Aggregation behaviour of amphiphilic cyclodextrins: The nucleation stage by atomistic molecular dynamics simulations

Amphiphilically modified cyclodextrins may form various supramolecular aggregates. Here we report a theoretical study of the aggregation of a few amphiphilic cyclodextrins carrying hydrophobic thioalkyl groups and hydrophilic ethylene glycol moieties at opposite rims, focusing on the initial nucleation stage in an apolar solvent and in water. The study is based on atomistic molecular dynamics methods with a “bottom up” approach that can provide important information about the initial aggregates of few molecules. The focus is on the interaction pattern of amphiphilic cyclodextrin (aCD), which may interact by mutual inclusion of the substituent groups in the hydrophobic cavity of neighbouring molecules or by dispersion interactions at their lateral surface. We suggest that these aggregates can also form the nucleation stage of larger systems as well as the building blocks of micelles, vesicle, membranes, or generally nanoparticles thus opening new perspectives in the design of aggregates correlating their structures with the pharmaceutical properties

Modellazione molecolare di inibitori organici nel cemento (Molecular modeling of organic inhibitors in concrete)

Corrosion 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 [1] based on molecular mechanics and molecular dynamics methods [2-5] we considered organic inhibitors adsorbed on γ-FeOOH, comparing theoretical results with experimental data [1]. 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 γ-FeOOH surface, whereas the dimethylethanolamine film doesn’t have the same repulsion. The molecular simulations are a useful tool to better understand the behaviour of inhibitors in presence of chlorides that can start the corrosio

Aggregation behavior of amphiphilic cyclodextrins in a nonpolar solvent: Evidence of large-scale structures by atomistic molecular dynamics simulations and solution studies

Chemically modified cyclodextrins carrying both hydrophobic and hydrophilic substituents may form supramolecular aggregates or nanostructures of great interest. These systems have been usually investigated and characterized in water for their potential use as nanocarriers for drug delivery, but they can also aggregate in apolar solvents, as shown in the present paper through atomistic molecular dynamics simulations and dynamic light scattering measurements. The simulations, carried out with a large number of molecules in vacuo adopting an unbiased bottom-up approach, suggest the formation of bidimensional structures with characteristic length scales of the order of 10 nm, although some of these sizes are possibly affected by the assumed periodicity of the simulation cell, in particular at longer lengths. In any case, these nanostructures are stable at least from the kinetic viewpoint for relatively long times thanks to the large number of intermolecular interactions of dipolar and dispersive nature. The dynamic light scattering experiments indicate the presence of aggregates with a hydrodynamic radius of the order of 80 nm and a relatively modest polydispersity, even though smaller nanometer-sized aggregates cannot be fully ruled out. Taken together, these simulation and experimental results indicate that amphiphilic ally modified cyclodextrins do also form large-scale nanoaggregates even in apolar solvents

Inclusion complexes of β-cyclodextrin with tricyclic drugs: an X-ray diffraction, NMR and molecular dynamics study

Tricyclic fused-ring cyclobenzaprine (1) and amitriptyline (2) form 1:1 inclusion complexes with β-cyclodextrin (β-CD) in the solid state and in water solution. Rotating frame NOE experiments (ROESY) showed the same geometry of inclusion for both 1/β-CD and 2/β-CD complexes, with the aromatic ring system entering the cavity from the large rim of the cyclodextrin and the alkylammonium chain protruding out of the cavity and facing the secondary OH rim. These features matched those found in the molecular dynamics (MD) simulations in solution and in the solid state from single-crystal X-ray diffraction of 1/β-CD and 2/β-CD complexes. The latter complex was found in a single conformation in the solid state, whilst the MD simulations in explicit water reproduced the conformational transitions observed experimentally for the free molecule

Classical atomistic simulations of protein adsorption on carbon nanomaterials

Carbon nanomaterials are receiving an increasingly large interest in a variety of fields, including also nanomedicine. In this area, much attention is devoted to investigating and modeling the behavior of these nanomaterials when they interact with biological fluids and with biological macromolecules, in particular proteins and oligopeptides. The interaction with these molecules is in fact crucial to understand and predict the efficacy of nanomaterials as drug carriers or therapeutic agents as well as their potential toxicity when they occupy the active site of a protein or severely affect the secondary and tertiary structure, or even the local dynamics, thus inhibiting their biological function. In this review, therefore, we describe the most recent work carried out in the last few years to model the interaction between carbon nanomaterials, either pristine or functionalized, and proteins or oligopeptides using classical atomistic methods, mainly molecular dynamics simulations. The attention is focused on 0-dimensional fullerenes, mainly C 60 , on 1-dimensional carbon nanotubes, mostly the single-walled armchair and some chiral ones, and on 2-dimensional graphene and graphyne, the latter containing also sp hybridized atoms in addition to the sp 2 ones common to the other carbon nanomaterials