Description of a Non-Canonical AsPt Blue Species Originating from the Aerobic Oxidation of AP-1 in Aqueous Solution.

The peculiar behavior of arsenoplatin-1, ([Pt(µ-NHC(CH3)O)2ClAs(OH)2], AP-1), in aqueous solution and the progressive appearance of a characteristic and intense blue color led us to carry out a more extensive investigation to determine the nature of this elusive chemical species, which we named "AsPt blue". A multi-technique approach was therefore implemented to describe the processes involved in the formation of AsPt blue, and some characteristic features of this intriguing species were revealed.

Characterization of a Ruthenium(II) Complex in Singlet Oxygen-Mediated Photoelectrochemical Sensing.

A water-soluble ruthenium(II) complex (L), capable of producing singlet oxygen (1O2) when irradiated with visible light, was used to modify the surface of an indium-tin oxide (ITO) electrode decorated with a nanostructured layer of TiO2 (TiO2/ITO). Singlet oxygen triggers the appearance of a cathodic photocurrent when the electrode is illuminated and biased at a proper reduction potential value. The L/TiO2/ITO electrode was first characterized with cyclic voltammetry, impedance spectroscopy, NMR, and Raman spectroscopy. The rate constant of singlet oxygen production was evaluated by spectrophotometric measurements. Taking advantage of the oxidative process initiated by 1O2, the analysis of phenolic compounds was accomplished. Particularly, the 1O2-driven oxidation of hydroquinone (HQ) produced quinone moieties, which could be reduced back at the electrode surface, biased at -0.3 V vs Ag/AgCl. Such a light-actuated redox cycle produced a photocurrent dependent on the concentration of HQ in solution, exhibiting a limit of detection (LOD) of 0.3 µmol dm-3. The L/TiO2/ITO platform was also evaluated for the analysis of p-aminophenol, a commonly used reagent in affinity sensing based on alkaline phosphatase.

Combining cross-coupling reaction and Knoevenagel condensation in the synthesis of glyco-BODIPY probes for DC-SIGN super-resolution bioimaging.

Lectins are involved in a wide range of carbohydrate mediated recognition processes. Therefore, the availability of highly performant fluorescent tools tailored for lectin targeting and able to efficiently track events related to such key targets is in high demand. We report here on the synthesis of the glyco-BODIPYs 1 and 2, based on the efficient combination of a Heck-like cross coupling and a Knoevenagel condensation, which revealed efficient in addressing lectins. In particular, glyco-BODIPY 1 has two glycosidase stable C-mannose residues, which act as DC-SIGN (dendritic cell-specific intercellular adhesion molecule-3-grabbing non-integrin) targeting modules. By using live-cell fluorescence microscopy, we proved that BODIPY-mannose 1 was efficiently taken up by immune cells expressing DC-SIGN receptors. Super-resolution stimulated emission depletion (STED) microscopy further revealed that the internalized 1 localized in membranes of endosomes, proving that 1 is a reliable tool also in STED applications. Of note, glyco-BODIPY 1 contains an aryl-azido group, which allows further functionalization of the glycoprobe with bioactive molecules, thus paving the way for the use of 1 for tracking lectin-mediated cell internalization in diverse biological settings.

Highly Charged Ruthenium(II) Polypyridyl Complexes as Effective Photosensitizer in Photodynamic Therapy.

A comparative study between two novel, highly water soluble, ruthenium(II) polypyridyl complexes, [Ru(phen)2 L'] and [Ru(phen)2 Cu(II)L'] (L and L-CuII ), containing the polyaazamacrocyclic unit 4,4'-(2,5,8,11,14-pentaaza[15])-2,2'-bipyridilophane (L'), is herein reported. L and L-CuII interact with calf-thymus DNA and efficiently cleave DNA plasmid when light-activated. They also possess great penetration abilities and photo-induced biological activities, evaluated on an A375 human melanoma cell line, with L-CuII being the most effective. Our study highlights the key role of the Fenton active CuII center within the macrocycle framework, that would play a synergistic role with light activation in the formation of cytotoxic ROS species. Based on these results, an optimal design of RuII polypyridyl systems featuring specific CuII -chelating polyamine units could represent a suitable strategy for the development of novel and effective photosensitizers in photodynamic therapy.

Computational Investigation of the Selective Cleavage of Diastereotopic Cyclopropane Bonds in 5-Spirocyclopropane Isoxazolidines Rearrangement.

The complete path of the Brandi-Guarna rearrangement of 5-spirocyclopropane isoxazolidines has been investigated by means of density functional theory calculations to rationalize the competing formation of tetrahydropyridones and enaminones by the determination of the minimum energy reaction paths. Our calculations confirm that the rearrangement is triggered by the homolysis of the isoxazolidine N-O bond followed by cleavage of one of the two C-CH2 cyclopropane bonds as previously proposed by the Fabian group [ Eur. J. Org. Chem. 2001, 2001, 4223]. In addition, the results of this work suggest that in the presence of a stereogenic center at isoxazolidine C-4', the formation of a piperidinone or an enaminone as the final product depends on which of the two diastereotopic C-CH2 bonds of cyclopropane is cleaved in the second step of the process. The result can be of great interest for the understanding of other processes involving the opening of a cyclopropane ring.

Surface Enhanced Raman Spectroscopy for In-Field Detection of Pesticides: A Test on Dimethoate Residues in Water and on Olive Leaves.

Dimethoate (DMT) is an organophosphate insecticide commonly used to protect fruit trees and in particular olive trees. Since it is highly water-soluble, its use on olive trees is considered quite safe, because it flows away in the residual water during the oil extraction process. However, its use is strictly regulated, specially on organic cultures. The organic production chain certification is not trivial, since DMT rapidly degrades to omethoate (OMT) and both disappear in about two months. Therefore, simple, sensitive, cost-effective and accurate methods for the determination of dimethoate, possibly suitable for in-field application, can be of great interest. In this work, a quick screening method, possibly useful for organic cultures certification will be presented. DMT and OMT in water and on olive leaves have been detected by surface enhanced Raman spectroscopy (SERS) using portable instrumentations. On leaves, the SERS signals were measured with a reasonably good S/N ratio, allowing us to detect DMT at a concentration up to two orders of magnitude lower than the one usually recommended for in-field treatments. Moreover, detailed information on the DMT distribution on the leaves has been obtained by Raman line- (or area-) scanning experiments.

Correspondence between light-absorption spectrum and nonequilibrium work distribution as a mean to access free energy differences between electronic states.

The problem of recovering the free energy difference between two electronic states has been investigated by Frezzato [Chem. Phys. Lett. 533, 106 (2012)], exploring the equivalence between light-absorption spectra and work distribution, hence opening to the application of a spectroscopic version of the Jarzynski equality (JE) [Phys. Rev. Lett. 78, 2690 (1997)]. Here, assuming the validity of the time-dependent perturbation theory, we demonstrate that such equivalence does not lead to the known form of the JE. This is ascribed to the fact that light-absorption processes cannot be described as stochastic processes. To emphasize such an aspect, we devise a stochastic model for the UV-vis (ultraviolet and visible) absorption, suitable for determining the free energy difference between two generic quantum manifolds in a JE-like fashion. However, the model would require explicit knowledge of the transition dipole moments, which are in general not available. Nonetheless, we derive a spectroscopic version of the JE that allows us to recover the free energy difference between the ground and an excited electronic state when the latter state is the only one observed in the spectrum.

Photochemical Reactivity of 1,6-Methano[10]annulene.

1,6-Methano[10]annulene solutions in cyclohexane have been subjected to continuous and pulsed UV irradiation. Photolysis occurs in both cases, giving naphthalene as a minor and major product, respectively. The wavelength dependence of the reaction in solution indicates that the photochemical process occurs, exciting 1,6-methano[10]annulene in the second and third singlet electronic excited states. The reaction kinetics has been determined under pulsed irradiation. From the time dependence of concentrations, along with support of density functional theory calculations and early published data, two mechanisms are proposed for naphthalene production. Reaction steps such as direct migration of the bridging methylene of 1,6-methano[10]annulene to cyclohexane and 1,6-methano[10]annulene isomerization to benzotropilidene have been identified. The calculated energy diagrams relative to the ground and lowest excited states allow one to relate these steps to processes such as electrocyclic closure and sigmatropic shift. The norcaradienic form of 1,6-methano[10]annulene results in the critical species for methylene migration and the sigmatropic [1,5] shift. The present results and those arising from photolysis in the gas phase are good examples of the photochemical reactivity of 1,6-methano[10]annulene.

A fluorescent receptor for halide recognition: clues for the design of anion chemosensors.

The chemosensing properties of the polyaza-macrocycle 1-(6,7)-acridine-3,6,9,12-tetraaza-tridecaphane have been investigated by means of emission fluorescence spectroscopy, considering halide ions as substrates. As in the case of the free ligand, the fluorescence emission of the complexes is due to the acridinium species which are formed after photoinduced proton transfer reaction. The complexation constants have been obtained for the bi- and tri-protonated ligands in deoxygenated aqueous solutions. Two different emission behaviours have been observed varying the anion. Fluoride and chloride give rise to fluorescence enhancement whereas bromide and iodide strongly quench the emission. The macrocycle shows an unusual higher selectivity towards the chloride anion rather than fluoride. The fluorescence emission has been modelled considering a modified Stern-Volmer equation, taking into account the quenching effects of the largest anions, which can be considered negligible for fluoride and chloride anions. Ab initio calculations allow us to interpret the fluorescence emission of the complexes in terms of activation energy related to the proton transfer reaction responsible for the emission process.

Annealed importance sampling with constant cooling rate.

Annealed importance sampling is a simulation method devised by Neal [Stat. Comput. 11, 125 (2001)] to assign weights to configurations generated by simulated annealing trajectories. In particular, the equilibrium average of a generic physical quantity can be computed by a weighted average exploiting weights and estimates of this quantity associated to the final configurations of the annealed trajectories. Here, we review annealed importance sampling from the perspective of nonequilibrium path-ensemble averages [G. E. Crooks, Phys. Rev. E 61, 2361 (2000)]. The equivalence of Neal's and Crooks' treatments highlights the generality of the method, which goes beyond the mere thermal-based protocols. Furthermore, we show that a temperature schedule based on a constant cooling rate outperforms stepwise cooling schedules and that, for a given elapsed computer time, performances of annealed importance sampling are, in general, improved by increasing the number of intermediate temperatures.

Combining path-breaking with bidirectional nonequilibrium simulations to improve efficiency in free energy calculations.

An important limitation of unidirectional nonequilibrium simulations is the amount of realizations of the process necessary to reach suitable convergence of free energy estimates via Jarzynski's relationship [C. Jarzynski, Phys. Rev. Lett. 78, 2690 (1997)]. To this regard, an improvement of the method has been achieved by means of path-breaking schemes [R. Chelli et al., J. Chem. Phys. 138, 214109 (2013)] based on stopping highly dissipative trajectories before their normal end, under the founded assumption that such trajectories contribute marginally to the work exponential averages. Here, we combine the path-breaking scheme, called probability threshold scheme, to bidirectional nonequilibrium methods for free energy calculations [G. E. Crooks, Phys. Rev. E 61, 2361 (2000); R. Chelli and P. Procacci, Phys. Chem. Chem. Phys. 11, 1152 (2009)]. The method is illustrated and tested on a benchmark system, i.e., the helix-coil transition of deca-alanine. By using path-breaking in our test system, the computer time needed to carry out a series of nonequilibrium trajectories can be reduced up to a factor 4, with marginal loss of accuracy in free energy estimates.

Toward quantitative estimates of binding affinities for protein-ligand systems involving large inhibitor compounds: a steered molecular dynamics simulation route.

Understanding binding mechanisms between enzymes and potential inhibitors and quantifying protein-ligand affinities in terms of binding free energy is of primary importance in drug design studies. In this respect, several approaches based on molecular dynamics simulations, often combined with docking techniques, have been exploited to investigate the physicochemical properties of complexes of pharmaceutical interest. Even if the geometric properties of a modeled protein-ligand complex can be well predicted by computational methods, it is still challenging to rank with chemical accuracy a series of ligand analogues in a consistent way. In this article, we face this issue calculating relative binding free energies of a focal adhesion kinase, an important target for the development of anticancer drugs, with pyrrolopyrimidine-based ligands having different inhibitory power. To this aim, we employ steered molecular dynamics simulations combined with nonequilibrium work theorems for free energy calculations. This technique proves very powerful when a series of ligand analogues is considered, allowing one to tackle estimation of protein-ligand relative binding free energies in a reasonable time. In our cases, the calculated binding affinities are comparable with those recovered from experiments by exploiting the Michaelis-Menten mechanism with a competitive inhibitor.

Excited-state absorption and ultrafast relaxation dynamics of protoporphyrin IX and hemin.

The transient evolution of protoporphyrin IX (PPIX) and hemin following the Soret band excitation was measured in the 410-600 nm spectral region with sub-picosecond time resolution. In PPIX the relaxation pathway was characterized in the femto- and picosecond time scale by two processes with time constants of 350 fs and ~6 ps, describing the evolution of the system through internal Q(y) → Q(x) conversion and vibrational relaxation and cooling in the Q(x) state. The lifetime of the Q(x) state was found to be 10.4 ns by time resolved fluorescence measurements. In hemin, the ground state is completely recovered in tens of picoseconds through pathways involving CT and (d,d) states. The experimentally observed vibrational dynamics is mainly due to "hot" ground state transitions.

Tuning the emission properties of fluorescent ligands by changing pH: the unusual case of an acridine-containing polyamine macrocycle.

Synthesis and characterization of a new macrocyclic compound, composed by a triethylentetraamine chain linking the 4 and 5 positions of an acridine moiety, are reported. The molecule, devised as a fluorescent chemosensor for anions, has revealed an intriguing pH-dependent spectroscopic behavior, whose features are the specific object of this article. Ligand protonation in aqueous solution has been analyzed by means of potentiometric, (1)H NMR, UV-vis, and fluorescence emission measurements. The molecule binds up to four protons in the pH range 2-11. Protonation takes place on the aliphatic tetraamine chain, while the acridine nitrogen does not participate to proton binding even at very low pH. Differently from acridine, the UV-vis spectra are almost unaffected by the pH. On the opposite, the emission spectra are strongly pH-dependent. In fact, at low pH values, the spectra show a blue-shifted emission, resembling that of unprotonated acridine, while at slightly acidic and alkaline pH the fluorescence features a red-shifted band similar to that of acridinium cation. This unusual behavior occurs in the mono-, bi-, and triprotonated forms of the compound and is interpreted as due to an excited state proton transfer from an aliphatic ammonium group adjacent to the acridine moiety to the acridine nitrogen. In the fully protonated state, this process is prevented owing to unfavorable molecular arrangements mainly determined by electrostatic repulsions. This interpretation is supported by quantum mechanical calculations as well as molecular dynamics simulations.

Path-breaking schemes for nonequilibrium free energy calculations.

We propose a path-breaking route to the enhancement of unidirectional nonequilibrium simulations for the calculation of free energy differences via Jarzynski's equality [C. Jarzynski, Phys. Rev. Lett. 78, 2690 (1997)]. One of the most important limitations of unidirectional nonequilibrium simulations is the amount of realizations necessary to reach suitable convergence of the work exponential average featuring the Jarzynski's relationship. In this respect, a significant improvement of the performances could be obtained by finding a way of stopping trajectories with negligible contribution to the work exponential average, before their normal end. This is achieved using path-breaking schemes which are essentially based on periodic checks of the work dissipated during the pulling trajectories. Such schemes can be based either on breaking trajectories whose dissipated work exceeds a given threshold or on breaking trajectories with a probability increasing with the dissipated work. In both cases, the computer time needed to carry out a series of nonequilibrium trajectories is reduced up to a factor ranging from 2 to more than 10, at least for the processes under consideration in the present study. The efficiency depends on several aspects, such as the type of process, the number of check-points along the pathway and the pulling rate as well. The method is illustrated through radically different processes, i.e., the helix-coil transition of deca-alanine and the pulling of the distance between two methane molecules in water solution.

Nanostructured Ag platforms as biosensors of nucleobase chains.

Nanostructured Ag platforms have been obtained by simple chemical procedure and characterized by AFM (atomic force microscopy) measurements, for use in biosensing by means of SERS (surface-enhanced Raman scattering) spectroscopy. The SERS efficiency of these substrates has been verified by microRaman measurements on small RNA chains with different nucleobase content, showing sensitivity near attomole level. It is our opinion that these metal substrates may be widely used as appropriate sensors for detecting biomolecules in many applications concerning medical diagnostics, pharmacological research and nanomaterials technology.

Optothermal properties of plasmonic inorganic nanoparticles for photoacoustic applications.

Plasmonic systems are becoming a favourable alternative to dye molecules in the generation of photoacoustic signals for spectroscopy and imaging. In particular, inorganic nanoparticles are appealing because of their versatility. In fact, as the shape, size and chemical composition of nanoparticles are directly correlated with their plasmonic properties, the excitation wavelength can be tuned to their plasmon resonance by adjusting such traits. This feature enables an extensive spectral range to be covered. In addition, surface chemical modifications can be performed to provide the nanoparticles with designed functionalities, e.g., selective affinity for specific macromolecules. The efficiency of the conversion of absorbed photon energy into heat, which is the physical basis of the photoacoustic signal, can be accurately determined by photoacoustic methods. This review contrasts studies that evaluate photoconversion in various kinds of nanomaterials by different methods, with the objective of facilitating the researchers' choice of suitable plasmonic nanoparticles for photoacoustic applications.

Adsorption Geometry of Alizarin on Silver Nanoparticles: A Computational and Spectroscopic Study.

The knowledge of the adsorption geometry of an analyte on a metal substrate employed in surface enhanced Raman scattering (SERS) spectroscopy is important information for the correct interpretation of experimental data. The adsorption geometry of alizarin on silver nanoparticles was studied through ab initio calculations in the framework of density functional theory (DFT) by modeling alizarin taking into account all the different charged species present in solution as a function of pH. The calculations allowed a faithful reproduction of the measured SERS spectra and to elucidate the adsorption geometry of this dye on the silver substrate.

Surface-Enhanced Raman Spectroscopy for Bisphenols Detection: Toward a Better Understanding of the Analyte-Nanosystem Interactions.

Silver nanoparticles functionalized with thiolated ß-cyclodextrin (CD-SH) were employed for the detection of bisphenols (BPs) A, B, and S by means of surface-enhanced Raman spectroscopy (SERS). The functionalization of Ag nanoparticles with CD-SH leads to an improvement of the sensitivity of the implemented SERS nanosensor. Using a multivariate analysis of the SERS data, the limit of detection of these compounds was estimated at about 10-7 M, in the range of the tens of ppb. Structural analysis of the CD-SH/BP complex was performed by density functional theory (DFT) calculations. Theoretical results allowed the assignment of key structural vibrational bands related to ring breathing motions and the inter-ring vibrations and pointed out an external interaction due to four hydrogen bonds between the hydroxyl groups of BP and CD located at the external top of the CD cone. DFT calculations allowed also checking the interaction energies of the different molecular species on the Ag surface and testing the effect of the presence of CD-SH on the BPs' affinity. These findings were in agreement with the experimental evidences that there is not an actual inclusion of BP inside the CD cavity. The SERS sensor and the analysis procedure of data based on partial least square regression proposed here were tested in a real sample consisting of the detection of BPs in milk extracts to validate the detection performance of the SERS sensor.

Infinite supramolecular pseudo-polyrotaxane with poly[3]catenane axle: assembling nanosized rings from mono- and diatomic I- and I2 tectons.

Mono- and diatomic I- and I2 building blocks, despite their simplicity, can be used to generate complex hierarchical self-assembled architectures. Herein, the construction of a modular supramolecular poly[3]catenane and its conversion into the axle of an infinite supramolecular pseudo-polyrotaxane were achieved in a seamless process from the starting materials. The unique structural features, directionality, and iodine density of the obtained crystals demonstrate the benefits of a supramolecular design for polyiodide networks intended as solid-state conductors.