Nanoactuator for Neuronal Optoporation.

Light-driven modulation of neuronal activity at high spatial-temporal resolution is becoming of high interest in neuroscience. In addition to optogenetics, nongenetic membrane-targeted nanomachines that alter the electrical state of the neuronal membranes are in demand. Here, we engineered and characterized a photoswitchable conjugated compound (BV-1) that spontaneously partitions into the neuronal membrane and undergoes a charge transfer upon light stimulation. The activity of primary neurons is not affected in the dark, whereas millisecond light pulses of cyan light induce a progressive decrease in membrane resistance and an increase in inward current matched to a progressive depolarization and action potential firing. We found that illumination of BV-1 induces oxidation of membrane phospholipids, which is necessary for the electrophysiological effects and is associated with decreased membrane tension and increased membrane fluidity. Time-resolved atomic force microscopy and molecular dynamics simulations performed on planar lipid bilayers revealed that the underlying mechanism is a light-driven formation of pore-like structures across the plasma membrane. Such a phenomenon decreases membrane resistance and increases permeability to monovalent cations, namely, Na+, mimicking the effects of antifungal polyenes. The same effect on membrane resistance was also observed in nonexcitable cells. When sustained light stimulations are applied, neuronal swelling and death occur. The light-controlled pore-forming properties of BV-1 allow performing "on-demand" light-induced membrane poration to rapidly shift from cell-attached to perforated whole-cell patch-clamp configuration. Administration of BV-1 to ex vivo retinal explants or in vivo primary visual cortex elicited neuronal firing in response to short trains of light stimuli, followed by activity silencing upon prolonged light stimulations. BV-1 represents a versatile molecular nanomachine whose properties can be exploited to induce either photostimulation or space-specific cell death, depending on the pattern and duration of light stimulation.

Effect of Protonation on the Molecular Structure of Adenosine 5'-Triphosphate: A Combined Theoretical and Near Edge X-ray Absorption Fine Structure Study.

The present work combines the near edge X-ray absorption mass spectrometry of a protonated adenosine 5'-triphosphate (ATP) molecule isolated in an ion trap with (time-dependent) density functional theory calculations. Our study unravels the effect of protonation on the ATP structure and its spectral properties, providing structure-property relationships at atomistic resolution for protonated ATP (ATPH) isolated in the gas-phase conditions. On the other hand, the present C and N K-edge X-ray absorption spectra of isolated ATPH appear closely like those previously reported for solvated ATP at low pH. Therefore, the present work should be relevant for further investigation and modeling of structure-function properties of protonated adenine and ATP in complex biological environments.

A membrane intercalating metal-free conjugated organic photosensitizer for bacterial photodynamic inactivation.

Photodynamic inhibition (PDI) of bacteria represents a powerful strategy for dealing with multidrug-resistant pathogens and infections, as it exhibits minimal development of antibiotic resistance. The PDI action stems from the generation of a triplet state in the photosensitizer (PS), which subsequently transfers energy or electrons to molecular oxygen, resulting in the formation of reactive oxygen species (ROS). These ROS are then able to damage cells, eventually causing bacterial eradication. Enhancing the efficacy of PDI includes the introduction of heavy atoms to augment triplet generation in the PS, as well as membrane intercalation to circumvent the problem of the short lifetime of ROS. However, the former approach can pose safety and environmental concerns, while achieving stable membrane partitioning remains challenging due to the complex outer envelope of bacteria. Here, we introduce a novel PS, consisting of a metal-free donor-acceptor thiophene-based conjugate molecule (BV-1). It presents several advantageous features for achieving effective PDI, namely: (i) it exhibits strong light absorption due to the conjugated donor-acceptor moieties; (ii) it exhibits spontaneous and stable membrane partitioning thanks to its amphiphilicity, accompanied by a strong fluorescence turn-on; (iii) it undergoes metal-free intersystem crossing, which occurs preferentially when the molecule resides in the membrane. All these properties, which we rationalized via optical spectroscopies and calculations, enable the effective eradication of Escherichia coli, with an inhibition concentration that is below that of current state-of-the-art treatments. Our approach holds significant potential for the development of new PS for controlling bacterial infections, particularly those caused by Gram-negative bacteria.

A study of the valence photoelectron spectrum of uracil and mixed water-uracil clusters.

The valence ionization of uracil and mixed water-uracil clusters has been studied experimentally and by ab initio calculations. In both measurements, the spectrum onset shows a red shift with respect to the uracil molecule, with the mixed cluster characterized by peculiar features unexplained by the sum of independent contributions of the water or uracil aggregation. To interpret and assign all the contributions, we performed a series of multi-level calculations, starting from an exploration of several cluster structures using automated conformer-search algorithms based on a tight-binding approach. Ionization energies have been assessed on smaller clusters via a comparison between accurate wavefunction-based approaches and cost-effective DFT-based simulations, the latter of which were applied to clusters up to 12 uracil and 36 water molecules. The results confirm that (i) the bottom-up approach based on a multilevel method [Mattioli et al. Phys. Chem. Chem. Phys. 23, 1859 (2021)] to the structure of neutral clusters of unknown experimental composition converges to precise structure-property relationships and (ii) the coexistence of pure and mixed clusters in the water-uracil samples. A natural bond orbital (NBO) analysis performed on a subset of clusters highlighted the special role of H-bonds in the formation of the aggregates. The NBO analysis yields second-order perturbative energy between the H-bond donor and acceptor orbitals correlated with the calculated ionization energies. This sheds light on the role of the oxygen lone-pairs of the uracil CO group in the formation of strong H-bonds, with a stronger directionality in mixed clusters, giving a quantitative explanation for the formation of core-shell structures.

Insights into the Thermally Activated Cyclization Mechanism in a Linear Phenylalanine-Alanine Dipeptide.

Dipeptides, the prototype peptides, exist in both linear (l-) and cyclo (c-) structures. Since the first mass spectrometry experiments, it has been observed that some l-structures may turn into the cyclo ones, likely via a temperature-induced process. In this work, combining several different experimental techniques (mass spectrometry, infrared and Raman spectroscopy, and thermogravimetric analysis) with tight-binding and ab initio simulations, we provide evidence that, in the case of l-phenylalanyl-l-alanine, an irreversible cyclization mechanism, catalyzed by water and driven by temperature, occurs in the condensed phase. This process can be considered as a very efficient strategy to improve dipeptide stability by turning the comparatively fragile linear structure into the robust and more stable cyclic one. This mechanism may have played a role in prebiotic chemistry and can be further exploited in the preparation of nanomaterials and drugs.

A systematic study of the valence electronic structure of cyclo(Gly-Phe), cyclo(Trp-Tyr) and cyclo(Trp-Trp) dipeptides in the gas phase.

The electronic energy levels of cyclo(glycine-phenylalanine), cyclo(tryptophan-tyrosine) and cyclo(tryptophan-tryptophan) dipeptides are investigated with a joint experimental and theoretical approach. Experimentally, valence photoelectron spectra in the gas phase are measured using VUV radiation. Theoretically, we first obtain low-energy conformers through an automated conformer-rotamer ensemble sampling scheme based on tight-binding simulations. Then, different first principles computational schemes are considered to simulate the spectra: Hartree-Fock (HF), density functional theory (DFT) within the B3LYP approximation, the quasi-particle GW correction, and the quantum-chemistry CCSD method. Theory allows assignment of the main features of the spectra. A discussion on the role of electronic correlation is provided, by comparing computationally cheaper DFT scheme (and GW) results with the accurate CCSD method.

Water-biomolecule clusters studied by photoemission spectroscopy and multilevel atomistic simulations: hydration or solvation?

The properties of mixed water-uracil nanoaggregates have been probed by core electron-photoemission measurements to investigate supramolecular assembly in the gas phase driven by weak interactions. The interpretation of the measurements has been assisted by multilevel atomistic simulations, based on semi-empirical tight-binding and DFT-based methods. Our protocol established a positive-feedback loop between experimental and computational techniques, which has enabled a sound and detailed atomistic description of such complex heterogeneous molecular aggregates. Among biomolecules, uracil offers interesting and generalized skeletal features; its structure encompasses an alternation of hydrophilic H-bond donor and acceptor sites and hydrophobic moieties, typical in biomolecular systems, that induces a supramolecular core-shell-like organization of the mixed clusters with a water core and an uracil shell. This structure is far from typical models of both solid-state hydration, with water molecules in defined positions, or liquid solvation, where disconnected uracil molecules are completely surrounded by water.

Unravelling molecular interactions in uracil clusters by XPS measurements assisted by ab initio and tight-binding simulations.

The C, N and O 1s XPS spectra of uracil clusters in the gas phase have been measured. A new bottom-up approach, which relies on computational simulations starting from the crystallographic structure of uracil, has been adopted to interpret the measured spectra. This approach sheds light on the different molecular interactions (H-bond, π-stacking, dispersion interactions) at work in the cluster and provides a good understanding of the observed XPS chemical shifts with respect to the isolated molecule in terms of intramolecular and intermolecular screening occurring after the core-hole ionization. The proposed bottom-up approach, reasonably expensive in terms of computational resources, has been validated by finite-temperature molecular dynamics simulations of clusters composed of up to fifty molecules.

[1]Benzothieno[3,2-b][1]benzothiophene-Phthalocyanine Derivatives: A Subclass of Solution-Processable Electron-Rich Hole Transport Materials.

The [1]benzothieno[3,2-b][1]benzothiophene (BTBT) planar system was used to functionalize the phthalocyanine ring aiming at synthesizing novel electron-rich π-conjugated macrocycles. The resulting ZnPc-BTBT and ZnPc-(BTBT)4 derivatives are the first two examples of a phthalocyanine subclass having potential use as solution-processable p-type organic semiconductors. In particular, the combination of experimental characterizations and theoretical calculations suggests compatible energy level alignments with mixed halide hybrid perovskite-based devices. Furthermore, ZnPc-(BTBT)4 features a high aggregation tendency, a useful tool to design compact molecular films. When tested as hole transport materials in perovskite solar cells under 100 mA cm-2 standard AM 1.5G solar illumination, ZnPc-(BTBT)4 gave power conversion efficiencies as high as 14.13 %, irrespective of the doping process generally required to achieve high photovoltaic performances. This work is a first step toward a new phthalocyanine core engineerization to obtain robust, yet more efficient and cost-effective materials for organic electronics and optoelectronics.

Suzuki-Miyaura Micellar One-Pot Synthesis of Symmetrical and Unsymmetrical 4,7-Diaryl-5,6-difluoro-2,1,3-benzothiadiazole Luminescent Derivatives in Water and under Air.

The Suzuki-Miyaura cross-coupling reaction of 4,7-dibromo-5,6-difluoro-2,1,3-benzothiadiazole with different arylboronic acids can be efficiently carried out in water and under air by means of micellar coupling. The careful tuning of reaction conditions enables preparation of symmetrically and unsymmetrically substituted derivatives. The moderate to good yields obtained, along with the wide variety of available substitution patterns, makes this sustainable methodology very useful for the preparation of building blocks for luminescent optoelectronic materials.

Unexpected Rotamerism at the Origin of a Chessboard Supramolecular Assembly of Ruthenium Phthalocyanine.

We have investigated the formation and the properties of ultrathin films of ruthenium phthalocyanine (RuPc)2 vacuum deposited on graphite by scanning tunneling microscopy and synchrotron photoemission spectroscopy measurements, interpreted in close conjunction with ab initio simulations. Thanks to its unique dimeric structure connected by a direct Ru-Ru bond, (RuPc)2 can be found in two stable rotameric forms separated by a low-energy barrier. Such isomerism leads to a peculiar organization of the molecules in flat, horizontal layers on the graphite surface, characterized by a chessboard-like alternation of the two rotamers. Moreover, the molecules are vertically connected to form π-stacked columnar pillars of akin rotamers, compatible with the high conductivity measured in (RuPc)2 powders. Such features yield an unprecedented supramolecular assembly of phthalocyanine films, which could open interesting perspectives toward the realization of new architectures of organic electronic devices.

A Spotlight on the Compatibility between XFEL and Ab Initio Structures of the Oxygen Evolving Complex in Photosystem†II.

The Mn4 CaO5 cluster of photosystem II promotes a crucial step in the oxygenic photosynthesis, namely, the water-splitting reaction. The structure of such cluster in the S1 state of the Kok-Joliot's cycle has been recently resolved by femtosecond X-ray free-electron laser (XFEL) measurements. However, the XFEL results are characterized by appreciable discrepancies with previous X-ray diffraction (XRD), as well as with S1 models based on ab initio calculations. We provide here a unifying picture based on a combined set of DFT-based structures and molecular dynamics simulations of the S0 and S1 states. Our findings indicate that the XFEL results cannot be interpreted on the grounds of a single structure. A combination of two S1 stable isomers together with a minority contribution of the S0 state is necessary to reproduce XFEL results within 0.16 Å.

A Ru-Ru pair housed in ruthenium phthalocyanine: the role of a "cage" architecture in the molecule coupling with the Ag(111) surface.

A number of studies have investigated the properties of monomeric and double-decker phthalocyanines (Pcs) adsorbed on metal surfaces, in view of applications in spintronics devices. In a combined experimental and theoretical study, we consider here a different member of the Pcs family, the (RuPc)2 dimer, whose structure is characterized by two paired up magnetic centers embedded in a double-decker architecture. For (RuPc)2 on Ag(111), we show that this architecture works as a preserving cage by shielding the Ru-Ru pair from a direct interaction with the surface atoms. In fact, while noticeable surface-to-molecule charge transfer occurs with the ensuing quenching of the molecular magnetic moment, such phenomena occur here in the absence of a direct Ru-Ag coupling or structural rearrangement, at variance with other Pcs and thanks to the above shielding effect. These unique properties of the (RuPc)2 architecture are expected to permit an easy control of the surface-to-molecule charge-transfer process as well as of the molecular magnetic properties, thus making the (RuPc)2 dimer a significant paradigm for innovative "cage" structures as well as a promising candidate for applications in spintronics nano or single-molecule devices.

Atomistic Texture of Amorphous Manganese Oxides for Electrochemical Water Splitting Revealed by Ab Initio Calculations Combined with X-ray Spectroscopy.

Amorphous transition-metal (hydr)oxides are considered as the most promising catalysts that promote the oxidation of water to molecular oxygen, protons, and "energized" electrons, and, in turn, as fundamental parts of "artificial leaves" that can be exploited for large scale generation of chemical fuels (e.g., hydrogen) directly from sunlight. We present here a joint theoretical-experimental investigation of electrodeposited amorphous manganese oxides with different catalytic activities toward water oxidation (MnCats). Combining the information content of X-ray absorption fine structure (XAFS) measurements with the predictive power of ab initio calculations based on density functional theory, we have been able to identify the essential structural and electronic properties of MnCats. We have elucidated (i) the localization and structural connection of Mn(II), Mn(III), and Mn(IV) ions in such amorphous oxides and (ii) the distribution of protons at the MnCat/water interface. Our calculations result in realistic 3D models of the MnCat atomistic texture, formed by the interconnection of small planar Mn-oxo sheets cross-linked through different kinds of defective Mn atoms, isolated or arranged in closed cubane-like units. Essential for the catalytic activity is the presence of undercoordinated Mn(III)O5 units located at the boundary of the amorphous network, where they are ready to act as hole traps that trigger the oxidation of neighboring water molecules when the catalyst is exposed to an external positive potential. The present validation of a sound 3D model of MnCat improves the accuracy of XAFS fits and opens the way for the development of mechanistic schemes of its functioning beyond a speculative level.

Reaction pathways for oxygen evolution promoted by cobalt catalyst.

The in-depth understanding of the molecular mechanisms regulating the water oxidation catalysis is of key relevance for the rationalization and the design of efficient oxygen evolution catalysts based on earth-abundant transition metals. Performing ab initio DFT+U molecular dynamics calculations of cluster models in explicit water solution, we provide insight into the pathways for oxygen evolution of a cobalt-based catalyst (CoCat). The fast motion of protons at the CoCat/water interface and the occurrence of cubane-like Co-oxo units at the catalyst boundaries are the keys to unlock the fast formation of O-O bonds. Along the resulting pathways, we identified the formation of Co(IV)-oxyl species as the driving ingredient for the activation of the catalytic mechanism, followed by their geminal coupling with O atoms coordinated by the same Co. Concurrent nucleophilic attack of water molecules coming directly from the water solution is discouraged by high activation barriers. The achieved results suggest also interesting similarities between the CoCat and the Mn4Ca-oxo oxygen evolving complex of photosystem II.

Clusters and magnetic anchoring points in (Ga,Fe)N condensed magnetic semiconductors.

The stability and magnetic properties of Fe clusters in the (Ga,Fe)N magnetic semiconductor is investigated by using first-principles density functional theory and local spin density+Hubbard U theoretical methods. The present results reveal the existence of ferrimagnetic clusters formed by three or four peripheral Fe atoms neighboring a central Fe atom acting as a robust magnetic anchoring point. These clusters have magnetic moments 2 or 3 times that of a single Fe atom and, when connected by sharing peripheral Fe atoms, can form stable, ordered magnetic regions where all of the central atoms are ferromagnetically coupled. The formation of these ferrimagnetic clusters is proposed here to be at the origin of the ferromagnetic behavior observed in (Ga,Fe)N samples showing chemical phase separation.

Protonation states in a cobalt-oxide catalyst for water oxidation: fine comparison of ab initio molecular dynamics and X-ray absorption spectroscopy results.

Ab initio molecular dynamics simulations of a recently proposed cobalt-based catalyst for water oxidation provide insight into the properties of protons at the water/oxide interface. Calculations and X-ray absorption spectroscopy data indicate a cubane-like structure of the catalyst, support the occurrence of protonated µ(2)-O atoms, suggest deprotonated µ(3)-O atoms and the presence of sites promoting low-barrier hydrogen bonds.

Synthesis of a novel unsymmetrical Zn(II) phthalocyanine bearing a phenyl ethynyl moiety as sensitizer for dye-sensitized solar cells.

A new unsymmetrical zinc phthalocyanine sensitizer has been synthesised. The anchoring of the molecule to nanocrystalline TiO(2) films is realised by a carboxylic group connected to a phenyl ethynyl moiety. Density Functional Theory (DFT) calculations show significant and positive effects of such a functionalization. Electron injection into the semiconductor and photocurrent generation in DSSC are also presented.

Reaction intermediates in the photoreduction of oxygen molecules at the (101) TiO2 (anatase) surface.

The structural, electronic, and vibrational properties of intermediates of the O(2) photoreduction at the (101) TiO(2) (anatase) surface have been investigated by performing ab initio density functional calculations. In detail, a recently proposed approach has been used where molecules on the surface are treated like surface defects. Thus, by applying theoretical methods generally used in the physics of semiconductors, we successfully estimate the location and donor/acceptor character of the electronic levels induced by an adsorbed molecule in the TiO(2) energy gap, both crucial for the surface-molecule charge-transfer processes, and investigate the formation and the properties of charged intermediates. The present approach permits a view of the O(2) photoreduction process through several facets, which elucidates the molecule-surface charge-transfer conditions and reveals the key role played by charged intermediates. A comparison of present results with those of a highly sensitive IR (infrared) spectroscopy study of intermediates of the O(2) photoreduction leads to a deeper understanding of this process and to revised vibrational-line assignments and reaction paths.