H⋯π, N-H⋯π, and Cl⋯π nonbonded interactions of the endohedral system with the CNT wall explains the lower barrier and lower endothermicity. The hybrid QM/MM approach (MM = UFF force field) does not reproduce satisfactorily the QM energy ΔE (18.1 vs 13.5 kcal mol-1), while optimum agreement is found in the barrier Ea (25.8 vs 25.7 kcal mol-1). These results suggest that the simple Qeq formalism (included in the MM potential) does not describe properly the effect of CNT polarization in the presence of the net charge separation featuring the final product. A more accurate estimate of the tube polarization was obtained with single-point QM/MM computations including PCM corrections (using the benzene dielectric constant) on the QM/MM optimized structures. After PCM corrections, Ea changes slightly (from 25.8 to 24.5 kcal mol-1), but a more significant variation is observed for ΔE that becomes 13.1 kcal mol-1, in rather good agreement with the full QM. This level of theory (QM/MM with PCM correction, MM = UFF) represents a more general approach suitable for describing CNT-confined chemical processes involving significant charge separation. QM/MM computations were extended to CNTs of different radii: (4,4), (5,5), (7,7), (8,8), (9,9), (10,10), (12,12), (14,14) CNTs and, as a limit case, a graphene sheet. The lack of space available in the small tube (4,4) causes a strong structural distortion and a consequent increase in Ea and ΔE (40.8 and 44.0 kcal mol-1, respectively). These quantities suddenly decrease with the augmented volume inside the (5,5) tube. For larger tubes, different structural arrangements of the endohedral system are possible, and Ea and ΔE remain almost constant until the limiting case of graphene
A dichotomy in the enantioselective oxidation of aryl benzyl sulfides: A combined experimental and computational work
No full textPentafluorobenzyl pentafluorophenyl sulfide is oxidised with moderate e.e. value and a low yield by the usually highly successful oxidation protocol based upon tert-butyl hydroperoxide (TBHP) in the presence of a titanium/hydrobenzoin complex. This disappointing result resisted until the present work, in which the switch of the oxidation agent (from TBHP to cumene hydroperoxide), suggested by our previous computations, yielded the enantiopure sulfoxide. This valuable chiral compound was obtained in good yields (76%) without resorting to a chromatographic separation. DFT computations uncovered that this favourable reactivity was originated by a stabilizing π−π−stacking between the phenyl group of the oxidant and the pentafluorophenyl moiety of the substrate
Supramolecular Binding with Lectins: A New Route for Non-Covalent Functionalization of Polysaccharide Matrices
Full text linkThe chemical functionalization of polysaccharides to obtain functional materials has been of great interest in the last decades. This traditional synthetic approach has drawbacks, such as changing the crystallinity of the material or altering its morphology or texture. These modifications are crucial when a biogenic matrix is exploited for its hierarchical structure. In this work, the use of lectins and carbohydrate-binding proteins as supramolecular linkers for polysaccharide functionalization is proposed. As proof of concept, a deproteinized squid pen, a hierarchically-organized β-chitin matrix, was functionalized using a dye (FITC) labeled lectin; the lectin used was the wheat germ agglutinin (WGA). It has been observed that the binding of this functionalized protein homogenously introduces a new property (fluorescence) into the β-chitin matrix without altering its crystallographic and hierarchical structure. The supramolecular functionalization of polysaccharides with protein/lectin molecules opens up new routes for the chemical modification of polysaccharides. This novel approach can be of interest in various scientific fields, overcoming the synthetic limits that have hitherto hindered the technological exploitation of polysaccharides-based materials
Fullerenes against COVID-19: Repurposing C60 and C70 to Clog the Active Site of SARS-CoV-2 Protease
Full text linkThe persistency of COVID-19 in the world and the continuous rise of its variants demand new treatments to complement vaccines. Computational chemistry can assist in the identification of moieties able to lead to new drugs to fight the disease. Fullerenes and carbon nanomaterials can interact with proteins and are considered promising antiviral agents. Here, we propose the possibility to repurpose fullerenes to clog the active site of the SARS-CoV-2 protease, Mpro. Through the use of docking, molecular dynamics, and energy decomposition techniques, it is shown that C60 has a substantial binding energy to the main protease of the SARS-CoV-2 virus, Mpro, higher than masitinib, a known inhibitor of the protein. Furthermore, we suggest the use of C70 as an innovative scaffold for the inhibition of SARS-CoV-2 Mpro. At odds with masitinib, both C60 and C70 interact more strongly with SARS-CoV-2 Mpro when different protonation states of the catalytic dyad are considered. The binding of fullerenes to Mpro is due to shape complementarity, i.e., vdW interactions, and is aspecific. As such, it is not sensitive to mutations that can eliminate or invert the charges of the amino acids composing the binding pocket. Fullerenic cages should therefore be more effective against the SARS-CoV-2 virus than the available inhibitors such as masinitib, where the electrostatic term plays a crucial role in the binding
Use of a Coordination Complex or Compound for the Measurement of Temperature
No full textUse for measuring temperatures of a coordination complex presenting formula I, wherein M1, M2, M3, M4, M5 are chosen, each independently of the others, in the group consisting of: CuI, AgI, AuI, PdII; n is equal to the sum of the oxidation states of M1, M2, M3, M4, M5 minus 3; II represents a respective portion of each tridentate ligand having the formula III in which R1 is chosen in the group consisting of: Ph, C1-C4 alkyl, halo-alkyl C1-C4 substituted phenyl; R2 is chosen in the group consisting of: Ph, C1-C4 alkyl, C1-C4 halo-alkyl-, substituted phenyl; R3 is chosen in the group consisting of: C3-C18 alkyl, benzyl, substituted benzyl, C1-C20 hydroxy-alkyl, C1-C20 alkoxy silane
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