86,591 research outputs found
Molecular modelling of organic inhibitors in concrete
No full textCorrosion inhibitors are largely used to prevent chloride-induced corrosion in reinforced concrete structures. The interaction mechanisms with the passive film present on steel still requires deeper understanding. In a previous work based on molecular mechanics and molecular dynamics methods [M. V. Diamanti, E.A. Pérez Rosales, G. Raffaini, F. Ganazzoli, A. Brenna, M. Pedeferri, M. Ormellese, Corrosion Science, 2015] we considered organic inhibitors adsorbed on gamma-FeOOH, comparing theoretical results with experimental data.
Here we considered the initial interaction with the inhibitor film and chlorides. In particular, the adsorbed tartrate monolayer show the best behavior thanks to the repulsions by the COO- groups exposed to chlorides, more distant from the gamma-FeOOH surface, whereas the dimethylethanolamine film doesn’t have the same repulsion.
Based on these observations, molecular mechanics and molecular dynamics confirm to be an additional, powerful tool to understand the behaviour of inhibitors in the presence of a bare or passivated metallic surface, as well as to predict their potential efficiency in inhibiting steel corrosion in the chosen environmental conditions
Molecular dynamics simulation of the adsorption of a fibronectin module on a graphite surface
No full textWe report atomistic simulations of the adsorption of a fibronectin type I module on a hydrophobic graphite surface. This module comprises only beta-sheets, unlike the albumin fragments previously investigated by us which contained only alpha-helices (Raffaini, G.; Ganazzoli, F. Langmuir 2003, 19, 3403-3412). As done in the latter case, most simulations are carried out in an effective dielectric medium by energy minimizations and molecular dynamics (MD). Further optimizations and MD runs in the explicit presence of water are also performed to assess the stability of the geometries found and to describe the solvation of the adsorbed
fibronectin module. The initial adsorption is accompanied by local rearrangements of the strands in contact with the surface, but the overall molecular structure is largely preserved. Much larger rearrangements take place at longer times as found through the MD runs, with the molecule spreading as much as possible so as to maximize the surface coverage, hence the interaction energy, despite a significant strain energy. Energetic aspects of adsorption together with the concomitant size change are discussed in comparison
with our previous results for two albumin fragments
ADSORPTION OF AN ALBUMIN SUBDOMAIN ON DIFFERENT CRYSTALLOGRAPHIC SURFACES OF ANATASE TiO2: A MOLECULAR DYNAMICS STUDY
No full textA Molecular Dynamics Study of a Photodynamic Sensitizer for Cancer Cells: Inclusion Complexes of γ-Cyclodextrins with C70
No full textPhotodynamic therapy is an emerging treatment of tumor diseases. The complexes with γ-cyclodextrins (γ-CD) and fullerenes or their derivatives can be used as photosensitizers by direct injection into cancer cells. Using molecular mechanics and molecular dynamics methods, the stability and the geometry of the 2:1 complexes [(γ-CD)2/C70] are investigated analyzing the differences with the analogous C60 complexes, studied in a previous theoretical work and experimentally found to be much less efficient in cancer therapy. The inclusion complex of γ-CD and C70 has a 2:1 stoichiometry, the same as C60, but is significantly less stable and displays an unlike arrangement. In vacuo, mimicking an apolar solvent, the complex is compact, whereas in water the two γ-CDs encapsulate C70 forming a relatively stable complex by interacting through their primary rims, however exposing part of C70 to the solvent. Other higher-energy complexes with the γ-CDs facing different rims can form in water, but in all cases part of the hydrophobic C70 surface remains exposed to water. The stability and arrangement of these peculiar amphiphilic inclusion complexes having non-covalent interactions in water can be an important key for cancer therapy to enhance both the solubilization and the fullerene insertion into liposomes or cell membranes
Dendrimer dynamics: A review of analytical theories and molecular simulation methods
No full textThe theoretical study of dendrimers is reviewed, considering both analytical approaches and molecular simulation methods. We discuss the effect of molecular symmetry on the degeneracy of the relaxation times, and then the calculation of observable quantities, in particular the intrinsic viscosity, and then the viscoelastic complex modulus and the dynamic structure factor, in comparison with the available experimental data. In particular, the maximum intrinsic viscosity with increasing molar mass is analyzed in some detail. The approximations and/or assumptions of the adopted methods are also described in connection with analogous results for polymer of a different topology, in particular linear and star polymers
Understanding Surface Interaction and Inclusion Complexes between Piroxicam and Native or Crosslinked β-Cyclodextrins: The Role of Drug Concentration
No full textDrug concentration plays an important role in the interaction with drug carriers affecting the kinetics of release process and toxicology effects. Cyclodextrins (CDs) can solubilize hydrophobic drugs in water enhancing their bioavailability. In this theoretical study based on molecular mechanics and molecular dynamics methods, the interactions between beta-cyclodextrin and piroxicam, an important nonsteroidal anti-inflammatory drug, were investigated. At first, both host–guest complexes with native β-CD in the 1:1 and in 2:1 stoichiometry were considered without assuming any initial a priori inclusion: the resulting inclusion complexes were in good agreement with literature NMR data. The interaction between piroxicam and a beta-CD nanosponge (NS) was then modeled at different concentrations. Two inclusion mechanisms were found. Moreover, piroxicam can interact with the external NS surface or with its crosslinkers, also forming one nanopore. At larger concentration, a nucleation process of drug aggregation induced by the first layer of adsorbed piroxicam molecules is observed. The flexibility of crosslinked beta-CDs, which may be swollen or quite compact, changing the surface area accessible to drug molecules, and the dimension of the aggregate nucleated on the NS surface are important factors possibly affecting the kinetics of release, which shall be theoretically studied in more detail at specific concentrations
Structural studies of radical reaction products. II. 2,4-Bis(4-chlorophenyl)-5,5-dimethyl-3-pyrazolidinone
No full textThe title compd. is triclinic, space group P ̅1, with a 12.280(3), b 10.191(3), c 6.663(2) Å, α 83.93(7), β 100.05(8), and γ 87.70(8)°; d = 1.37 for Z = 2. The final R = 0.056 for 2285 reflections. The compd., which shows pharmacol. activity in vitro, presents a puckered pyrazolidionone ring puckering angle 36.0(2)° with an N-N bond 1.445(4) Å longer than those usually found in hydrazidic moieties. Geometric and electronic features of this part of the mol. have a close similarity with those of antipyrine, a 3H-pyrazol-3-one deriv. used as an antiinflammatory drug. The at. coordinates are give
Structural studies of radical reaction products. I. The structure of an asymmetrically substituted diazene: 3-(p-chlorophenyl)-4-(p-chlorophenylazo)-4-methyl-2-pentanone, C18H18Cl2N2O
No full textThe title compd., from the decompn. of 4-chlorobenzenediazonium chloride by Ti ions in the presence of 4-methyl-3penten-2-one, is triclinic, space group P ̅1, with a 15.863(7), b 10.226(4), c 5.765(4) Å, α 92.30(8), β 88.37(8), and γ 108.70(9)°; d.(exptl.) = 1.30 and d.(calcd.) = 1.31 for Z = 2. Final R 0.0415 for 2176 obsd. reflections [having I ≥ 3σ(I)]. At. parameters are given. The distance between the N atoms of the azo group (1.240(3) Å) is equal to the expected bond length between doubly bonded sp2-hybridized N atoms, and there is no evidence of π delocalization between the azo group and the Ph rings. This structure proves unambiguously that aryl radical addn. to a sterically hindered olefin is governed by steric factor
CONFORMATIONS AND DYNAMICS OF STARS AND DENDRIMERS: THE GAUSSIAN SELF-CONSISTENT APPROACH
No full textSome conformational and dynamical aspects of branched polymer are reviewed. We discuss the theoretical Gaussian Self-Consistent (GSC) approach proposed in our group and used to study the behaviour of regular star polymers and dendrimers in different solvent conditions. Within a single framework, we consider the unperturbed Theta state, as well as the good-solvent state in comparison with other theoretical or simulation approaches, and with some experimental results. We also briefly report the further results obtained for amphiphilic copolymer stars in selective solvents so as to highlight the potentialities of the method, as well as its strengths and its shortcomings
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