A dynamical study of the Si(+) + H(2)O reaction

A dynamical study of the Si(+) + H(2)O reaction has been carried out by means of a quasiclassical trajectory method that decomposes the reaction into a capture step, for which an accurate analytical potential is employed, and an unimolecular step, in which the evolution of the collision complex is studied through a direct dynamics BHandHLYP/6-31G(d,p) method. The capture rate coefficient has been computed for thermal conditions corresponding to temperatures ranging from 50 to 1000 K. It is concluded that the main reason why the reaction rate is about 10 times smaller than the capture rate (at T = 298 K) is the topology of the potential energy surface of the ground state. It is also concluded that the ratio between the rates of product and reactant generation from the collision complex decreases quite steeply with increasing temperature, and therefore, the reaction rate decreases even more sharply. Exciting the stretching normal modes of water substantially increases that ratio, and moderate rotational excitation does not appear to have a relevant effect. The collision complex is always initially SiOH(2)(+), but in some trajectories, it becomes HSiOH(+), which generates the products, although the former species is the main intermediate.     

Electron capture by polarizable dipolar targets: numerical and analytically approximated capture probabilities

Numerically accurate and analytically approximated partial wave probabilities for the capture of a charged particle by a stationary polarizable dipole are presented over wide ranges of collision energies. The results facilitate the analysis of electron-molecule attachment in terms of capture rates, contributions from electron-phonon coupling, and kinetic properties when metastable anions are formed.     

Dynamic aspects of small bubble and hydrophilic solid encounters

The capture of solid particles suspended in aqueous solution by rising gas bubbles involves hydrodynamic and physicochemical processes that are central to colloid science. Of the collision, attachment and aggregate stability aspects to the bubble-particle interaction, the crucial attachment process is least understood. This is especially true of hydrophilic solids. We review the current literature regarding each component of the bubble-particle attachment process, from the free-rise of a small, clean single bubble, to the collision, film drainage and interactions which dominate the attachment rate. There is a particular focus on recent studies which employ single, very small bubbles as analysis probes, enabling the dynamic bubble-hydrophilic particle interaction to be investigated, avoiding complications which arise from fluid inertia, deformation of the liquid-vapour interface and the possibility of surfactant contamination.     

Does double electron capture lead to the formation of biradicals? An ECD-SORI-CID study on lacticin 481

We studied lacticin 481, a small lantibiotic with three lanthionine bridges, by electron capture dissociation (ECD) in a Fourier transform ion cyclotron resonance (FTICR) mass spectrometer. Following electron capture, very little fragmentation was observed, but species formed by nondissociative single and multiple electron capture were abundant. Ions formed by double electron capture were subjected to sustained off resonance irradiation collision induced dissociation (SORI-CID) to determine whether stable biradicals were formed. In the SORI-CID spectra of the ions formed by double electron capture, some, but minor, H* radical loss was observed, which was not observed at all for regularly protonated ions. A small part of the ions formed by double electron capture are thus long-lived biradicals. Apart from the observed H* loss, the SORI-CID spectra of ions that captured two electrons was similar to that of regularly protonated ions and quite different from the SORI-CID spectra of radical ions formed by single electron capture. This implies that recombination of the two radical sites is the dominant process in biradical lacticin 481 ions, at least on the time scale of our SORI-CID experiments.     

Charge transfer collisions between fullerenes: C 60 3+ + C60

Charge transfer collisions between C ₆₀ ³⁺ and C₆₀ are studied for collision energies between 400 and 3600 eV. Single and double electron transfers are observed, both occuring under single collision conditions. Absolute charge transfer cross sections are determined as a function of collision energy. The cross section for single electron capture of approx. 300 Ų is about two times larger than that for double electron transfer. For both processes the cross section increases slightly with increasing collision energy.     

Electron-electron interaction in slow charge exchange collisions

The influence of excited projectile electrons on the charge exchange mechanism is studied in slow collisions of multiply charged ions with atoms. Translational energy spectra for single electron capture are measured for projectile ions being prepared in the ground state and in an excited metastable state. The differences are discussed in terms of the electron-electron interaction, which turns out to be more important in collision systems with projectiles in low charge states.     

Single electron capture by C3+ ions in He,Ne and Ar

Translational energy spectra have been obtained for 6 keV C²⁺ ions resulting from single-electron capture by 6 keV C³⁺ ions in collision with He, Ne and Ar. Our data for He and Ne are in good agreement with previous measurements, while data for the Ar target have not appeared in the literature. The spectrum for C³⁺ in Ar is complex and appears to contain many strong spectral features which involve capture with excitation of the target product ion in Ar⁺.     

Collision Energetics in a Tandem Time-of-Flight (TOF/TOF) Mass Spectrometer with a Curved-Field Reflectron

Collisions of fullerene ions (C(60) (+)) with helium and neon were carried out over a range of laboratory energies (3-20 keV) on a unique tandem time-of-flight (TOF/TOF) mass spectrometer equipped with a curved-field reflectron (CFR). The CFR enables focusing of product ions over a wide kinetic energy range. Thus, ions extracted from a laser desorption/ionization (LDI) source are not decelerated prior to collision, and collision energies in the laboratory frame are determined by the source extraction voltages. Comparison of product ion mass spectra obtained following collisions with inert gases show a time (and apparent mass) shift for product ions relative to those observed in spectra obtained by metastable dissociation (unimolecular decay), consistent with impulse collision models, in which interactions of helium with fullerene in the high energy range are primarily with a single carbon atom. In addition, within a narrow range of kinetic energies an additional peak corresponding to the capture of helium is observed for fragment ions C(50) (+), C(52) (+), C(54) (+), C(56) (+) and C(58) (+).     

Capture and dissociation in the complex-forming CH + H2 → CH2 + H, CH + H2 reactions

The rate coefficients for the capture process CH + H(2)→ CH(3) and the reactions CH + H(2)→ CH(2) + H (abstraction), CH + H(2) (exchange) have been calculated in the 200-800 K temperature range, using the quasiclassical trajectory (QCT) method and the most recent global potential energy surface. The reactions, which are of interest in combustion and in astrochemistry, proceed via the formation of long-lived CH(3) collision complexes, and the three H atoms become equivalent. QCT rate coefficients for capture are in quite good agreement with experiments. However, an important zero point energy (ZPE) leakage problem occurs in the QCT calculations for the abstraction, exchange and inelastic exit channels. To account for this issue, a pragmatic but accurate approach has been applied, leading to a good agreement with experimental abstraction rate coefficients. Exchange rate coefficients have also been calculated using this approach. Finally, calculations employing QCT capture/phase space theory (PST) models have been carried out, leading to similar values for the abstraction rate coefficients as the QCT and previous quantum mechanical capture/PST methods. This suggests that QCT capture/PST models are a good alternative to the QCT method for this and similar systems.     

Side-chain fragmentation of alkylated cysteine residues in electron capture dissociation mass spectrometry

The recent development of novel fragmentation processes based on either electron capture directly or transfer from an anion show great potential for solving problems in proteomics that are intractable by the more widely employed thermal-based fragmentation processes such as collision induced dissociation. The dominant fragmentation occurring upon electron capture dissociation of peptides is cleavage of N-C alpha bonds in the peptide backbone to form c and z* ions. In the case of disulfide-linked peptides, it has also been shown that electron capture on one of the cystine sulfur atoms is favored, resulting in cleavage of the disulfide bond. In this study, we report that electron capture on the sulfur of alkylated cysteine residues is also a dominant process, causing cysteine side-chain loss from z* ions.     

A perturbation molecular orbital theory of gas-phase dissociative electron-transfer rates

Gasphase dissociative electron-transfer (ET) reactions are examined in the light of modern electron-transfer theory and a perturbation molecular orbital (PMO) model for ion-molecule collision rates. Two dissociative ET reactions reported by Knighton and Grimsrud—the reaction of azulene anion with dibromodifluoromethane and with carbon tetrachloride—happened in the inverted region of the relationship between reaction rate and free energy. Carbon-halogen vibration participation in dissociative ET reactions is demonstrated in two reaction series. Carbon-hydrogen stretch (3050 cm^?1) activation of electron transfer happened in the most exothermic reaction series: dissociative capture to form bromide from bromotrichloromethane The reasons for the failure of classical ion-molecule collision theory to give a quantitative account of reactive ion-molecule collision rates are presented in some detail. The fundamental failure is a result of a previously unappreciated change in the polarizability of a molecule when the orbitals on the molecule overlap with those on an adjacent ion. The molecular orbital-based collision model used here avoids the need to evaluate the changes in the polarizability tensor with overlap.     

Influence of the Excited States of Atomic Nitrogen N(<Superscript>2</Superscript>D) and N(<Superscript>2</Superscript>P) on the Transport Properties of Nitrogen. Part I: Atomic Nitrogen Properties

In this paper, calculated values of the viscosity and thermal conductivity of atomic nitrogen, taking into account three species (the ground and two excited states), are presented. The calculations, which assume that the temperature dependent probability of occupation of the states is given by the Boltzmann factor, are performed for atmospheric-pressure in the temperature range from 1,000 to 20,000 K. Six collision integrals are used in calculating the transport coefficients and we have introduced new averaged collision integrals where the weight associated at each interacting species pair is the probable collision frequency. The influence of the collision integral values and energy transfer between two different species is studied. These results are compared which those of published theoretical studies.     

Collision statistics, thermodynamics, and transport coefficients of hard hyperspheres in three, four, and five dimensions

The collision statistics of hard hyperspheres are investigated. An exact, analytical formula is developed for the distribution of speeds of a sphere on collision, which is shown to be related to the average time between collisions for a sphere with a particular velocity. In addition, the relationship between the collision rate and the compressibility factor is generalized to arbitrary dimensions. Molecular dynamics simulations are performed for d=3, 4, and 5 dimensional hard-hypersphere fluids. From these simulations, the equation of state of these systems, the self-diffusion coefficient, the shear viscosity, and the thermal conductivity are determined as a function of density. Various aspects of the collision statistics and their dependence on the density and dimensionality of the system are also studied.     

Trajectory-based solution of the nonadiabatic quantum dynamics equations: an on-the-fly approach for molecular dynamics simulations

The non-relativistic quantum dynamics of nuclei and electrons is solved within the framework of quantum hydrodynamics using the adiabatic representation of the electronic states. An on-the-fly trajectory-based nonadiabatic molecular dynamics algorithm is derived, which is also able to capture nuclear quantum effects that are missing in the traditional trajectory surface hopping approach based on the independent trajectory approximation. The use of correlated trajectories produces quantum dynamics, which is in principle exact and computationally very efficient. The method is first tested on a series of model potentials and then applied to study the molecular collision of H with H(2) using on-the-fly TDDFT potential energy surfaces and nonadiabatic coupling vectors.     

Electron attachment processes in halomethanes

We have investigated thermal electron capture processes in the mixtures of halomethanes and carbon dioxide (in excess) using the electron swarm method. We have found that except the very slow second order reactions (single collision) there occur processes involving homo-(RX)₂ or heterogeniouos (RX·CO₂) van der Waals complexes (multi-body pressure dependent processes) which are at least a few times faster at atmospheric pressures. The mechanism and the kinetics of some of these processes are presented.     

Electronic excitation in potassium alkyl iodide collisions

The production of highly excited states of the alkyl iodides by collision with fast potassium atoms has been studied by a time of flight molecular beam technique. A simple electron capture and recapture mechanism is advanced to account for the observations.     

Exploring the importance of quantum effects in nucleation: the archetypical Ne(n) case

The effect of quantum mechanics (QM) on the details of the nucleation process is explored employing Ne clusters as test cases due to their semi-quantal nature. In particular, we investigate the impact of quantum mechanics on both condensation and dissociation rates in the framework of the microcanonical ensemble. Using both classical trajectories and two semi-quantal approaches (zero point averaged dynamics, ZPAD, and Gaussian-based time dependent Hartree, G-TDH) to model cluster and collision dynamics, we simulate the dissociation and monomer capture for Ne(8) as a function of the cluster internal energy, impact parameter and collision speed. The results for the capture probability P(s)(b) as a function of the impact parameter suggest that classical trajectories always underestimate capture probabilities with respect to ZPAD, albeit at most by 15%-20% in the cases we studied. They also do so in some important situations when using G-TDH. More interestingly, dissociation rates k(diss) are grossly overestimated by classical mechanics, at least by one order of magnitude. We interpret both behaviours as mainly due to the reduced amount of kinetic energy available to a quantum cluster for a chosen total internal energy. We also find that the decrease in monomer dissociation energy due to zero point energy effects plays a key role in defining dissociation rates. In fact, semi-quantal and classical results for k(diss) seem to follow a common "corresponding states" behaviour when the proper definition of internal and dissociation energies are used in a transition state model estimation of the evaporation rate constants.     

Low energy charge-transfer collisions of rare gas dications: Ne + Ne and Kr + Kr

We report measurements of the double charge transfer reactions Ne²⁺ + Ne → Ne + Ne²⁺ and Kr²⁺ + Kr → Kr + Kr²⁺ at hyperthermal energies. At collision energies below 0.8 eV, the experimental results are well reproduced by the capture (Langevin) cross section multiplied by the factor 1/2. For the single charge transfer channel, Ne²⁺ + Ne → Ne⁺ + Ne⁺, our experiment suggests that the process has a very small cross section.     

An improved collision efficiency model for particle aggregation

A generalized geometric model is presented which describes the collision efficiency factor of aggregation (the probability of a binary particle or aggregate collision resulting in adhesion) for systems comprised of two oppositely charged species. Application of the general model to specific systems requires calculation of the area of each species available for collision with a second species. This is in contrast to previous models developed for polymer-particle flocculation that are based on the fractional surface coverage of adsorbed polymer. The difference between these approaches is suggested as an explanation for previously observed discrepancies between theory and observation. In the current work the specific case of oppositely charged nondeformable spherical particles (heteroaggregation) is quantitatively addressed. The optimum concentration of oppositely charged particles for rapid aggregation (maximum collision efficiency) as a function of relative particle size is calculated and an excellent correlation is found with data taken from literature.     

Primary and secondary structure dependence of peptide flexibility assessed by fluorescence-based measurement of end-to-end collision rates

The intrachain fluorescence quenching of the fluorophore 2,3-diazabicyclo[2.2.2]oct-2-ene (DBO) is measured in short peptide fragments, namely the two strands and the turn of the N-terminal beta-hairpin of ubiquitin. The investigated peptides adopt a random-coil conformation in aqueous solution according to CD and NMR experiments. The combination of quenchers with different quenching efficiencies, namely tryptophan and tyrosine, allows the extrapolation of the rate constants for end-to-end collision rates as well as the dissociation of the end-to-end encounter complex. The measured activation energies for fluorescence quenching demonstrate that the end-to-end collision process in peptides is partially controlled by internal friction within the backbone, while measurements in solvents of different viscosities (H2O, D2O, and 7.0 M guanidinium chloride) suggest that solvent friction is an additional important factor in determining the collision rate. The extrapolated end-to-end collision rates, which are only slightly larger than the experimental rates for the DBO/Trp probe/quencher system, provide a measure of the conformational flexibility of the peptide backbone. The chain flexibility is found to be strongly dependent on the type of secondary structure that the peptides represent. The collision rates for peptides derived from the beta-strand motifs (ca. 1 x 10(7) s(-1)) are ca. 4 times slower than that derived from the beta-turn. The results provide further support for the hypothesis that chain flexibility is an important factor in the preorganization of protein fragments during protein folding. Mutations to the beta-turn peptide show that subtle sequence changes strongly affect the flexibility of peptides as well. The protonation and charge status of the peptides, however, are shown to have no significant effect on the flexibility of the investigated peptides. The meaning and definition of end-to-end collision rates in the context of protein folding are critically discussed.