Competition between Loss of H2 versus H+H in the Fragmentation of the Fluorene Cation.

The fluorene cation is a frequently studied molecule in the context of fragmentation experiments. This is because of its potential role in interstellar chemistry, notably as a precursor of PAH cages. In this paper, we analyze H, H+ , H2 and H 2 + ${{\rm{H}}_2^ + }$ losses from the fluorene cation using the SMF (Statistical Molecular Fragmentation) model. We calculate the probabilities of all the 534 possible fragmentation channels as a function of the excitation energy, up to the loss of three hydrogens. Four different types of hydrogen atom pairings (from the same carbon, from the same ring, from different rings and across-the-bay) have been tested in order to determine which types contribute to the actual production of hydrogen molecules. The simulated breakdown curves are in very good agreement with different experimental results when same ring pairing is taken into account. It was possible to deduce from the model the locations of the emitted H, H+ , H2 and H 2 + ${{\rm{H}}_2^ + }$ species.

Use of Gaussian-Type Functions for Describing Fast Ion-Matter Irradiation with Time-Dependent Density Functional Theory.

The electronic stopping power is an observable property that quantifies the ability of swift ions to penetrate matter to transfer energy to the electron cloud. The recent literature has proven the value of Real-Time Time-Dependent Density Functional Theory to accurately evaluate this property from first-principles, but questions remain regarding the capability of computer codes relying on atom-centered basis functions to capture the physics at play. In this Perspective, we draw attention to the fact that irradiation by swift ions triggers electron emission into the continuum, especially at the Bragg peak. We investigate the ability of Gaussian atomic orbitals (AOC), which were fitted to mimic continuum wave functions, to improve electronic stopping power predictions. AOC are added to standard correlation-consistent basis sets or STO minimal basis sets. Our benchmarks for water irradiation by fast protons clearly advocate for the use of AOC, especially near the Bragg peak. We show that AOC only need to be placed on the molecules struck by the ion. The number of AOC that are added to the usual basis set is relatively small compared to the total number of atomic orbitals, making the use of such a basis set an excellent choice from a computational cost point of view. The optimum basis set combination is applied for the calculation of the stopping power of a proton in water with encouraging agreement with experimental data.

In-depth theoretical understanding of the chemical interaction of aromatic compounds with a gold nanoparticle.

Gold Nanoparticles (GNPs), owing to their unique properties and versatile preparation strategy, have been demonstrated to exhibit promising applications in diverse fields, which include bio-sensors, catalysts, nanomedicines and radiotherapy. Yet, the nature of the interfacial interaction of GNPs with their chemical environment remains elusive. Experimental vibrational spectroscopy can reveal different interactions of aromatic biological molecules absorbed on GNPs, that may result from changes in the orientation of the molecule. However, the presence of multiple functional groups and the aqueous solvent introduces competition, and complexifies the spectral interpretations. Therefore, our objective is to theoretically investigate the adsorption of aromatic molecules containing various functional groups on the surface of GNPs to comparatively study their preferred adsorption modes. The interaction between Au32, as a model of GNPs, and a series of substituted aromatic compounds that includes benzene, aniline, phenol, toluene, benzoic acid, acetophenone, methyl benzoate, and thiophenol, is investigated. Our computed interaction energies highlight the preference of the aromatic ring to lie flat on the surface. The orientations of the molecules can be distinguished using infrared spectroscopy along with strong changes in intensity and significant shifts of some vibrational modes when the molecule interacts with the GNP. The interaction energy and the electron transfer between the nanoparticle and the aromatic molecule are not found to correlate, possibly because of significant back donation of electrons from GNPs to organic molecules as revealed by charge decomposition analysis. A thorough quantum topological analysis identifies multiple non-covalent interactions and assigns the nature of the interaction mostly to dative interactions between the aromatic ring and the GNP as well as dispersive interaction. Finally, energy decomposition analyses point out the role of the charge transfer energy contribution in the subtle balance of the different physical components.

Multiple dehydrogenation of fluorene cation and neutral fluorene using the statistical molecular fragmentation model.

The statistical molecular fragmentation (SMF) model was used to analyze the 306 fragmentation channels (containing 611 different species) that result from the fluorene (C13H10+) cation losing up to three hydrogen atoms (neutral radicals and/or a proton). Breakdown curves from such analysis permit one to extract experimentally inaccessible information about the fragmentation of the fluorene cation, such as the locations of the lost hydrogen atoms (or proton), yields of the neutral fragments, electronic states of the residues, and quantification of very low probability channels that would be difficult to detect. Charge localization during the fragmentation pathways was studied to provide a qualitative understanding of the fragmentation process. Breakdown curves for both the fluorene cation and neutral fluorene were compared. The SMF results match the rise and fall of the one hydrogen loss yield experimentally measured by imaging photoelectron-photoion coincidence spectroscopy using a VUV synchrotron.

Probing the structural properties of the water solvation shell around gold nanoparticles: A computational study.

While subjected to radiation, gold nanoparticles (GNPs) have been shown to enhance the production of radicals when added to aqueous solutions. It has been proposed that the arrangement of water solvation layers near the water-gold interface plays a significant role. As such, the structural and electronic properties of the first water solvation layer surrounding GNPs of varying sizes were compared to bulk water using classical molecular dynamics and quantum and semi-empirical methods. Classical molecular dynamics was used to understand the change in macroscopic properties of bulk water in the presence of different sizes of GNP, as well as by including salt ions. The analysis of these macroscopic properties has led to the conclusion that larger GNPs induce the rearrangement of water molecules to form a 2D hydrogen-bond network at the interface. Quantum methods were employed to understand the electronic nature of the interaction between water molecules and GNPs along with the change in the water orientation and the vibrational density of states. The stretching region of vibrational density of states was found to extend into the higher wavenumber region, as the size of the GNP increases. This extension represents the dangling water molecules at the interface, as a result of reorientation of the water molecules in the first solvation shell. This multi-level study suggests that in the presence of GNP of increasing sizes, the first water solvation shell undergoes a rearrangement to maximize the water-water interactions as well as the water-GNP interactions.

The statistical molecular fragmentation model compared to experimental plasma induced hydrocarbon decays.

We compare the predictions of our recently developed statistical molecular fragmentation (SMF) model with experimental results from plasma induced hydrocarbon decay. The SMF model is an exactly solvable statistical model, able to calculate the probabilities for all possible fragmentation channels as a function of the deposited excitation energy. The weights of the channels are calculated from the corresponding volume of the accessible phase space of the system, taking into account all relevant degeneracies, symmetries and density functions. An experiment designed to study the abatement of propene in N2 using a photo-triggered discharge producing a homogeneous plasma at sub-atmospheric pressure was also performed. Using a 0D model that simulates the complex chemical kinetics in the plasma, it was possible to assess the percentages of the original parent hydrocarbon's fragmentation channels based on the detected species. These results were compared to those obtained from the SMF model. Previous plasma induced hydrocarbon fragmentation experiments for ethene, ethane and propane, were also compared to the predictions of the SMF model. For energies below that of metastable dinitrogen (i.e. below 6.17 eV and 8.4 eV), the SMF model and the experimental fragmentation channels coincide. This study allows one to draw conclusions both on the range of excitation energies transferred to the parent hydrocarbon molecules during plasma discharge and on the probability of the dynamical coupling of two H atoms from neighbouring carbon atoms to form H2 molecules.

Statistical molecular fragmentation: which parameters influence the branching ratios?

The fragmentation of molecules under conditions that result in yields of products that are thermodynamically controlled can be readily studied with statistical models. We explore which parameters influence the branching ratios using our recently developed Statistical Molecular Fragmentation model (SMF) and apply it to the decomposition of propane. We find that the fragmentation process has low sensitivity to the differences between the molecular descriptions given by commonly used ab initio methods (B3LYP, CCSD(T) and composite methods with different atom-centered basis sets). However, the branching ratios are most influenced by the vibrational frequencies of the molecules and radicals present in the decomposition pathways.

A Statistical Model and DFT Study of the Fragmentation Mechanisms of Metronidazole by Advanced Oxidation Processes.

The degradation pathway of the antibiotic metronidazole (MNZ) in wastewater was investigated computationally with a physical statistical method and a quantum chemical approach. In both cases, density functional theory (DFT) at the M06-2X/6-311+G(d,p) level was used to calculate the structures and property parameters of all molecules. On one hand, decay of the isolated MNZ molecule excited at a given excitation energy was studied using the statistical molecular fragmentation (SMF) model. On the other hand, the reaction mechanisms of MNZ oxidized by hydroxyl radicals (•OH) in advanced oxidation processes (AOPs) were analyzed. Both studies show that the main reaction sites in MNZ are, by decreasing importance, -NO2, -CH2OH, and -CH2CH2OH. The main degradation reactions are (i) alcohol group oxidation including the abstraction of hydrogen on C in the -CH2OH group and oxidation of the hydroxyl group to the aldehyde and further to the carboxylic acid and (ii) addition-elimination reactions happening on the imidazole ring which finally replace the nitro by hydroxyl radicals. The results gained are in a good agreement with the available experimental data on MNZ degradation by AOPs. The structures of intermediates, transition states, and free energy surfaces are helpful in elucidating the details of the elimination mechanism, supplementing current experimental knowledge.

Molecular Mechanism of the Cell Membrane Pore Formation Induced by Bubble Stable Cavitation.

Microbubbles in combination with ultrasound provide a new and promising way to deliver drugs into living cells. It is believed that the stable vibration or the collapse of the bubbles under ultrasound are the two main mechanisms that induce the formation of pores in the cell membranes, through which drugs may get inside the cell cytoplasm. The bubble collapse hypothesis is not only intuitive since released shock waves can easily penetrate and create pores in the membrane, but it is also confirmed by both experiment and theory. In contrast, the molecular mechanism of stable vibration is not well-understood because of experimental difficulties resulting from the fragility of bubbles and the lack of molecular dynamics simulation studies. To obtain a better understanding of this mechanism, we developed a lipid-coated bubble model that we applied to simulate the stable cavitation of the bubble in the presence of a lipid bilayer. We show that the wall shear stress generated by the bubble vibration does not induce the membrane pore formation. Instead, the bubble fuses with the membrane and subsequent cavitation pulls lipid molecules out of the membrane, creating pores. This could help one to choose the best combination of the bubble shell materials, the ultrasound frequency, and intensity, so that the opening and closing of pores will be optimized.

Picosecond infrared laser-induced all-atom nonequilibrium molecular dynamics simulation of dissociation of viruses.

Since the discovery of the plant pathogen tobacco mosaic virus as the first viral entity in the late 1800s, viruses traditionally have been mainly thought of as pathogens for disease-resistances. However, viruses have recently been exploited as nanoplatforms with applications in biomedicine and materials science. To this aim, a large majority of current methods and tools have been developed to improve the physical stability of viral particles, which may be critical to the extreme physical or chemical conditions that viruses may encounter during purification, fabrication processes, storage and use. However, considerably fewer studies are devoted to developing efficient methods to degrade or recycle such enhanced stability biomaterials. With this in mind, we carry out all-atom nonequilibrium molecular dynamics simulation, inspired by the recently developed mid-infrared free-electron laser pulse technology, to dissociate viruses. Adopting the poliovirus as a representative example, we find that the primary step in the dissociation process is due to the strong resonance between the amide I vibrational modes of the virus and the tuned laser frequencies. This process is determined by a balance between the formation and dissociation of the protein shell, reflecting the highly plasticity of the virus. Furthermore, our method should provide a feasible approach to simulate viruses, which is otherwise too expensive for conventional equilibrium all-atom simulations of such very large systems. Our work shows a proof of concept which may open a new, efficient way to cleave or to recycle virus-based materials, provide an extremely valuable tool for elucidating mechanical aspects of viruses, and may well play an important role in future fighting against virus-related diseases.

Vibrational spectra of polyatomic molecules assisted by quantum thermal baths.

We assess the performance of colored-noise thermostats to generate quantum mechanical initial conditions for molecular dynamics simulations, in the context of infrared spectra of large polyatomic molecules. Comparison with centroid molecular dynamics simulations taken as reference shows that the method is accurate in predicting line shifts and band widths in the ionic cluster (NaCl)(32) and in the naphthalene molecule. As illustrated on much larger polycyclic aromatic hydrocarbons, the method also allows fundamental spectra to be evaluated in the limit of T = 0, taking into account anharmonicities and vibrational delocalization.

Improving anharmonic infrared spectra using semiclassically prepared molecular dynamics simulations.

Classical molecular dynamics is a convenient method for computing anharmonic infrared spectra of polyatomic molecules and condensed phase systems. However it does not perform well for predicting accurate intensities and it lacks nuclear quantization, two deficiencies that are usually accounted for by empirical scaling factors. In this paper we show on the examples of the trans isomer of nitrous acid and naphthalene that both issues can be alleviated by preparing the initial conditions according to semiclassical quantization based on a normal mode representation. The method correctly reproduces fundamental frequencies obtained with quantum mechanical methods. At increasing temperatures, the effective frequencies are found to follow the same trends as path-integral based methods. In the low-temperature limit, the band intensities predicted by the method are also found to agree with quantum mechanical considerations.

Temperature dependent absorption spectra of Br(-), Br2(•-), and Br3(-) in aqueous solutions.

The absorption spectra of Br(2)(•-) and Br(3)(-) in aqueous solutions are investigated by pulse radiolysis techniques from room temperature to 380 and 350 °C, respectively. Br(2)(•-) can be observed even in supercritical conditions, showing that this species could be used as a probe in pulse radiolysis at high temperature and even under supercritical conditions. The weak temperature effect on the absorption spectra of Br(2)(•-) and Br(3)(-) is because, in these two systems, the transition occurs between two valence states; for example, for Br(2)(-) we have (2)Σ(u) → (2)Σ(g) transition. These valence transitions involve no diffuse final state. However, the absorption band of Br(-) undergoes an important red shift to longer wavelengths. We performed classical dynamics of hydrated Br(-) system at 20 and 300 °C under pressure of 25 MPa. The radial distribution functions (rdf's) show that the strong temperature increase (from 20 to 300 °C) does not change the radius of the solvent first shell. On the other hand, it shifts dramatically (by 1 Å) the second maximum of the Br-O rdf and introduces much disorder. This shows that the first water shell is strongly bound to the anion whatever the temperature. The first two water shells form a cavity of a roughly spherical shape around the anion. By TDDFT method, we calculated the absorption spectra of hydrated Br(-) at two temperatures and we compared the results with the experimental data.

Far-infrared spectroscopy of small polycyclic aromatic hydrocarbons.

Both experimental and theoretical spectroscopic studies on small gas phase polycyclic aromatic hydrocarbons in the far-infrared spectral region are reported. The experimental set-up based on thermal emission and Fourier transform far infrared analysis led to the detection of relatively broad vibrational bands, unresolved in rotation, representative of each molecule. Detailed theoretical investigations were performed, including both ab initio calculations and spectral simulations. For the majority of the samples, this study provides the first detection of the vibrational modes associated with the skeleton motions.

Photofragmentation of the fluorene cation: I. New experimental procedure using sequential multiphoton absorption.

The hydrogen-loss channel, induced by sequential multiphoton absorption, of the vapor-phase fluorene cation was investigated using a supersonic molecular beam and a time-of-flight mass spectrometer. The fluorene cation was prepared by resonantly enhanced multiphoton ionization. The ultimate goal of this experiment is the determination of the evolution of the dissociation rate constant in a wide energy range. In this paper, we give a description of the original experimental procedure, show that the absorption process is non-Poissonian, and determine the absolute photon absorption cross section.

Photofragmentation of the fluorene cation: II. Determination of the H-loss energy-dependent rate constant.

The hydrogen-loss channel, induced by sequential multiphoton absorption, of the vapor-phase fluorene cation was investigated using a pulsed supersonic molecular beam, a time-of-flight mass spectrometer, and pulsed nanosecond lasers. Our new method leads to the determination of the absolute absorption cross section. Its attenuation with the number of absorbed photons has been approximated by means of statistical models. A model-free determination of the evolution of the dissociation rate constant in a relatively large energy range was obtained by solving the set of coupled differential kinetic equations numerically. Particular attention was focused on the data analysis techniques. The free fit of these rate constants is close to the photothermodissociation statistical model, but shows a discrepancy with the Rice and Ramsperger and Kassel model mainly at high energy. The resulting activation energy is in agreement with both that deduced from the ab initio calculations and that from the tight-binding energy potential surface model.

Intramolecular anharmonicity in the naphthalene molecule: thermodynamics and spectral effects.

The anharmonicity of the ground electronic state of the naphthalene molecule has been investigated using a tight-binding potential energy surface model. The vibrational density of states is calculated from a mixed classical quantum theoretical approach. The primary assumption of this model is that the evolution of the mean anharmonic quantum energy as a function of temperature follows the classical evolution. From the thermal expansion of the classical free energy obtained using a reversible-scaling method, the mean vibrational frequency has also been determined as a function of temperature.