Understanding the influence of disorder on the exciton dynamics and energy transfer in Zn-phthalocyanine H-aggregates.

The photophysics of 9(19),16(17),23(24)-tri-tert-butyl-2-[ethynyl-(4-carboxymethyl)phenyl]phthalocyaninatozinc(ii) and its H-aggregates is studied in different solvents by means of ultrafast non-linear optical spectroscopy and computational modeling. In non-coordinating solvents, both stationary and time-resolved spectroscopies highlight the formation of extended molecular aggregates, whose dimension and spectral properties depends on the concentration. In all the explored experimental conditions, time-resolved transient absorption experiments show multi exponential decay of the signals. Additional insights into the excited state relaxation mechanisms of the system is obtained with 2D electronic spectroscopy, which is employed to compare the deactivation channels in the absence or presence of aggregates. In ethanol and diethylether, where only monomers are present, an ultrafast relaxation process among the two non-degenerate Q-states of the molecule is evidenced by the appearance of a cross peak in the 2D-maps. In chloroform or CCl4, where disordered H-aggregates are formed, an energy transfer channel among aggregates with different composition and size is observed, leading to the non-radiative decay towards the lower energy dark state of the aggregates. Efficient coupling between less and more aggregated species is highlighted in two-dimensional electronic spectra by the appearance of a cross peak. The kinetics and intensity of the latter depend on the concentration of the solution. Finally, the linear spectroscopic properties of the aggregate are reproduced using a simplified structural model of an extended aggregate, based on Frenkel Hamiltonian Calculations and on an estimate of the electronic couplings between each dimer composing the aggregate computed at DFT level.

Spin Dynamics and Low Energy Vibrations: Insights from Vanadyl-Based Potential Molecular Qubits.

Here we report the investigation of the magnetization dynamics of a vanadyl complex with diethyldithiocarbamate (Et2dtc-) ligands, namely [VO(Et2dtc)2] (1), in both solid-state and frozen solution. This showed an anomalous and unprecedentedly observed field dependence of the relaxation time, which was modeled with three contributions to the relaxation mechanism. The temperature dependence of the weight of the two processes dominating at low fields was found to well correlate with the low energy vibrations as determined by THz spectroscopy. This detailed experimental comparative study represents a fundamental step to understand the spin dynamics of potential molecular quantum bits, and enriches the guidelines to design molecule-based systems with enhanced quantum coherence.

Femtosecond transient infrared and stimulated Raman spectroscopy shed light on the relaxation mechanisms of photo-excited peridinin.

By means of one- and two-dimensional transient infrared spectroscopy and femtosecond stimulated Raman spectroscopy, we investigated the excited state dynamics of peridinin, a carbonyl carotenoid occurring in natural light harvesting complexes. The presence of singly and doubly excited states, as well as of an intramolecular charge transfer (ICT) state, makes the behavior of carbonyl carotenoids in the excited state very complex. In this work, we investigated by time resolved spectroscopy the relaxation of photo-excited peridinin in solvents of different polarities and as a function of the excitation wavelength. Our experimental results show that a characteristic pattern of one- and two-dimensional infrared bands in the C=C stretching region allows monitoring the relaxation pathway. In polar solvents, moderate distortions of the molecular geometry cause a variation of the single/double carbon bond character, so that the partially ionic ICT state is largely stabilized by the solvent reorganization. After vertical photoexcitation at 400 nm of the S2 state, the off-equilibrium population moves to the S1 state with ca. 175 fs time constant; from there, in less than 5 ps, the non-Franck Condon ICT state is reached, and finally, the ground state is recovered in 70 ps. That the relevant excited state dynamics takes place far from the Franck Condon region is demonstrated by its noticeable dependence on the excitation wavelength.

Ultrafast resonance energy transfer in the umbelliferone-alizarin bichromophore.

In this work we present the synthesis, time-resolved spectroscopic characterization and computational analysis of a bichromophore composed of two very well-known naturally occurring dyes: 7-hydroxycoumarin (umbelliferone) and 1,2-dihydroxyanthraquinone (alizarin). The umbelliferone donor (Dn) and alizarin acceptor (Ac) moieties are linked to a triazole ring viaσ bonds, providing a flexible structure. By measuring the fluorescence quantum yields and the ultrafast transient absorption spectra we demonstrate the high efficiency (∼85%) and the fast nature (∼1.5 ps) of the energy transfer in this compound. Quantum chemical calculations, within the density functional theory (DFT) approach, are used to characterize the electronic structure of the bichromophore (Bi) in the ground and excited states. We simulate the absorption and fluorescence spectra using the TD-DFT methods and the vertical gradient approach (VG), and include the solvent effects by adopting the conductor-like polarizable continuum model (CPCM). The calculated electronic structure suggests the occurrence of weak interactions between the electron densities of Dn and Ac in the excited state, indicating that the Förster-type transfer is the appropriate model for describing the energy transfer in this system. The average distance between Dn and Ac moieties calculated from the conformational analysis (12 Å) is in very good agreement with the value estimated from the Förster equation (∼11 Å). At the same time, the calculated rate constant for energy transfer, averaged over multiple conformations of the system (3.6 ps), is in reasonable agreement with the experimental value (1.6 ps) estimated by transient absorption spectroscopy. The agreement between experimental results and computational data leads us to conclude that the energy transfer in Bi is well described by the Förster mechanism.

Transient infrared spectroscopy: a new approach to investigate valence tautomerism.

In this work we present, to our knowledge for the first time, the results of a transient infrared spectroscopic study of the photoinduced valence tautomerism process in cobalt-dioxolene complexes with sub-picosecond time resolution. The molecular systems investigated were [Co(tpa)(diox)]PF(6) (1) and [Co(Me(3)tpa)(diox)]PF(6) (2), where diox = 3,5-di-tert-butyl-1,2-dioxolene; tpa = tris(2-pyridylmethyl)amine and Me(3)tpa its 6-methylated analogue. Complex (1) is present in solution as ls-Co(III)(catecholate) (1-CAT), while (2) as hs-Co(II)(semiquinonate) (2-SQ). DFT calculation of the harmonic frequencies for (1) and (2) allowed us to identify the vibrational markers of catecholate and semiquinonate redox isomers. Irradiation with 405 and 810 nm pulses (~35 fs) of (1-CAT) induces the formation of an intermediate excited species from which the ground state population is recovered with a time constant of 1.5 ± 0.3 ns. Comparing the 1 ns transient infrared spectrum with the experimental difference spectrum FTIR(2-SQ)-FTIR(1-CAT) and with the calculated difference spectrum IR(c)(1-SQ)-IR(c)(1-CAT) we are able to unequivocally identify the long lived species as the semiquinonate redox isomer of (1). On the other hand, no evidence of photoconversion is observed upon irradiation of (2) with 405 nm. Temporal evolution of transient spectra was analyzed with the combined approach consisting of singular values decomposition and global fitting (global analysis). After 405 and 810 nm excitation of (1-CAT), the semiquinonate excited species is formed on an ultrafast time scale (<200 fs) and cools down within the first 50 ps. Excitation of (2-SQ) with 405 nm wavelength produces a short lived excited state in which the semiquinonate nature of dioxolene is preserved and the ground state recovery is completed within 30 ps.

Bifurcated hydrogen bond in lithium nitrate trihydrate probed by ab initio molecular dynamics.

The hydrogen-bond dynamics of lithium nitrate trihydrate has been studied by a combined approach based on ab initio molecular dynamics simulations and wavelet analysis. The simultaneous bifurcated interaction between one hydrogen atom of water molecules and two oxygen atoms of nitrate ions is the pivotal feature of the crystal structure: this bifurcated interaction has deep effects on the O-H stretching region of the vibrational spectrum. The structural, dynamic, spectroscopic, and electronic properties of the bifurcated hydrogen bond have been investigated computationally, elucidating at the molecular level the differences with weak and strong hydrogen bonds present in the crystal. These studies corroborate the very recent IR experiments performed on the lithium nitrate trihydrate crystal, offering new perspectives to interpreting the vibrational spectra. In fact, this approach allows obtaining two-dimensional plots, which summarize the essential features of both the hydrogen-bond network and IR spectra, resulting in a peculiar "signature" of the bifurcated interaction.

Hydrogen bond effects in the vibrational spectra of 1,3-propanediol in acetonitrile: ab initio and experimental study.

Hydrogen bond interactions strongly affect vibrational properties and frequencies, the most common consequence being a redshift of the stretching vibration involved; there are, however, few exceptions to this general trend. In previous works, we have proved the effectiveness of ab initio simulations combined with wavelet analysis to investigate these effects and put them into relation to structural environment. In this work, we investigate the hydrogen bond effects on the structural and vibrational properties of 1,3-propanediol in acetonitrile by a combined experimental and computational approach. We explain the appearance of two spectral components in the O-H stretching band on the basis of intra- and intermolecular hydrogen bond interactions. We also elucidate the blueshift of the C≡N stretching band as due to a hydrogen bond interaction between the glycol and acetonitrile that modify the electron density distribution inside the CN group. This effect is well reproduced by ab initio molecular dynamics simulations and density functional calculations reported in this work.

Excitonic effects in two-dimensional vibrational spectra of liquid formamide.

The linear and two-dimensional infrared (2DIR) responses of the amide I vibrational mode in liquid formamide are investigated experimentally and theoretically using molecular dynamics simulations. The recent method based on the numerical integration of the Schrödinger equation is employed to calculate the 2DIR spectra. Special attention is devoted to the interplay of the structural dynamics and the excitonic nature of the amide I modes in determining the optical response of the studied system. In particular, combining experimental data, simulated spectra and analysis of the simulated atomic trajectory in terms of a transition dipole coupling model, we provide a convincing explanation of the peculiar features of the 2DIR spectra, which show a substantial increase of the antidiagonal bandwidth with increasing frequency. We point out that, at variance with liquid water, the 2DIR spectral profile of formamide is determined more by the excitonic nature of the vibrational states than by the fast structural dynamics responsible for the frequency fluctuations.

Temperature Dependence of Spin-Phonon Coupling in [VO(acac)2]: A Computational and Spectroscopic Study.

Molecular electronic spins are good candidates as qubits since they are characterized by a large tunability of their electronic and magnetic properties through a rational chemical design. Coordination compounds of light transition metals are promising systems for spin-based quantum information technologies, thanks to their long spin coherence times up to room temperature. Our work aims at presenting an in-depth study on how the spin-phonon coupling in vanadyl-acetylacetonate, [VO(acac)2], can change as a function of temperature using terahertz time-domain spectroscopy and density functional theory (DFT) calculations. Powder THz spectra were recorded between 10 and 300 K. The temperature dependence of vibrational frequencies was then accounted for in the periodic DFT calculations using unit-cell parameters measured at two different temperatures and the optimized ones, as usually reported in the literature. In this way, it was possible to calculate the observed THz anharmonic frequency shift with high accuracy. The overall differences in the spin-phonon coupling magnitudes as a function of temperature were also highlighted showing that the computed trends have to be ascribed to the anisotropic variation of cell parameters.

Serum albumin-bound proteomic signature for early detection and staging of hepatocarcinoma: sample variability and data classification.

BACKGROUND: Matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) proteomic signature might be of interest for the early detection and staging of hepatocellular carcinoma (HCC). However, published procedures have been criticized for the lack of data about analytical reproducibility, and the use of inadequate data processing. METHODS: MALDI-TOF profiling of peptides bound to serum albumin ("albuminome") was performed using 90 µL of serum from 45 study subjects (HCV-related cirrhosis, small, unifocal HCCs and advanced HCCs). To overcome the large intra-sample variability, a Quality Assurance protocol was implemented, and 4-8 samples for each subject were processed and analyzed. Overall, 522 subject samples and 299 quality-control spectra were analyzed. A machine-learning approach (Random Forest) was applied to analyze the data sets. RESULTS: Mean intra-sample coefficient of variation (CV) of the analytical procedure was 17.6%-30.0%; inter-subject CV was in the range 48.8%-71.3% among the three study groups. The Random Forest procedure correctly classified 433/522 "patient samples" and 295/299 "reference samples"; 43/45 patients were correctly classified following this approach. CONCLUSIONS: Our data suggest that, notwithstanding the large analytical variability found, multiple proteomic profiles obtained from each subject can differentiate cirrhosis with and without HCC, and HCCs with and without vascular invasion, warranting further investigation in a prospective setting.

Structural relaxation in supercooled water by time-resolved spectroscopy.

Water has many kinetic and thermodynamic properties that exhibit an anomalous dependence on temperature, in particular in the supercooled phase. These anomalies have long been interpreted in terms of underlying structural causes, and their experimental characterization points to the existence of a singularity at a temperature of about 225 K. Further insights into the nature and origin of this singularity might be gained by completely characterizing the structural relaxation in supercooled water. But until now, such a characterization has only been realized in simulations that agree with the predictions of simple mode-coupling theory; unambiguous experimental support for this surprising conclusion is, however, not yet available. Here we report time-resolved optical Kerr effect measurements that unambiguously demonstrate that the structural relaxation of liquid and weakly supercooled water follows the behaviour predicted by simple mode-coupling theory. Our findings thus support the interpretation of the singularity as a purely dynamical transition. That is, the anomalous behaviour of weakly supercooled water can be explained using a fully dynamic model and without needing to invoke a thermodynamic origin. In this regard, water behaves like many other, normal molecular liquids that are fragile glass-formers.

Pressure Effects on Water Dynamics by Time-Resolved Optical Kerr Effect.

Despite water being the most common and most widely studied substance in the world, it still presents unknown aspects. In particular, water shows several thermodynamic and dynamical anomalies in the liquid and supercooled metastable phases, and the natures of these phases are still hotly debated. Here, we report measurements of water using the optical Kerr effect as a function of pressure along two isotherms, at 273 K from 0.1 to 750 MPa and at 297 K from 0.1 to 1350 MPa, reaching the supercooled metastable phase. The structural relaxation and the low frequency vibrational dynamics of water show a peculiar pressure dependence similar to that of other dynamical properties. The data analysis suggests the presence in the water phase diagram of a crossover area that divides two regions characterized by different dynamic regimes, which appear to be related to two liquid forms, one dominated by the high density water and the other by the low density water.

Pyrene-excimers-based antenna systems.

A series of dendrimeric compounds bearing pyrene units were synthesized to afford light-harvesting antennae based on the formation of intramolecular excimers. The synthetic plan profited from the efficiency of the Huisgen reaction, the 1,3-dipolar cycloaddition of azides and terminal alkynes, which allowed ready assembly of the different building blocks. The three molecular antennae obtained, of increasing generation, revealed efficient energy transfer both in solution and in the solid state.

What are the sites water occupies at the interface of a phospholipid membrane?

We explore the two-dimensional infrared response of D(2)O and of OD impurity at the interface of phospholipid membrane fragments. The spectra of the two aqueous states are inhomogeneously broadened due to the absorption of water molecule associated with the membrane interface in different structural sites. The nonlinear spectra of the two species allow disentangling of the spectral contributions of the aqueous states of two types: where the stretching modes are under effective mixing and where the stretching modes are uncoupled. By reviewing the results of the experimental studies with the support of molecular dynamic simulation we identify the spectral signatures of the main structural motives responsible for the inhomogeneous distribution of resonances in the infrared OD stretching region. Our analysis provides a quantitative estimate of the statistical population of the different aqueous species at the polar interface of the bilayer.

Hydration of phospholipid interface: carbonyl-water hydrogen bond association.

Being largely driven by electrostatic interactions, hydration compensates hydrophobic repulsion and, thus, contributes decisively in structural expressions of molecules in a phospholipid membrane environment. Here, we explore the nature of the aqueous state associated with carbonyl moieties of a phospholipid bilayer. The task is of an obvious difficulty, since water clustering at a membrane interface implies the presence of various aqueous states giving rise to spectral inhomogeneity. The resultant frequency overlap of the optical response from states of differing nature obscures the structural analysis. We extract the information on water next to phospholipid carbonyls by monitoring the O-D stretch perturbation upon direct infrared excitation of lipid carbonyl groups. Modelling the signal with the help of quantum computations and molecular dynamics simulation, we extract the geometry for the optimal placement of water next to carbonyl moieties, and anticipate the time scale of the water molecule displacement, leading to the disruption of the hydrogen bond, upon direct excitation of the C=O group. The picture we provide here is of general and applied value. The practical importance stems from the necessity of experimentally characterizing the hydration of polar moieties in polypeptides (of pharmacological significance) when in a phospholipid environment, a task not yet achieved.

Chemical equilibrium probed by two-dimensional IR spectroscopy: hydrogen bond dynamics of methyl acetate in water.

The solvation dynamics of methyl acetate in heavy water are analyzed by means of two-dimensional infrared spectroscopy, in conjunction with Car-Parrinello molecular dynamics simulations. The C horizontal lineO stretching infrared band of methyl acetate in water splits into a doublet as a consequence of the hydrogen bond interaction with the solvent, which leads to the equilibrium between two solvated species, consisting of one methyl acetate molecule bonded to one and two water molecules. The structure and dynamics of the water molecules bound to methyl acetate are characterized by means of experiments and simulations, allowing an accurate description of the kinetics of the exchange process and the lifetime of the hydrogen bond.

Two-dimensional infrared spectroscopy of a structured liquid: neat formamide.

Vibrational dynamics of liquid formamide is studied in the spectral region of the amide I mode by means of linear and two-dimensional infrared spectroscopies. The two-dimensional spectrum has a complex structure to be connected to the partially excitonic nature of the vibrational states. The measurements performed on a 1:10 (12)C:(13)C formamide isotopic mixture allow separating the broadening contribution due to the inhomogeneous frequency distribution of the local oscillators from that of excitonic origin. A model based on the Kubo picture of the line broadening is used, together with the dynamic information obtained from a molecular dynamics simulation, to fit the spectra of the (12)C formamide impurity in the isotopic mixture. The relevant dynamical information, such as the amplitude of the frequency fluctuations, lifetime of the second vibrational excited state, and anharmonicity, is thus recovered. By appropriately combining the outcomes of experiments and molecular dynamics simulation, we demonstrate that motional narrowing determines the line shape of the amide I resonance to a large extent. The same analysis provides an estimate of the transition dipole moment of formamide, which results in good agreement with an ab initio calculation. The calculated frequency fluctuation correlation time is found to be comparable to the hydrogen-bond lifetime, which defines the basic structural relaxation rate of the networked liquid.

Retrieval of spectral and dynamic properties from two-dimensional infrared pump-probe experiments.

We have developed a fitting algorithm able to extract spectral and dynamic properties of a three level oscillator from a two-dimensional infrared spectrum (2D-IR) detected in time resolved nonlinear experiments. Such properties go from the frequencies of the ground-to-first and first-to-second vibrational transitions (and hence anharmonicity) to the frequency-fluctuation correlation function. This last is represented through a general expression that allows one to approach the various strategies of modeling proposed in the literature. The model is based on the Kubo picture of stochastic fluctuations of the transition frequency as a result of perturbations by a fluctuating surrounding. To account for the line-shape broadening due to pump pulse spectral width in double-resonance measurements, we supply the fitting algorithm with the option to perform the convolution of the spectral signal with a Lorentzian function in the pump-frequency dimension. The algorithm is tested here on 2D-IR pump-probe spectra of a Gly-Ala dipeptide recorded at various pump-probe delay times. Speedup benchmarks have been performed on a small Beowulf cluster. The program is written in FORTRAN language for both serial and parallel architectures and is available free of charge to the interested reader.

Real time contrast enhanced ultrasonography in detection of liver metastases from gastrointestinal cancer.

BACKGROUND: Contrast enhanced ultrasound (CEUS) is an imaging technique which appeared on the market around the year 2000 and proposed for the detection of liver metastases in gastrointestinal cancer patients, a setting in which accurate staging plays a significant role in the choice of treatment. METHODS: A total of 109 patients with colorectal (n = 92) or gastric cancer prospectively underwent computed tomography (CT) scan and conventional US evaluation followed by real time CEUS. A diagnosis of metastases was made by CT or, for lesions not visible at CT, the diagnosis was achieved by histopathology or by a malignant behavior during follow-up. RESULTS: Of 109 patients, 65 were found to have metastases at presentation. CEUS improved sensitivity in metastatic livers from 76.9% of patients (US) to 95.4% (p <0.01), while CT scan reached 90.8% (p = n.s. vs CEUS, p < 0.01 vs US). CEUS and CT were more sensitive than US also for detection of single lesions (87 with US, 122 with CEUS, 113 with CT). In 15 patients (13.8%), CEUS revealed more metastases than CT, while CT revealed more metastases than CEUS in 9 patients (8.2%) (p = n.s.). CONCLUSION: CEUS is more sensitive than conventional US in the detection of liver metastases and could be usefully employed in the staging of patients with gastrointestinal cancer. Findings at CEUS and CT appear to be complementary in achieving maximum sensitivity.

Heterogeneity of water at the phospholipid membrane interface.

Femtosecond infrared (IR) two-color pump-probe experiments were used to investigate the nonlinear response of the D2O stretching vibration in weakly hydrated dimyristoyl-phosphatidylcholine (DMPC) membrane fragments. The vibrational lifetime is comparable to or longer than that in bulk D2O and is frequency dependent, as it decreases with increasing probe frequency. Also, the lifetime increases when the water content of the sample is lowered. The measured lifetimes range between 903 and 390 fs. A long-lived spectral feature grows in following the excitation and is attributed to photoinduced D-bond breaking. The photoproduct spectrum differs from the steady state difference Fourier transform infrared (FTIR) spectrum, showing that the full thermalization of the excitation energy happens on a much longer time scale than the time interval considered (12 ps). Further evidence of the inhomogeneous character of the water residing in the polar region of the bilayer comes from the spectral anisotropy. The water molecules absorbing on the low frequency side of the absorption band show no decay at all of the anisotropy, while an ultrafast partial decay appears when the high frequency side of the spectrum is probed. The overall behavior differs remarkably from that observed with similar experiments in bulk water and in water segregated in inverse micelles. In weakly hydrated phospholipid membranes, water molecules are present mostly as isolated species, prevalently involved in strong, rigid, and persistent hydrogen bonds with the polar groups of the bilayer molecules. This specific character appears to have a direct effect on the structural stability and thermal properties of the membrane.