Thermodynamics of Adsorption on Graphenic Surfaces from Aqueous Solution.

Adsorption of organic molecules from aqueous solution to the surface of carbon nanotubes or graphene is an important process in many applications of these materials. Here we use molecular dynamics simulation, supplemented by analytical chemistry, to explore in detail the adsorption thermodynamics of a diverse set of aromatic compounds on graphenic materials, elucidating the effects of the solvent, surface coverage, surface curvature, defects, and functionalization by hydroxy groups. We decompose the adsorption free energies into entropic and enthalpic components and find that different classes of compounds-such as phenols, benzoates, and alkylbenzenes-can easily be distinguished by the relative contributions of entropy and enthalpy to their adsorption free energies. Overall, entropy dominates for the more hydrophobic compounds, while enthalpy plays the greatest role for more hydrophilic compounds. Experiments and independent simulations using two different force field frameworks (CHARMM and Amber) support the robustness of these conclusions. We determine that concave curvature is generally associated with greater adsorption affinity, more favorable enthalpy, and greater contact area, while convex curvature reduces both adsorption enthalpy and contact area. Defects on the graphene surfaces can create concave curvature, resulting in localized binding sites. As the graphene surface becomes covered with aromatic solutes, the affinity for adsorbing an additional solute increases until a complete monolayer is formed, driven by more favorable enthalpy and partially canceled by less favorable entropy. Similarly, hydroxylation of the surface leads to preferential adsorption of the aromatic solutes to remaining regions of bare graphene, resulting in less favorable adsorption entropy, but compensated by an increase in favorable enthalpic interactions.

Experimental and Computational Characterization of the Interaction between Gold Nanoparticles and Polyamidoamine Dendrimers.

Dendrimers provide a means to control the synthesis of gold nanoparticles and stabilize their suspensions. However, design of improved dendrimers for this application is hindered by a lack of understanding how the dendrimers and synthesis conditions determine nanoparticle morphology and suspension stability. In the present work, we evaluate the effect of polyamidoamine (PAMAM) dendrimers terminated with different functional groups (-OH or -NH3+) and different synthesis conditions on the morphology of the resulting gold nanoparticles and their stability in solution. We leverage molecular dynamics (MD) simulations to identify the atomic interactions that underlie adsorption of PAMAM dendrimers to gold surface and how the thermodynamics of this adsorption depends on the terminal functional groups of the dendrimers. We find that gold nanoparticles formed with hydroxyl-terminated PAMAM (PAMAM-OH) rapidly aggregate, whereas those formed with PAMAM-NH3+ are stable in solution for months of storage. Synthesis under ultrasound sonication is shown to be more rapid than that under agitation, with sonication producing smaller nanoparticles. Free-energy calculations in MD simulations show that all dendrimers have a high affinity for the gold surface, although PAMAM-OH and its oxidized aldehyde form (PAMAM-CHO) have a greater affinity for the nanoparticle surface than PAMAM-NH3+. Although adsorption of PAMAM-OH and PAMAM-CHO has both favorable entropy and enthalpy, adsorption of PAMAM-NH3+ is driven by a strong enthalpic component subject to an unfavorable entropic component.

Molecular clustering and percolation characteristics near the glass transition in aqueous trehalose and choline dihydrogen phosphate solutions.

Spatial and temporal characteristics of molecular structure in ternary solutions of trehalose and choline dihydrogen phosphate (CDHP) are studied using molecular dynamics simulations at 300 K for a range of solute concentrations with a 2 : 1 stoichiometric ratio of trehalose to CDHP. For a given molecular configuration, water molecules are classified as interior (only neighboring other water molecules) or interfacial (at least one solute neighbor). As a tagged water molecule diffuses, it dynamically exchanges between interior and interfacial type as its local environment changes, with differences in hydrogen-bond strength between different molecular species creating a persistent preference for interfacial water. At high solute concentrations, interfacial and interior water have similar diffusivity, which allows for water to collectively act as a plasticizer. The percolation threshold for water, defined as the maximum solute concentration at which there still exists a water cluster that spans the simulation box, was found to be slightly under the liquid-glass transition, estimated to be near 84.5% solute concentration based on the onset of a volume hysteresis effect, which was not previously studied in the computational literature. The systems were observed to be highly inhomogeneous, with interlaced percolating networks of water and solute coexisting at intermediate concentrations. The density of interior water was found to decrease with increasing solute concentration, creating low-density regions within the matrix.

Interaction of collagen like peptides with gold nanosurfaces: a molecular dynamics investigation.

In this study, an attempt has been made to understand the interaction between collagen like peptides (CPs) with a gold nanosurface (AuNS) using a classical molecular dynamics simulation. Results reveal that the adsorption of CPs onto the gold surface depends on the amino acid composition of the collagen like peptides. It is evident from the findings that the Hyp residue of collagen interacts favorably with the AuNS. It is interesting to note that the model CP without a Hyp residue does not adsorb well on the surface. Results indicate that gold nanosurfaces or gold nanoparticles can be exploited to detect breast cancer due to the increased content of Hyp residues in the Gly-XAA-YAA triplet of collagen in breast cancer tissues. These results provide useful information for designing collagen based scaffolds for tissues engineering applications.

Discovery of potent inhibitor for matrix metalloproteinase-9 by pharmacophore based modeling and dynamics simulation studies.

Matrix metalloproteinase-9 (MMP-9) is an attractive target for anticancer therapy. In the present study ligand based pharmacophore modeling was performed to elucidate the structural elements for a diverse class of MMP-9 inhibitors. The pharmacophore model was validated through Güner-Henry (GH) scoring method. The final pharmacophore model consisted of three hydrogen bond acceptors (HBA), and two ring aromatic regions (RA). This model was utilized to screen the natural compound database to seek novel compounds as MMP-9 inhibitors. The identified hits were validated using molecular docking and molecular dynamics simulation studies. Finally, one compound named Hinokiflavone from Juniperus communis had high binding free energy of -26.54kJ/mol compared with the known inhibitors of MMP-9. Cytotoxicity for hinokiflavone was evaluated by MTT assay. Inhibition of MMP-9 in the presence of hinokiflavone was detected by gelatin zymography and gelatinolytic inhibition assay. Results revealed that the natural compounds derived based on the developed pharmacophore model would be useful for further design and development of MMP-9 inhibitors.

Molecular dynamics simulation study on the interaction of collagen-like peptides with gelatinase-A (MMP-2).

Although several models have been proposed for the interaction of collagen with gelatinase-A (matrix metalloproteinases-2 (MMP-2)), the extensive role of each domain of gelatinase A in hydrolyzing the collagens with and without interruptions is still elusive. Molecular docking, molecular dynamics (MD) simulation, normal mode analysis (NMA) and framework rigidity optimized dynamics algorithm (FRODAN) based analysis were carried out to understand the function of various domains of MMP-2 upon interaction with collagen like peptides. The results reveal that the collagen binding domain (CBD) binds to the C-terminal of collagen like peptide with interruption. CBD helps in unwinding the loosely packed interrupted region of triple helical structure to a greater extent. It can be possible to speculate that the role of hemopexin (HPX) domain is to prevent further unwinding of collagen like peptide by binding to the other end of the collagen like peptide. The catalytic (CAT) domain then reorients itself to interact with the part of the unwound region of collagen like peptide for further hydrolysis. In conclusion the CBD of MMP-2 recognizes the collagen and aids in unwinding the collagen like peptide with interruptions, and the HPX domain of MMP-2 binds to the other end of the collagen allowing CAT domain to access the cleavage site. This study provides a comprehensive understanding of the structural basis of collagenolysis by MMP-2.