Probing the conformational dynamics of an Ago-RNA complex in water/methanol solution.

Argonaute (Ago) proteins mediate target recognition guiding miRNA to bind complementary mRNA primarily in the seed region. However, additional pairing can occur beyond the seed, forming a supplementary duplex that can contribute to the guide-target affinity. In order to shed light on the connection, between protein-RNA interactions and miRNA-mRNA seed and supplementary duplex mobility, we carried out molecular dynamics simulations at the microsecond time-scale using a different approach compared to the ones normally used. Until now, theoretical investigations with classical MD on Ago-RNA complexes have been focused primarily on pure water solvent, which mimics the natural environment of biological molecules. Here, we explored the conformational space of a human Ago2 (hAgo2) bound to the seed + supplementary miRNA-mRNA duplex, using the solvent environment as a molecular probe. MD simulations have been performed in a mixture of water/MeOH at a molar ratio of 70 : 30 as well as in pure water for comparison. Our findings revealed that the mixed solvent promotes protein RNA association, principally enhancing salt-linkages between basic amino acid side-chains and acidic phosphates of the sugar-phosphate backbone. The primary effect registered was the restriction of supplementary duplex flexibility and the stabilization of the miRNA 3' terminus. Interestingly, we observed that the influence of the solvent appears to have almost no impact on the conformation of the seed duplex.

Ionization of 2- and 4(5)-Nitroimidazoles Radiosensitizers: A "Kinetic Competition" Between NO2 and NO Losses.

Nitroimidazoles are a class of chemicals with a remarkable broad spectrum of applications from the production of explosives to the use as radiosensitizers in radiotherapy. The understanding of thedynamics of their fragmentation induced by ionizing sources is of fundamental interest. The goal of this work is to theoretically investigate the kinetic competition between the two most important decomposition channels of 2, 4 and 5-Nitroimidazole cations: the NO and NO2 losses. The calculated rate constants of the two processes are in very good agreement with the experimental Photoelectron-Photoion Coincidence (PEPICO) branching ratio. This study solves the intriguing and theoretically unexplained experimental observation that 2-Nitroimidazole, at variance with the other two regio-isomers is a source for only NO at low energies (<12.76 eV). This is a key point for biomedical application of the nitroimidazoles, because NO is the vasodilator that favors the reoxigenation of hypoxic tumor tissues.

VUV Photofragmentation of Chloroiodomethane: The Iso-CH2I-Cl and Iso-CH2Cl-I Radical Cation Formation.

Dihalomethanes XCH2Y (X and Y = F, Cl, Br, and I) are a class of compounds involved in several processes leading to the release of halogen atoms, ozone consumption, and aerosol particle formation. Neutral dihalomethanes have been largely studied, but chemical physics properties and processes involving their radical ions, like the pathways of their decomposition, have not been completely investigated. In this work the photodissociation dynamics of the ClCH2I molecule has been explored in the photon energy range 9-21 eV using both VUV rare gas discharge lamps and synchrotron radiation. The experiments show that, among the different fragment ions, CH2I+ and CH2Cl+, which correspond to the Cl- and I-losses, respectively, play a dominant role. The experimental ionization energy of ClCH2I and the appearance energies of the CH2I+ and CH2Cl+ ions are in agreement with the theoretical results obtained at the MP2/CCSD(T) level of theory. Computational investigations have been also performed to study the isomerization of geminal [ClCH2I]•+ into the iso-chloroiodomethane isomers: [CH2I-Cl]•+ and [CH2Cl-I]•+.

VUV Photofragmentation of CH2I2: The [CH2I-I](•+) Iso-diiodomethane Intermediate in the I-Loss Channel from [CH2I2](•.).

Diiodomethane is an important halocarbon responsible for several atmospheric processes like ozone depletion and aerosol particle formation. Despite this, the thermochemical data and a detailed analysis of the pathways for the decomposition of this halomethane and its molecular ion [CH2I2](•+) are scarce. In this paper an investigation of the photodissociation dynamics of the CH2I2 molecule focused on the I-loss channel by the photoelectron-photoion coincidence (PEPICO) technique and computational methods is reported. The experimental results show that upon VUV irradiation the dissociation of the lower electronic ionic states of diiodomethane leads only to the CH2I(+) ion and the I atom. The theoretical calculations point out that isomerization of [CH2I2](•+) into iso-diiodomethane [CH2I-I](•+) may play an important role in the emission of iodine atom as compared to direct C-I bond breaking.

A joint theoretical and experimental study on diiodomethane: Ions and neutrals in the gas phase.

The chemical physics of halomethanes is an important and challenging topic in several areas of chemistry in particular in the chemistry of the atmosphere. Among the class of halomethanes, the diiodomethane molecule has attracted some interest in the last years, but despite this, the information on its radical cation [CH2I2](⋅+) is still limited. In this work, we measured and calculated the appearance energy (AE) of the ionic fragments I2(⋅+) and CH2(⋅+) and correlated the different fragmentation channels to the electronic states of the cation via photoelectron-photoion coincidence (PEPICO) experiments. In the case of the CH2/I2(⋅+) channel, the experimentally determined AE is in excellent agreement with the adiabatic theoretical value while a discrepancy is observed for the CH2(⋅+)/I2 channel. This discrepancy can be understood accounting for a fragmentation involving the formation of two I atoms (CH2(⋅+)/2I channel), which, as explained by time dependent density functional theory (TD-DFT) calculations, occurs when [CH2I2](⋅+) excited states are involved.

Radiation Damage Mechanisms of Chemotherapeutically Active Nitroimidazole Derived Compounds.

Photoionization mass spectrometry, photoelectron-photoion coincidence spectroscopic technique, and computational methods have been combined to investigate the fragmentation of two nitroimidazole derived compounds: the metronidazole and misonidazole. These molecules are used in radiotherapy thanks to their capability to sensitize hypoxic tumor cells to radiation by "mimicking" the effects of the presence of oxygen as a damaging agent. Previous investigations of the fragmentation patterns of the nitroimidazole isomers (Bolognesi et al., 2016; Cartoni et al., 2018) have shown their capacity to produce reactive molecular species such as nitric oxide, carbon monoxide or hydrogen cyanide, and their potential impact on the biological system. The results of the present work suggest that different mechanisms are active for the more complex metronidazole and misonidazole molecules. The release of nitric oxide is hampered by the efficient formation of nitrous acid or nitrogen dioxide. Although both metronidazole and misonidazole contain imidazole ring in the backbone, the side branches of these molecules lead to very different bonding mechanisms and properties.

Photofragmentation of halogenated pyrimidine molecules in the VUV range.

In the present work, we studied the photoinduced ion chemistry of the halogenated pyrimidines, a class of prototype radiosensitizing molecules, in the energy region 9-15 eV. The work was stimulated by previous studies on inner shell site-selective fragmentation of the pyrimidine molecule, which have shown that the fragmentation is governed by the population/formation of specific ionic states with a hole in valence orbitals, which in turn correlate to accessible dissociation limits. The combined experimental and theoretical study of the appearance energies of the main fragments provides information on the geometric structure of the products and on the role played by the specific halogen atom and the site of halogenation in the dissociation process. This information can be used to gain new insights on the elementary mechanisms that could possibly explain the enhanced radiation damage to the DNA bases or to the medium in which the bases are embedded, thereby contributing to their radiosensitizing effect.

Experimental and theoretical investigation of laser-induced plasma of a titanium target.

We present a theoretical approach to interpreting optical emission spectroscopy measurements for nonequilibrium conditions. In this approach both the fluid dynamics and the kinetics of laser-induced plasma are taken into account, and the results obtained by the numerical model are applied to the spectroscopic observation of the plasma induced by the interaction between a KrF laser and a metallic Ti target. We have generalized the theoretical method to calculate the initial conditions for the plume expansion that show the best agreement with experimental results.