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Beilstein Journal of Nanotechnology (1)
PLoS ONE (1)
The journal of physical chemistry. B (1)
Corni, Stefano (3)
Benassi, Enrico (1)
Cohen, Sidney R (1)
Di Felice, Rosa (1)
Fraternali, Franca (1)
Frydman, Veronica (1)
Gottschalk, Kay Eberhard (1)
Gölzhäuser, Armin (1)
Hoefling, Martin (1)
Klein, Michael L. (1)
Mayor, Marcel (1)
Migliore, Agostino (1)
Monti, Susanna (1)
Pipolo, Silvio (1)
Tirosh, Einat (1)
Valášek, Michal (1)
Varsano, Daniele (1)
Year of Publication
Direct monitoring of opto-mechanical switching of self-assembled monolayer films containing the azobenzene group
Cohen, Sidney R
Beilstein Journal of Nanotechnology
The potential for manipulation and control inherent in molecule-based motors holds great scientific and technological promise. Molecules containing the azobenzene group have been heavily studied in this context. While the effects of the cis–trans isomerization of the azo group in such molecules have been examined macroscopically by a number of techniques, modulations of the elastic modulus upon isomerization in self-assembled films were not yet measured directly. Here, we examine the mechanical response upon optical switching of bis[(1,1'-biphenyl)-4-yl]diazene organized in a self-assembled film on Au islands, using atomic force microscopy. Analysis of higher harmonics by means of a torsional harmonic cantilever allowed real-time extraction of mechanical data. Quantitative analysis of elastic modulus maps obtained simultaneously with topographic images show that the modulus of the cis-form is approximately twice that of the trans-isomer. Quantum mechanical and molecular dynamics studies show good agreement with this experimental result, and indicate that the stiffer response in the cis-form comprises contributions both from the individual molecular bonds and from intermolecular interactions in the film. These results demonstrate the power and insights gained from cutting-edge AFM technologies, and advanced computational methods.
AFM; azobenzene; elastic modulus; molecular dynamics; nanomechanics; photoswitch; quantum mechanics computation; self-assembled monolayer
Interaction of β-Sheet Folds with a Gold Surface
Gottschalk, Kay Eberhard
The adsorption of proteins on inorganic surfaces is of fundamental biological importance. Further, biomedical and nanotechnological applications increasingly use interfaces between inorganic material and polypeptides. Yet, the underlying adsorption mechanism of polypeptides on surfaces is not well understood and experimentally difficult to analyze. Therefore, we investigate here the interactions of polypeptides with a gold(111) surface using computational molecular dynamics (MD) simulations with a polarizable gold model in explicit water. Our focus in this paper is the investigation of the interaction of polypeptides with β-sheet folds. First, we concentrate on a β-sheet forming model peptide. Second, we investigate the interactions of two domains with high β-sheet content of the biologically important extracellular matrix protein fibronectin (FN). We find that adsorption occurs in a stepwise mechanism both for the model peptide and the protein. The positively charged amino acid Arg facilitates the initial contact formation between protein and gold surface. Our results suggest that an effective gold-binding surface patch is overall uncharged, but contains Arg for contact initiation. The polypeptides do not unfold on the gold surface within the simulation time. However, for the two FN domains, the relative domain-domain orientation changes. The observation of a very fast and strong adsorption indicates that in a biological matrix, no bare gold surfaces will be present. Hence, the bioactivity of gold surfaces (like bare gold nanoparticles) will critically depend on the history of particle administration and the proteins present during initial contact between gold and biological material. Further, gold particles may act as seeds for protein aggregation. Structural re-organization and protein aggregation are potentially of immunological importance.
First principles effective electronic couplings for hole transfer in natural and size-expanded DNA
Klein, Michael L.
Di Felice, Rosa
The journal of physical chemistry. B
Hole transfer processes between base pairs in natural DNA and size-expanded DNA (xDNA) are studied and compared, by means of an accurate first principles evaluation of the effective electronic couplings (also known as transfer integrals), in order to assess the effect of the base augmentation on the efficiency of charge transport through double-stranded DNA. According to our results, the size expansion increases the average electronic coupling, and thus the CT rate, with potential implications in molecular biology and in the implementation of molecular nanoelectronics. Our analysis shows that the effect of the nucleobase expansion on the charge-transfer (CT) rate is sensitive to the sequence of base pairs. Furthermore, we find that conformational variability is an important factor for the modulation of the CT rate. From a theoretical point of view, this work offers a contribution to the CT chemistry in π-stacked arrays. Indeed, we compare our methodology against other standard computational frameworks that have been adopted to tackle the problem of CT in DNA, and unravel basic principles that should be accounted for in selecting an appropriate theoretical level.
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