First-principle-based MD description of azobenzene molecular rods

Pipolo, Silvio; Benassi, Enrico; Brancolini, Giorgia; Valášek, Michal; Mayor, Marcel; Corni, Stefano

doi:10.1007/s00214-012-1274-z

Cited by 19 publications

(30 citation statements)

References 50 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…To gain a better understanding of the interactions of the azobenzene molecules with graphene, we perform molecular dynamics simulations (see Supplementary Note 7 for details). All calculations are done using the Groningen Machine for Chemical Simulations (GROMACS) 50 package and a modified version of the all-atom Optimized Potentials for Liquid Simulations (OPLSAA) force field developed for azobenzenes 51 52 . To assess the relative adsorption affinity of the trans versus cis conformations, we first compute the interaction energy for a single azobenzene molecule by running a 1-ns simulation in vacuum.…”

Section: Resultsmentioning

confidence: 99%

Light-enhanced liquid-phase exfoliation and current photoswitching in graphene–azobenzene composites

et al. 2016

View full text Add to dashboard Cite

Multifunctional materials can be engineered by combining multiple chemical components, each conferring a well-defined function to the ensemble. Graphene is at the centre of an ever-growing research effort due to its combination of unique properties. Here we show that the large conformational change associated with the trans–cis photochemical isomerization of alkyl-substituted azobenzenes can be used to improve the efficiency of liquid-phase exfoliation of graphite, with the photochromic molecules acting as dispersion-stabilizing agents. We also demonstrate reversible photo-modulated current in two-terminal devices based on graphene–azobenzene composites. We assign this tuneable electrical characteristics to the intercalation of the azobenzene between adjacent graphene layers and the resulting increase in the interlayer distance on (photo)switching from the linear trans-form to the bulky cis-form of the photochromes. These findings pave the way to the development of new optically controlled memories for light-assisted programming and high-sensitive photosensors.

show abstract

Section: Resultsmentioning

confidence: 99%

Light-enhanced liquid-phase exfoliation and current photoswitching in graphene–azobenzene composites

et al. 2016

View full text Add to dashboard Cite

show abstract

“…In addition to the tabulated parameters of PCFF, a small number of parameters related to the azobenzene and dimethylamino groups have been supplemented from additional sources. Parameters of the torsional potentials of the CCNN and CNNC groups are adopted from Pipolo et al for the NCCH torsional potential from Sun, and a further set of values for the dimethylamino group are taken from ref . The cutoff distance of the LJ interactions is set to 2.0 nm.…”

Section: Models and Methodsmentioning

confidence: 99%

Do Columns of Azobenzene Stars Disassemble under Light Illumination?

2019

View full text Add to dashboard Cite

The clustering properties of star-shaped molecules comprising three photochromic azobenzene-containing arms are investigated with specific focus on the influence of light on these structures. Previous experimental works report self-assembly of azobenzene stars in aqueous solution into long columnar clusters that are detectable using optical microscopy. These clusters appear to vanish under UV irradiation, which is known to induce trans-to-cis photoisomerization of the azobenzene groups. We have performed MD simulations, density functional theory, and density functional tight binding calculations to determine conformational properties and binding energies of these clusters. Our simulation data suggest that the binding strength of the clusters is large enough to prevent a breaking along their main axis. We conclude that very likely other mechanisms lead to the apparent disappearance of the clusters.

show abstract

“…We thank S. Pipolo for making available the code required to t classical parameters based on ab initio results. 53…”

Section: Acknowledgementsmentioning

confidence: 99%

Can small hydrophobic gold nanoparticles inhibit β₂-microglobulin fibrillation?

2014

Self Cite

View full text Add to dashboard Cite

Inorganic nanoparticles stabilized by a shell of organic ligands can enhance or suppress the natural propensity of proteins to form fibrils. Functionalization facilitates targeted delivery of the nanoparticles to various cell types, bioimaging, drug delivery and other therapeutic and diagnostic applications. In this study, we provide a computational model of the effect of a prototypical thiol-protected gold nanoparticle, Au₂₅L₁₈(-) (L = S(CH₂)₂Ph) on the β₂-microglobulin natural fibrillation propensity. To reveal the molecular basis of the protein-nanoparticle association process, we performed various simulations at multiple levels (Classical Molecular Dynamics and Brownian Dynamics) that cover multiple length- and timescales. The results provide a model of the ensemble of structures constituting the protein-gold nanoparticle complexes, and insights into the driving forces for the binding of β₂-microglobulin to hydrophobic small size gold nanoparticles. We have found that the small nanoparticles can bind the protein to form persistent complexes. This binding of nanoparticles is able to block the active sites of domains from binding to another protein, thus leading to potential inhibition of the fibrillation activity. A comparison with the binding patches identified for the interaction of the protein with a known inhibitor of fibrillation, supports our conclusion.

show abstract

First-principle-based MD description of azobenzene molecular rods

Cited by 19 publications

References 50 publications

Light-enhanced liquid-phase exfoliation and current photoswitching in graphene–azobenzene composites

Light-enhanced liquid-phase exfoliation and current photoswitching in graphene–azobenzene composites

Do Columns of Azobenzene Stars Disassemble under Light Illumination?

Can small hydrophobic gold nanoparticles inhibit β₂-microglobulin fibrillation?

Contact Info

Product

Resources

About

First-principle-based MD description of azobenzene molecular rods

Cited by 19 publications

References 50 publications

Light-enhanced liquid-phase exfoliation and current photoswitching in graphene–azobenzene composites

Light-enhanced liquid-phase exfoliation and current photoswitching in graphene–azobenzene composites

Do Columns of Azobenzene Stars Disassemble under Light Illumination?

Can small hydrophobic gold nanoparticles inhibit β2-microglobulin fibrillation?

Contact Info

Product

Resources

About

Can small hydrophobic gold nanoparticles inhibit β₂-microglobulin fibrillation?