Photosensitizers Based on Bichromophoric Dyads Combining Ru(II)-Polypyridyl Complexes and Dissymmetric Perylene Monoimide Derivatives: The Nontrivial Role of Ligand Substitution.

The covalent modification of Ru(II) polypyridyl complexes (RPCs) with organic chromophores is a powerful strategy to obtain metal-based photosensitizer agents (PSs) with improved performance for application in photodynamic therapy (PDT). In this respect, perylene-imides are of particular interest due to their rich chemical-physical repertoire, and it is therefore quite surprising that their combination with RPCs has been poorly considered so far. Herein, we report on the photophysical behavior of two newly synthesized RPCs bearing a perylene monoimide appendant (PMI-Ad). Differently from the majority of RPCs-perylene-imides dyads, these chromophores are dissymmetric and are tethered to the metal centers through a single C-C bond in the 3- or 5-position of 1,10-phenanthroline (Ru-3PMI-Ad and Ru-5PMI-Ad). Both compounds show excellent singlet oxygen photosensitizing activity, with quantum yields reaching >90% in the case of Ru-3PMI-Ad. A combined spectroscopic and theoretical analysis, also involving transient absorption and luminescence lifetime measurements, demonstrates that both compounds undergo intersystem crossing on a very fast time scale (tens of picoseconds) and with high efficiency. Our results further demonstrate that the increased electron delocalization between the metal center and the PMI-Ad chromophore observed for Ru-3PMI-Ad additionally contributes to increase the singlet oxygen quantum yields by prolonging the lifetime of the triplet state.

Nitroimidazole-Based Ruthenium(II) Complexes: Playing with Structural Parameters to Design Photostable and Light-Responsive Antibacterial Agents.

5-Nitroimidazole (5NIMH), chosen as a molecular model of nitroimidazole derivatives, which represent a broad-spectrum class of antimicrobials, was incorporated into the ruthenium complexes [Ru(tpy)(phen)(5NIM)]PF6 (1) and [Ru(tpy)(dmp)(5NIM)]PF6 (2) (tpy = terpyridine, phen = phenanthroline, dmp = 2,9-dimethyl-1,10-phenanthroline). Besides the uncommon metal coordination of 5-nitroimidazole in its imidazolate form (5NIM), the different architectures of the spectator ligands (phen and dmp) were exploited to tune the "mode of action" of the resulting complexes, passing from a photostable compound where the redox properties of 5NIMH are preserved (1) to one suitable for the nitroimidazole phototriggered release (2) and whose antibacterial activity against B. subtilis, chosen as cellular model, is effectively improved upon light exposure. This study may provide a fundamental knowledge on the use of Ru(II)-polypyridyl complexes to incorporate and/or photorelease biologically relevant nitroimidazole derivatives in the design of a novel class of antimicrobials.

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.

A Photochromic Azobenzene Peptidomimetic of a ß-Turn Model Peptide Structure as a Conformational Switch.

The insertion of azobenzene moiety in complex molecular protein or peptide systems can lead to molecular switches to be used to determine kinetics of folding/unfolding properties of secondary structures, such as α-helix, ß-turn, or ß-hairpin. In fact, in azobenzene, absorption of light induces a reversible trans ↔ cis isomerization, which in turns generates a strain or a structure relaxation in the chain that causes peptide folding/unfolding. In particular azobenzene may permit reversible conformational control of hairpin formation. In the present work a synthetic photochromic azobenzene amino acid derivative was incorporated as a turn element to modify the synthetic peptide [Pro7,Asn8,Thr10]CSF114 previously designed to fold as a type I ß-turn structure in biomimetic HFA/water solution. In particular, the P-N-H fragment at positions 7-9, involved in a ß-hairpin, was replaced by an azobenzene amino acid derivative (synthesized ad hoc) to investigate if the electronic properties of the novel peptidomimetic analog could induce variations in the isomerization process. The absorption spectra of the azopeptidomimetic analog of the type I ß-turn structure and of the azobenzene amino acid as control were measured as a function of the irradiation time exciting into the respective first ππ* and nπ* transition bands. Isomerization of the azopeptidomimetic results strongly favored by exciting into the ππ* transition. Moreover, conformational changes induced by the cis↔ trans azopeptidomimetic switch were investigated by NMR in different solvents.

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.

Silver nanowires as infrared-active materials for surface-enhanced Raman scattering.

Surface-enhanced Raman scattering (SERS) is increasing in significance as a bioanalytical tool. Novel nanostructured metal substrates are required to improve performances and versatility of SERS spectroscopy. In particular, as biological tissues are relatively transparent in the infrared wavelength range, SERS-active materials suitable for infrared laser excitation are needed. Nanowires appear interesting in this respect as they show a very broad localized surface plasmon resonance band, ranging from near UV to near infrared wavelengths. The SERS activity of silver nanowires has been tested at three wavelengths and a fair enhancement at 1064 and 514 nm has been observed, whereas a very weak enhancement was present when exciting close to the nanowire extinction maximum. These experimentally measured optical properties have been contrasted with finite element method simulations. Furthermore, laser-induced optoacoustic spectroscopy measurements have shown that the extinction at 1064 nm is completely due to scattering. This result has an important implication that no heating occurs when silver nanowires are utilized as SERS-active substrates, thereby preventing possible thermal damage.

Non-covalent interactions in anisole-(CO2)n (n = 1, 2) complexes.

Non-covalent interactions are ubiquitous and represent a very important binding motif. The direct experimental measurement of binding energies in complexes has been elusive for a long time despite its importance, for instance, for understanding and predicting the structure of bio-macromolecules. Here, we report a combined experimental and computational analysis on the 1 : 1 and 1 : 2 clusters formed by anisole (methoxybenzene) and carbon dioxide molecules. We have obtained a detailed description of the interaction between CO2 and anisole. This system represents quite a challenging test for the presently available experimental and theoretical methods for the characterization of weakly bound molecular complexes. The results, evaluated in the framework of previous studies on anisole clusters, show a very good agreement between experimental and theoretical data. A comparison of the experimental and computational data enabled the binding energy values of the 1 : 1 and 1 : 2 clusters to be determined in the ground electronic state of the neutral and cation complex and in the first excited singlet state of the neutral complex. In addition, it was possible to adduce the presence of different 1 : 1+ conformers, prepared by direct ionization of the 1 : 1 complex or by dissociative ionization of the 1 : 2 complex.

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.

Computing Free Energy Differences of Configurational Basins.

A simulation-based approach is proposed to estimate free energy differences between configurational states A and B, defined in terms of collective coordinates of the molecular system. The computational protocol is organized into three stages that can be carried on simultaneously. Two of them consist of independent simulations aimed at sampling, in turn, A and B states. In order to limit the evolution of the system around A and B, biased sampling simulations such as umbrella sampling can be employed. These simulations allow us to estimate local configuration integrals associated with A and B, which can be viewed as vibrational contributions to the free energy. Free energy evaluation is completed by the linking-path stage, in which the potential of mean force difference is estimated between two arbitrary points of the configurational surface, located the first around A and the second around B. The linking path in the space of the collective coordinates is arbitrary and can be computed with any method, starting from adaptive biasing potential/force approaches to nonequilibrium techniques. As an illustrative example, we present the calculation of free energy differences between conformational states of the alanine dipeptide in the space of backbone dihedral angles. The basic advantage of this method, that we term "path-linked domains" scheme, is to prevent accurate calculation of the whole free energy hypersurface in the space of the collective coordinates, thus limiting the statistical sampling to a minimum. Path-linked domains schemes can be applied to a variety of biochemical processes, such as protein-ligand complexation or folding-unfolding interconversion.

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.

Binding energies of the π-stacked anisole dimer: new molecular beam-laser spectroscopy experiments and CCSD(T) calculations.

Among noncovalent interactions, π-π stacking is a very important binding motif governed mainly by London dispersion. Despite its importance, for instance, for the structure of bio-macromolecules, the direct experimental measurement of binding energies in π-π stacked complexes has been elusive for a long time. Only recently, an experimental value for the binding energy of the anisole dimer was presented, determined by velocity mapping ion imaging in a two-photon resonant ionisation molecular beam experiment. However, in that paper, a discrepancy was already noted between the obtained experimental value and a theoretical estimate. Here, we present an accurate recalculation of the binding energy based on the combination of the CCSD(T)/CBS interaction energy and a DFT-D3 vibrational analysis. This proves unambiguously that the previously reported experimental value is too high and a new series of measurements with a different, more sensitive apparatus was performed. The new experimental value of 1800±100 cm(-1) (5.15±0.29 kcal mol(-1)) is close to the present theoretical prediction of 5.04±0.40 kcal mol(-1). Additional calculations of the properties of the cationic and excited states involved in the photodissociation of the dimer were used to identify and rationalise the difficulties encountered in the experimental work.

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.

Nonequilibrium Candidate Monte Carlo Simulations with Configurational Freezing Schemes.

Nonequilibrium Candidate Monte Carlo simulation [Nilmeier et al., Proc. Natl. Acad. Sci. U.S.A. 2011, 108, E1009-E1018] is a tool devised to design Monte Carlo moves with high acceptance probabilities that connect uncorrelated configurations. Such moves are generated through nonequilibrium driven dynamics, producing candidate configurations accepted with a Monte Carlo-like criterion that preserves the equilibrium distribution. The probability of accepting a candidate configuration as the next sample in the Markov chain basically depends on the work performed on the system during the nonequilibrium trajectory and increases with decreasing such a work. It is thus strategically relevant to find ways of producing nonequilibrium moves with low work, namely moves where dissipation is as low as possible. This is the goal of our methodology, in which we combine Nonequilibrium Candidate Monte Carlo with Configurational Freezing schemes developed by Nicolini et al. (J. Chem. Theory Comput. 2011, 7, 582-593). The idea is to limit the configurational sampling to particles of a well-established region of the simulation sample, namely the region where dissipation occurs, while leaving fixed the other particles. This allows to make the system relaxation faster around the region perturbed by the finite-time switching move and hence to reduce the dissipated work, eventually enhancing the probability of accepting the generated move. Our combined approach enhances significantly configurational sampling, as shown by the case of a bistable dimer immersed in a dense fluid.

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.

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.

Noncovalent interactions in the gas phase: the anisole-phenol complex.

The present paper reports on an integrated spectroscopic study of the anisole-phenol complex in a molecular beam environment. Combining REMPI and HR-LIF spectroscopy experimental data with density functional computations (TD-M05-2X/M05-2X//N07D) and first principle spectra simulations, it was possible to locate the band origin of the S(1) ← S(0) electronic transition and determine the equilibrium structure of the complex, both in the S(0) and S(1) electronic states. Experimental and computational evidence indicates that the observed band origin is due to an electronic transition localized on the phenol frame, while it was not possible to localize experimentally another band origin due to the electronic transition localized on the anisole molecule. The observed structure of the complex is stabilized by a hydrogen bond between the phenol, acting as a proton donor, and the anisole molecule, acting as an acceptor through the lone pairs of the oxygen atom. A secondary interaction involving the hydrogen atoms of the anisole methyl group and the π electron system of the phenol molecule stabilizes the complex in a nonplanar configuration. Additional insights about the landscapes of the potential energy surfaces governing the ground and first excited electronic states of the anisole-phenol complex, with the issuing implications on the system photodynamic, can be extracted from the combined experimental and computational studies.

Integrated experimental and computational spectroscopy study on π-stacking interaction: the anisole dimer.

Integrated experimental and computational results help to clarify the nature of the intermolecular interactions in a simple, isolated π-stacked dimer prepared in a molecular beam. The properties of bimolecular anisole complexes are examined and discussed in terms of the local/supramolecular nature of the electronic wavefunctions. Experimental resonance-enhanced multi-photon ionization spectra of clusters with different isotopic compositions confirmed the fundamentally localized nature of the S(1)←S(0) electronic transition. A detail analysis of the experimental results however shows the existence of non-negligible excitonic coupling for the excited-state wavefunctions leading to the doubling of the single-molecule vibronic levels in the S(1) state, with a splitting of about 30 cm(-1). Theoretical simulation of the vibrationally resolved electronic spectra and computations of the excitonic coupling convincingly support the experimental findings. The overall combined experimental/theoretical study allows a detailed description of the stacking interaction in the anisole dimer.

Isotopomeric conformational changes in the anisole-water complex: new insights from HR-UV spectroscopy and theoretical studies.

Resonance enhanced multiphoton ionization and rotationally resolved S1<--S0 electronic spectra of the anisole-2H2O complex have been obtained. The experimental results are compared with high level quantum mechanical calculations and with data already available in the literature. Quite surprisingly, the equilibrium structure of the anisole-2H2O complex in the S0 state shows some non-negligible differences from that of the isotopomer anisole-1H2O complex. Actually, the structure of the deuterated complex is more similar to the corresponding structure of the anisole-1H2O complex in the S1 state. In anisole-water, two equivalent H(D) atoms exist as revealed by line splitting in the rotationally resolved spectra. It is possible to suggest a mechanism for the proton/deuteron exchange ruled by a bifurcated transition state for the exchange reaction, with both water hydrogen atoms interacting with the anisole oxygen atom. From the analysis of all of the available experimental data and of computational results, we can demonstrate that in the S1 excited state the hydrogen bond in which the water molecule acts as an acid is weaker than in the electronic ground state but is still the principal interaction between water and the anisole molecules.

On the properties of microsolvated molecules in the ground (S0) and excited (S1) states: the anisole-ammonia 1:1 complex.

State-of-the-art spectroscopic and theoretical methods have been exploited in a joint effort to elucidate the subtle features of the structure and the energetics of the anisole-ammonia 1:1 complex, a prototype of microsolvation processes. Resonance enhanced multiphoton ionization and laser-induced fluorescence spectra are discussed and compared to high-level first-principles theoretical models, based on density functional, many body second order perturbation, and coupled cluster theories. In the most stable nonplanar structure of the complex, the ammonia interacts with the delocalized pi electron density of the anisole ring: hydrogen bonding and dispersive forces provide a comparable stabilization energy in the ground state, whereas in the excited state the dispersion term is negligible because of electron density transfer from the oxygen to the aromatic ring. Ground and excited state geometrical parameters deduced from experimental data and computed by quantum mechanical methods are in very good agreement and allow us to unambiguously determine the molecular structure of the anisole-ammonia complex.