Boosting the Modeling of Infrared and Raman Spectra of Bulk Phase Chromophores with Machine Learning.

In the field of vibrational spectroscopy simulation, hybrid approximations to Kohn-Sham density-functional theory (KS-DFT) are often considered computationally prohibitive due to the significant effort required to evaluate the exchange-correlation potential in planewave codes. In this Letter, we show that by leveraging the porting of KS-DFT on GPU and incorporating machine-learning techniques, simulating IR and Raman spectra of real-life chromophores in bulk aqueous solution becomes a routine application at this level of theory.

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. , and prepared using aldehydes derived from almonds, corncobs and cinnamon, respectively, were studied as promising quinoid materials for optoelectronic applications.

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-S and R. Two types of building blocks can be formed; block I is enantiomer-pure and is built up of the same motifs (format SS or RR) whereas block II is enantiomer-mixed and composes both motifs (format SR), 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.

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.

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.

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

Maghemite (γ-FeO) nanoparticles (MNPs) were functionalized with 3-aminopropyltriethoxysilane (APTES) to give APTES@FeO (AMNP) which was then reacted with diethylenetriamine-pentaacetic acid (DTPA) to give a nanohybrid DTPA-APTES@FeO (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 UO with different stoichiometries.

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.

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.

Photoisomerization of a 4-dicyanomethylene-2-methyl-6-(-dimethylaminostyryl)-4-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-(-dimethylaminostyryl)-4-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.

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.

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.

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.

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.

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.

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 close to the value obtained by theoretical modeling. The Au-C(alkyl) bond energy is also calculated, it reaches -36.

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 (δ =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 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 O ) 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.

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.

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.

Supramolecular chiral host-guest nanoarchitecture induced by the selective assembly of barbituric acid derivative enantiomers.

Barbituric acid derivatives are prochiral molecules, i.e. they are chiral upon adsorption on surfaces.

Association of symmetrical alkane diols with pyridine: DFT/GIAO calculation of H NMR chemical shifts.

Proton nuclear magnetic resonance (NMR) shifts of the free diol and of its 1 : 1 and 1 : 2 hydrogen-bonded complexes with pyridine have been computed for five symmetrical alkane diols on the basis of density functional theory, by applying the gauge-including atomic orbital method to geometry-optimized conformers. For certain conformers, intramolecular OH···OH interactions, evidenced by high NMR OH proton shifts, are further enhanced on going from the free diol to the corresponding 1 : 1 diol/pyridine complex. This is confirmed by atoms-in-molecules and non-covalent interaction plots.

Striking HIV-1 Entry by Targeting HIV-1 gp41. But, Where Should We Target?

HIV-1 gp41 facilitates the viral fusion through a conformational switch involving the association of three C-terminal helices along the conserved hydrophobic grooves of three N-terminal helices coiled-coil. The control of these structural rearrangements is thought to be central to HIV-1 entry and, therefore, different strategies of intervention are being developed. Herewith, we describe a procedure to simulate the folding of an HIV-1 gp41 simplified model.