Modeling the Absorbance Properties of a Pyrene Chromophore Grafted onto a Au₂₅ Nanocluster: A TD-DFT Study

Using ab initio spectroscopic tools, we have studied the structural and electronic properties of a pyrene chromophore grafted onto a Au₂₅ nanocluster synthesized by Devadas and co-workers [<i>J. Phys. Chem. Lett.</i> <b>2010</b>, <i>1</i>, 1497]. To simulate the electronic absorption spectra of this hybrid metallic/organic structure, we relied on a three-step approach: (1) Molecular Dynamics simulations based on Force Field Classical Mechanics, (2) geometry optimizations at the ZORA-BP86/TZP level, and (3) TD-DFT calculations with the CAM-B3LYP functional. This procedure allowed us to reproduce and rationalize the experimental observations. Because of small spatial overlap and energy matching between the organic and metallic frontier orbitals, the absorption spectrum of the hybrid system is a simple addition of the pyrene and nanocluster optical spectra. To tune the optical properties of the organic moiety and enable the electronic communication within the hybrid system, a modification of the pyrene skeleton is proposed. This study thus paves the way toward the simulation of UV–visible absorption spectra of hybrid metallic–organic systems

Density Functional Theory Study of the Conformation and Optical Properties of Hybrid Au_<i>n</i>–Dithienylethene Systems (<i>n</i> = 3, 19, 25)

We present a theoretical study of Au_<i>n</i>–dithienylethene hybrid systems (<i>n</i> = 3, 19, 25), where the organic molecule is covalently linked to a nanometer-scaled gold nanoparticle (NP). We aim at gaining insights on the optical properties of such photochromic devices and proposing a size-limited gold aggregate model able to recover the optical properties of the experimental system. We thus present a DFT-based calculation scheme to model the ground-state (conformation, energetic parameters) and excited-state properties (UV–visible absorption spectra) of this type of hybrid systems. Within this framework, the structural parameters (adsorption site, orientation, and internal structure of the photochrome) are found to be slightly dependent on the size/shape of the gold aggregate. The influence of the gold fragment on the optical properties of the resulting hybrid system is then discussed with the help of TD-DFT combined with an analysis of the virtual orbitals involved in the photochromic transitions. We show that, for the open hybrid isomer, the number of gold atoms is the key parameter to recover the photoactive properties that are experimentally observed. On the contrary, for hybrid closed systems, the three-dimensional structure of the metallic aggregate is of high impact. We thus conclude that Au₂₅ corresponds to the most appropriate fragment to model nanometer-sized NP–DTE hybrid device

Simulation of the Properties of a Photochromic Triad

To increase the contrast between the “on” and “off” states, photochromic units may be coupled together through delocalized bridges. However, such a procedure is practically limited by the impossibility to achieve the conversion of all photochromes. In this letter, we investigate the structures and properties of a dithienylethene trimer in order to apprehend its excited-state properties in the framework of a procedure combining the simulations of the electronic spectrum with time-dependent density functional theory and the analysis of the topology of the relevant molecular orbitals. Using a range-separated hybrid, this level of theory is able to perfectly reproduce the patterns of the absorption spectrum but only yields partially correct insights regarding the ring-closure of the three dithienylethene units. These theoretical simulations are a first step toward the development of more efficient molecular switches

Molecular Dynamics Simulation of a RNA Aptasensor

Single-stranded RNA aptamers have emerged as novel biosensor tools. However, the immobilization procedure of the aptamer onto a surface generally induces a loss of affinity. To understand this molecular process, we conducted a complete simulation study for the Flavin mononucleotide aptamer for which experimental data are available. Several molecular dynamics simulations (MD) of the Flavin in complex with its RNA aptamer were conducted in solution, linked with six thymidines (T6) and, finally, immobilized on an hexanol-thiol-functionalized gold surface. First, we demonstrated that our MD computations were able to reproduce the experimental solution structure and to provide a meaningful estimation of the Flavin free energy of binding. We also demonstrated that the T6 linkage, by itself, does not generate a perturbation of the Flavin recognition process. From the simulation of the complete biosensor system, we observed that the aptamer stays oriented parallel to the surface at a distance around 36 Å avoiding, this way, interaction with the surface. We evidenced a structural reorganization of the Flavin aptamer binding mode related to the loss of affinity and induced by an anisotropic distribution of sodium cationic densities. This means that ionic diffusion is different between the surface and the aptamer than above this last one. We suggest that these findings might be extrapolated to other nucleic acids systems for the future design of biosensors with higher efficiency and selectivity

Some Theoretical and Experimental Insights on the Mechanistic Routes Leading to the Spontaneous Grafting of Gold Surfaces by Diazonium Salts

The spontaneous grafting of diazonium salts on gold may involve the carbocation obtained by heterolytic dediazonation and not necessarily the radical, as usually observed on reducing surfaces. The mechanism is addressed on the basis of DFT calculations and experiments carried out under conditions where the carbocation and the radical are produced selectively. The calculations indicate that the driving force of the reaction leading from a gold cluster, used as a gold model surface, and the carbocation to the modified cluster is higher than that of the analogous reaction starting from the radical. The experiments performed under conditions of heterolytic dediazonation show the formation of thin films on the surface of gold. The grafting of a carbocation is therefore possible, but a mechanism where the cleavage of the Ar–N bond is catalyzed by the surface of gold cannot be excluded

Diazonium Salt-Derived 4-(Dimethylamino)phenyl Groups as Hydrogen Donors in Surface-Confined Radical Photopolymerization for Bioactive Poly(2-hydroxyethyl methacrylate) Grafts

In this paper we describe a novel methodology for grafting polymers via radical photopolymerization initiated on gold surfaces by aryl layers from diazonium salt precursors. The parent 4-(dimethylamino)­benzenediazonium salt was electroreduced on a gold surface to provide 4-(dimethylamino)­phenyl (DMA) hydrogen donor layers; free benzophenone in solution was used as a photosensitizer to strip hydrogen from the grafted DMA. This system permitted efficient surface initiation of photopolymerization of 2-hydroxyethyl methacrylate. The resulting poly­(2-hydroxyethyl methacrylate) (PHEMA) grafts were found to be very adherent to the surface as they resist total failure after being soaked in the well-known paint stripper methyl ethyl ketone. The PHEMA grafts were reacted with 1,1′-carbonyldiimidazole to yield carbamate groups that are able to react readily with amino groups from proteins. The final surface consisted of protein-functionalized PHEMA grafts where bovine serum albumin (BSA) protein is specifically linked to the grafts by covalent bonds. We used X-ray photoelectron spectroscopy to monitor the chemical changes at the gold surface all along the process from the neat gold to the end-protein-functionalized polymer grafts: the PHEMA graft thickness ranged from 7 to 27 nm, and the activation by 1,1′-carbonyldiimidazole reached 37% of the OH groups, which was sufficient for 90% surface coverage of the grafts by BSA. This work conclusively provides a new approach for bridging reactive and functional polymers to surfaces via aryl diazonium salts in a simple, fast, and efficient approach of importance in biomedical and other applications