The prediction of chemical reactivity from first principles: Collision and reaction dynamics

Aquest treball fa una revisió de mesures experimentals i càlculs teòrics sobre la dinàmica de col·lisions i reaccions moleculars. Els experiments se centren en col·lisions, a energies intermèdies, que involucren sistemes del tipus ió-àtom i iómolècula, per les quals es mesuren seccions eficaces totals, estat a estat, així com aquelles que discerneixen les diferents contribucions del moment angular d'espín. Els resultats obtinguts s'interpreten satisfactòriament en termes d'acoblaments no adiabàtics entre els diferents estats electrònics dels sistemes col·lisionants. Els càlculs teòrics utilitzen la metodologia quasiclàssica, així com metodologies mecanoquàntiques recentment desenvolupades, tant aproximades com exactes. S'han obtingut resultats totalment convergits per sistemes tipus, mentre que s'han analitzat, de manera detallada i extensiva, les característiques dinàmiques de sistemes triatòmic, tetraatòmic i pentaatòmic.

Performance Analysis of Two Quantum Reaction Dynamics Codes: Time-Dependent and Time-Independent Strategies

The computer simulation of reaction dynamics has nowadays reached a remarkable degree of accuracy. Triatomic elementary reactions are rigorously studied with great detail on a straightforward basis using a considerable variety of Quantum Dynamics computational tools available to the scientific community. In our contribution we compare the performance of two quantum scattering codes in the computation of reaction cross sections of a triatomic benchmark reaction such as the gas phase reaction Ne + H2+ %12. NeH++ H. The computational codes are selected as representative of time-dependent (Real Wave Packet [ ]) and time-independent (ABC [ ]) methodologies. The main conclusion to be drawn from our study is that both strategies are, to a great extent, not competing but rather complementary. While time-dependent calculations advantages with respect to the energy range that can be covered in a single simulation, time-independent approaches offer much more detailed information from each single energy calculation. Further details such as the calculation of reactivity at very low collision energies or the computational effort related to account for the Coriolis couplings are analyzed in this paper.

Performance Analysis of Two Quantum Reaction Dynamics Codes: Time-Dependent and Time-Independent Strategies

The computer simulation of reaction dynamics has nowadays reached a remarkable degree of accuracy. Triatomic elementary reactions are rigorously studied with great detail on a straightforward basis using a considerable variety of Quantum Dynamics computational tools available to the scientific community. In our contribution we compare the performance of two quantum scattering codes in the computation of reaction cross sections of a triatomic benchmark reaction such as the gas phase reaction Ne + H2+ %12. NeH++ H. The computational codes are selected as representative of time-dependent (Real Wave Packet [ ]) and time-independent (ABC [ ]) methodologies. The main conclusion to be drawn from our study is that both strategies are, to a great extent, not competing but rather complementary. While time-dependent calculations advantages with respect to the energy range that can be covered in a single simulation, time-independent approaches offer much more detailed information from each single energy calculation. Further details such as the calculation of reactivity at very low collision energies or the computational effort related to account for the Coriolis couplings are analyzed in this paper.

Selectivity and Mechanisms Driven by Reaction Dynamics: The Case of the Gas-Phase OH-+CH3ONO2 Reaction

Well-established statistical approaches such as transition-state theory based on high-level calculated potential energy profiles are unable to account for the selectivity observed in the gas-phase OH- + CH3ONO2 reaction. This reaction can undergo bimolecular nucleophilic displacement at either the carbon center (S(N)2@C) or the nitrogen center (S(N)2@N) as well as a proton abstraction followed by dissociation (E(CO)2) pathway. Direct dynamics simulations yield an S(N)2:E(CO)2 product ratio in close agreement with experiment and show that the lack of reactivity at the nitrogen atom is due to the highly negative electrostatic potential generated by the oxygen atoms in the ONO2 group that scatters the incoming OH-. In addition to these dynamical effects, the nonstatistical behavior of these reactions is attributed to the absence of equilibrated reactant complexes and to the large number of recrossings, which might be present in several ion-molecule gas-phase reactions.

Chemical Reaction Dynamics of the Liquid/Vapor Interface Studied by Mass Spectrometry

This thesis presents investigations of chemical reactions occurring at the liquid/vapor interface studied using novel sampling methodologies coupled with detection by mass spectrometry. Chapters 2 and 3 utilize the recently developed technique of field-induced droplet ionization mass spectrometry (FIDI-MS), in which the application of a strong electric field to a pendant microliter droplet results in the ejection of highly charged progeny droplets from the liquid surface. In Chapter 2, this method is employed to study the base-catalyzed dissociation of a surfactant molecule at the liquid/vapor interface upon uptake of ammonia from the gas phase. This process is observed to occur without significant modulation of the bulk solution pH, suggesting a transient increase in surface pH following the uptake of gaseous ammonia. Chapter 3 presents real-time studies of the oxidation of the model tropospheric organic compound glycolaldehyde by photodissociation of iron (III) oxalate complexes. The oxidation products of glycolaldehyde formed in this process are identified, and experiments in a deoxygenated environment identify the role of oxygen in the oxidation pathway and in the regeneration of iron (III) following photo-initiated reduction. Chapter 4 explores alternative methods for the study of heterogeneous reaction processes by mass spectrometric sampling from liquid surfaces. Bursting bubble ionization (BBI) and interfacial sampling with an acoustic transducer (ISAT) generate nanoliter droplets from a liquid surface that can be sampled via the atmospheric pressure interface of a mass spectrometer. Experiments on the oxidation of oleic acid by ozone using ISAT are also presented. Chapters 5 and 6 detail mechanistic studies and applications of free-radical-initiated peptide sequencing (FRIPS), a technique employing gas-phase free radical chemistry to the sequencing of peptides and proteins by mass spectrometry. Chapter 5 presents experimental and theoretical studies on the anomalous mechanism of dissociation observed in the presence of serine and threonine residues in peptides. Chapter 6 demonstrates the combination of FRIPS with ion mobility-mass spectrometry (IM-MS) for the separation of isomeric peptides.

Effects of the target spin on the reaction mechanism of the (16)O+(63)Cu system

Precise quasielastic and alpha-transfer excitation functions, at theta(lab) = 161 degrees, have been measured at energies near the Coulomb barrier for the (16)O + (63)Cu system. This is the first time reported quasielastic barrier distribution for a medium odd-A nucleus target deduced from the data. Additional elastic scattering angular distributions data available in the literature for this system were also used in the investigation of the role of several individual channels in the reaction dynamics, by comparing the data with free-parameter coupled-channels calculations. In order to do so, the nucleus-nucleus bare potential has a double-folding potential as the real component and only a very short-range imaginary potential. The quasielastic barrier distribution has been shown to be a powerful tool in this analysis at the barrier region. A high collectivity of the (63)Cu was observed, mainly due to the strong influence of its 5/2-and 7/2-states on all reaction channels investigated. A striking influence of the reorientation of the ground-state target-spin on the elastic cross sections, taken at backward angles, was also observed.

Femtosecond dynamics of molecules and clusters

The real-time dynamics of multiphoton ionization and fragmentation of molecules - Na_2 , Na_3 - and clusters - Na_n, Hg_n - has been studied in molecular beam experiments employing ion and electron spectroscopy together with femtosecond pump-probe techniques. Experiments with Na_2 and Na_3 reveal unexpected features of the dynamics of the absorption of several photons as seen in the one- and three dimensional vibrational wave packet motion in different potential surfaces and in high laser fields. Cluster size dependent studies of physical properties such as absorption resonances, lifetimes and decay channels have been performed using tunable femtosecond light pulses in resonance enhanced multiphoton ionization (REMPI) of the cluster size under investigation. This method failed in ns-laser experiments due to the ultrafast decay of the studied cluster. For Na_n, cluster we find that for cluster sizes n \le 21 molecular excitations and properties prevail over collective excitations of plasmon-like resonances. In the case of Hg_n cluster prompt formation of singly and doubly charged cluster are observed up to n \approx 60. The transient multiphoton ionization spectra show a 'short' time wave packet dynamics, which is identical for singly and doubly charged mercury clusters while the 'long' time fragmentation dynamics is different.

Structure, Dynamics and Reactivity in the Organic Solid State: Anthracene Derivatives and Charge Transfer Crystals

The work presented in this thesis tackles some important points concerning the collective properties of two typical categories of molecular crystals, i.e., anthracene derivatives and charge transfer crystals. Anthracene derivatives have constituted the class of materials from which systematical investigations of crystal-to-crystal photodimerization reactions started, developed and have been the subject of a new awakening in the recent years. In this work some of these compounds, namely, 9-cyanoanthacene, 9-anthacenecarboxylic acid and 9-methylanthracene, have been selected as model systems for a phenomenological approach to some key properties of the solid state, investigated by spectroscopic methods. The present results show that, on the basis of the solid state organization and the chemical nature of each compound, photo-reaction dynamics and kinetics display distinctive behaviors, which allows for a classification of the various processes in topochemical, non topochemical, reversible or topophysical. The second part of the thesis was focused on charge transfer crystals, binary systems formed by stoichiometric combinations of the charge donating perylene (D) and the charge accepting tetracyano-quinodimethane (A), this latter also in its fluorinated derivatives. The work was focused on the growth of single crystals, some of which not yet reported in the literature, by PVT technique. Structural and spectroscopic characterizations have been performed, with the aim of determining the degree of charge transfer between donor and acceptor in the co-crystals. An interesting outcome of the systematic search performed in this work is the definition of the experimental conditions which drive the crystal growth of the binary systems either towards the low (1:1) or the high ratio (3:1 or 3:2) stoichiometries.

Maximizing Product Formation and Minimizing Degradation: A Look at Buffering Conditions and Post-Reaction Degradation for the In-Line Jaffe Reaction with Capillary Electrophoresis

Creatinine levels in blood serum are typically used to assess renal function. Clinical determination of creatinine is often based on the Jaffe reaction, in which creatinine in the serum reacts with sodium picrate, resulting in a spectrophotometrically quantifiable product. Previous work from our lab has introduced an electrophoretically mediated initiation of this reaction, in which nanoliter plugs of individual reagent solutions can be added to the capillary and then mixed and reacted. Following electrophoretic separation of the product from excess reactant(s), the product can be directly determined on column. This work aims to gain a detailed understanding of the in-capillary reagent mixing dynamics, in-line reaction yield, and product degradation during electrophoresis, with an overall goal of improving assay sensitivity. One set of experiments focuses on maximizing product formation through manipulation of various conditions such as pH, voltage applied, and timing of the applied voltage, in addition to manipulations in the identity, concentration, and pH of the background electrolyte. Through this work, it was determined that dramatic changes in local voltage fields within the various reagent zones lead to ineffective reagent overlapping. Use of the software simulation program Simul 5 enabled visualization of the reaction dynamics within the capillary, specifically the wide variance between the electric field intensities within the creatinine and picrate zones. Because of this simulation work, the experimental method was modified to increase the ionic strength of the creatinine reagent zone to lower the local voltage field, thus producing more predictable and effective overlap conditions for the reagents and allowing the formation of more Jaffe product. As second set of experiments focuses on controlling the post-reaction product degradation. In that vein, we have systematically explored the importance of the identity, concentration, and pH of the background electrolyte on the post-reaction degradation rate of the product. Although prior work with borate background electrolytes indicated that product degradation was probably a function of the ionic strength of the background electrolyte, this work with a glycine background electrolyte demonstrates that degradation is in fact not a function of ionic strength of the background electrolyte. As the concentration and pH of the glycine background increased, the rate of degradation of product did not change dramatically, whereas in borate-buffered systems, the rate of Jaffe product degradation increased linearly with background electrolyte concentration above 100.0 mM borate. Similarly, increasing pH of the glycine background electrolyte did not result in a corresponding increase in product degradation, as it had with the borate background electrolyte. Other general trends that were observed include: increasing background electrolyte concentration increases peak efficiency and higher pH favors product formation; thus, it appears that use of a background electrolyte other than borate, such as glycine, the rate of degradation of the Jaffe product can be slowed, increasing the sensitivity of this in-line assay.

Lanczos subspace time-independent wave packet calculations of S(D-1)+H-2 reactive scattering

In this paper. we present the results of quantum dynamical simulations of the S (D-1) + H-2 insertion reaction on a newly developed potential energy surface (J. Chem. Phys. 2001, 114, 320). State-to-state reaction probabilities. product state distributions, and initial-state resolved cumulative reaction probabilities from a given incoming reactant channel are obtained from a time-independent wave packet analysis, performed within a single Lanczos subspace. Integral reaction cross sections are then estimated by J-shifting method and compared with the results from molecular beam experiment and QCT calculations.

Calculation of bound and resonance states of HO2 for nonzero total angular momentum

Bound and resonance states of HO2 have been calculated quantum mechanically by the Lanczos homogeneous filter diagonalization method [Zhang and Smith, Phys. Chem. Chem. Phys. 3, 2282 (2001); J. Chem. Phys. 115, 5751 (2001)] for nonzero total angular momentum J = 1,2,3. For lower bound states, agreement between the results in this paper and previous work is quite satisfactory; while for high lying bound states and resonances these are the first reported results. A helicity quantum number V assignment (within the helicity conserving approximation) is performed and the results indicate that for lower bound states it is possible to assign the V quantum numbers unambiguously, but for resonances it is impossible to assign the V helicity quantum numbers due to strong mixing. In fact, for the high-lying bound states, the mixing has already appeared. These results indicate that the helicity conserving approximation is not good for the resonance state calculations and exact quantum calculations are needed to accurately describe the reaction dynamics for HO2 system. Analysis of the resonance widths shows that most of the resonances are overlapping and the interferences between them lead to large fluctuations from one resonance to another. In accord with the conclusions from earlier J = 0 calculations, this indicates that the dissociation of HO2 is essentially irregular. (C) 2003 American Institute of Physics.

Structure-function relationships in a glycosyltransferase, a phosphatase and an oxidoreductase

Dissertation presented to obtain the Ph.D degree in Biochemistry

Dinámica de reacciones unimoleculares en fase gas: Desviaciones del comportamiento estadístico

The present review summarizes the most relevant results of our research group obtained recently in the field of unimolecular reaction dynamics. The following processes are specifically analyzed: the isomerization, dissociation and elimination in methyl nitrite, the fragmentation reactions of the mercaptomethyl cation, the C-CO dissociation in the acetyl and propionyl radicals, and the decomposition of vinyl fluoride. In all the cases, only state- or energy-selected systems are considered. Special emphasis is paid to the possibility of systems exhibiting non-statistical behavior.

Femtosecond real-time probing of reactions

Femtosecond reaction dynamics of OClO in a supersonic molecular beam are reported. The system is excited to the A^2A_2 state with a femtosecond pulse, covering a range of excitation in the symmetric stretch between v_1 = 17 to v_1 = 11 (308-352 nm). A time-delayed femtosecond probe pulse ionizes the OClO, and OClO^+ is detected. This ion has not been observed in previous experiments because of its ultrafast fragmentation. Transients are reported for the mass of the parent OClO as well as the mass of the ClO. Apparent biexponential decays are observed and related to the fragmentation dynamics: OClO+hv \rightarrow (OClO)^{(++)*} \rightarrow ClO+O \rightarrow Cl+O_2. Clusters of OClO with water (OClO)_n (H_2 0)_m with n from 1 to 3 and m from 0 to 3 are also observed. The dynamics of the fragmentation reveal the nuclear motions and the electronic coupling between surfaces. The time scale for bond breakage is in the range of 300-500 fs, depending on v_1; surface crossing to form new intermediates is a pathway for the two channels of fragmentation: ClO+O (primary) and Cl+O_2 (minor). Comparisons with results of ab initio calculations are made.

State-resolved gas-surface reactivity of methane in the symmetric C-H stretch vibration on Ni(100)

The state-resolved reactivity of CH4 in its totally symmetric C-H stretch vibration (�1) has been measured on a Ni(100) surface. Methane molecules were accelerated to kinetic energies of 49 and 63:5 kJ=mol in a molecular beam and vibrationally excited to �1 by stimulated Raman pumping before surface impact at normal incidence. The reactivity of the symmetric-stretch excited CH4 is about an order of magnitude higher than that of methane excited to the antisymmetric stretch (�3) reported by Juurlink et al. [Phys. Rev. Lett. 83, 868 (1999)] and is similar to that we have previously observed for the excitation of the first overtone (2�3). The difference between the state-resolved reactivity for �1 and �3 is consistent with predictions of a vibrationally adiabatic model of the methane reaction dynamics and indicates that statistical models cannot correctly describe the chemisorption of CH4 on nickel.