Marcus Theory and Long-Range Activationless Transport in Molecular Junctions.

Intrachain transport in molecular junctions (MJs) longer than 5 nm has been modeled within the theoretical framework of Marcus theory. We show that in oligo(bisthienylbenzene)-based MJs, electronic transport involves polarons, localized on three monomers that are close to 4 nm in length. They hop and tunnel between adjacent localized sites with reorganization energies λ close to 400-600 meV and electronic coupling parameters Hab close to λ/2. As a consequence, the activation energy for intrachain transport, given by the equation ΔG* = (λ/4)(1 - 2Hab/λ)2, is close to zero, and transport along the chain is activationless, in agreement with experimental observation. On the contrary, similar calculations on conjugated oligonaphthalenefluoreneimine wires show that Hab is much less than λ/2 and predict that the activation energies for intrachain hopping between adjacent sites, close to λ/4, are ∼115 meV. This work proposes a new perspective for understanding long-range activationless transport in MJs beyond the tunneling regime.

Two-Dimensional Hetero- to Homochiral Phase Transition from Dynamic Adsorption of Barbituric Acid Derivatives.

Barbituric acid derivative (TDPT) is an achiral molecule, and its adsorption on a surface results in two opposite enantiomerically oriented motifs, namely TDPT-Sp and Rp. Two types of building blocks can be formed; block I is enantiomer-pure and is built up of the same motifs (format SpSp or RpRp) whereas block II is enantiomer-mixed and composes both motifs (format SpRp), respectively. The organization of the building blocks determines the formation of different nanoarchitectures which are investigated using scanning tunneling microscopy at a liquid/HOPG interface. Sophisticated, highly symmetric "nanowaves" are first formed from both building blocks I and II and are heterochiral. The "nanowaves" are metastable and evolve stepwisely into more close-packed "nanowires" which are formed from enantiomer-pure building block I and are homochiral. A dynamic hetero- to homochiral transformation and simultaneous multi-scale phase transitions are demonstrated at the single-molecule level. Our work provides novel insights into the control and the origin of chiral assemblies and chiral transitions, revealing the various roles of enantiomeric selection and chiral competition, driving forces, stability and molecular coverage.

DockSurf: A Molecular Modeling Software for the Prediction of Protein/Surface Adhesion.

The elucidation of structural interfaces between proteins and inorganic surfaces is a crucial aspect of bionanotechnology development. Despite its significance, the interfacial structures between proteins and metallic surfaces are yet to be fully understood, and the lack of experimental investigation has impeded the development of many devices. To overcome this limitation, we suggest considering the generation of protein/surface structures as a molecular docking problem with a homogenous plan as the target. To this extent, we propose a new software, DockSurf, which aims to quickly propose reliable protein/surface structures. Our approach considers the conformational exploration with Euler's angles, which provide a cartography instead of a unique structure. Interaction energies were derived from quantum mechanics computations for a set of small molecules that describe protein atom types and implemented in a Derjaguin, Landau, Verwey, and Overbeek potential for the consideration of large systems such as proteins. The validation of DockSurf software was conducted with molecular dynamics for corona proteins with gold surfaces and provided enthusiastic results. This software is implemented in the RPBS platform to facilitate widespread access to the scientific community.

Tuning the photochemical ring-closing reaction efficiency in diarylethene-based photoswitches through engineering of internal charge transfer.

The photochemical quantum yield is one of the key features for a photoswitch and its tuning is challenging. In an attempt to tackle this issue within the popular diarylethene-based switches, we have explored the potential to use internal charge transfer (CT), a readily controllable parameter, for an effective modulation of the photocyclization quantum yield. For this, a homogeneous family of terarylenes, a sub-class of diarylethenes, with different CT characters, but the same photochromic core was designed and its photochromic properties were fully investigated. A clear correlation was found between the cyclization quantum yield and the CT character of the switch. More precisely, almost linear relationships were established between the ring-closing quantum yield and (i) the electron density variation accompanying the S0 → S1 transition and (ii) the percentage of LUMO on the reactive carbon atoms. Such a correlation was rationalized by a joint spectroscopic analysis and theoretical modelling of both ground and first excited states, introducing the concept of "early" or "late" photochromes. Encouragingly, such a potentally predictive model also seemed relevant when applied to some other diarylethene-based switches reported in the literature.

Functionalized maghemite nanoparticles for enhanced adsorption of uranium from simulated wastewater and magnetic harvesting.

Maghemite (γ-Fe2O3) nanoparticles (MNPs) were functionalized with 3-aminopropyltriethoxysilane (APTES) to give APTES@Fe2O3 (AMNP) which was then reacted with diethylenetriamine-pentaacetic acid (DTPA) to give a nanohybrid DTPA-APTES@Fe2O3 (DAMNP). Nano-isothermal titration calorimetry shows that DTPA complexation with uranyl ions in water is exothermic and has a stoichiometry of two DTPA to three uranyl ions. Density functional theory calculations indicate the possibility of several complexes between DTPA and UO22+ with different stoichiometries. Interactions between uranyl ions and DAMNP functional groups are revealed by X-photoelectron and Fourier transform infrared spectroscopies. Spherical aberration-corrected Scanning Transmission Electron Microscopy visualizes uranium on the particle surface. Adsorbent performance metrics were evaluated by batch adsorption studies under different conditions of pH, initial uranium concentration and contact time, and the results expressed in terms of equilibrium adsorption capacities (qe) and partition coefficients (PC). By either criterion, performance increases from MNP to AMNP to DAMNP, with the maximum uptake at pH 5.5 in all cases: MNP, qe = 63 mg g-1, PC = 127 mg g-1 mM-1; AMNP, qe = 165 mg g-1, PC = 584 mg g-1 mM-1; DAMNP, qe = 249 mg g-1, PC = 2318 mg g-1 mM-1 (at 25 °C; initial U concentration 0.63 mM; 5 mg adsorbent in 10 mL of solution; contact time, 3 h). The pH maximum is related to the predominance of mono- and di-cationic uranium species. Uptake by DAMNPs follows a pseudo-first-order or pseudo-second-order kinetic model and fits a variety of adsorption models. The maximum adsorption capacity for DAMNPs is higher than for other functionalized magnetic nanohybrids. This adsorbent can be regenerated and recycled for at least 10 cycles with less than 10% loss in activity, and shows high selectivity. These findings suggest that DAMNP could be a promising adsorbent for the recovery of uranium from nuclear wastewaters.

New Quinoid Bio-Inspired Materials Using Para-Azaquinodimethane Moiety.

Quinoid single molecules are regarded as promising materials for electronic applications due to their tunable chemical structure-driven properties. A series of three single bio-inspired quinoid materials containing para-azaquinodimethane (p-AQM) moiety were designed, synthesized and characterized. AQM1, AQM2 and AQM3, prepared using aldehydes derived from almonds, corncobs and cinnamon, respectively, were studied as promising quinoid materials for optoelectronic applications. The significance of facile synthetic procedures is highlighted through a straightforward two-step synthesis, using Knoevenagel condensation. The synthesized molecules showed molar extinction coefficients of 22,000, 32,000 and 61,000 L mol-1 cm-1, respectively, for AQM1, AQM2 and AQM3. The HOMO-LUMO energy gaps were calculated experimentally, theoretically showing the same trends: AQM3 < AQM2 < AQM1. The role of the aryl substituent was studied and showed an impact on the electronic properties. DFT calculations show planar structures with quinoidal bond length alternation, in agreement with the experimental results. Finally, these bio-based materials showed high thermal stabilities between 290 °C and 340 °C and a glassy behavior after the first heating-cooling scan. These results highlight these bio-based single molecules as potential candidates for electronic or biomedical applications.

Competitive Photoisomerization and Energy Transfer Processes in Fluorescent Multichromophoric Systems.

Multichromophoric systems showing both fluorescence and photoisomerization are fascinating, with complex interchromophoric interactions. The experimental and theoretical study of a series of compounds, bearing a variable number of 4-dicyanomethylene-2-tert-butyl-6-(p-(N-(2-azidoethyl)-N-methyl)aminostyryl)-4H-pyran (DCM) units are reported. The photophysical properties of multi-DCM derivatives, namely 2DCM and 3DCM, were compared to the single model azido-functionalized DCM, in the E and Z isomers. The (EE)-2DCM and (EEE)-3DCM were synthesized via the click reaction. Steady-state spectroscopy and photokinetics experiments under UV or visible irradiation indicated the presence of intramolecular energy transfer processes among the DCM units. Homo- and hetero-energy transfer processes between adjacent chromophores were confirmed by fluorescence anisotropy and decays. Molecular dynamics simulations for 2DCM were carried out and analyzed using a Markov state model, providing geometrical parameters (orientation and distance between chromophores) and energy transfer efficiency. This work contributes to a better understanding and rationalization of multiple energy transfer processes occuring within multichromophoric systems.

An accurate vibrational signature in halogen bonded molecular crystals.

The far infrared (FIR) and Raman fingerprints of the halogen bond in two representative 1D halogen bonded networks based on the recognition of TFIB, tetrafluorodiiodobenzene, with piperazine or azopyridine, have been accurately identified. It was demonstrated that the signature of the halogen bonding in the solid state, especially the N⋯I signal can be simply and directly evidenced in the far infrared region. The DFT theoretical calculations identified the N⋯I interaction in the molecular crystals and allowed estimation of the corresponding energies and distances of the involved halogen bonds, in accordance with the cristallographic data.

Visualization and Comprehension of Electronic and Topographic Contrasts on Cooperatively Switched Diarylethene-Bridged Ditopic Ligand.

Diarylethene is a prototypical molecular switch that can be reversibly photoisomerized between its open and closed forms. Ligands bpy-DAE-bpy, consisting of a phenyl-diarylethene-phenyl (DAE) central core and bipyridine (bpy) terminal substituents, are able to self-organize. They are investigated by scanning tunneling microscopy at the solid-liquid interface. Upon light irradiation, cooperative photochromic switching of the ligands is recognized down to the submolecular level. The closed isomers show different electron density of states (DOS) contrasts, attributed to the HOMO or LUMO molecular orbitals observed. More importantly, the LUMO images show remarkable differences between the open and closed isomers, attributed to combined topographic and electronic contrasts mainly on the DAE moieties. The electronic contrasts from multiple HOMO or LUMO distributions, combined with topographic distortion of the open or closed DAE, are interpreted by density functional theory (DFT) calculations.

Photoisomerization of a 4-dicyanomethylene-2-methyl-6-(p-dimethylaminostyryl)-4H-pyran analog dye: a combined photophysical and theoretical investigation.

A combination of experimental and theoretical investigations of a photoisomerizable analog of 4-dicyanomethylene-2-methyl-6-(p-dimethylaminostyryl)-4H-pyran (DCM) dye molecule is presented. We provide evidence that the 4 main isomers and conformers of DCM contribute to its photochemical and photophysical processes. The absorption and emission spectra, as well as time-resolved fluorescence experimental results, are discussed and compared to DFT/TDDFT calculations. The E ↔ Z isomerization is induced photochemically, whereas the s-cis ↔ s-trans conformational interconversion is a thermal process which may also happen during irradiation. The photoreaction pathways from the first excited state down to the ground state are shown to be mediated by two conical intersections, as revealed using spin-flip TDDFT calculations. The rationalization of these isomerization schemes provides important insights into the photophysical properties of DCM, responsible for its photoswitchable fluorescence.

A Photo- and Redox-Driven Two-Directional Terthiazole-Based Switch: A Combined Experimental and Computational Investigation.

Terthiazoles with redox-active substituents like an N-methyl pyridinium group and ferrocene have been synthesized and their photo- and electro-chromic behaviors were investigated. The presence of two lateral N-methyl pyridinium substituents in the structure of terthiazole proved to be effective in inducing not only the reductive ring-closure of the terthiazole core but also its oxidative ring-opening reaction, leading to the first terarylene-based switch able to fully operate both photochemically and electrochemically. Moreover, the large increase in the redox potential between its open and closed form (700 mV) means that a part of the photon energy necessary to trigger the cyclization is stored in the form of chemical potential available for other works. Introduction of a second redox-active unit such as ferrocene onto the central thiazolyl moiety is found to inhibit the photochromism of the switch but not its redox switchability, which, instead, got improved for the ring-opening reaction via the redox properties of the ferrocenyl unit. The optical and redox properties of the switch in its different oxidation states are analyzed with the aid of DFT calculations in order to rationalize different switching processes.

Triangulenium dyes: the comprehensive photo-absorption and emission story of a versatile family of chromophores.

The triangulenium dyes constitute a family of versatile chromophores whose impressive photo-absorption and emission properties are currently highlighted in numerous novel experimental applications. In this investigation, we provide a comprehensive TDDFT characterization of their spectroscopic properties elucidating the origin of their large and complex absorption and emission vibronic spectra spread over the (whole) visible region. More precisely, by benchmarking the performance of 10 commonly-used exchange-correlation density functionals belonging to different classes of approximation, we develop and validate a computational protocol allowing the accurate modeling of both the position and optical line-shape of their vibrationally-resolved absorption and emission band structures. We find that semilocal approximations provide the best estimate of the structure of the vibronic spectra, however they spuriously and strongly underestimate their position. We finally show that global-hybrid density functionals mixing between 20 and 30% of exact-like exchange are an excellent compromise to get a satisfactory estimate of both of these properties.

Intramolecular Path Determination of Active Electrons on Push-Pull Oligocarbazole Dyes-Sensitized Solar Cells.

Several push-pull oligocarbazole dye-sensitizers have been studied using theoretical methods in order to better understand the relationship between structural electronic or optical properties and intramolecular path of active electrons during the ionization and injection processes. DFT/TD-DFT calculations were performed on a series of five dye sensitizers. They differ by the presence of electron donating group (EDG) by inductive effect (noted+I) or electron releasing group (ERG) by mesomeric effect (noted+M) or electron withdrawing group by inductive effect (noted-I) on the pushed part of the dyes studied. Our work focused on the internal distribution of electrons in the different parts of dye that are the push/pull moieties and the π-bridge. The study concerned the ground state, the electronic transition process and the excited state. In each situation, the fragment acting in the ionization or transition phenomena were identified. In the ground state, the electrons of the push part appear to be the least bound because they have the highest probabilities of ionization. In the excited state, the ionized atoms are essentially positioned in the pushing part and some neighboring atoms of the bridge. In the electronic transition, the active atoms are located in the π-conjugated part but only on the side adjacent to the acceptor group. To arrive to this conclusion, we optimized the structures of the five dyes in their ground and excited states. We calculated the atomic charges, the wavelengths and intensities of electronic transitions in the visible domain, the reorganization energies as well as the oxidation potential. It appears that +M donor ligands improve the performance of a dye because the great distribution of atoms to be ionized in the push parts.

Four Major Channels Detected in the Cytochrome P450 3A4: A Step toward Understanding Its Multispecificity.

We computed the network of channels of the 3A4 isoform of the cytochrome P450 (CYP) on the basis of 16 crystal structures extracted from the Protein Data Bank (PDB). The calculations were performed with version 2 of the CCCPP software that we developed for this research project. We identified the minimal cost paths (MCPs) output by CCCPP as probable ways to access to the buried active site. The algorithm of calculation of the MCPs is presented in this paper, with its original method of visualization of the channels. We found that these MCPs constitute four major channels in CYP3A4. Among the many channels proposed by Cojocaru et al. in 2007, we found that only four of them open in 3A4. We provide a refined description of these channels together with associated quantitative data.

Development of XIAP Antagonists Based On De Novo 8,5-Fused Bicyclic Lactams.

In order to develop original water soluble antagonists of X-linked inhibitor of apoptosis protein (XIAP), a novel bicyclic scaffold was designed based on 8,5-fused bicyclic lactam. During its preparation, a spontaneous rearrangement from 8,5- to 7,5-fused bicyclic lactam was observed and confirmed by MS and NMR analyses, in particular the HMBC spectra. DFT calculations were performed to understand the corresponding mechanism. It was finally prevented through changing the reaction order in the synthesis route and a Smac mimetic with this core structure, ZJ-1 was successfully obtained. The structure of this new bicyclic scaffold was well confirmed by HRMS and NMR (1H, 13C, NOESY) analyses. ZJ-1 presented in addition a binding affinity to XIAP-BIR3, nearly 6 times better than that of AVPI, similar to the reported SM-128 in an in vitro fluorescence polarization (FP) assay. This preliminary result suggests that this new bicyclic scaffold could be very attractive in the development of novel anticancer agents targeting XIAP.

Alkyl-Modified Gold Surfaces: Characterization of the Au-C Bond.

The surface of gold can be modified with alkyl groups through a radical crossover reaction involving alkyliodides or bromides in the presence of a sterically hindered diazonium salt. In this paper, we characterize the Au-C(alkyl) bond by surface-enhanced Raman spectroscopy (SERS); the corresponding peak appears at 387 cm-1 close to the value obtained by theoretical modeling. The Au-C(alkyl) bond energy is also calculated, it reaches -36.9 kcal mol-1 similar to that of an Au-S-alkyl bond but also of an Au-C(aryl) bond. In agreement with the similar energies of Au-C(alkyl) and Au-S-(alkyl), we demonstrate experimentally that these groups can be exchanged on the surface of gold.

Photoinduced Electron Transfer (PET)-Mediated Fragmentation of Picolinium-Derived Redox Probes.

The photolysis of covalently linked N-alkyl picolinium phenylacetate-carbazole dyads was analyzed experimentally and by using density functional theory (DFT) and time dependent-DFT (TD-DFT) calculations. In contrast to earlier observations efficient one and two-photon fragmentations conditions were found for 15 c (δu =0.16 GM at 730 nm) opening the way for the design of a novel class of "caged" compounds.

Light-induced piston nanoengines: ultrafast shuttling of a styryl dye inside cucurbit[7]uril.

The combination of photoactive styryl(pyridinium) dyes and cucurbit[7]uril (CB[7]) in an integrated supramolecular system allowed us to design a novel high speed molecular machine based on the fully reversible shuttling motion of the dye inside the CB[7] host cavity. The driving force of this movement is the electrostatic potential change after the occurrence of intramolecular charge transfer in the excited state of the dye molecule that can be externally controlled by light. Steady-state and time-resolved optical spectroscopy as well as DFT calculations provided an unambiguous evidence for the ultrafast piston-like movement of the system between two states. The shuttling process occurs in the picosecond timescale and its bistability depends on the strength of the dye donor fragment.

The Cytochrome P450 3A4 has three Major Conformations: New Clues to Drug Recognition by this Promiscuous Enzyme.

We computed the channels of the 3A4 isoform of the cytochrome P450 3A4 (CYP) on the basis of 24 crystal structures extracted from the Protein Data Bank (PDB). We identified three major conformations (denoted C, O1 and O2) using an enhanced version of the CCCPP software that we developed for the present work, while only two conformations (C and O2 ) are considered in the literature. We established the flowchart of definition of these three conformations in function of the structural and physicochemical parameters of the ligand. The channels are characterized with qualitative and quantitative parameters, and not only with their surrounding secondary structures as it is usually done in the literature.

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.